Key: PMID, Value: 37874098 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20231101 Key: LR, Value: 20231101 Key: IS, Value: 2426-0266 (Electronic) Key: IS, Value: 2274-5807 (Linking) Key: VI, Value: 10 Key: IP, Value: 4 Key: DP, Value: 2023 Key: TI, Value: Initial Experiences with Amyloid-Related Imaging Abnormalities in Patients Key: Receiving Aducanumab Following Accelerated Approval., Value: Key: PG, Value: 765-770 Key: LID, Value: 10.14283/jpad.2023.96 [doi] Key: AB, Value: Aducanumab is the first FDA-approved amyloid-lowering immunotherapy for Key: Alzheimer's disease. There is little real-world data to guide management of, Value: Key: amyloid-related imaging abnormalities (ARIA), a potentially serious side-effect, Value: Key: which requires surveillance with magnetic resonance imaging. We report our, Value: Key: experiences in managing ARIA in patients receiving aducanumab at the Butler, Value: Key: Hospital Memory and Aging Program during the year following FDA approval. We, Value: Key: followed the Appropriate Use Recommendations for aducanumab to guide patient, Value: Key: selection, detection, and management of ARIA (1). ARIA-E occurred in 6 out of 24, Value: Key: participants treated; all APOE-ε4 carriers. Treatment was discontinued in 4 cases, Value: Key: of moderate-severe ARIA-E, temporarily held in 1 moderate case, and dosed through, Value: Key: in 1 mild case (mean duration = 3 months, range, 1-6 months). No participants, Value: Key: required hospitalization or high dose corticosteroids. Participants on, Value: Key: anticoagulation were excluded and no macrohemorrhages occurred. These data, Value: Key: support the measured approaches to treatment outlined in the Appropriate Use, Value: Key: Recommendations., Value: Key: FAU, Value: Howe, M D Key: AU, Value: Howe MD Key: AD, Value: Dr. Matthew Howe, Butler Hospital Memory and Aging Program, 345 Blackstone Key: Boulevard, Providence, RI 02906, USA, Phone: 401-455-6403, Fax: 401-455-6405,, Value: Key: Email: matthew_howe@brown.edu., Value: Key: FAU, Value: Britton, K J Key: AU, Value: Britton KJ Key: FAU, Value: Joyce, H E Key: AU, Value: Joyce HE Key: FAU, Value: Pappas, G J Key: AU, Value: Pappas GJ Key: FAU, Value: Faust, M A Key: AU, Value: Faust MA Key: FAU, Value: Dawson, B C Key: AU, Value: Dawson BC Key: FAU, Value: Riddle, M C Key: AU, Value: Riddle MC Key: FAU, Value: Salloway, S P Key: AU, Value: Salloway SP Key: LA, Value: eng Key: PT, Value: Journal Article Key: PL, Value: Switzerland Key: TA, Value: J Prev Alzheimers Dis Key: JT, Value: The journal of prevention of Alzheimer's disease Key: JID, Value: 101638820 Key: RN, Value: 105J35OE21 (aducanumab) Key: RN, Value: 0 (Antibodies, Monoclonal, Humanized) Key: RN, Value: 0 (Amyloid) Key: SB, Value: IM Key: MH, Value: Humans Key: MH, Value: *Alzheimer Disease/diagnostic imaging/drug therapy Key: MH, Value: Antibodies, Monoclonal, Humanized/adverse effects Key: MH, Value: Amyloid Key: MH, Value: Magnetic Resonance Imaging Key: OTO, Value: NOTNLM Key: OT, Value: Alzheimer’s disease Key: OT, Value: amyloid-β Key: OT, Value: clinical practice Key: OT, Value: neuroimaging Key: OT, Value: neurology Key: COIS, Value: M. Howe: None to disclose. K. Britton: None to disclose. H. Joyce: None to Key: disclose. G. Pappas: None to disclose. M. Faust: None to disclose. B. Dawson:, Value: Key: None to disclose. M. Riddle: None to disclose. S. Salloway: Dr. Salloway has, Value: Key: provided consultation to Biogen, Eisai, Avid, Lilly, Genentech, and Roche; he was, Value: Key: a site principal investigator on the PRIME and ENGAGE studies and co-chair of the, Value: Key: Investigator Steering Committee for the ENGAGE study. Dr. Salloway is an author, Value: Key: on the AUR for Aducanumab (1) and Lecanemab (15) and is the first author on the, Value: Key: report of ARIA in the aducanumab phase 3 program (5). Butler Hospital has, Value: Key: received research grants from Biogen, Eisai, Avid, Roche, Genentech, Janssen and, Value: Key: Lilly., Value: Key: EDAT, Value: 2023/10/24 12:42 Key: MHDA, Value: 2023/11/01 12:43 Key: CRDT, Value: 2023/10/24 08:43 Key: PHST, Value: 2023/11/01 12:43 [medline] Key: PHST, Value: 2023/10/24 12:42 [pubmed] Key: PHST, Value: 2023/10/24 08:43 [entrez] Key: AID, Value: 10.14283/jpad.2023.96 [doi] Key: PST, Value: ppublish Key: SO, Value: J Prev Alzheimers Dis. 2023;10(4):765-770. doi: 10.14283/jpad.2023.96. Key: PMID, Value: 34794383 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20211122 Key: LR, Value: 20240404 Key: IS, Value: 1471-2105 (Electronic) Key: IS, Value: 1471-2105 (Linking) Key: VI, Value: 22 Key: IP, Value: 1 Key: DP, Value: 2021 Nov 18 Key: TI, Value: Asc-Seurat: analytical single-cell Seurat-based web application. Key: PG, Value: 556 Key: LID, Value: 10.1186/s12859-021-04472-2 [doi] Key: LID, Value: 556 Key: AB, Value: BACKGROUND: Single-cell RNA sequencing (scRNA-seq) has revolutionized the study Key: of transcriptomes, arising as a powerful tool for discovering and characterizing, Value: Key: cell types and their developmental trajectories. However, scRNA-seq analysis is, Value: Key: complex, requiring a continuous, iterative process to refine the data and uncover, Value: Key: relevant biological information. A diversity of tools has been developed to, Value: Key: address the multiple aspects of scRNA-seq data analysis. However, an easy-to-use, Value: Key: web application capable of conducting all critical steps of scRNA-seq data, Value: Key: analysis is still lacking. We present Asc-Seurat, a feature-rich workbench,, Value: Key: providing an user-friendly and easy-to-install web application encapsulating, Value: Key: tools for an all-encompassing and fluid scRNA-seq data analysis. Asc-Seurat, Value: Key: implements functions from the Seurat package for quality control, clustering, and, Value: Key: genes differential expression. In addition, Asc-Seurat provides a pseudotime, Value: Key: module containing dozens of models for the trajectory inference and a functional, Value: Key: annotation module that allows recovering gene annotation and detecting gene, Value: Key: ontology enriched terms. We showcase Asc-Seurat's capabilities by analyzing a, Value: Key: peripheral blood mononuclear cell dataset. CONCLUSIONS: Asc-Seurat is a, Value: Key: comprehensive workbench providing an accessible graphical interface for scRNA-seq, Value: Key: analysis by biologists. Asc-Seurat significantly reduces the time and effort, Value: Key: required to analyze and interpret the information in scRNA-seq datasets., Value: Key: CI, Value: © 2021. The Author(s). Key: FAU, Value: Pereira, W J Key: AU, Value: Pereira WJ Key: AUID, Value: ORCID: 0000-0003-1019-6281 Key: AD, Value: School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Key: Gainesville, FL, 32611, USA. wendelljpereira@gmail.com., Value: Key: FAU, Value: Almeida, F M Key: AU, Value: Almeida FM Key: AD, Value: Department of Cell Biology, Institute of Biological Sciences, University of Key: Brasília, Brasília, DF, 70910-900, Brazil., Value: Key: FAU, Value: Conde, D Key: AU, Value: Conde D Key: AD, Value: School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Key: Gainesville, FL, 32611, USA., Value: Key: FAU, Value: Balmant, K M Key: AU, Value: Balmant KM Key: AD, Value: School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Key: Gainesville, FL, 32611, USA., Value: Key: FAU, Value: Triozzi, P M Key: AU, Value: Triozzi PM Key: AD, Value: School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Key: Gainesville, FL, 32611, USA., Value: Key: FAU, Value: Schmidt, H W Key: AU, Value: Schmidt HW Key: AD, Value: School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Key: Gainesville, FL, 32611, USA., Value: Key: FAU, Value: Dervinis, C Key: AU, Value: Dervinis C Key: AD, Value: School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Key: Gainesville, FL, 32611, USA., Value: Key: FAU, Value: Pappas, G J Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Department of Cell Biology, Institute of Biological Sciences, University of Key: Brasília, Brasília, DF, 70910-900, Brazil., Value: Key: FAU, Value: Kirst, M Key: AU, Value: Kirst M Key: AD, Value: School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Key: Gainesville, FL, 32611, USA., Value: Key: AD, Value: Genetics Institute, University of Florida, Gainesville, FL, 32611, USA. Key: LA, Value: eng Key: GR, Value: DE-SC0018247/Office of Science/ Key: PT, Value: Journal Article Key: DEP, Value: 20211118 Key: PL, Value: England Key: TA, Value: BMC Bioinformatics Key: JT, Value: BMC bioinformatics Key: JID, Value: 100965194 Key: SB, Value: IM Key: MH, Value: Cluster Analysis Key: MH, Value: Gene Expression Profiling Key: MH, Value: Leukocytes, Mononuclear Key: MH, Value: Sequence Analysis, RNA Key: MH, Value: *Single-Cell Analysis Key: MH, Value: *Software Key: PMC, Value: PMC8600690 Key: OTO, Value: NOTNLM Key: OT, Value: Gene expression Key: OT, Value: Single-cell RNA sequencing Key: OT, Value: Web application Key: OT, Value: scRNA-seq Key: COIS, Value: The authors declare that they have no competing interests. Key: EDAT, Value: 2021/11/20 06:00 Key: MHDA, Value: 2021/11/23 06:00 Key: PMCR, Value: 2021/11/18 Key: CRDT, Value: 2021/11/19 05:32 Key: PHST, Value: 2021/09/07 00:00 [received] Key: PHST, Value: 2021/11/10 00:00 [accepted] Key: PHST, Value: 2021/11/19 05:32 [entrez] Key: PHST, Value: 2021/11/20 06:00 [pubmed] Key: PHST, Value: 2021/11/23 06:00 [medline] Key: PHST, Value: 2021/11/18 00:00 [pmc-release] Key: AID, Value: 10.1186/s12859-021-04472-2 [pii] Key: AID, Value: 4472 [pii] Key: AID, Value: 10.1186/s12859-021-04472-2 [doi] Key: PST, Value: epublish Key: SO, Value: BMC Bioinformatics. 2021 Nov 18;22(1):556. doi: 10.1186/s12859-021-04472-2. Key: PMID, Value: 37970066 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20240214 Key: LR, Value: 20240214 Key: IS, Value: 2046-1402 (Electronic) Key: IS, Value: 2046-1402 (Linking) Key: VI, Value: 12 Key: DP, Value: 2023 Key: TI, Value: Scalable and versatile container-based pipelines for de novo genome assembly and Key: bacterial annotation., Value: Key: PG, Value: 1205 Key: LID, Value: 10.12688/f1000research.139488.1 [doi] Key: LID, Value: 1205 Key: AB, Value: Background: Advancements in DNA sequencing technology have transformed the field Key: of bacterial genomics, allowing for faster and more cost effective chromosome, Value: Key: level assemblies compared to a decade ago. However, transforming raw reads into a, Value: Key: complete genome model is a significant computational challenge due to the varying, Value: Key: quality and quantity of data obtained from different sequencing instruments, as, Value: Key: well as intrinsic characteristics of the genome and desired analyses. To address, Value: Key: this issue, we have developed a set of container-based pipelines using Nextflow,, Value: Key: offering both common workflows for inexperienced users and high levels of, Value: Key: customization for experienced ones. Their processing strategies are adaptable, Value: Key: based on the sequencing data type, and their modularity enables the incorporation, Value: Key: of new components to address the community's evolving needs. Methods: These, Value: Key: pipelines consist of three parts: quality control, de novo genome assembly, and, Value: Key: bacterial genome annotation. In particular, the genome annotation pipeline, Value: Key: provides a comprehensive overview of the genome, including standard gene, Value: Key: prediction and functional inference, as well as predictions relevant to clinical, Value: Key: applications such as virulence and resistance gene annotation, secondary, Value: Key: metabolite detection, prophage and plasmid prediction, and more. Results: The, Value: Key: annotation results are presented in reports, genome browsers, and a web-based, Value: Key: application that enables users to explore and interact with the genome annotation, Value: Key: results. Conclusions: Overall, our user-friendly pipelines offer a seamless, Value: Key: integration of computational tools to facilitate routine bacterial genomics, Value: Key: research. The effectiveness of these is illustrated by examining the sequencing, Value: Key: data of a clinical sample of Klebsiella pneumoniae., Value: Key: CI, Value: Copyright: © 2023 Almeida FMd et al. Key: FAU, Value: de Almeida, Felipe Marques Key: AU, Value: de Almeida FM Key: AUID, Value: ORCID: 0000-0002-6855-3379 Key: AD, Value: Programa de Pós-graduação em Biologia Molecular, Universidade de Brasilia, Key: Brasília, FD, 70910-900, Brazil., Value: Key: AD, Value: Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Key: 70910-900, Brazil., Value: Key: FAU, Value: de Campos, Tatiana Amabile Key: AU, Value: de Campos TA Key: AD, Value: Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Key: 70910-900, Brazil., Value: Key: AD, Value: Programa de Pós-graduação em Biologia Microbiana, Universidade de Brasília, Key: Brasília, DF, 70910-900, Brazil., Value: Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: AUID, Value: ORCID: 0000-0002-1100-976X Key: AD, Value: Programa de Pós-graduação em Biologia Molecular, Universidade de Brasilia, Key: Brasília, FD, 70910-900, Brazil., Value: Key: AD, Value: Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Key: 70910-900, Brazil., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Review Key: DEP, Value: 20230925 Key: PL, Value: England Key: TA, Value: F1000Res Key: JT, Value: F1000Research Key: JID, Value: 101594320 Key: SB, Value: IM Key: MH, Value: Sequence Analysis, DNA/methods Key: MH, Value: *Software Key: MH, Value: Molecular Sequence Annotation Key: MH, Value: *Genome, Bacterial Key: MH, Value: Base Sequence Key: PMC, Value: PMC10646344 Key: OTO, Value: NOTNLM Key: OT, Value: antibiotic resistance Key: OT, Value: bacterial genomics Key: OT, Value: nextflow Key: OT, Value: pipelines Key: OT, Value: public health Key: OT, Value: virulence Key: COIS, Value: No competing interests were disclosed. Key: EDAT, Value: 2023/11/16 06:45 Key: MHDA, Value: 2024/02/13 12:45 Key: PMCR, Value: 2023/09/25 Key: CRDT, Value: 2023/11/16 04:27 Key: PHST, Value: 2023/08/16 00:00 [accepted] Key: PHST, Value: 2024/02/13 12:45 [medline] Key: PHST, Value: 2023/11/16 06:45 [pubmed] Key: PHST, Value: 2023/11/16 04:27 [entrez] Key: PHST, Value: 2023/09/25 00:00 [pmc-release] Key: AID, Value: 10.12688/f1000research.139488.1 [doi] Key: PST, Value: epublish Key: SO, Value: F1000Res. 2023 Sep 25;12:1205. doi: 10.12688/f1000research.139488.1. eCollection Key: 2023., Value: Key: PMID, Value: 32103826 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20210625 Key: LR, Value: 20240403 Key: IS, Value: 1741-2552 (Electronic) Key: IS, Value: 1741-2560 (Print) Key: IS, Value: 1741-2552 (Linking) Key: VI, Value: 17 Key: IP, Value: 2 Key: DP, Value: 2020 Mar 26 Key: TI, Value: Model-based design for seizure control by stimulation. Key: PG, Value: 026009 Key: LID, Value: 10.1088/1741-2552/ab7a4e [doi] Key: AB, Value: OBJECTIVE: Current brain stimulation paradigms are largely empirical rather than Key: theoretical. An opportunity exists to improve upon their modest effectiveness in, Value: Key: closed-loop control strategies with the development of theoretically grounded,, Value: Key: model-based designs. APPROACH: Inspired by this need, here we couple experimental, Value: Key: data and mathematical modeling with a control-theoretic strategy for seizure, Value: Key: termination. We begin by exercising a dynamical systems approach to model, Value: Key: seizures (n = 94) recorded using intracranial EEG (iEEG) from 21 patients with, Value: Key: medication-resistant, localization-related epilepsy. MAIN RESULTS: Although each, Value: Key: patient's seizures displayed unique spatial and temporal patterns, their, Value: Key: evolution can be parsimoniously characterized by the same model form., Value: Key: Idiosyncracies of the model can inform individualized intervention strategies,, Value: Key: specifically in iEEG samples with well-localized seizure onset zones. Temporal, Value: Key: fluctuations in the spatial profiles of the oscillatory modes show that seizure, Value: Key: onset marks a transition into a regime in which the underlying system supports, Value: Key: prolonged rhythmic and focal activity. Based on these observations, we propose a, Value: Key: control-theoretic strategy that aims to stabilize ictal activity using static, Value: Key: output feedback for linear time-invariant switching systems. Finally, we, Value: Key: demonstrate in silico that our proposed strategy allows us to dampen the emerging, Value: Key: focal oscillatory sources using only a small set of electrodes. SIGNIFICANCE: Our, Value: Key: integrative study informs the development of modulation and control algorithms, Value: Key: for neurostimulation that could improve the effectiveness of implantable,, Value: Key: closed-loop anti-epileptic devices., Value: Key: FAU, Value: Ashourvan, Arian Key: AU, Value: Ashourvan A Key: AD, Value: Department of Bioengineering, School of Engineering and Applied Science, Key: University of Pennsylvania, Philadelphia, PA 19104, United States of America., Value: Key: U.S. Army Research Laboratory, Aberdeen Proving Ground, MD 21005, United States, Value: Key: of America., Value: Key: FAU, Value: Pequito, Sérgio Key: AU, Value: Pequito S Key: FAU, Value: Khambhati, Ankit N Key: AU, Value: Khambhati AN Key: FAU, Value: Mikhail, Fadi Key: AU, Value: Mikhail F Key: FAU, Value: Baldassano, Steven N Key: AU, Value: Baldassano SN Key: FAU, Value: Davis, Kathryn A Key: AU, Value: Davis KA Key: FAU, Value: Lucas, Timothy H Key: AU, Value: Lucas TH Key: FAU, Value: Vettel, Jean M Key: AU, Value: Vettel JM Key: FAU, Value: Litt, Brian Key: AU, Value: Litt B Key: FAU, Value: Pappas, George J Key: AU, Value: Pappas GJ Key: FAU, Value: Bassett, Danielle S Key: AU, Value: Bassett DS Key: LA, Value: eng Key: GR, Value: T32 NS091006/NS/NINDS NIH HHS/United States Key: GR, Value: R01 NS099348/NS/NINDS NIH HHS/United States Key: GR, Value: K23 NS092973/NS/NINDS NIH HHS/United States Key: GR, Value: R01 MH107235/MH/NIMH NIH HHS/United States Key: GR, Value: R01 DC009209/DC/NIDCD NIH HHS/United States Key: GR, Value: R21 MH106799/MH/NIMH NIH HHS/United States Key: GR, Value: R01 HD086888/HD/NICHD NIH HHS/United States Key: GR, Value: R01 MH109520/MH/NIMH NIH HHS/United States Key: GR, Value: R01 MH107703/MH/NIMH NIH HHS/United States Key: GR, Value: R01 NS092882/NS/NINDS NIH HHS/United States Key: GR, Value: DP1 NS122038/NS/NINDS NIH HHS/United States Key: GR, Value: UH2 NS095495/NS/NINDS NIH HHS/United States Key: PT, Value: Journal Article Key: PT, Value: Research Support, N.I.H., Extramural Key: PT, Value: Research Support, Non-U.S. Gov't Key: PT, Value: Research Support, U.S. Gov't, Non-P.H.S. Key: DEP, Value: 20200326 Key: PL, Value: England Key: TA, Value: J Neural Eng Key: JT, Value: Journal of neural engineering Key: JID, Value: 101217933 Key: SB, Value: IM Key: MH, Value: Algorithms Key: MH, Value: *Drug Resistant Epilepsy Key: MH, Value: Electrocorticography Key: MH, Value: Electroencephalography Key: MH, Value: *Epilepsies, Partial Key: MH, Value: Humans Key: MH, Value: Seizures/therapy Key: PMC, Value: PMC8341467 Key: MID, Value: NIHMS1703860 Key: EDAT, Value: 2020/02/28 06:00 Key: MHDA, Value: 2021/06/29 06:00 Key: PMCR, Value: 2021/08/05 Key: CRDT, Value: 2020/02/28 06:00 Key: PHST, Value: 2020/02/28 06:00 [pubmed] Key: PHST, Value: 2021/06/29 06:00 [medline] Key: PHST, Value: 2020/02/28 06:00 [entrez] Key: PHST, Value: 2021/08/05 00:00 [pmc-release] Key: AID, Value: 10.1088/1741-2552/ab7a4e [doi] Key: PST, Value: epublish Key: SO, Value: J Neural Eng. 2020 Mar 26;17(2):026009. doi: 10.1088/1741-2552/ab7a4e. Key: PMID, Value: 24919147 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20140717 Key: LR, Value: 20220310 Key: IS, Value: 1476-4687 (Electronic) Key: IS, Value: 0028-0836 (Linking) Key: VI, Value: 510 Key: IP, Value: 7505 Key: DP, Value: 2014 Jun 19 Key: TI, Value: The genome of Eucalyptus grandis. Key: PG, Value: 356-62 Key: LID, Value: 10.1038/nature13308 [doi] Key: AB, Value: Eucalypts are the world's most widely planted hardwood trees. Their outstanding Key: diversity, adaptability and growth have made them a global renewable resource of, Value: Key: fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of, Value: Key: Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem, Value: Key: duplications, the largest proportion thus far in plant genomes. Eucalyptus also, Value: Key: shows the highest diversity of genes for specialized metabolites such as terpenes, Value: Key: that act as chemical defence and provide unique pharmaceutical oils. Genome, Value: Key: sequencing of the E. grandis sister species E. globulus and a set of inbred E., Value: Key: grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding, Value: Key: depression. The E. grandis genome is the first reference for the eudicot order, Value: Key: Myrtales and is placed here sister to the eurosids. This resource expands our, Value: Key: understanding of the unique biology of large woody perennials and provides a, Value: Key: powerful tool to accelerate comparative biology, breeding and biotechnology., Value: Key: FAU, Value: Myburg, Alexander A Key: AU, Value: Myburg AA Key: AD, Value: 1] Department of Genetics, Forestry and Agricultural Biotechnology Institute Key: (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2], Value: Key: Genomics Research Institute (GRI), University of Pretoria, Private bag X20,, Value: Key: Pretoria 0028, South Africa., Value: Key: FAU, Value: Grattapaglia, Dario Key: AU, Value: Grattapaglia D Key: AD, Value: 1] Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, Key: EPQB Final W5 Norte, 70770-917 Brasília, Brazil [2] Programa de Ciências, Value: Key: Genômicas e Biotecnologia, Value: Universidade Católica de Brasília SGAN 916, 70790-160 Key: Brasília, Brazil., Value: Key: FAU, Value: Tuskan, Gerald A Key: AU, Value: Tuskan GA Key: AD, Value: 1] US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Key: Creek, California 94598, USA [2] Biosciences Division, Oak Ridge National, Value: Key: Laboratory, Oak Ridge, Tennessee 37831, USA., Value: Key: FAU, Value: Hellsten, Uffe Key: AU, Value: Hellsten U Key: AD, Value: US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Key: Creek, California 94598, USA., Value: Key: FAU, Value: Hayes, Richard D Key: AU, Value: Hayes RD Key: AD, Value: US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Key: Creek, California 94598, USA., Value: Key: FAU, Value: Grimwood, Jane Key: AU, Value: Grimwood J Key: AD, Value: HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama Key: 35801, USA., Value: Key: FAU, Value: Jenkins, Jerry Key: AU, Value: Jenkins J Key: AD, Value: HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama Key: 35801, USA., Value: Key: FAU, Value: Lindquist, Erika Key: AU, Value: Lindquist E Key: AD, Value: US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Key: Creek, California 94598, USA., Value: Key: FAU, Value: Tice, Hope Key: AU, Value: Tice H Key: AD, Value: US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Key: Creek, California 94598, USA., Value: Key: FAU, Value: Bauer, Diane Key: AU, Value: Bauer D Key: AD, Value: US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Key: Creek, California 94598, USA., Value: Key: FAU, Value: Goodstein, David M Key: AU, Value: Goodstein DM Key: AD, Value: US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Key: Creek, California 94598, USA., Value: Key: FAU, Value: Dubchak, Inna Key: AU, Value: Dubchak I Key: AD, Value: US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Key: Creek, California 94598, USA., Value: Key: FAU, Value: Poliakov, Alexandre Key: AU, Value: Poliakov A Key: AD, Value: US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Key: Creek, California 94598, USA., Value: Key: FAU, Value: Mizrachi, Eshchar Key: AU, Value: Mizrachi E Key: AD, Value: 1] Department of Genetics, Forestry and Agricultural Biotechnology Institute Key: (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2], Value: Key: Genomics Research Institute (GRI), University of Pretoria, Private bag X20,, Value: Key: Pretoria 0028, South Africa., Value: Key: FAU, Value: Kullan, Anand R K Key: AU, Value: Kullan AR Key: AD, Value: 1] Department of Genetics, Forestry and Agricultural Biotechnology Institute Key: (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2], Value: Key: Genomics Research Institute (GRI), University of Pretoria, Private bag X20,, Value: Key: Pretoria 0028, South Africa., Value: Key: FAU, Value: Hussey, Steven G Key: AU, Value: Hussey SG Key: AD, Value: 1] Department of Genetics, Forestry and Agricultural Biotechnology Institute Key: (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2], Value: Key: Genomics Research Institute (GRI), University of Pretoria, Private bag X20,, Value: Key: Pretoria 0028, South Africa., Value: Key: FAU, Value: Pinard, Desre Key: AU, Value: Pinard D Key: AD, Value: 1] Department of Genetics, Forestry and Agricultural Biotechnology Institute Key: (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2], Value: Key: Genomics Research Institute (GRI), University of Pretoria, Private bag X20,, Value: Key: Pretoria 0028, South Africa., Value: Key: FAU, Value: van der Merwe, Karen Key: AU, Value: van der Merwe K Key: AD, Value: 1] Department of Genetics, Forestry and Agricultural Biotechnology Institute Key: (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2], Value: Key: Genomics Research Institute (GRI), University of Pretoria, Private bag X20,, Value: Key: Pretoria 0028, South Africa., Value: Key: FAU, Value: Singh, Pooja Key: AU, Value: Singh P Key: AD, Value: 1] Department of Genetics, Forestry and Agricultural Biotechnology Institute Key: (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2], Value: Key: Genomics Research Institute (GRI), University of Pretoria, Private bag X20,, Value: Key: Pretoria 0028, South Africa., Value: Key: FAU, Value: van Jaarsveld, Ida Key: AU, Value: van Jaarsveld I Key: AD, Value: Bioinformatics and Computational Biology Unit, Department of Biochemistry, Key: University of Pretoria, Pretoria, Private bag X20, Pretoria 0028, South Africa., Value: Key: FAU, Value: Silva-Junior, Orzenil B Key: AU, Value: Silva-Junior OB Key: AD, Value: Laboratório de Bioinformática, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Key: Final W5 Norte, 70770-917 Brasília, Brazil., Value: Key: FAU, Value: Togawa, Roberto C Key: AU, Value: Togawa RC Key: AD, Value: Laboratório de Bioinformática, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Key: Final W5 Norte, 70770-917 Brasília, Brazil., Value: Key: FAU, Value: Pappas, Marilia R Key: AU, Value: Pappas MR Key: AD, Value: Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Key: Final W5 Norte, 70770-917 Brasília, Brazil., Value: Key: FAU, Value: Faria, Danielle A Key: AU, Value: Faria DA Key: AD, Value: Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Key: Final W5 Norte, 70770-917 Brasília, Brazil., Value: Key: FAU, Value: Sansaloni, Carolina P Key: AU, Value: Sansaloni CP Key: AD, Value: Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Key: Final W5 Norte, 70770-917 Brasília, Brazil., Value: Key: FAU, Value: Petroli, Cesar D Key: AU, Value: Petroli CD Key: AD, Value: Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Key: Final W5 Norte, 70770-917 Brasília, Brazil., Value: Key: FAU, Value: Yang, Xiaohan Key: AU, Value: Yang X Key: AD, Value: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Key: USA., Value: Key: FAU, Value: Ranjan, Priya Key: AU, Value: Ranjan P Key: AD, Value: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Key: USA., Value: Key: FAU, Value: Tschaplinski, Timothy J Key: AU, Value: Tschaplinski TJ Key: AD, Value: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Key: USA., Value: Key: FAU, Value: Ye, Chu-Yu Key: AU, Value: Ye CY Key: AD, Value: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Key: USA., Value: Key: FAU, Value: Li, Ting Key: AU, Value: Li T Key: AD, Value: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Key: USA., Value: Key: FAU, Value: Sterck, Lieven Key: AU, Value: Sterck L Key: AD, Value: Department of Plant Biotechnology and Bioinformatics (VIB), Ghent University, Key: Technologiepark 927, B-9000 Ghent, Belgium., Value: Key: FAU, Value: Vanneste, Kevin Key: AU, Value: Vanneste K Key: AD, Value: Department of Plant Biotechnology and Bioinformatics (VIB), Ghent University, Key: Technologiepark 927, B-9000 Ghent, Belgium., Value: Key: FAU, Value: Murat, Florent Key: AU, Value: Murat F Key: AD, Value: INRA/UBP UMR 1095, 5 Avenue de Beaulieu, 63100 Clermont Ferrand, France. Key: FAU, Value: Soler, Marçal Key: AU, Value: Soler M Key: AD, Value: Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse Key: III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France., Value: Key: FAU, Value: Clemente, Hélène San Key: AU, Value: Clemente HS Key: AD, Value: Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse Key: III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France., Value: Key: FAU, Value: Saidi, Naijib Key: AU, Value: Saidi N Key: AD, Value: Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse Key: III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France., Value: Key: FAU, Value: Cassan-Wang, Hua Key: AU, Value: Cassan-Wang H Key: AD, Value: Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse Key: III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France., Value: Key: FAU, Value: Dunand, Christophe Key: AU, Value: Dunand C Key: AD, Value: Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse Key: III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France., Value: Key: FAU, Value: Hefer, Charles A Key: AU, Value: Hefer CA Key: AD, Value: 1] Bioinformatics and Computational Biology Unit, Department of Biochemistry, Key: University of Pretoria, Pretoria, Private bag X20, Pretoria 0028, South Africa, Value: Key: [2] Department of Botany, University of British Columbia, 3529-6270 University, Value: Key: Blvd, Vancouver V6T 1Z4, Canada., Value: Key: FAU, Value: Bornberg-Bauer, Erich Key: AU, Value: Bornberg-Bauer E Key: AD, Value: Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, University Key: of Muenster, Huefferstrasse 1, D-48149, Muenster, Germany., Value: Key: FAU, Value: Kersting, Anna R Key: AU, Value: Kersting AR Key: AD, Value: 1] Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, Key: University of Muenster, Huefferstrasse 1, D-48149, Muenster, Germany [2], Value: Key: Department of Bioinformatics, Institute for Computer Science, University of, Value: Key: Duesseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany., Value: Key: FAU, Value: Vining, Kelly Key: AU, Value: Vining K Key: AD, Value: Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Key: Oregon 97331, USA., Value: Key: FAU, Value: Amarasinghe, Vindhya Key: AU, Value: Amarasinghe V Key: AD, Value: Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Key: Oregon 97331, USA., Value: Key: FAU, Value: Ranik, Martin Key: AU, Value: Ranik M Key: AD, Value: Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Key: Oregon 97331, USA., Value: Key: FAU, Value: Naithani, Sushma Key: AU, Value: Naithani S Key: AD, Value: 1] Department of Botany and Plant Pathology, Oregon State University, Key: 2082-Cordley Hall, Corvallis, Oregon 97331, USA [2] Center for Genome Research, Value: Key: and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA., Value: Key: FAU, Value: Elser, Justin Key: AU, Value: Elser J Key: AD, Value: Department of Botany and Plant Pathology, Oregon State University, 2082-Cordley Key: Hall, Corvallis, Oregon 97331, USA., Value: Key: FAU, Value: Boyd, Alexander E Key: AU, Value: Boyd AE Key: AD, Value: Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Key: Oregon 97331, USA., Value: Key: FAU, Value: Liston, Aaron Key: AU, Value: Liston A Key: AD, Value: 1] Department of Botany and Plant Pathology, Oregon State University, Key: 2082-Cordley Hall, Corvallis, Oregon 97331, USA [2] Center for Genome Research, Value: Key: and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA., Value: Key: FAU, Value: Spatafora, Joseph W Key: AU, Value: Spatafora JW Key: AD, Value: 1] Department of Botany and Plant Pathology, Oregon State University, Key: 2082-Cordley Hall, Corvallis, Oregon 97331, USA [2] Center for Genome Research, Value: Key: and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA., Value: Key: FAU, Value: Dharmwardhana, Palitha Key: AU, Value: Dharmwardhana P Key: AD, Value: Department of Botany and Plant Pathology, Oregon State University, 2082-Cordley Key: Hall, Corvallis, Oregon 97331, USA., Value: Key: FAU, Value: Raja, Rajani Key: AU, Value: Raja R Key: AD, Value: Department of Botany and Plant Pathology, Oregon State University, 2082-Cordley Key: Hall, Corvallis, Oregon 97331, USA., Value: Key: FAU, Value: Sullivan, Christopher Key: AU, Value: Sullivan C Key: AD, Value: Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Key: Oregon 97331, USA., Value: Key: FAU, Value: Romanel, Elisson Key: AU, Value: Romanel E Key: AD, Value: 1] Laboratório de Biologia Evolutiva Teórica e Aplicada, Departamento de Key: Genética, Universidade Federal do Rio de Janeiro (UFRJ), Av. Prof. Rodolpho Paulo, Value: Key: Rocco, 21949900 Rio de Janeiro, Brazil [2] Departamento de Biotecnologia, Escola, Value: Key: de Engenharia de Lorena-Universidade de São Paulo (EEL-USP), CP116, 12602-810,, Value: Key: Lorena-SP, Brazil [3] Laboratório de Genética Molecular Vegetal (LGMV),, Value: Key: Departamento de Genética, Universidade Federal do Rio de Janeiro (UFRJ), Av., Value: Key: Prof. Rodolpho Paulo Rocco, 21949900 Rio de Janeiro, Brazil., Value: Key: FAU, Value: Alves-Ferreira, Marcio Key: AU, Value: Alves-Ferreira M Key: AD, Value: Laboratório de Genética Molecular Vegetal (LGMV), Departamento de Genética, Key: Universidade Federal do Rio de Janeiro (UFRJ), Av. Prof. Rodolpho Paulo Rocco,, Value: Key: 21949900 Rio de Janeiro, Brazil., Value: Key: FAU, Value: Külheim, Carsten Key: AU, Value: Külheim C Key: AD, Value: Research School of Biology, Australian National University, Canberra 0200, Key: Australia., Value: Key: FAU, Value: Foley, William Key: AU, Value: Foley W Key: AD, Value: Research School of Biology, Australian National University, Canberra 0200, Key: Australia., Value: Key: FAU, Value: Carocha, Victor Key: AU, Value: Carocha V Key: AD, Value: 1] Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse Key: III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France [2] IICT/MNE; Palácio, Value: Key: Burnay, Value: Rua da Junqueira, 30, 1349-007 Lisboa, Portugal [3] IBET/ITQB, Av. Key: República, Quinta do Marquês, 2781-901 Oeiras, Portugal., Value: Key: FAU, Value: Paiva, Jorge Key: AU, Value: Paiva J Key: AD, Value: 1] IICT/MNE; Palácio Burnay |Rua da Junqueira, 30, 1349-007 Lisboa, Portugal [2] Key: IBET/ITQB, Av. República, Quinta do Marquês, 2781-901 Oeiras, Portugal., Value: Key: FAU, Value: Kudrna, David Key: AU, Value: Kudrna D Key: AD, Value: Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721, USA. Key: FAU, Value: Brommonschenkel, Sergio H Key: AU, Value: Brommonschenkel SH Key: AD, Value: Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-000, Brazil. Key: FAU, Value: Pasquali, Giancarlo Key: AU, Value: Pasquali G Key: AD, Value: Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, 91501-970 Key: Porto Alegre, Brazil., Value: Key: FAU, Value: Byrne, Margaret Key: AU, Value: Byrne M Key: AD, Value: Science and Conservation Division, Department of Parks and Wildlife, Locked Bag Key: 104, Bentley Delivery Centre, Western Australia 6983, Australia., Value: Key: FAU, Value: Rigault, Philippe Key: AU, Value: Rigault P Key: AD, Value: GYDLE, 1363 av. Maguire, suite 301, Québec, Quebec G1T 1Z2, Canada. Key: FAU, Value: Tibbits, Josquin Key: AU, Value: Tibbits J Key: AD, Value: Department of Environment and Primary Industries, Victorian Government, Key: Melbourne, Victoria 3085, Australia., Value: Key: FAU, Value: Spokevicius, Antanas Key: AU, Value: Spokevicius A Key: AD, Value: Melbourne School of Land and Environment, University of Melbourne, Melbourne, Key: Victoria 3010, Australia., Value: Key: FAU, Value: Jones, Rebecca C Key: AU, Value: Jones RC Key: AD, Value: School of Biological Sciences and National Centre for Future Forest Industries, Key: University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia., Value: Key: FAU, Value: Steane, Dorothy A Key: AU, Value: Steane DA Key: AD, Value: 1] School of Biological Sciences and National Centre for Future Forest Key: Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001,, Value: Key: Australia [2] Faculty of Science, Health, Education and Engineering, University, Value: Key: of the Sunshine Coast, Queensland 4558, Australia., Value: Key: FAU, Value: Vaillancourt, René E Key: AU, Value: Vaillancourt RE Key: AD, Value: School of Biological Sciences and National Centre for Future Forest Industries, Key: University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia., Value: Key: FAU, Value: Potts, Brad M Key: AU, Value: Potts BM Key: AD, Value: School of Biological Sciences and National Centre for Future Forest Industries, Key: University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia., Value: Key: FAU, Value: Joubert, Fourie Key: AU, Value: Joubert F Key: AD, Value: 1] Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Key: Pretoria 0028, South Africa [2] Bioinformatics and Computational Biology Unit,, Value: Key: Department of Biochemistry, University of Pretoria, Pretoria, Private bag X20,, Value: Key: Pretoria 0028, South Africa., Value: Key: FAU, Value: Barry, Kerrie Key: AU, Value: Barry K Key: AD, Value: US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Key: Creek, California 94598, USA., Value: Key: FAU, Value: Pappas, Georgios J Key: AU, Value: Pappas GJ Key: AD, Value: Departamento de Biologia Celular, Universidade de Brasília, Brasília 70910-900, Key: Brazil., Value: Key: FAU, Value: Strauss, Steven H Key: AU, Value: Strauss SH Key: AD, Value: Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Key: Oregon 97331, USA., Value: Key: FAU, Value: Jaiswal, Pankaj Key: AU, Value: Jaiswal P Key: AD, Value: 1] Department of Botany and Plant Pathology, Oregon State University, Key: 2082-Cordley Hall, Corvallis, Oregon 97331, USA [2] Center for Genome Research, Value: Key: and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA., Value: Key: FAU, Value: Grima-Pettenati, Jacqueline Key: AU, Value: Grima-Pettenati J Key: AD, Value: Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse Key: III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France., Value: Key: FAU, Value: Salse, Jérôme Key: AU, Value: Salse J Key: AD, Value: INRA/UBP UMR 1095, 5 Avenue de Beaulieu, 63100 Clermont Ferrand, France. Key: FAU, Value: Van de Peer, Yves Key: AU, Value: Van de Peer Y Key: AD, Value: 1] Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Key: Pretoria 0028, South Africa [2] Department of Plant Biotechnology and, Value: Key: Bioinformatics (VIB), Ghent University, Technologiepark 927, B-9000 Ghent,, Value: Key: Belgium., Value: Key: FAU, Value: Rokhsar, Daniel S Key: AU, Value: Rokhsar DS Key: AD, Value: US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Key: Creek, California 94598, USA., Value: Key: FAU, Value: Schmutz, Jeremy Key: AU, Value: Schmutz J Key: AD, Value: 1] US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Key: Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601, Value: Key: Genome Way, Huntsville, Alabama 35801, USA., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: PT, Value: Research Support, U.S. Gov't, Non-P.H.S. Key: DEP, Value: 20140611 Key: PL, Value: England Key: TA, Value: Nature Key: JT, Value: Nature Key: JID, Value: 0410462 Key: SB, Value: IM Key: MH, Value: Eucalyptus/classification/*genetics Key: MH, Value: Evolution, Molecular Key: MH, Value: Genetic Variation Key: MH, Value: *Genome, Plant Key: MH, Value: Inbreeding Key: MH, Value: Phylogeny Key: EDAT, Value: 2014/06/12 06:00 Key: MHDA, Value: 2014/07/18 06:00 Key: CRDT, Value: 2014/06/12 06:00 Key: PHST, Value: 2013/09/08 00:00 [received] Key: PHST, Value: 2014/04/02 00:00 [accepted] Key: PHST, Value: 2014/06/12 06:00 [entrez] Key: PHST, Value: 2014/06/12 06:00 [pubmed] Key: PHST, Value: 2014/07/18 06:00 [medline] Key: AID, Value: nature13308 [pii] Key: AID, Value: 10.1038/nature13308 [doi] Key: PST, Value: ppublish Key: SO, Value: Nature. 2014 Jun 19;510(7505):356-62. doi: 10.1038/nature13308. Epub 2014 Jun 11. Key: PMID, Value: 36781633 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20230215 Key: LR, Value: 20230426 Key: IS, Value: 1940-6029 (Electronic) Key: IS, Value: 1064-3745 (Linking) Key: VI, Value: 2638 Key: DP, Value: 2023 Key: TI, Value: Computational Protocol for DNA Methylation Profiling in Plants Using Restriction Key: Enzyme-Based Genome Reduction., Value: Key: PG, Value: 23-36 Key: LID, Value: 10.1007/978-1-0716-3024-2_3 [doi] Key: AB, Value: Epigenetics can be described as heritable phenotype changes that do not involve Key: alterations in the underlying DNA sequence. Having widespread implications in, Value: Key: fundamental biological phenomena, there is an increased interest in, Value: Key: characterizing epigenetic modifications and studying their functional, Value: Key: implications. DNA methylation, particularly 5-methylcytosine (5mC), stands out as, Value: Key: the most studied epigenetic mark and several methodologies have been created to, Value: Key: investigate it. With the development of next-generation sequencing technologies,, Value: Key: several approaches to DNA methylation profiling were conceived, with differences, Value: Key: in resolution and genomic scope. Besides the gold standard whole-genome bisulfite, Value: Key: sequencing, which is costly for population-scale studies, genomic reduced, Value: Key: representation methods emerged as viable alternatives to investigate methylation, Value: Key: loci. Whole-genome bisulfite sequencing provides single-base methylation, Value: Key: resolution but is costly for population-scale studies. Genomic reduction methods, Value: Key: emerged as viable alternatives to investigate a fraction of methylated loci. One, Value: Key: of such approaches uses double digestion with the restriction enzymes PstI and, Value: Key: one of the isoschizomers, MspI and HpaII, with differential sensitivity to 5mC at, Value: Key: the restriction site. Statistical comparison of sequencing reads counts obtained, Value: Key: from the two libraries for each sample (PstI-MspI and PstI-HpaII) is used to, Value: Key: infer the methylation status of thousands of cytosines. Here, we describe a, Value: Key: general overview of the technique and a computational protocol to process the, Value: Key: generated data to provide a medium-scale inventory of methylated sites in plant, Value: Key: genomes. The software is available at, Value: Key: https://github.com/wendelljpereira/DArTseqMet ., Value: Key: CI, Value: © 2023. The Author(s), under exclusive license to Springer Science+Business Key: Media, LLC, part of Springer Nature., Value: Key: FAU, Value: Pereira, Wendell Jacinto Key: AU, Value: Pereira WJ Key: AD, Value: School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Key: Gainesville, FL, USA., Value: Key: AD, Value: Department of Cell Biology, University of Brasilia, Brasilia, Distrito Federal, Key: Brazil., Value: Key: FAU, Value: de Castro Rodrigues Pappas, Marília Key: AU, Value: de Castro Rodrigues Pappas M Key: AD, Value: Embrapa Genetic Resources and Biotechnology, Brasilia, Distrito Federal, Brazil. Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Department of Cell Biology, University of Brasilia, Brasilia, Distrito Federal, Key: Brazil. gpappas@unb.br., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: PL, Value: United States Key: TA, Value: Methods Mol Biol Key: JT, Value: Methods in molecular biology (Clifton, N.J.) Key: JID, Value: 9214969 Key: RN, Value: OJ9787WBLU (hydrogen sulfite) Key: RN, Value: 0 (Sulfites) Key: RN, Value: EC 3.1.21.|(DNA Restriction Enzymes) Key: SB, Value: IM Key: MH, Value: *DNA Methylation Key: MH, Value: *Genomics/methods Key: MH, Value: Sulfites Key: MH, Value: Epigenesis, Genetic Key: MH, Value: DNA Restriction Enzymes/genetics Key: MH, Value: Sequence Analysis, DNA/methods Key: OTO, Value: NOTNLM Key: OT, Value: Computational protocol Key: OT, Value: DNA methylation Key: OT, Value: Differential expression Key: OT, Value: Methylation sensitivity Key: OT, Value: Next-generation sequencing Key: OT, Value: Restriction enzymes Key: EDAT, Value: 2023/02/14 06:00 Key: MHDA, Value: 2023/02/16 06:00 Key: CRDT, Value: 2023/02/13 23:26 Key: PHST, Value: 2023/02/13 23:26 [entrez] Key: PHST, Value: 2023/02/14 06:00 [pubmed] Key: PHST, Value: 2023/02/16 06:00 [medline] Key: AID, Value: 10.1007/978-1-0716-3024-2_3 [doi] Key: PST, Value: ppublish Key: SO, Value: Methods Mol Biol. 2023;2638:23-36. doi: 10.1007/978-1-0716-3024-2_3. Key: PMID, Value: 28054597 Key: OWN, Value: NLM Key: STAT, Value: PubMed-not-MEDLINE Key: DCOM, Value: 20180620 Key: LR, Value: 20231112 Key: IS, Value: 2045-2322 (Electronic) Key: IS, Value: 2045-2322 (Linking) Key: VI, Value: 7 Key: DP, Value: 2017 Jan 5 Key: TI, Value: Trade-offs between driving nodes and time-to-control in complex networks. Key: PG, Value: 39978 Key: LID, Value: 10.1038/srep39978 [doi] Key: LID, Value: 39978 Key: AB, Value: Recent advances in control theory provide us with efficient tools to determine Key: the minimum number of driving (or driven) nodes to steer a complex network, Value: Key: towards a desired state. Furthermore, we often need to do it within a given time, Value: Key: window, so it is of practical importance to understand the trade-offs between the, Value: Key: minimum number of driving/driven nodes and the minimum time required to reach a, Value: Key: desired state. Therefore, we introduce the notion of actuation spectrum to, Value: Key: capture such trade-offs, which we used to find that in many complex networks only, Value: Key: a small fraction of driving (or driven) nodes is required to steer the network to, Value: Key: a desired state within a relatively small time window. Furthermore, our empirical, Value: Key: studies reveal that, even though synthetic network models are designed to present, Value: Key: structural properties similar to those observed in real networks, their actuation, Value: Key: spectra can be dramatically different. Thus, it supports the need to develop new, Value: Key: synthetic network models able to replicate controllability properties of, Value: Key: real-world networks., Value: Key: FAU, Value: Pequito, Sérgio Key: AU, Value: Pequito S Key: AD, Value: Department of Electrical and Systems Engineering, School of Engineering and Key: Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104,, Value: Key: USA., Value: Key: FAU, Value: Preciado, Victor M Key: AU, Value: Preciado VM Key: AD, Value: Department of Electrical and Systems Engineering, School of Engineering and Key: Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104,, Value: Key: USA., Value: Key: FAU, Value: Barabási, Albert-László Key: AU, Value: Barabási AL Key: AD, Value: Center for Complex Network Research and Departments of Physics, Computer Science Key: and Biology, Northeastern University, Boston, Massachusetts 02115, USA., Value: Key: AD, Value: Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, Key: Massachusetts 02115, USA., Value: Key: AD, Value: Department of Medicine, Brighamand Women's Hospital, Harvard Medical School, Key: Boston, Massachusetts 02115, USA., Value: Key: FAU, Value: Pappas, George J Key: AU, Value: Pappas GJ Key: AD, Value: Department of Electrical and Systems Engineering, School of Engineering and Key: Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104,, Value: Key: USA., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: PT, Value: Research Support, U.S. Gov't, Non-P.H.S. Key: DEP, Value: 20170105 Key: PL, Value: England Key: TA, Value: Sci Rep Key: JT, Value: Scientific reports Key: JID, Value: 101563288 Key: EIN, Value: Sci Rep. 2017 Mar 09;7:43194. PMID: 28276443 Key: PMC, Value: PMC5215470 Key: EDAT, Value: 2017/01/06 06:00 Key: MHDA, Value: 2017/01/06 06:01 Key: PMCR, Value: 2017/01/05 Key: CRDT, Value: 2017/01/06 06:00 Key: PHST, Value: 2016/09/28 00:00 [received] Key: PHST, Value: 2016/11/29 00:00 [accepted] Key: PHST, Value: 2017/01/06 06:00 [entrez] Key: PHST, Value: 2017/01/06 06:00 [pubmed] Key: PHST, Value: 2017/01/06 06:01 [medline] Key: PHST, Value: 2017/01/05 00:00 [pmc-release] Key: AID, Value: srep39978 [pii] Key: AID, Value: 10.1038/srep39978 [doi] Key: PST, Value: epublish Key: SO, Value: Sci Rep. 2017 Jan 5;7:39978. doi: 10.1038/srep39978. Key: PMID, Value: 30483479 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20190904 Key: LR, Value: 20190904 Key: IS, Value: 2235-2988 (Electronic) Key: IS, Value: 2235-2988 (Linking) Key: VI, Value: 8 Key: DP, Value: 2018 Key: TI, Value: A Wor1-Like Transcription Factor Is Essential for Virulence of Cryptococcus Key: neoformans., Value: Key: PG, Value: 369 Key: LID, Value: 10.3389/fcimb.2018.00369 [doi] Key: LID, Value: 369 Key: AB, Value: Gti1/Pac2 transcription factors occur exclusively in fungi and their roles vary Key: according to species, including regulating morphological transition and, Value: Key: virulence, mating and secondary metabolism. Many of these functions are important, Value: Key: for fungal pathogenesis. We therefore hypothesized that one of the two proteins, Value: Key: of this family in Cryptococcus neoformans, a major pathogen of humans, would also, Value: Key: control virulence-associated cellular processes. Elimination of this protein in, Value: Key: C. neoformans results in reduced polysaccharide capsule expression and defective, Value: Key: cytokinesis and growth at 37°C. The mutant loses virulence in a mouse model of, Value: Key: cryptococcal infection and retains only partial virulence in the Galleria, Value: Key: mellonella alternative model at 30°C. We performed RNA-Seq experiments on the, Value: Key: mutant and found abolished transcription of genes that, in combination, are known, Value: Key: to account for all the observed phenotypes. The protein has been named Required, Value: Key: for cytokinesis and virulence 1 (Rcv1)., Value: Key: FAU, Value: Paes, Hugo Costa Key: AU, Value: Paes HC Key: AD, Value: Clinical Medicine Division, University of Brasília Medical School, Brasília, Key: Brazil., Value: Key: FAU, Value: Derengowski, Lorena da Silveira Key: AU, Value: Derengowski LDS Key: AD, Value: Military College, Brasília, Brazil. Key: FAU, Value: Peconick, Luisa Defranco Ferreira Key: AU, Value: Peconick LDF Key: AD, Value: Ceilândia College, University of Brasília, Brasília, Brazil. Key: FAU, Value: Albuquerque, Patrícia Key: AU, Value: Albuquerque P Key: AD, Value: Ceilândia College, University of Brasília, Brasília, Brazil. Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Department of Cell Biology, Institute of Biological Sciences, University of Key: Brasília, Brasília, Brazil., Value: Key: FAU, Value: Nicola, André Moraes Key: AU, Value: Nicola AM Key: AD, Value: Pathology Division, University of Brasília Medical School, Brasília, Brazil. Key: FAU, Value: Silva, Fabiana Brandão Alves Key: AU, Value: Silva FBA Key: AD, Value: Department of Biomedicine, Paulista University, Brasília, Brazil. Key: FAU, Value: Vallim, Marcelo Afonso Key: AU, Value: Vallim MA Key: AD, Value: Cellular and Molecular Biology Division, Biological Sciences Department, São Key: Paulo Federal University, São Paulo, Brazil., Value: Key: FAU, Value: Alspaugh, J Andrew Key: AU, Value: Alspaugh JA Key: AD, Value: Department of Medicine, School of Medicine, Duke University, Durham, NC, United Key: States., Value: Key: FAU, Value: Felipe, Maria Sueli Soares Key: AU, Value: Felipe MSS Key: AD, Value: Graduate School in Genomic Sciences, Catholic University of Brasília, Brasília, Key: Brazil., Value: Key: FAU, Value: Fernandes, Larissa Key: AU, Value: Fernandes L Key: AD, Value: Ceilândia College, University of Brasília, Brasília, Brazil. Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20181113 Key: PL, Value: Switzerland Key: TA, Value: Front Cell Infect Microbiol Key: JT, Value: Frontiers in cellular and infection microbiology Key: JID, Value: 101585359 Key: RN, Value: 0 (Polysaccharides) Key: RN, Value: 0 (Transcription Factors) Key: SB, Value: IM Key: MH, Value: Animals Key: MH, Value: Cryptococcosis/microbiology/*pathology Key: MH, Value: Cryptococcus neoformans/*enzymology/growth & development/*pathogenicity Key: MH, Value: Cytokinesis Key: MH, Value: Disease Models, Animal Key: MH, Value: Gene Deletion Key: MH, Value: Gene Expression Profiling Key: MH, Value: Lepidoptera Key: MH, Value: Mice Key: MH, Value: Polysaccharides/metabolism Key: MH, Value: Sequence Analysis, RNA Key: MH, Value: Temperature Key: MH, Value: Transcription Factors/genetics/*metabolism Key: MH, Value: Virulence Key: PMC, Value: PMC6243373 Key: OTO, Value: NOTNLM Key: OT, Value: Cryptococcus neoformans Key: OT, Value: capsule Key: OT, Value: cytokinesis Key: OT, Value: transcription factor Key: OT, Value: virulence Key: EDAT, Value: 2018/11/30 06:00 Key: MHDA, Value: 2019/09/05 06:00 Key: PMCR, Value: 2018/01/01 Key: CRDT, Value: 2018/11/29 06:00 Key: PHST, Value: 2018/08/01 00:00 [received] Key: PHST, Value: 2018/10/03 00:00 [accepted] Key: PHST, Value: 2018/11/29 06:00 [entrez] Key: PHST, Value: 2018/11/30 06:00 [pubmed] Key: PHST, Value: 2019/09/05 06:00 [medline] Key: PHST, Value: 2018/01/01 00:00 [pmc-release] Key: AID, Value: 10.3389/fcimb.2018.00369 [doi] Key: PST, Value: epublish Key: SO, Value: Front Cell Infect Microbiol. 2018 Nov 13;8:369. doi: 10.3389/fcimb.2018.00369. Key: eCollection 2018., Value: Key: PMID, Value: 29954895 Key: OWN, Value: NLM Key: STAT, Value: PubMed-not-MEDLINE Key: LR, Value: 20240328 Key: IS, Value: 2169-8287 (Electronic) Key: VI, Value: 6 Key: IP, Value: 26 Key: DP, Value: 2018 Jun 28 Key: TI, Value: Draft Genome Sequence of the Antimicrobial-Producing Strain Paenibacillus elgii Key: AC13., Value: Key: LID, Value: 10.1128/genomeA.00573-18 [doi] Key: LID, Value: e00573-18 Key: AB, Value: A Paenibacillus elgii strain isolated from soil samples from Cerrado, Brazil, Key: showed antimicrobial activity. Its genome sequence was acquired (GS20 FLX, Value: Key: Titanium 454 platform) and comprises 108 contigs (N(50), 198,427 bp) and 6,810, Value: Key: predicted sequences. Here, we shed some light on the antimicrobial genes of the, Value: Key: strain, including a nonribosomal peptide synthetase (NRPS) module identified as, Value: Key: part of a pelgipeptin gene cluster., Value: Key: CI, Value: Copyright © 2018 Ortega et al. Key: FAU, Value: Ortega, Daniel Barros Key: AU, Value: Ortega DB Key: AUID, Value: ORCID: 0000-0003-0721-7010 Key: AD, Value: Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Key: Brasília, Brasília, Distrito Federal, Brazil., Value: Key: FAU, Value: Costa, Rosiane Andrade Key: AU, Value: Costa RA Key: AD, Value: Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Key: Brasília, Brasília, Distrito Federal, Brazil., Value: Key: FAU, Value: Pires, Allan Silva Key: AU, Value: Pires AS Key: AD, Value: Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Key: Brasília, Brasília, Distrito Federal, Brazil., Value: Key: FAU, Value: Araújo, Thiago Fellipe Key: AU, Value: Araújo TF Key: AD, Value: Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Key: Brasília, Brasília, Distrito Federal, Brazil., Value: Key: FAU, Value: Araújo, Janaina Fernandez Key: AU, Value: Araújo JF Key: AD, Value: Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Key: Brasília, Brasília, Distrito Federal, Brazil., Value: Key: FAU, Value: Kurokawa, Adriane Silva Key: AU, Value: Kurokawa AS Key: AD, Value: Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Key: Brasília, Brasília, Distrito Federal, Brazil., Value: Key: FAU, Value: Magalhães, Beatriz Simas Key: AU, Value: Magalhães BS Key: AD, Value: Integra Bioprocessos e Análises, Brasília, Distrito Federal, Brazil. Key: FAU, Value: Reis, Alessandra Maria Moreira Key: AU, Value: Reis AMM Key: AD, Value: Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Key: Brasília, Brasília, Distrito Federal, Brazil., Value: Key: FAU, Value: Franco, Octávio Luís Key: AU, Value: Franco OL Key: AUID, Value: ORCID: 0000-0001-9546-0525 Key: AD, Value: Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Key: Brasília, Brasília, Distrito Federal, Brazil., Value: Key: AD, Value: S-Inova Biotech, Biotechnology Postgraduate Program, Universidade Católica Dom Key: Bosco, Campo Grande, Mato Grosso do Sul, Brazil., Value: Key: FAU, Value: Kruger, Ricardo Henrique Key: AU, Value: Kruger RH Key: AD, Value: Graduate Program in Molecular Biology, Universidade de Brasília, Brasília, Key: Distrito Federal, Brazil., Value: Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Graduate Program in Molecular Biology, Universidade de Brasília, Brasília, Key: Distrito Federal, Brazil., Value: Key: FAU, Value: Barreto, Cristine Chaves Key: AU, Value: Barreto CC Key: AD, Value: Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Key: Brasília, Brasília, Distrito Federal, Brazil criscbarreto@gmail.com., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: DEP, Value: 20180628 Key: PL, Value: United States Key: TA, Value: Genome Announc Key: JT, Value: Genome announcements Key: JID, Value: 101595808 Key: PMC, Value: PMC6025928 Key: EDAT, Value: 2018/06/30 06:00 Key: MHDA, Value: 2018/06/30 06:01 Key: PMCR, Value: 2018/06/28 Key: CRDT, Value: 2018/06/30 06:00 Key: PHST, Value: 2018/06/30 06:00 [entrez] Key: PHST, Value: 2018/06/30 06:00 [pubmed] Key: PHST, Value: 2018/06/30 06:01 [medline] Key: PHST, Value: 2018/06/28 00:00 [pmc-release] Key: AID, Value: 6/26/e00573-18 [pii] Key: AID, Value: genomeA00573-18 [pii] Key: AID, Value: 10.1128/genomeA.00573-18 [doi] Key: PST, Value: epublish Key: SO, Value: Genome Announc. 2018 Jun 28;6(26):e00573-18. doi: 10.1128/genomeA.00573-18. Key: PMID, Value: 38082179 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20240125 Key: LR, Value: 20240131 Key: IS, Value: 2157-846X (Electronic) Key: IS, Value: 2157-846X (Linking) Key: VI, Value: 8 Key: IP, Value: 1 Key: DP, Value: 2024 Jan Key: TI, Value: Macroscopic resting-state brain dynamics are best described by linear models. Key: PG, Value: 68-84 Key: LID, Value: 10.1038/s41551-023-01117-y [doi] Key: AB, Value: It is typically assumed that large networks of neurons exhibit a large repertoire Key: of nonlinear behaviours. Here we challenge this assumption by leveraging, Value: Key: mathematical models derived from measurements of local field potentials via, Value: Key: intracranial electroencephalography and of whole-brain, Value: Key: blood-oxygen-level-dependent brain activity via functional magnetic resonance, Value: Key: imaging. We used state-of-the-art linear and nonlinear families of models to, Value: Key: describe spontaneous resting-state activity of 700 participants in the Human, Value: Key: Connectome Project and 122 participants in the Restoring Active Memory project., Value: Key: We found that linear autoregressive models provide the best fit across both data, Value: Key: types and three performance metrics: predictive power, computational complexity, Value: Key: and the extent of the residual dynamics unexplained by the model. To explain this, Value: Key: observation, we show that microscopic nonlinear dynamics can be counteracted or, Value: Key: masked by four factors associated with macroscopic dynamics: averaging over space, Value: Key: and over time, which are inherent to aggregated macroscopic brain activity, and, Value: Key: observation noise and limited data samples, which stem from technological, Value: Key: limitations. We therefore argue that easier-to-interpret linear models can, Value: Key: faithfully describe macroscopic brain dynamics during resting-state conditions., Value: Key: CI, Value: © 2023. The Author(s). Key: FAU, Value: Nozari, Erfan Key: AU, Value: Nozari E Key: AUID, Value: ORCID: 0000-0002-1981-8959 Key: AD, Value: Department of Mechanical Engineering, University of California, Riverside, CA, Key: USA., Value: Key: AD, Value: Department of Electrical and Computer Engineering, University of California, Key: Riverside, CA, USA., Value: Key: AD, Value: Department of Bioengineering, University of California, Riverside, CA, USA. Key: FAU, Value: Bertolero, Maxwell A Key: AU, Value: Bertolero MA Key: AD, Value: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA. Key: FAU, Value: Stiso, Jennifer Key: AU, Value: Stiso J Key: AUID, Value: ORCID: 0000-0002-3295-586X Key: AD, Value: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA. Key: AD, Value: Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA. Key: FAU, Value: Caciagli, Lorenzo Key: AU, Value: Caciagli L Key: AD, Value: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA. Key: FAU, Value: Cornblath, Eli J Key: AU, Value: Cornblath EJ Key: AUID, Value: ORCID: 0000-0002-2619-8778 Key: AD, Value: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA. Key: AD, Value: Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA. Key: FAU, Value: He, Xiaosong Key: AU, Value: He X Key: AUID, Value: ORCID: 0000-0002-7941-2918 Key: AD, Value: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA. Key: FAU, Value: Mahadevan, Arun S Key: AU, Value: Mahadevan AS Key: AD, Value: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA. Key: FAU, Value: Pappas, George J Key: AU, Value: Pappas GJ Key: AUID, Value: ORCID: 0000-0001-9081-0637 Key: AD, Value: Department of Electrical and Systems Engineering, University of Pennsylvania, Key: Philadelphia, PA, USA., Value: Key: FAU, Value: Bassett, Dani S Key: AU, Value: Bassett DS Key: AUID, Value: ORCID: 0000-0002-6183-4493 Key: AD, Value: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA. Key: dsb@seas.upenn.edu., Value: Key: AD, Value: Department of Electrical and Systems Engineering, University of Pennsylvania, Key: Philadelphia, PA, USA. dsb@seas.upenn.edu., Value: Key: AD, Value: Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Key: PA, USA. dsb@seas.upenn.edu., Value: Key: AD, Value: Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA. Key: dsb@seas.upenn.edu., Value: Key: AD, Value: Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA. Key: dsb@seas.upenn.edu., Value: Key: AD, Value: Santa Fe Institute, Santa Fe, NM, USA. dsb@seas.upenn.edu. Key: LA, Value: eng Key: GR, Value: 1926757/National Science Foundation (NSF)/ Key: GR, Value: 1F31MH120925-01A/U.S. Department of Health & Human Services | NIH | National Key: Institute of Mental Health (NIMH)/, Value: Key: GR, Value: F30 MH118871-01/U.S. Department of Health & Human Services | NIH | National Key: Institute of Mental Health (NIMH)/, Value: Key: GR, Value: W911NF-16-1-0474/United States Department of Defense | United States Army | U.S. Key: Army Research, Development and Engineering Command, Value: Army Research Office (ARO)/ Key: PT, Value: Journal Article Key: DEP, Value: 20231211 Key: PL, Value: England Key: TA, Value: Nat Biomed Eng Key: JT, Value: Nature biomedical engineering Key: JID, Value: 101696896 Key: SB, Value: IM Key: MH, Value: Humans Key: MH, Value: Linear Models Key: MH, Value: *Brain/physiology Key: MH, Value: *Connectome/methods Key: MH, Value: Magnetic Resonance Imaging/methods Key: MH, Value: Models, Theoretical Key: EDAT, Value: 2023/12/12 00:42 Key: MHDA, Value: 2024/01/25 06:44 Key: CRDT, Value: 2023/12/11 23:51 Key: PHST, Value: 2020/12/23 00:00 [received] Key: PHST, Value: 2023/09/26 00:00 [accepted] Key: PHST, Value: 2024/01/25 06:44 [medline] Key: PHST, Value: 2023/12/12 00:42 [pubmed] Key: PHST, Value: 2023/12/11 23:51 [entrez] Key: AID, Value: 10.1038/s41551-023-01117-y [pii] Key: AID, Value: 10.1038/s41551-023-01117-y [doi] Key: PST, Value: ppublish Key: SO, Value: Nat Biomed Eng. 2024 Jan;8(1):68-84. doi: 10.1038/s41551-023-01117-y. Epub 2023 Key: Dec 11., Value: Key: PMID, Value: 32497070 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20200821 Key: LR, Value: 20200821 Key: IS, Value: 1932-6203 (Electronic) Key: IS, Value: 1932-6203 (Linking) Key: VI, Value: 15 Key: IP, Value: 6 Key: DP, Value: 2020 Key: TI, Value: A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT Key: sequencing., Value: Key: PG, Value: e0233800 Key: LID, Value: 10.1371/journal.pone.0233800 [doi] Key: LID, Value: e0233800 Key: AB, Value: Several studies suggest the relation of DNA methylation to diseases in humans and Key: important phenotypes in plants drawing attention to this epigenetic mark as an, Value: Key: important source of variability. In the last decades, several methodologies were, Value: Key: developed to assess the methylation state of a genome. However, there is still a, Value: Key: lack of affordable and precise methods for genome wide analysis in large sample, Value: Key: size studies. Methyl sensitive double digestion MS-DArT sequencing method emerges, Value: Key: as a promising alternative for methylation profiling. We developed a, Value: Key: computational pipeline for the identification of DNA methylation using, Value: Key: MS-DArT-seq data and carried out a pilot study using the Eucalyptus grandis tree, Value: Key: sequenced for the species reference genome. Using a statistic framework as in, Value: Key: differential expression analysis, 72,515 genomic sites were investigated and, Value: Key: 5,846 methylated sites identified, several tissue specific, distributed along the, Value: Key: species 11 chromosomes. We highlight a bias towards identification of DNA, Value: Key: methylation in genic regions and the identification of 2,783 genes and 842, Value: Key: transposons containing methylated sites. Comparison with WGBS, DNA sequencing, Value: Key: after treatment with bisulfite, data demonstrated a precision rate higher than, Value: Key: 95% for our approach. The availability of a reference genome is useful for, Value: Key: determining the genomic context of methylated sites but not imperative, making, Value: Key: this approach suitable for any species. Our approach provides a cost effective,, Value: Key: broad and reliable examination of DNA methylation profile on MspI/HpaII, Value: Key: restriction sites, is fully reproducible and the source code is available on, Value: Key: GitHub (https://github.com/wendelljpereira/ms-dart-seq)., Value: Key: FAU, Value: Pereira, Wendell Jacinto Key: AU, Value: Pereira WJ Key: AUID, Value: ORCID: 0000-0003-1019-6281 Key: AD, Value: Department of Cell Biology, University of Brasília, Brasília, Distrito Federal, Key: Brazil., Value: Key: FAU, Value: Pappas, Marília de Castro Rodrigues Key: AU, Value: Pappas MCR Key: AD, Value: Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil. Key: FAU, Value: Grattapaglia, Dario Key: AU, Value: Grattapaglia D Key: AUID, Value: ORCID: 0000-0002-0050-970X Key: AD, Value: Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil. Key: AD, Value: Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil. Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Department of Cell Biology, University of Brasília, Brasília, Distrito Federal, Key: Brazil., Value: Key: LA, Value: eng Key: SI, Value: figshare/10.6084/m9.figshare.10305431 Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20200604 Key: PL, Value: United States Key: TA, Value: PLoS One Key: JT, Value: PloS one Key: JID, Value: 101285081 Key: RN, Value: 0 (DNA Transposable Elements) Key: RN, Value: 0 (Sulfites) Key: RN, Value: EC 3.1.21.|(DNA Restriction Enzymes) Key: RN, Value: OJ9787WBLU (hydrogen sulfite) Key: SB, Value: IM Key: MH, Value: Chromosomes, Plant/genetics Key: MH, Value: *Cost-Benefit Analysis Key: MH, Value: DNA Methylation/*genetics Key: MH, Value: DNA Restriction Enzymes/genetics Key: MH, Value: DNA Transposable Elements/genetics Key: MH, Value: Eucalyptus/*genetics Key: MH, Value: Genes, Plant/genetics Key: MH, Value: Genotyping Techniques/economics/*methods Key: MH, Value: High-Throughput Nucleotide Sequencing/economics/*methods Key: MH, Value: Pilot Projects Key: MH, Value: Plant Leaves/*genetics Key: MH, Value: Reproducibility of Results Key: MH, Value: Restriction Mapping Key: MH, Value: Sequence Analysis, DNA/economics/*methods Key: MH, Value: Sulfites/pharmacology Key: MH, Value: Trees/*genetics Key: PMC, Value: PMC7272069 Key: COIS, Value: Authors MRP and DG are employed by EMBRAPA, but this commercial affiliation does Key: not alter our adherence to all PLOS ONE policies on sharing data and materials., Value: Key: EDAT, Value: 2020/06/05 06:00 Key: MHDA, Value: 2020/08/22 06:00 Key: PMCR, Value: 2020/06/04 Key: CRDT, Value: 2020/06/05 06:00 Key: PHST, Value: 2019/12/11 00:00 [received] Key: PHST, Value: 2020/05/12 00:00 [accepted] Key: PHST, Value: 2020/06/05 06:00 [entrez] Key: PHST, Value: 2020/06/05 06:00 [pubmed] Key: PHST, Value: 2020/08/22 06:00 [medline] Key: PHST, Value: 2020/06/04 00:00 [pmc-release] Key: AID, Value: PONE-D-19-34321 [pii] Key: AID, Value: 10.1371/journal.pone.0233800 [doi] Key: PST, Value: epublish Key: SO, Value: PLoS One. 2020 Jun 4;15(6):e0233800. doi: 10.1371/journal.pone.0233800. Key: eCollection 2020., Value: Key: PMID, Value: 33935984 Key: OWN, Value: NLM Key: STAT, Value: PubMed-not-MEDLINE Key: LR, Value: 20210504 Key: IS, Value: 1664-302X (Print) Key: IS, Value: 1664-302X (Electronic) Key: IS, Value: 1664-302X (Linking) Key: VI, Value: 12 Key: DP, Value: 2021 Key: TI, Value: Multidrug-Resistant (MDR) Klebsiella variicola Strains Isolated in a Brazilian Key: Hospital Belong to New Clones., Value: Key: PG, Value: 604031 Key: LID, Value: 10.3389/fmicb.2021.604031 [doi] Key: LID, Value: 604031 Key: AB, Value: Klebsiella variicola is mainly associated with opportunistic infections and Key: frequently identified as Klebsiella pneumoniae. This misidentification implies a, Value: Key: wrong epidemiology result as well as incorrect attribution to K. pneumoniae as, Value: Key: the etiology of some severe infections. Recently, huge efforts have been made to, Value: Key: study K. variicola, however, the biological aspects of this species are still, Value: Key: unclear. Here we characterized five K. variicola strains initially identified as, Value: Key: K. pneumoniae, with a Vitek-2 System and 16S rRNA sequencing. One-step multiplex, Value: Key: polymerase chain reaction and Whole Genome Sequencing (WGS) identified them as K., Value: Key: variicola. Additionally, WGS analysis showed that all the strains are closely, Value: Key: related with K. variicola genomes, forming a clustered group, apart from K., Value: Key: pneumoniae and K. quasipneumoniae. Multilocus sequence typing analysis showed, Value: Key: four different sequence types (STs) among the strains and for two of them (Kv97, Value: Key: and Kv104) the same ST was assigned. All strains were multidrug-resistant (MDR), Value: Key: and three showed virulence phenotypes including invasion capacity to epithelial, Value: Key: cells, and survival in human blood and serum. These results showed the emergence, Value: Key: of new K. variicola clones with pathogenic potential to colonize and cause, Value: Key: infection in different tissues. These characteristics associated with MDR strains, Value: Key: raise great concern for human health., Value: Key: CI, Value: Copyright © 2021 Campos, Almeida, Almeida, Nakamura-Silva, Oliveira-Silva, Sousa, Key: Cerdeira, Lincopan, Pappas and Pitondo-Silva., Value: Key: FAU, Value: de Campos, Tatiana Amabile Key: AU, Value: de Campos TA Key: AD, Value: Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade Key: de Brasília, Brasília, Brazil., Value: Key: AD, Value: Programa de Pós-graduação em Biologia Microbiana, Universidade de Brasília, Key: Brasília, Brazil., Value: Key: FAU, Value: de Almeida, Felipe Marques Key: AU, Value: de Almeida FM Key: AD, Value: Programa de Pós-graduação em Biologia Molecular, Universidade de Brasília, Key: Brasília, Brazil., Value: Key: FAU, Value: de Almeida, Ana Paula Cardoso Key: AU, Value: de Almeida APC Key: AD, Value: Programa de Pós-graduação em Biologia Microbiana, Universidade de Brasília, Key: Brasília, Brazil., Value: Key: FAU, Value: Nakamura-Silva, Rafael Key: AU, Value: Nakamura-Silva R Key: AD, Value: Programa de Pós-graduação em Tecnologia Ambiental, Universidade de Ribeirão Key: Preto, Ribeirão Preto, Brazil., Value: Key: FAU, Value: Oliveira-Silva, Mariana Key: AU, Value: Oliveira-Silva M Key: AD, Value: Programa de Pós-graduação em Tecnologia Ambiental, Universidade de Ribeirão Key: Preto, Ribeirão Preto, Brazil., Value: Key: FAU, Value: de Sousa, Isabela Felix Alencar Key: AU, Value: de Sousa IFA Key: AD, Value: Programa de Pós-graduação em Biologia Molecular, Universidade de Brasília, Key: Brasília, Brazil., Value: Key: FAU, Value: Cerdeira, Louise Key: AU, Value: Cerdeira L Key: AD, Value: Instituto de Ciências Biológicas, Universidade de São Paulo, São Paulo, Brazil. Key: AD, Value: Department of Infectious Diseases, Central Clinical School, Monash University, Key: Melbourne, VIC, Australia., Value: Key: FAU, Value: Lincopan, Nilton Key: AU, Value: Lincopan N Key: AD, Value: Department of Infectious Diseases, Central Clinical School, Monash University, Key: Melbourne, VIC, Australia., Value: Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade Key: de Brasília, Brasília, Brazil., Value: Key: AD, Value: Programa de Pós-graduação em Biologia Molecular, Universidade de Brasília, Key: Brasília, Brazil., Value: Key: FAU, Value: Pitondo-Silva, André Key: AU, Value: Pitondo-Silva A Key: AD, Value: Programa de Pós-graduação em Tecnologia Ambiental, Universidade de Ribeirão Key: Preto, Ribeirão Preto, Brazil., Value: Key: AD, Value: Programa de Pós-graduação em Odontologia, Universidade de Ribeirão Preto, Key: Ribeirão Preto, Brazil., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: DEP, Value: 20210416 Key: PL, Value: Switzerland Key: TA, Value: Front Microbiol Key: JT, Value: Frontiers in microbiology Key: JID, Value: 101548977 Key: PMC, Value: PMC8085564 Key: OTO, Value: NOTNLM Key: OT, Value: Klebsiella variicola Key: OT, Value: antimicrobial resistance Key: OT, Value: brazilian clones Key: OT, Value: multidrug-resistant Key: OT, Value: pathogenicity Key: OT, Value: whole genome sequence Key: COIS, Value: The authors declare that the research was conducted in the absence of any Key: commercial or financial relationships that could be construed as a potential, Value: Key: conflict of interest., Value: Key: EDAT, Value: 2021/05/04 06:00 Key: MHDA, Value: 2021/05/04 06:01 Key: PMCR, Value: 2021/04/16 Key: CRDT, Value: 2021/05/03 06:11 Key: PHST, Value: 2020/09/08 00:00 [received] Key: PHST, Value: 2021/03/25 00:00 [accepted] Key: PHST, Value: 2021/05/03 06:11 [entrez] Key: PHST, Value: 2021/05/04 06:00 [pubmed] Key: PHST, Value: 2021/05/04 06:01 [medline] Key: PHST, Value: 2021/04/16 00:00 [pmc-release] Key: AID, Value: 10.3389/fmicb.2021.604031 [doi] Key: PST, Value: epublish Key: SO, Value: Front Microbiol. 2021 Apr 16;12:604031. doi: 10.3389/fmicb.2021.604031. Key: eCollection 2021., Value: Key: PMID, Value: 37512901 Key: OWN, Value: NLM Key: STAT, Value: PubMed-not-MEDLINE Key: LR, Value: 20230801 Key: IS, Value: 2076-2607 (Print) Key: IS, Value: 2076-2607 (Electronic) Key: IS, Value: 2076-2607 (Linking) Key: VI, Value: 11 Key: IP, Value: 7 Key: DP, Value: 2023 Jun 30 Key: TI, Value: Complete Genome Sequence of Pantoea stewartii RON18713 from Brazil Nut Tree Key: Phyllosphere Reveals Genes Involved in Plant Growth Promotion., Value: Key: LID, Value: 10.3390/microorganisms11071729 [doi] Key: LID, Value: 1729 Key: AB, Value: The Amazonian rainforest is a hyper-diverse ecosystem in the number of species Key: and the myriad of intertaxon relationships that are mostly understudied. In order, Value: Key: to characterize a dominant and economically important Amazonian species, the, Value: Key: Brazil nut tree (Bertholletia excelsa Bonpl.), at the genome level, wegenerated, Value: Key: high-coverage long-read sequencing data from the leaves of a single individual., Value: Key: The genome assembly revealed an unexpected discovery: two circular contigs that, Value: Key: could be assigned to the chromosome and a plasmid of a Pantoea stewartii strain., Value: Key: Comparative genomics revealed that this strain belongs to the indologenes, Value: Key: subspecies and displays high synteny with other strains isolated from diseased, Value: Key: leaves of the neotropical palm Bactris gasipaes Kunth. Investigation of, Value: Key: pathogenicity-related genes revealed the absence of the entire type III secretion, Value: Key: system gene cluster in the plasmid, which was otherwise highly similar to a, Value: Key: plasmid from an isolate known to cause disease in Dracaena sanderiana Mast. In, Value: Key: contrast, several genes associated with plant-growth promoting traits were, Value: Key: detected, including genes involved in indole-3-acetic acid (IAA) production,, Value: Key: phosphate solubilization, and biosynthesis of siderophores. In summary, we report, Value: Key: the genome of an uncultivated P. stewartii subsp. indologenes strain associated, Value: Key: with the Brazil nut tree and potentially a plant growth-promoting bacteria., Value: Key: FAU, Value: Rocha, Rodrigo Theodoro Key: AU, Value: Rocha RT Key: AUID, Value: ORCID: 0000-0001-5624-8644 Key: AD, Value: Department of Cell Biology, University of Brasília, Brasília 70910-900, DF, Key: Brazil., Value: Key: FAU, Value: de Almeida, Felipe Marques Key: AU, Value: de Almeida FM Key: AUID, Value: ORCID: 0000-0002-6855-3379 Key: AD, Value: Department of Cell Biology, University of Brasília, Brasília 70910-900, DF, Key: Brazil., Value: Key: FAU, Value: Pappas, Marília C R Key: AU, Value: Pappas MCR Key: AUID, Value: ORCID: 0000-0002-4680-0199 Key: AD, Value: EMBRAPA Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil. Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: AUID, Value: ORCID: 0000-0002-1100-976X Key: AD, Value: Department of Cell Biology, University of Brasília, Brasília 70910-900, DF, Key: Brazil., Value: Key: FAU, Value: Martins, Karina Key: AU, Value: Martins K Key: AUID, Value: ORCID: 0000-0002-9272-1475 Key: AD, Value: Department of Biology, Federal University of São Carlos, Sorocaba 18052-780, SP, Key: Brazil., Value: Key: LA, Value: eng Key: GR, Value: 17/06102-0/São Paulo Research Foundation/ Key: PT, Value: Journal Article Key: DEP, Value: 20230630 Key: PL, Value: Switzerland Key: TA, Value: Microorganisms Key: JT, Value: Microorganisms Key: JID, Value: 101625893 Key: PMC, Value: PMC10383142 Key: OTO, Value: NOTNLM Key: OT, Value: Amazon rainforest Key: OT, Value: Brazil nut tree Key: OT, Value: Pantoea stewartii subsp. indologenes Key: OT, Value: genome Key: OT, Value: plant–microbe interaction Key: OT, Value: type III secretion system Key: COIS, Value: The authors declare no conflict of interest. Key: EDAT, Value: 2023/07/29 11:45 Key: MHDA, Value: 2023/07/29 11:46 Key: PMCR, Value: 2023/06/30 Key: CRDT, Value: 2023/07/29 01:32 Key: PHST, Value: 2023/04/17 00:00 [received] Key: PHST, Value: 2023/06/09 00:00 [revised] Key: PHST, Value: 2023/06/26 00:00 [accepted] Key: PHST, Value: 2023/07/29 11:46 [medline] Key: PHST, Value: 2023/07/29 11:45 [pubmed] Key: PHST, Value: 2023/07/29 01:32 [entrez] Key: PHST, Value: 2023/06/30 00:00 [pmc-release] Key: AID, Value: microorganisms11071729 [pii] Key: AID, Value: microorganisms-11-01729 [pii] Key: AID, Value: 10.3390/microorganisms11071729 [doi] Key: PST, Value: epublish Key: SO, Value: Microorganisms. 2023 Jun 30;11(7):1729. doi: 10.3390/microorganisms11071729. Key: PMID, Value: 32198121 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20210419 Key: LR, Value: 20210419 Key: IS, Value: 1096-0937 (Electronic) Key: IS, Value: 1087-1845 (Linking) Key: VI, Value: 138 Key: DP, Value: 2020 May Key: TI, Value: Exploring the Brazilian diversity of Aspergillus sp. strains for lovastatin and Key: itaconic acid production., Value: Key: PG, Value: 103367 Key: LID, Value: S1087-1845(20)30058-X [pii] Key: LID, Value: 10.1016/j.fgb.2020.103367 [doi] Key: AB, Value: Filamentous fungi are well known for producing secondary metabolites applied in Key: various industrial segments. Among these, lovastatin and itaconic acid, produced, Value: Key: by Aspergillus terreus, have applications in the pharmaceutical and chemical, Value: Key: industries. Lovastatin is primarily used for the control of hypercholesterolemia,, Value: Key: while itaconic acid is a building block for the production of synthetic fibers,, Value: Key: coating adhesives, among others. In this study, for the first time, 35 strains of, Value: Key: Aspergillus sp. from four Brazilian culture collections were evaluated for, Value: Key: lovastatin and itaconic acid production and compared to a reference strain, ATCC, Value: Key: 20542. From an initial screening, the strains ATCC 20542, URM 224, URM1876, URM, Value: Key: 5061, URM 5254, URM 5256, URM 5650, and URM 5961 were selected for genomic, Value: Key: comparison. Among tested strains, the locus corresponding to the lovastatin, Value: Key: genomic cluster was assembled, showing that all genes essential for lovastatin, Value: Key: biosynthesis were present in producing URM 5961 and URM 5650 strains, with 100%, Value: Key: and 98.5% similarity to ATCC 20542, respectively. However, in the no producing, Value: Key: URM 1876, URM 224, URM 5254, URM 5061, and URM 5256 strains, this cluster was, Value: Key: either fragmented or missing. Among the 35 strains evaluated for itaconic acid, Value: Key: production in this study, only three strains had titers above 0.5 g/L, 16 strains, Value: Key: had production below 0.5 g/L, and the remaining 18 strains had no production,, Value: Key: with the highest production of itaconic acid observed in the URM 5254 strain with, Value: Key: 2.2 g/L. The essential genes for itaconic acid production, mttA, cadA msfA were, Value: Key: also mapped, where all three genes linked to itaconic acid production were found, Value: Key: in a single contig in the assembly of each strain. In contrast to lovastatin, Value: Key: loci, there is no correlation between the level of itaconic acid production and, Value: Key: genetic polymorphisms in the genes associated with its biosynthesis., Value: Key: CI, Value: Copyright © 2020 Elsevier Inc. All rights reserved. Key: FAU, Value: Rodrigues, Kelly Assis Key: AU, Value: Rodrigues KA Key: AD, Value: Grupo Engenharia de Biocatalisadores, Instituto de Ciências Biológicas, Key: Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil; Pós-Graduação em, Value: Key: Biologia Molecular, Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil., Value: Key: FAU, Value: Rocha, Rodrigo Theodoro Key: AU, Value: Rocha RT Key: AD, Value: Pós-Graduação em Biologia Molecular, Universidade de Brasília, Brasília, DF CEP Key: 70790-900, Brazil; Computational Genomics Group, Instituto de Ciências, Value: Key: Biológicas, Universidade de Brasília, Brasília, CEP 70790-900, Brazil., Value: Key: FAU, Value: Mulinari, Flávia Furtado Key: AU, Value: Mulinari FF Key: AD, Value: Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Key: Brasília, Brasília, DF CEP 70790-160, Brazil., Value: Key: FAU, Value: Guedes, Adevilton Viana Key: AU, Value: Guedes AV Key: AD, Value: Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Key: Brasília, Brasília, DF CEP 70790-160, Brazil., Value: Key: FAU, Value: Teixeira, Marcus de Melo Key: AU, Value: Teixeira MM Key: AD, Value: Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Key: Brasília, Brasília, DF CEP 70790-160, Brazil; Faculdade de Medicina, Universidade, Value: Key: de Medicina, Brasília, DF CEP 70910-900, Brazil., Value: Key: FAU, Value: Motta, Dielle de Oliveira Key: AU, Value: Motta DO Key: AD, Value: Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Key: Brasília, Brasília, DF CEP 70790-160, Brazil., Value: Key: FAU, Value: Fernandes, Larissa Key: AU, Value: Fernandes L Key: AD, Value: Laboratório de Imunologia Aplicada, Instituto de Biologia, Departamento de Key: Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil., Value: Key: FAU, Value: Magalhães, Beatriz Simas Key: AU, Value: Magalhães BS Key: AD, Value: Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Key: Brasília, Brasília, DF CEP 70790-160, Brazil., Value: Key: FAU, Value: Felipe, Maria Sueli Soares Key: AU, Value: Felipe MSS Key: AD, Value: Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Key: Brasília, Brasília, DF CEP 70790-160, Brazil., Value: Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Pós-Graduação em Biologia Molecular, Universidade de Brasília, Brasília, DF CEP Key: 70790-900, Brazil; Computational Genomics Group, Instituto de Ciências, Value: Key: Biológicas, Universidade de Brasília, Brasília, CEP 70790-900, Brazil., Value: Key: FAU, Value: Parachin, Nádia Skorupa Key: AU, Value: Parachin NS Key: AD, Value: Grupo Engenharia de Biocatalisadores, Instituto de Ciências Biológicas, Key: Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil; Pós-Graduação em, Value: Key: Biologia Molecular, Universidade de Brasília, Brasília, DF CEP 70790-900, Brazil;, Value: Key: Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de, Value: Key: Brasília, Brasília, DF CEP 70790-160, Brazil. Electronic address: nadiasp@unb.br., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20200318 Key: PL, Value: United States Key: TA, Value: Fungal Genet Biol Key: JT, Value: Fungal genetics and biology : FG & B Key: JID, Value: 9607601 Key: RN, Value: 0 (Succinates) Key: RN, Value: 9LHU78OQFD (Lovastatin) Key: RN, Value: Q4516562YH (itaconic acid) Key: RN, Value: Aspergillus terreus Key: SB, Value: IM Key: MH, Value: *Aspergillus/genetics/metabolism Key: MH, Value: Biodiversity Key: MH, Value: Brazil Key: MH, Value: Genes, Fungal Key: MH, Value: Genetic Variation Key: MH, Value: Genome, Fungal Key: MH, Value: *Lovastatin/biosynthesis/genetics Key: MH, Value: Phylogeny Key: MH, Value: *Succinates/metabolism Key: OTO, Value: NOTNLM Key: OT, Value: Aspergillus terreus Key: OT, Value: Brazillian biodiversity Key: OT, Value: Lovastatin Key: OT, Value: Lovastatin transporter Key: OT, Value: Secondary metabolite Key: EDAT, Value: 2020/03/22 06:00 Key: MHDA, Value: 2021/04/20 06:00 Key: CRDT, Value: 2020/03/22 06:00 Key: PHST, Value: 2019/10/31 00:00 [received] Key: PHST, Value: 2020/03/09 00:00 [revised] Key: PHST, Value: 2020/03/10 00:00 [accepted] Key: PHST, Value: 2020/03/22 06:00 [pubmed] Key: PHST, Value: 2021/04/20 06:00 [medline] Key: PHST, Value: 2020/03/22 06:00 [entrez] Key: AID, Value: S1087-1845(20)30058-X [pii] Key: AID, Value: 10.1016/j.fgb.2020.103367 [doi] Key: PST, Value: ppublish Key: SO, Value: Fungal Genet Biol. 2020 May;138:103367. doi: 10.1016/j.fgb.2020.103367. Epub 2020 Key: Mar 18., Value: Key: PMID, Value: 33195951 Key: OWN, Value: NLM Key: STAT, Value: PubMed-not-MEDLINE Key: LR, Value: 20240330 Key: IS, Value: 2472-1751 (Electronic) Key: IS, Value: 2472-1751 (Linking) Key: VI, Value: 4 Key: IP, Value: 4 Key: DP, Value: 2020 Key: TI, Value: Models of communication and control for brain networks: distinctions, Key: convergence, and future outlook., Value: Key: PG, Value: 1122-1159 Key: LID, Value: 10.1162/netn_a_00158 [doi] Key: AB, Value: Recent advances in computational models of signal propagation and routing in the Key: human brain have underscored the critical role of white-matter structure. A, Value: Key: complementary approach has utilized the framework of network control theory to, Value: Key: better understand how white matter constrains the manner in which a region or set, Value: Key: of regions can direct or control the activity of other regions. Despite the, Value: Key: potential for both of these approaches to enhance our understanding of the role, Value: Key: of network structure in brain function, little work has sought to understand the, Value: Key: relations between them. Here, we seek to explicitly bridge computational models, Value: Key: of communication and principles of network control in a conceptual review of the, Value: Key: current literature. By drawing comparisons between communication and control, Value: Key: models in terms of the level of abstraction, the dynamical complexity, the, Value: Key: dependence on network attributes, and the interplay of multiple spatiotemporal, Value: Key: scales, we highlight the convergence of and distinctions between the two, Value: Key: frameworks. Based on the understanding of the intertwined nature of communication, Value: Key: and control in human brain networks, this work provides an integrative, Value: Key: perspective for the field and outlines exciting directions for future work., Value: Key: CI, Value: © 2020 Massachusetts Institute of Technology. Key: FAU, Value: Srivastava, Pragya Key: AU, Value: Srivastava P Key: AD, Value: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA USA. Key: FAU, Value: Nozari, Erfan Key: AU, Value: Nozari E Key: AD, Value: Department of Electrical & Systems Engineering, University of Pennsylvania, Key: Philadelphia, PA USA., Value: Key: FAU, Value: Kim, Jason Z Key: AU, Value: Kim JZ Key: AD, Value: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA USA. Key: FAU, Value: Ju, Harang Key: AU, Value: Ju H Key: AD, Value: Neuroscience Graduate Group, Perelman School of Medicine, University of Key: Pennsylvania, Philadelphia, PA USA., Value: Key: FAU, Value: Zhou, Dale Key: AU, Value: Zhou D Key: AD, Value: Neuroscience Graduate Group, Perelman School of Medicine, University of Key: Pennsylvania, Philadelphia, PA USA., Value: Key: FAU, Value: Becker, Cassiano Key: AU, Value: Becker C Key: AD, Value: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA USA. Key: FAU, Value: Pasqualetti, Fabio Key: AU, Value: Pasqualetti F Key: AD, Value: Department of Mechanical Engineering, University of California, Riverside, CA Key: USA., Value: Key: FAU, Value: Pappas, George J Key: AU, Value: Pappas GJ Key: AD, Value: Department of Electrical & Systems Engineering, University of Pennsylvania, Key: Philadelphia, PA USA., Value: Key: FAU, Value: Bassett, Danielle S Key: AU, Value: Bassett DS Key: AUID, Value: ORCID: 0000-0002-6183-4493 Key: AD, Value: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA USA. Key: LA, Value: eng Key: PT, Value: Journal Article Key: DEP, Value: 20201101 Key: PL, Value: United States Key: TA, Value: Netw Neurosci Key: JT, Value: Network neuroscience (Cambridge, Mass.) Key: JID, Value: 101719149 Key: PMC, Value: PMC7655113 Key: OTO, Value: NOTNLM Key: OT, Value: Brain dynamics Key: OT, Value: Causality Key: OT, Value: Communication models Key: OT, Value: Control models for brain networks Key: OT, Value: Integrated models Key: OT, Value: Linear control Key: OT, Value: Nonlinear control Key: OT, Value: Spatiotemporal scales in brain Key: OT, Value: System identification Key: OT, Value: Time-varying control Key: COIS, Value: Competing Interests: The authors have declared that no competing interests exist. Key: EDAT, Value: 2020/11/17 06:00 Key: MHDA, Value: 2020/11/17 06:01 Key: PMCR, Value: 2020/11/01 Key: CRDT, Value: 2020/11/16 08:56 Key: PHST, Value: 2020/02/14 00:00 [received] Key: PHST, Value: 2020/07/21 00:00 [accepted] Key: PHST, Value: 2020/11/16 08:56 [entrez] Key: PHST, Value: 2020/11/17 06:00 [pubmed] Key: PHST, Value: 2020/11/17 06:01 [medline] Key: PHST, Value: 2020/11/01 00:00 [pmc-release] Key: AID, Value: netn_a_00158 [pii] Key: AID, Value: 10.1162/netn_a_00158 [doi] Key: PST, Value: epublish Key: SO, Value: Netw Neurosci. 2020 Nov 1;4(4):1122-1159. doi: 10.1162/netn_a_00158. eCollection Key: 2020., Value: Key: PMID, Value: 29800320 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20190806 Key: LR, Value: 20190806 Key: IS, Value: 1362-4962 (Electronic) Key: IS, Value: 0305-1048 (Print) Key: IS, Value: 0305-1048 (Linking) Key: VI, Value: 46 Key: IP, Value: W1 Key: DP, Value: 2018 Jul 2 Key: TI, Value: PaintOmics 3: a web resource for the pathway analysis and visualization of Key: multi-omics data., Value: Key: PG, Value: W503-W509 Key: LID, Value: 10.1093/nar/gky466 [doi] Key: AB, Value: The increasing availability of multi-omic platforms poses new challenges to data Key: analysis. Joint visualization of multi-omics data is instrumental in better, Value: Key: understanding interconnections across molecular layers and in fully utilizing the, Value: Key: multi-omic resources available to make biological discoveries. We present here, Value: Key: PaintOmics 3, a web-based resource for the integrated visualization of multiple, Value: Key: omic data types onto KEGG pathway diagrams. PaintOmics 3 combines server-end, Value: Key: capabilities for data analysis with the potential of modern web resources for, Value: Key: data visualization, providing researchers with a powerful framework for, Value: Key: interactive exploration of their multi-omics information. Unlike other, Value: Key: visualization tools, PaintOmics 3 covers a comprehensive pathway analysis, Value: Key: workflow, including automatic feature name/identifier conversion, multi-layered, Value: Key: feature matching, pathway enrichment, network analysis, interactive heatmaps,, Value: Key: trend charts, and more. It accepts a wide variety of omic types, including, Value: Key: transcriptomics, proteomics and metabolomics, as well as region-based approaches, Value: Key: such as ATAC-seq or ChIP-seq data. The tool is freely available at, Value: Key: www.paintomics.org., Value: Key: FAU, Value: Hernández-de-Diego, Rafael Key: AU, Value: Hernández-de-Diego R Key: AD, Value: Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Key: Valencia, Spain., Value: Key: FAU, Value: Tarazona, Sonia Key: AU, Value: Tarazona S Key: AD, Value: Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Key: Valencia, Spain., Value: Key: AD, Value: Department of Applied Statistics, Operations Research and Quality, Universitat Key: Politècnica de València, Spain., Value: Key: FAU, Value: Martínez-Mira, Carlos Key: AU, Value: Martínez-Mira C Key: AD, Value: Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Key: Valencia, Spain., Value: Key: FAU, Value: Balzano-Nogueira, Leandro Key: AU, Value: Balzano-Nogueira L Key: AD, Value: Microbiology and Cell Science Department, Institute for Food and Agricultural Key: Sciences, University of Florida, Gainesville, FL, USA., Value: Key: AD, Value: Genetics Institute, University of Florida, Gainesville, FL, USA. Key: FAU, Value: Furió-Tarí, Pedro Key: AU, Value: Furió-Tarí P Key: AD, Value: Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Key: Valencia, Spain., Value: Key: FAU, Value: Pappas, Georgios J Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Department of Cellular Biology, University of Brasilia, Biological Sciences Key: Institute, Brasília, Brazil., Value: Key: FAU, Value: Conesa, Ana Key: AU, Value: Conesa A Key: AD, Value: Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Key: Valencia, Spain., Value: Key: AD, Value: Microbiology and Cell Science Department, Institute for Food and Agricultural Key: Sciences, University of Florida, Gainesville, FL, USA., Value: Key: AD, Value: Genetics Institute, University of Florida, Gainesville, FL, USA. Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: PL, Value: England Key: TA, Value: Nucleic Acids Res Key: JT, Value: Nucleic acids research Key: JID, Value: 0411011 Key: MH, Value: Cell Line, Transformed Key: MH, Value: Cellular Reprogramming Key: MH, Value: Computer Graphics Key: MH, Value: Fibroblasts/cytology/metabolism Key: MH, Value: *Gene Expression Regulation Key: MH, Value: Genomics/methods Key: MH, Value: Humans Key: MH, Value: Internet Key: MH, Value: Metabolic Networks and Pathways/*genetics Key: MH, Value: Metabolomics/methods Key: MH, Value: Molecular Sequence Annotation Key: MH, Value: Proteomics/methods Key: MH, Value: Signal Transduction/*genetics Key: MH, Value: *Software Key: MH, Value: *Transcriptome Key: PMC, Value: PMC6030972 Key: EDAT, Value: 2018/05/26 06:00 Key: MHDA, Value: 2019/08/07 06:00 Key: PMCR, Value: 2018/05/25 Key: CRDT, Value: 2018/05/26 06:00 Key: PHST, Value: 2018/02/22 00:00 [received] Key: PHST, Value: 2018/05/16 00:00 [accepted] Key: PHST, Value: 2018/05/26 06:00 [pubmed] Key: PHST, Value: 2019/08/07 06:00 [medline] Key: PHST, Value: 2018/05/26 06:00 [entrez] Key: PHST, Value: 2018/05/25 00:00 [pmc-release] Key: AID, Value: 5003457 [pii] Key: AID, Value: gky466 [pii] Key: AID, Value: 10.1093/nar/gky466 [doi] Key: PST, Value: ppublish Key: SO, Value: Nucleic Acids Res. 2018 Jul 2;46(W1):W503-W509. doi: 10.1093/nar/gky466. Key: PMID, Value: 36701110 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20230224 Key: LR, Value: 20240305 Key: IS, Value: 1678-4405 (Electronic) Key: IS, Value: 1517-8382 (Print) Key: IS, Value: 1517-8382 (Linking) Key: VI, Value: 54 Key: IP, Value: 1 Key: DP, Value: 2023 Mar Key: TI, Value: Genomic and physiological characterization of Novosphingobium terrae sp. nov., an Key: alphaproteobacterium isolated from Cerrado soil containing a mega-sized chromid., Value: Key: PG, Value: 239-258 Key: LID, Value: 10.1007/s42770-022-00900-4 [doi] Key: AB, Value: A novel bacterial strain, designated GeG2(T), was isolated from soils of the Key: native Cerrado, a highly biodiverse savanna-like Brazilian biome. 16S rRNA gene, Value: Key: analysis of GeG2(T) revealed high sequence identity (100%) to the, Value: Key: alphaproteobacterium Novosphingobium rosa; however, comparisons with N. rosa DSM, Value: Key: 7285(T) showed several distinctive features, prompting a full characterization of, Value: Key: the new strain in terms of physiology, morphology, and, ultimately, its genome., Value: Key: GeG2(T) cells were Gram-stain-negative bacilli, facultatively anaerobic, motile,, Value: Key: positive for catalase and oxidase activities, and starch hydrolysis. Strain, Value: Key: GeG2(T) presented planktonic-sessile dimorphism and cell aggregates surrounded by, Value: Key: extracellular matrix and nanometric spherical structures were observed,, Value: Key: suggesting the production of exopolysaccharides (EPS) and outer membrane vesicles, Value: Key: (OMVs). Despite high 16S rDNA identity, strain GeG2(T) showed 90.38% average, Value: Key: nucleotide identity and 42.60% digital DNA-DNA hybridization identity with N., Value: Key: rosa, below species threshold. Whole-genome assembly revealed four circular, Value: Key: replicons: a 4.1 Mb chromosome, a 2.7 Mb extrachromosomal megareplicon, and two, Value: Key: plasmids (212.7 and 68.6 kb). The megareplicon contains a few core genes and, Value: Key: plasmid-type replication/maintenance systems, consistent with its classification, Value: Key: as a chromid. Genome annotation shows a vast repertoire of carbohydrate-active, Value: Key: enzymes and genes involved in the degradation of aromatic compounds, highlighting, Value: Key: the biotechnological potential of the new isolate. Chemotaxonomic features,, Value: Key: including polar lipid and fatty acid profiles, as well as physiological,, Value: Key: molecular, and whole-genome comparisons showed significant differences between, Value: Key: strain GeG2(T) and N. rosa, indicating that it represents a novel species, for, Value: Key: which the name Novosphingobium terrae is proposed. The type strain is GeG2(T), Value: Key: (= CBMAI 2313(T) = CBAS 753( T))., Value: Key: CI, Value: © 2023. The Author(s) under exclusive licence to Sociedade Brasileira de Key: Microbiologia., Value: Key: FAU, Value: Belmok, Aline Key: AU, Value: Belmok A Key: AUID, Value: ORCID: 0000-0002-8524-3727 Key: AD, Value: Laboratório de Microbiologia, Departamento de Biologia Celular, Instituto de Key: Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil., Value: Key: abelmokadias@gmail.com., Value: Key: FAU, Value: de Almeida, Felipe Marques Key: AU, Value: de Almeida FM Key: AD, Value: Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Key: Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil., Value: Key: FAU, Value: Rocha, Rodrigo Theodoro Key: AU, Value: Rocha RT Key: AD, Value: Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Key: Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil., Value: Key: FAU, Value: Vizzotto, Carla Simone Key: AU, Value: Vizzotto CS Key: AD, Value: Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil e Key: Ambiental, Faculdade de Tecnologia, Universidade de Brasília, Brasilia, DF,, Value: Key: Brazil., Value: Key: AD, Value: Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto de Key: Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil., Value: Key: FAU, Value: Tótola, Marcos Rogério Key: AU, Value: Tótola MR Key: AD, Value: Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento Key: de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil., Value: Key: FAU, Value: Ramada, Marcelo Henrique Soller Key: AU, Value: Ramada MHS Key: AD, Value: Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Key: Católica de Brasília, Brasilia, DF, Brazil., Value: Key: AD, Value: Programa de Pós-Graduação em Gerontologia, Universidade Católica de Brasília, Key: Brasilia, DF, Brazil., Value: Key: FAU, Value: Krüger, Ricardo Henrique Key: AU, Value: Krüger RH Key: AD, Value: Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto de Key: Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil., Value: Key: FAU, Value: Kyaw, Cynthia Maria Key: AU, Value: Kyaw CM Key: AD, Value: Laboratório de Microbiologia, Departamento de Biologia Celular, Instituto de Key: Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil., Value: Key: malta@unb.br., Value: Key: FAU, Value: Pappas, Georgios J Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Key: Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil., Value: Key: gpappas@unb.br., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: DEP, Value: 20230126 Key: PL, Value: Brazil Key: TA, Value: Braz J Microbiol Key: JT, Value: Brazilian journal of microbiology : [publication of the Brazilian Society for Key: Microbiology], Value: Key: JID, Value: 101095924 Key: RN, Value: 0 (Phospholipids) Key: RN, Value: 0 (Soil) Key: RN, Value: 0 (RNA, Ribosomal, 16S) Key: RN, Value: 0 (DNA, Bacterial) Key: RN, Value: 1339-63-5 (Ubiquinone) Key: RN, Value: 0 (Fatty Acids) Key: SB, Value: IM Key: MH, Value: *Phospholipids Key: MH, Value: *Soil Key: MH, Value: RNA, Ribosomal, 16S/genetics Key: MH, Value: Sequence Analysis, DNA Key: MH, Value: DNA, Bacterial/genetics Key: MH, Value: Ubiquinone/chemistry/genetics Key: MH, Value: Phylogeny Key: MH, Value: Bacterial Typing Techniques Key: MH, Value: Soil Microbiology Key: MH, Value: Fatty Acids/chemistry Key: MH, Value: Genomics Key: PMC, Value: PMC9944591 Key: OTO, Value: NOTNLM Key: OT, Value: Cerrado Key: OT, Value: Chromid Key: OT, Value: Cultivation Key: OT, Value: Novosphingobium Key: OT, Value: Soils Key: OT, Value: Sphingomonadales Key: COIS, Value: The authors declare no competing interests. Key: EDAT, Value: 2023/01/27 06:00 Key: MHDA, Value: 2023/02/25 06:00 Key: PMCR, Value: 2024/01/26 Key: CRDT, Value: 2023/01/26 11:19 Key: PHST, Value: 2022/01/29 00:00 [received] Key: PHST, Value: 2022/10/02 00:00 [accepted] Key: PHST, Value: 2023/01/27 06:00 [pubmed] Key: PHST, Value: 2023/02/25 06:00 [medline] Key: PHST, Value: 2023/01/26 11:19 [entrez] Key: PHST, Value: 2024/01/26 00:00 [pmc-release] Key: AID, Value: 10.1007/s42770-022-00900-4 [pii] Key: AID, Value: 900 [pii] Key: AID, Value: 10.1007/s42770-022-00900-4 [doi] Key: PST, Value: ppublish Key: SO, Value: Braz J Microbiol. 2023 Mar;54(1):239-258. doi: 10.1007/s42770-022-00900-4. Epub Key: 2023 Jan 26., Value: Key: PMID, Value: 29362436 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20181211 Key: LR, Value: 20190123 Key: IS, Value: 2045-2322 (Electronic) Key: IS, Value: 2045-2322 (Linking) Key: VI, Value: 8 Key: IP, Value: 1 Key: DP, Value: 2018 Jan 23 Key: TI, Value: Spectral mapping of brain functional connectivity from diffusion imaging. Key: PG, Value: 1411 Key: LID, Value: 10.1038/s41598-017-18769-x [doi] Key: LID, Value: 1411 Key: AB, Value: Understanding the relationship between the dynamics of neural processes and the Key: anatomical substrate of the brain is a central question in neuroscience. On the, Value: Key: one hand, modern neuroimaging technologies, such as diffusion tensor imaging, can, Value: Key: be used to construct structural graphs representing the architecture of white, Value: Key: matter streamlines linking cortical and subcortical structures. On the other, Value: Key: hand, temporal patterns of neural activity can be used to construct functional, Value: Key: graphs representing temporal correlations between brain regions. Although some, Value: Key: studies provide evidence that whole-brain functional connectivity is shaped by, Value: Key: the underlying anatomy, the observed relationship between function and structure, Value: Key: is weak, and the rules by which anatomy constrains brain dynamics remain elusive., Value: Key: In this article, we introduce a methodology to map the functional connectivity of, Value: Key: a subject at rest from his or her structural graph. Using our methodology, we are, Value: Key: able to systematically account for the role of structural walks in the formation, Value: Key: of functional correlations. Furthermore, in our empirical evaluations, we observe, Value: Key: that the eigenmodes of the mapped functional connectivity are associated with, Value: Key: activity patterns associated with different cognitive systems., Value: Key: FAU, Value: Becker, Cassiano O Key: AU, Value: Becker CO Key: AD, Value: Department of Electrical and Systems Engineering, University of Pennsylvania, Key: Philadelphia, USA., Value: Key: FAU, Value: Pequito, Sérgio Key: AU, Value: Pequito S Key: AD, Value: Department of Industrial and Systems Engineering, Rensselaer Polytechnic Key: Institute, Troy, USA., Value: Key: FAU, Value: Pappas, George J Key: AU, Value: Pappas GJ Key: AD, Value: Department of Electrical and Systems Engineering, University of Pennsylvania, Key: Philadelphia, USA., Value: Key: FAU, Value: Miller, Michael B Key: AU, Value: Miller MB Key: AD, Value: Department of Psychological and Brain Sciences, University of California at Santa Key: Barbara, Santa Barbara, USA., Value: Key: FAU, Value: Grafton, Scott T Key: AU, Value: Grafton ST Key: AD, Value: Department of Psychological and Brain Sciences, University of California at Santa Key: Barbara, Santa Barbara, USA., Value: Key: FAU, Value: Bassett, Danielle S Key: AU, Value: Bassett DS Key: AUID, Value: ORCID: 0000-0002-6183-4493 Key: AD, Value: Department of Electrical and Systems Engineering, University of Pennsylvania, Key: Philadelphia, USA., Value: Key: AD, Value: Department of Bioengineering, University of Pennsylvania, Philadelphia, USA. Key: FAU, Value: Preciado, Victor M Key: AU, Value: Preciado VM Key: AD, Value: Department of Electrical and Systems Engineering, University of Pennsylvania, Key: Philadelphia, USA. preciado@seas.upenn.edu., Value: Key: LA, Value: eng Key: GR, Value: R01 DC009209/DC/NIDCD NIH HHS/United States Key: GR, Value: R01 HD086888/HD/NICHD NIH HHS/United States Key: GR, Value: U54 MH091657/MH/NIMH NIH HHS/United States Key: PT, Value: Journal Article Key: PT, Value: Research Support, N.I.H., Extramural Key: PT, Value: Research Support, Non-U.S. Gov't Key: PT, Value: Research Support, U.S. Gov't, Non-P.H.S. Key: DEP, Value: 20180123 Key: PL, Value: England Key: TA, Value: Sci Rep Key: JT, Value: Scientific reports Key: JID, Value: 101563288 Key: SB, Value: IM Key: MH, Value: Brain Mapping/*methods Key: MH, Value: Diffusion Tensor Imaging/*methods Key: MH, Value: Humans Key: MH, Value: Nerve Net/*diagnostic imaging/physiology Key: MH, Value: Temporal Lobe/physiology Key: MH, Value: White Matter/physiology Key: PMC, Value: PMC5780460 Key: COIS, Value: The authors declare that they have no competing interests. Key: EDAT, Value: 2018/01/25 06:00 Key: MHDA, Value: 2018/12/12 06:00 Key: PMCR, Value: 2018/01/23 Key: CRDT, Value: 2018/01/25 06:00 Key: PHST, Value: 2017/04/05 00:00 [received] Key: PHST, Value: 2017/12/15 00:00 [accepted] Key: PHST, Value: 2018/01/25 06:00 [entrez] Key: PHST, Value: 2018/01/25 06:00 [pubmed] Key: PHST, Value: 2018/12/12 06:00 [medline] Key: PHST, Value: 2018/01/23 00:00 [pmc-release] Key: AID, Value: 10.1038/s41598-017-18769-x [pii] Key: AID, Value: 18769 [pii] Key: AID, Value: 10.1038/s41598-017-18769-x [doi] Key: PST, Value: epublish Key: SO, Value: Sci Rep. 2018 Jan 23;8(1):1411. doi: 10.1038/s41598-017-18769-x. Key: PMID, Value: 28276443 Key: OWN, Value: NLM Key: STAT, Value: PubMed-not-MEDLINE Key: LR, Value: 20191120 Key: IS, Value: 2045-2322 (Electronic) Key: IS, Value: 2045-2322 (Linking) Key: VI, Value: 7 Key: DP, Value: 2017 Mar 9 Key: TI, Value: Corrigendum: Trade-offs between driving nodes and time-to-control in complex Key: networks., Value: Key: PG, Value: 43194 Key: LID, Value: 10.1038/srep43194 [doi] Key: LID, Value: 43194 Key: FAU, Value: Pequito, Sérgio Key: AU, Value: Pequito S Key: FAU, Value: Preciado, Victor M Key: AU, Value: Preciado VM Key: FAU, Value: Barabási, Albert-László Key: AU, Value: Barabási AL Key: FAU, Value: Pappas, George J Key: AU, Value: Pappas GJ Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Published Erratum Key: DEP, Value: 20170309 Key: PL, Value: England Key: TA, Value: Sci Rep Key: JT, Value: Scientific reports Key: JID, Value: 101563288 Key: EFR, Value: Sci Rep. 2017 Jan 05;7:39978. PMID: 28054597 Key: PMC, Value: PMC5343485 Key: EDAT, Value: 2017/03/10 06:00 Key: MHDA, Value: 2017/03/10 06:01 Key: PMCR, Value: 2017/03/09 Key: CRDT, Value: 2017/03/10 06:00 Key: PHST, Value: 2017/03/10 06:00 [entrez] Key: PHST, Value: 2017/03/10 06:00 [pubmed] Key: PHST, Value: 2017/03/10 06:01 [medline] Key: PHST, Value: 2017/03/09 00:00 [pmc-release] Key: AID, Value: srep43194 [pii] Key: AID, Value: 10.1038/srep43194 [doi] Key: PST, Value: epublish Key: SO, Value: Sci Rep. 2017 Mar 9;7:43194. doi: 10.1038/srep43194. Key: PMID, Value: 25706301 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20160122 Key: LR, Value: 20231104 Key: IS, Value: 1932-6203 (Electronic) Key: IS, Value: 1932-6203 (Linking) Key: VI, Value: 10 Key: IP, Value: 2 Key: DP, Value: 2015 Key: TI, Value: Sugarcane giant borer transcriptome analysis and identification of genes related Key: to digestion., Value: Key: PG, Value: e0118231 Key: LID, Value: 10.1371/journal.pone.0118231 [doi] Key: LID, Value: e0118231 Key: AB, Value: Sugarcane is a widely cultivated plant that serves primarily as a source of sugar Key: and ethanol. Its annual yield can be significantly reduced by the action of, Value: Key: several insect pests including the sugarcane giant borer (Telchin licus licus), a, Value: Key: lepidopteran that presents a long life cycle and which efforts to control it, Value: Key: using pesticides have been inefficient. Although its economical relevance, only a, Value: Key: few DNA sequences are available for this species in the GenBank. Pyrosequencing, Value: Key: technology was used to investigate the transcriptome of several developmental, Value: Key: stages of the insect. To maximize transcript diversity, a pool of total RNA was, Value: Key: extracted from whole body insects and used to construct a normalized cDNA, Value: Key: database. Sequencing produced over 650,000 reads, which were de novo assembled to, Value: Key: generate a reference library of 23,824 contigs. After quality score and, Value: Key: annotation, 43% of the contigs had at least one BLAST hit against the NCBI, Value: Key: non-redundant database, and 40% showed similarities with the lepidopteran Bombyx, Value: Key: mori. In a further analysis, we conducted a comparison with Manduca sexta midgut, Value: Key: sequences to identify transcripts of genes involved in digestion. Of these, Value: Key: transcripts, many presented an expansion or depletion in gene number, compared to, Value: Key: B. mori genome. From the sugarcane giant borer (SGB) transcriptome, a number of, Value: Key: aminopeptidase N (APN) cDNAs were characterized based on homology to those, Value: Key: reported as Cry toxin receptors. This is the first report that provides a, Value: Key: large-scale EST database for the species. Transcriptome analysis will certainly, Value: Key: be useful to identify novel developmental genes, to better understand the, Value: Key: insect's biology and to guide the development of new strategies for insect-pest, Value: Key: control., Value: Key: FAU, Value: Fonseca, Fernando Campos de Assis Key: AU, Value: Fonseca FC Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil; Key: Universidade de Brasília, Brasília, Distrito Federal, Brazil., Value: Key: FAU, Value: Firmino, Alexandre Augusto Pereira Key: AU, Value: Firmino AA Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil; Key: Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul,, Value: Key: Brazil., Value: Key: FAU, Value: de Macedo, Leonardo Lima Pepino Key: AU, Value: de Macedo LL Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil; Key: Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil., Value: Key: FAU, Value: Coelho, Roberta Ramos Key: AU, Value: Coelho RR Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil; Key: Universidade de Brasília, Brasília, Distrito Federal, Brazil., Value: Key: FAU, Value: de Souza Júnior, José Dijair Antonino Key: AU, Value: de Souza Júnior JD Key: FAU, Value: Silva-Junior, Orzenil Bonfim Key: AU, Value: Silva-Junior OB Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil; Key: Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil., Value: Key: FAU, Value: Togawa, Roberto Coiti Key: AU, Value: Togawa RC Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil. Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Universidade de Brasília, Brasília, Distrito Federal, Brazil. Key: FAU, Value: de Góis, Luiz Avelar Brandão Key: AU, Value: de Góis LA Key: AD, Value: Usina triunfo, Maceió, Alagoas, Brazil. Key: FAU, Value: da Silva, Maria Cristina Mattar Key: AU, Value: da Silva MC Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil. Key: FAU, Value: Grossi-de-Sá, Maria Fátima Key: AU, Value: Grossi-de-Sá MF Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil; Key: Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil., Value: Key: LA, Value: eng Key: SI, Value: GENBANK/JZ578314 Key: SI, Value: GENBANK/JZ578315 Key: SI, Value: GENBANK/JZ578316 Key: SI, Value: GENBANK/JZ578317 Key: SI, Value: GENBANK/JZ578318 Key: SI, Value: SRA/SRR1204999 Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20150223 Key: PL, Value: United States Key: TA, Value: PLoS One Key: JT, Value: PloS one Key: JID, Value: 101285081 Key: RN, Value: 0 (Insect Proteins) Key: RN, Value: EC 3.4.11.2 (CD13 Antigens) Key: SB, Value: IM Key: EIN, Value: PLoS One. 2015;10(4):e0123836. de Sousa Júnior, José Dijair Antonino [corrected Key: to de Souza Júnior, José Dijair Antonino]. PMID: 25835298, Value: Key: MH, Value: Amino Acid Sequence Key: MH, Value: Animals Key: MH, Value: CD13 Antigens/genetics Key: MH, Value: Digestion/*genetics Key: MH, Value: Expressed Sequence Tags/chemistry Key: MH, Value: Gene Expression Profiling/*methods Key: MH, Value: Gene Library Key: MH, Value: Gene Ontology Key: MH, Value: Insect Proteins/*genetics Key: MH, Value: Lepidoptera/*genetics/growth & development/physiology Key: MH, Value: Life Cycle Stages/genetics Key: MH, Value: Molecular Sequence Data Key: MH, Value: Reverse Transcriptase Polymerase Chain Reaction Key: MH, Value: Saccharum/*parasitology Key: MH, Value: Sequence Analysis, DNA Key: MH, Value: Sequence Homology, Amino Acid Key: PMC, Value: PMC4338194 Key: COIS, Value: Competing Interests: Luiz AvelarBrandao de Gois is affiliated with TRIUNFO Key: AGROINDUSTRIAL LTDA, Value: accordingly with current legislation, as a phytosanitary Key: and environmental coordination, occupying the position of biologist. The authors, Value: Key: declare that there is no interest from this company in patents or any other, Value: Key: products that may be obtained from the present study described in the manuscript., Value: Key: This does not alter the authors' adherence to all PLOS ONE policies on sharing, Value: Key: data and materials., Value: Key: EDAT, Value: 2015/02/24 06:00 Key: MHDA, Value: 2016/01/23 06:00 Key: PMCR, Value: 2015/02/23 Key: CRDT, Value: 2015/02/24 06:00 Key: PHST, Value: 2014/09/08 00:00 [received] Key: PHST, Value: 2015/01/11 00:00 [accepted] Key: PHST, Value: 2015/02/24 06:00 [entrez] Key: PHST, Value: 2015/02/24 06:00 [pubmed] Key: PHST, Value: 2016/01/23 06:00 [medline] Key: PHST, Value: 2015/02/23 00:00 [pmc-release] Key: AID, Value: PONE-D-14-39676 [pii] Key: AID, Value: 10.1371/journal.pone.0118231 [doi] Key: PST, Value: epublish Key: SO, Value: PLoS One. 2015 Feb 23;10(2):e0118231. doi: 10.1371/journal.pone.0118231. Key: eCollection 2015., Value: Key: PMID, Value: 34899623 Key: OWN, Value: NLM Key: STAT, Value: PubMed-not-MEDLINE Key: LR, Value: 20231108 Key: IS, Value: 1664-302X (Print) Key: IS, Value: 1664-302X (Electronic) Key: IS, Value: 1664-302X (Linking) Key: VI, Value: 12 Key: DP, Value: 2021 Key: TI, Value: A Novel Multidrug Resistant, Non-Tn4401 Genetic Element-Bearing, Strain of Key: Klebsiella pneumoniae Isolated From an Urban Lake With Drinking and Recreational, Value: Key: Water Reuse., Value: Key: PG, Value: 732324 Key: LID, Value: 10.3389/fmicb.2021.732324 [doi] Key: LID, Value: 732324 Key: AB, Value: Antimicrobial resistance (AMR) is an increasing and urgent issue for human health Key: worldwide, as it leads to the reduction of available antibiotics to treat, Value: Key: bacterial infections, in turn increasing hospital stays and lethality. Therefore,, Value: Key: the study and genomic surveillance of bacterial carriers of resistance in and, Value: Key: outside of clinical settings is of utter importance. A colony of multidrug, Value: Key: resistant (MDR) bacteria identified as Klebsiella spp., by 16S rDNA amplicon, Value: Key: sequencing, has been isolated from an urban lake in Brazil, during a, Value: Key: drug-degrading bacterial prospection. Genomic analyses revealed the bacteria as, Value: Key: Klebsiella pneumoniae species. Furthermore, the in silico Multilocus Sequence, Value: Key: Typing (MLST) identified the genome as a new sequence type, ST5236. The search, Value: Key: for antimicrobial resistance genes (ARGs) detected the presence of genes against, Value: Key: beta-lactams, fosfomycin, acriflavine and efflux pumps, as well as genes for, Value: Key: heavy metal resistance. Of particular note, an extended-spectrum beta-lactamase, Value: Key: gene (blaCTX-M-15) has been detected in close proximity to siphoviridae genes,, Value: Key: while a carbapenemase gene (KPC-2) has been found in an extrachromosomal contig,, Value: Key: within a novel non-Tn4401 genetic element (NTE(KPC)). An extrachromosomal contig, Value: Key: found in the V3 isolate is identical to a contig of a K. pneumoniae isolate from, Value: Key: a nearby hospital, which indicates a putative gene flow from the hospital network, Value: Key: into Paranoá lake. The discovery of a MDR isolate in this lake is worrisome, as, Value: Key: the region has recently undergone periods of water scarcity causing the lake,, Value: Key: which receives treated wastewater effluent, and is already used for recreational, Value: Key: purposes, to be used as an environmental buffer for drinking water reuse., Value: Key: Altogether, our results indicate an underrepresentation of environmental K., Value: Key: pneumoniae among available genomes, which may hamper the understanding of the, Value: Key: population dynamics of the species in the environment and its consequences in the, Value: Key: spread of ARGs and virulence genes., Value: Key: CI, Value: Copyright © 2021 Janssen, de Almeida, Damasceno, Baptista, Pappas, de Campos and Key: Martins., Value: Key: FAU, Value: Janssen, Luis Key: AU, Value: Janssen L Key: AD, Value: Department of Cellular Biology, Institute of Biological Sciences, University of Key: Brasilia, Brasília, Brazil., Value: Key: FAU, Value: de Almeida, Felipe Marques Key: AU, Value: de Almeida FM Key: AD, Value: Department of Cellular Biology, Institute of Biological Sciences, University of Key: Brasilia, Brasília, Brazil., Value: Key: FAU, Value: Damasceno, Thais Amanda Silva Key: AU, Value: Damasceno TAS Key: AD, Value: Department of Cellular Biology, Institute of Biological Sciences, University of Key: Brasilia, Brasília, Brazil., Value: Key: FAU, Value: Baptista, Rodrigo de Paula Key: AU, Value: Baptista RP Key: AD, Value: Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Key: GA, United States., Value: Key: AD, Value: Institute of Bioinformatics, University of Georgia, Athens, GA, United States. Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Department of Cellular Biology, Institute of Biological Sciences, University of Key: Brasilia, Brasília, Brazil., Value: Key: FAU, Value: de Campos, Tatiana Amabile Key: AU, Value: de Campos TA Key: AD, Value: Department of Cellular Biology, Institute of Biological Sciences, University of Key: Brasilia, Brasília, Brazil., Value: Key: FAU, Value: Martins, Vicente de Paulo Key: AU, Value: Martins VP Key: AD, Value: Department of Cellular Biology, Institute of Biological Sciences, University of Key: Brasilia, Brasília, Brazil., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: DEP, Value: 20211124 Key: PL, Value: Switzerland Key: TA, Value: Front Microbiol Key: JT, Value: Frontiers in microbiology Key: JID, Value: 101548977 Key: PMC, Value: PMC8654192 Key: OTO, Value: NOTNLM Key: OT, Value: Klebsiella pneumoniae Key: OT, Value: MLST Key: OT, Value: antimicrobial resistance Key: OT, Value: one health Key: OT, Value: strain type Key: OT, Value: water scarcity Key: COIS, Value: The authors declare that the research was conducted in the absence of any Key: commercial or financial relationships that could be construed as a potential, Value: Key: conflict of interest., Value: Key: EDAT, Value: 2021/12/14 06:00 Key: MHDA, Value: 2021/12/14 06:01 Key: PMCR, Value: 2021/11/24 Key: CRDT, Value: 2021/12/13 17:55 Key: PHST, Value: 2021/06/28 00:00 [received] Key: PHST, Value: 2021/11/01 00:00 [accepted] Key: PHST, Value: 2021/12/13 17:55 [entrez] Key: PHST, Value: 2021/12/14 06:00 [pubmed] Key: PHST, Value: 2021/12/14 06:01 [medline] Key: PHST, Value: 2021/11/24 00:00 [pmc-release] Key: AID, Value: 10.3389/fmicb.2021.732324 [doi] Key: PST, Value: epublish Key: SO, Value: Front Microbiol. 2021 Nov 24;12:732324. doi: 10.3389/fmicb.2021.732324. Key: eCollection 2021., Value: Key: PMID, Value: 17324564 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20090407 Key: LR, Value: 20090119 Key: IS, Value: 0944-5013 (Print) Key: IS, Value: 0944-5013 (Linking) Key: VI, Value: 164 Key: IP, Value: 1 Key: DP, Value: 2009 Key: TI, Value: Molecular phylogenetic diversity of bacteria associated with soil of the Key: savanna-like Cerrado vegetation., Value: Key: PG, Value: 59-70 Key: AB, Value: The Brazilian savanna-like vegetation of Cerrado is rapidly being converted to Key: pasture and agricultural fields. A 16S rDNA-based approach was taken to study the, Value: Key: bacterial community associated with the soil of a native cerrado area (sensu, Value: Key: stricto) and an area that has been converted to pasture. The bacterial group most, Value: Key: abundantly identified in cerrado sensu stricto soil was the alpha-Proteobacteria, Value: Key: while in cerrado converted to pasture the Actinobacteria were the most abundant., Value: Key: Rarefaction curves indicate that the species richness of cerrado sensu stricto is, Value: Key: greater than that of cerrado converted to pasture. Furthermore,, Value: Key: lineage-through-time plots show that the expected richness of species present in, Value: Key: cerrado sensu stricto soil is approximately 10 times greater than that of cerrado, Value: Key: converted to pasture., Value: Key: FAU, Value: Quirino, Betania F Key: AU, Value: Quirino BF Key: AD, Value: Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, Key: SGAN Quadra 916, Av. W5 Norte, 70790-160 Brasília, DF, Brazil., Value: Key: FAU, Value: Pappas, Georgios J Key: AU, Value: Pappas GJ Key: FAU, Value: Tagliaferro, Andrea C Key: AU, Value: Tagliaferro AC Key: FAU, Value: Collevatti, Rosane G Key: AU, Value: Collevatti RG Key: FAU, Value: Neto, Eduardo Leonardecz Key: AU, Value: Neto EL Key: FAU, Value: da Silva, Maria Regina S S Key: AU, Value: da Silva MR Key: FAU, Value: Bustamante, Mercedes M C Key: AU, Value: Bustamante MM Key: FAU, Value: Krüger, Ricardo H Key: AU, Value: Krüger RH Key: LA, Value: eng Key: SI, Value: GENBANK/DQ303929 Key: SI, Value: GENBANK/DQ303930 Key: SI, Value: GENBANK/DQ303931 Key: SI, Value: GENBANK/DQ303932 Key: SI, Value: GENBANK/DQ303933 Key: SI, Value: GENBANK/DQ303934 Key: SI, Value: GENBANK/DQ303935 Key: SI, Value: GENBANK/DQ303936 Key: SI, Value: GENBANK/DQ303937 Key: SI, Value: GENBANK/DQ303938 Key: SI, Value: GENBANK/DQ303939 Key: SI, Value: GENBANK/DQ303940 Key: SI, Value: GENBANK/DQ303941 Key: SI, Value: GENBANK/DQ303942 Key: SI, Value: GENBANK/DQ303943 Key: SI, Value: GENBANK/DQ303944 Key: SI, Value: GENBANK/DQ303945 Key: SI, Value: GENBANK/DQ303946 Key: SI, Value: GENBANK/DQ303947 Key: SI, Value: GENBANK/DQ303948 Key: SI, Value: GENBANK/DQ303949 Key: SI, Value: GENBANK/DQ303950 Key: SI, Value: GENBANK/DQ303951 Key: SI, Value: GENBANK/DQ303952 Key: SI, Value: GENBANK/DQ303953 Key: SI, Value: GENBANK/DQ303954 Key: SI, Value: GENBANK/DQ303955 Key: SI, Value: GENBANK/DQ303956 Key: SI, Value: GENBANK/DQ303957 Key: SI, Value: GENBANK/DQ303958 Key: SI, Value: GENBANK/DQ303959 Key: SI, Value: GENBANK/DQ303960 Key: SI, Value: GENBANK/DQ303961 Key: SI, Value: GENBANK/DQ303962 Key: SI, Value: GENBANK/DQ303963 Key: SI, Value: GENBANK/DQ303964 Key: SI, Value: GENBANK/DQ303965 Key: SI, Value: GENBANK/DQ303966 Key: SI, Value: GENBANK/DQ303967 Key: SI, Value: GENBANK/DQ303968 Key: SI, Value: GENBANK/DQ303969 Key: SI, Value: GENBANK/DQ303970 Key: SI, Value: GENBANK/DQ303971 Key: SI, Value: GENBANK/DQ303972 Key: SI, Value: GENBANK/DQ303973 Key: SI, Value: GENBANK/DQ303974 Key: SI, Value: GENBANK/DQ303975 Key: SI, Value: GENBANK/DQ303976 Key: SI, Value: GENBANK/DQ303977 Key: SI, Value: GENBANK/DQ303978 Key: SI, Value: GENBANK/DQ303979 Key: SI, Value: GENBANK/DQ303980 Key: SI, Value: GENBANK/DQ303981 Key: SI, Value: GENBANK/DQ303982 Key: SI, Value: GENBANK/DQ303983 Key: SI, Value: GENBANK/DQ303984 Key: SI, Value: GENBANK/DQ303985 Key: SI, Value: GENBANK/DQ303986 Key: SI, Value: GENBANK/DQ303987 Key: SI, Value: GENBANK/DQ303988 Key: SI, Value: GENBANK/DQ303989 Key: SI, Value: GENBANK/DQ303990 Key: SI, Value: GENBANK/DQ303991 Key: SI, Value: GENBANK/DQ303992 Key: SI, Value: GENBANK/DQ303993 Key: SI, Value: GENBANK/DQ303994 Key: SI, Value: GENBANK/DQ303995 Key: SI, Value: GENBANK/DQ303996 Key: SI, Value: GENBANK/DQ303997 Key: SI, Value: GENBANK/DQ303998 Key: SI, Value: GENBANK/DQ303999 Key: SI, Value: GENBANK/DQ304000 Key: SI, Value: GENBANK/DQ304001 Key: SI, Value: GENBANK/DQ304002 Key: SI, Value: GENBANK/DQ304003 Key: SI, Value: GENBANK/DQ304004 Key: SI, Value: GENBANK/DQ304005 Key: SI, Value: GENBANK/DQ304006 Key: SI, Value: GENBANK/DQ304007 Key: SI, Value: GENBANK/DQ304008 Key: SI, Value: GENBANK/DQ304009 Key: SI, Value: GENBANK/DQ304010 Key: SI, Value: GENBANK/DQ304011 Key: SI, Value: GENBANK/DQ304012 Key: SI, Value: GENBANK/DQ304013 Key: SI, Value: GENBANK/DQ304014 Key: SI, Value: GENBANK/DQ304015 Key: SI, Value: GENBANK/DQ304016 Key: SI, Value: GENBANK/DQ304017 Key: SI, Value: GENBANK/DQ304018 Key: SI, Value: GENBANK/DQ304019 Key: SI, Value: GENBANK/DQ304020 Key: SI, Value: GENBANK/DQ304021 Key: SI, Value: GENBANK/DQ304022 Key: SI, Value: GENBANK/DQ304023 Key: SI, Value: GENBANK/DQ304024 Key: SI, Value: GENBANK/DQ304025 Key: SI, Value: GENBANK/DQ304026 Key: SI, Value: GENBANK/DQ304027 Key: SI, Value: GENBANK/DQ304028 Key: SI, Value: GENBANK/DQ304029 Key: SI, Value: GENBANK/DQ304030 Key: SI, Value: GENBANK/DQ304031 Key: SI, Value: GENBANK/DQ304032 Key: SI, Value: GENBANK/DQ304033 Key: SI, Value: GENBANK/DQ304034 Key: SI, Value: GENBANK/DQ304035 Key: SI, Value: GENBANK/DQ304036 Key: SI, Value: GENBANK/DQ304037 Key: SI, Value: GENBANK/DQ304038 Key: SI, Value: GENBANK/DQ304039 Key: SI, Value: GENBANK/DQ304040 Key: SI, Value: GENBANK/DQ304041 Key: SI, Value: GENBANK/DQ304042 Key: SI, Value: GENBANK/DQ304043 Key: SI, Value: GENBANK/DQ304044 Key: SI, Value: GENBANK/DQ304045 Key: SI, Value: GENBANK/DQ304046 Key: SI, Value: GENBANK/DQ304047 Key: SI, Value: GENBANK/DQ304048 Key: SI, Value: GENBANK/DQ304049 Key: SI, Value: GENBANK/DQ304050 Key: SI, Value: GENBANK/DQ304051 Key: SI, Value: GENBANK/DQ304052 Key: SI, Value: GENBANK/DQ304053 Key: SI, Value: GENBANK/DQ304054 Key: SI, Value: GENBANK/DQ304055 Key: SI, Value: GENBANK/DQ304056 Key: SI, Value: GENBANK/DQ304057 Key: SI, Value: GENBANK/DQ304058 Key: SI, Value: GENBANK/DQ304059 Key: SI, Value: GENBANK/DQ304060 Key: SI, Value: GENBANK/DQ304061 Key: SI, Value: GENBANK/DQ304062 Key: SI, Value: GENBANK/DQ304063 Key: SI, Value: GENBANK/DQ304064 Key: SI, Value: GENBANK/DQ304065 Key: SI, Value: GENBANK/DQ304066 Key: SI, Value: GENBANK/DQ304067 Key: SI, Value: GENBANK/DQ304068 Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20070226 Key: PL, Value: Germany Key: TA, Value: Microbiol Res Key: JT, Value: Microbiological research Key: JID, Value: 9437794 Key: RN, Value: 0 (DNA, Bacterial) Key: RN, Value: 0 (DNA, Ribosomal) Key: RN, Value: 0 (RNA, Ribosomal, 16S) Key: SB, Value: IM Key: MH, Value: Bacteria/*classification/genetics/*isolation & purification Key: MH, Value: *Biodiversity Key: MH, Value: Brazil Key: MH, Value: DNA, Bacterial/genetics Key: MH, Value: DNA, Ribosomal/genetics Key: MH, Value: Molecular Sequence Data Key: MH, Value: *Phylogeny Key: MH, Value: RNA, Ribosomal, 16S/genetics Key: MH, Value: *Soil Microbiology Key: MH, Value: Tropical Climate Key: EDAT, Value: 2007/02/28 09:00 Key: MHDA, Value: 2009/04/08 09:00 Key: CRDT, Value: 2007/02/28 09:00 Key: PHST, Value: 2006/12/05 00:00 [accepted] Key: PHST, Value: 2007/02/28 09:00 [pubmed] Key: PHST, Value: 2009/04/08 09:00 [medline] Key: PHST, Value: 2007/02/28 09:00 [entrez] Key: AID, Value: S0944-5013(07)00002-X [pii] Key: AID, Value: 10.1016/j.micres.2006.12.001 [doi] Key: PST, Value: ppublish Key: SO, Value: Microbiol Res. 2009;164(1):59-70. doi: 10.1016/j.micres.2006.12.001. Epub 2007 Key: Feb 26., Value: Key: PMID, Value: 24386449 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20150223 Key: LR, Value: 20211021 Key: IS, Value: 1932-6203 (Electronic) Key: IS, Value: 1932-6203 (Linking) Key: VI, Value: 8 Key: IP, Value: 12 Key: DP, Value: 2013 Key: TI, Value: Transcriptome analysis in cotton boll weevil (Anthonomus grandis) and RNA Key: interference in insect pests., Value: Key: PG, Value: e85079 Key: LID, Value: 10.1371/journal.pone.0085079 [doi] Key: LID, Value: e85079 Key: AB, Value: Cotton plants are subjected to the attack of several insect pests. In Brazil, the Key: cotton boll weevil, Anthonomus grandis, is the most important cotton pest. The, Value: Key: use of insecticidal proteins and gene silencing by interference RNA (RNAi) as, Value: Key: techniques for insect control are promising strategies, which has been applied in, Value: Key: the last few years. For this insect, there are not much available molecular, Value: Key: information on databases. Using 454-pyrosequencing methodology, the transcriptome, Value: Key: of all developmental stages of the insect pest, A. grandis, was analyzed. The A., Value: Key: grandis transcriptome analysis resulted in more than 500.000 reads and a data set, Value: Key: of high quality 20,841 contigs. After sequence assembly and annotation, around, Value: Key: 10,600 contigs had at least one BLAST hit against NCBI non-redundant protein, Value: Key: database and 65.7% was similar to Tribolium castaneum sequences. A comparison of, Value: Key: A. grandis, Drosophila melanogaster and Bombyx mori protein families' data showed, Value: Key: higher similarity to dipteran than to lepidopteran sequences. Several contigs of, Value: Key: genes encoding proteins involved in RNAi mechanism were found. PAZ Domains, Value: Key: sequences extracted from the transcriptome showed high similarity and, Value: Key: conservation for the most important functional and structural motifs when, Value: Key: compared to PAZ Domains from 5 species. Two SID-like contigs were, Value: Key: phylogenetically analyzed and grouped with T. castaneum SID-like proteins. No, Value: Key: RdRP gene was found. A contig matching chitin synthase 1 was mined from the, Value: Key: transcriptome. dsRNA microinjection of a chitin synthase gene to A. grandis, Value: Key: female adults resulted in normal oviposition of unviable eggs and malformed alive, Value: Key: larvae that were unable to develop in artificial diet. This is the first study, Value: Key: that characterizes the transcriptome of the coleopteran, A. grandis. A new and, Value: Key: representative transcriptome database for this insect pest is now available. All, Value: Key: data support the state of the art of RNAi mechanism in insects., Value: Key: FAU, Value: Firmino, Alexandre Augusto Pereira Key: AU, Value: Firmino AA Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil ; Key: Graduate Program in Cellular and Molecular Biology, Center of Biotechnology,, Value: Key: Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul,, Value: Key: Brazil., Value: Key: FAU, Value: Fonseca, Fernando Campos de Assis Key: AU, Value: Fonseca FC Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil ; Key: Graduate Program in Biology Molecular, Universidade de Brasília, Brasília,, Value: Key: Distrito Federal, Brazil., Value: Key: FAU, Value: de Macedo, Leonardo Lima Pepino Key: AU, Value: de Macedo LL Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil ; Key: Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de, Value: Key: Brasília, Brasília, Distrito Federal, Brazil., Value: Key: FAU, Value: Coelho, Roberta Ramos Key: AU, Value: Coelho RR Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil ; Key: Graduate Program in Biology Molecular, Universidade de Brasília, Brasília,, Value: Key: Distrito Federal, Brazil., Value: Key: FAU, Value: Antonino de Souza, José Dijair Jr Key: AU, Value: Antonino de Souza JD Jr Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil ; Key: Graduate Program in Biology Molecular, Universidade de Brasília, Brasília,, Value: Key: Distrito Federal, Brazil., Value: Key: FAU, Value: Togawa, Roberto Coiti Key: AU, Value: Togawa RC Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil. Key: FAU, Value: Silva-Junior, Orzenil Bonfim Key: AU, Value: Silva-Junior OB Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil. Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Graduate Program in Biology Molecular, Universidade de Brasília, Brasília, Key: Distrito Federal, Brazil., Value: Key: FAU, Value: da Silva, Maria Cristina Mattar Key: AU, Value: da Silva MC Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil. Key: FAU, Value: Engler, Gilbert Key: AU, Value: Engler G Key: AD, Value: Plateau Microscopique, Institut National de la Recherche Agronomique, Key: Sophia-Antipolis, France., Value: Key: FAU, Value: Grossi-de-Sa, Maria Fatima Key: AU, Value: Grossi-de-Sa MF Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil ; Key: Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de, Value: Key: Brasília, Brasília, Distrito Federal, Brazil., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20131227 Key: PL, Value: United States Key: TA, Value: PLoS One Key: JT, Value: PloS one Key: JID, Value: 101285081 Key: RN, Value: 0 (Insect Proteins) Key: SB, Value: IM Key: MH, Value: Animals Key: MH, Value: Gossypium/parasitology Key: MH, Value: Insect Proteins/*biosynthesis/genetics Key: MH, Value: RNA Interference/*physiology Key: MH, Value: Species Specificity Key: MH, Value: Transcriptome/*physiology Key: MH, Value: Weevils/genetics/*metabolism Key: PMC, Value: PMC3874031 Key: COIS, Value: Competing Interests: The authors have declared that no competing interests exist. Key: EDAT, Value: 2014/01/05 06:00 Key: MHDA, Value: 2015/02/24 06:00 Key: PMCR, Value: 2013/12/27 Key: CRDT, Value: 2014/01/04 06:00 Key: PHST, Value: 2013/09/11 00:00 [received] Key: PHST, Value: 2013/11/22 00:00 [accepted] Key: PHST, Value: 2014/01/04 06:00 [entrez] Key: PHST, Value: 2014/01/05 06:00 [pubmed] Key: PHST, Value: 2015/02/24 06:00 [medline] Key: PHST, Value: 2013/12/27 00:00 [pmc-release] Key: AID, Value: PONE-D-13-37579 [pii] Key: AID, Value: 10.1371/journal.pone.0085079 [doi] Key: PST, Value: epublish Key: SO, Value: PLoS One. 2013 Dec 27;8(12):e85079. doi: 10.1371/journal.pone.0085079. Key: eCollection 2013., Value: Key: PMID, Value: 30930909 Key: OWN, Value: NLM Key: STAT, Value: PubMed-not-MEDLINE Key: LR, Value: 20201001 Key: IS, Value: 1664-462X (Print) Key: IS, Value: 1664-462X (Electronic) Key: IS, Value: 1664-462X (Linking) Key: VI, Value: 10 Key: DP, Value: 2019 Key: TI, Value: Spring Is Coming: Genetic Analyses of the Bud Break Date Locus Reveal Candidate Key: Genes From the Cold Perception Pathway to Dormancy Release in Apple (Malus ×, Value: Key: domestica Borkh.)., Value: Key: PG, Value: 33 Key: LID, Value: 10.3389/fpls.2019.00033 [doi] Key: LID, Value: 33 Key: AB, Value: Chilling requirement (CR) for bud dormancy completion determines the time of bud Key: break in apple (Malus × domestica Borkh.). The molecular control of bud dormancy, Value: Key: is highly heritable, suggesting a strong genetic control of the trait. An, Value: Key: available Infinium II SNP platform for genotyping containing 8,788 single, Value: Key: nucleotide polymorphic markers was employed, and linkage maps were constructed in, Value: Key: a F(1) cross from the low CR M13/91 and the moderate CR cv. Fred Hough. These, Value: Key: maps were used to identify quantitative trait loci (QTL) for bud break date as a, Value: Key: trait related to dormancy release. A major QTL for bud break was detected at the, Value: Key: beginning of linkage group 9 (LG9). This QTL remained stable during seven seasons, Value: Key: in two different growing sites. To increase mapping efficiency in detecting, Value: Key: contributing genes underlying this QTL, 182 additional SNP markers located at the, Value: Key: locus for bud break were used. Combining linkage mapping and structural, Value: Key: characterization of the region, the high proportion of the phenotypic variance in, Value: Key: the trait explained by the QTL is related to the coincident positioning of, Value: Key: Arabidopsis orthologs for ICE1, FLC, and PRE1 protein-coding genes. The proximity, Value: Key: of these genes from the most explanatory markers of this QTL for bud break, Value: Key: suggests potential genetic additive effects, reinforcing the hypothesis of, Value: Key: inter-dependent mechanisms controlling dormancy induction and release in apple, Value: Key: trees., Value: Key: FAU, Value: Miotto, Yohanna Evelyn Key: AU, Value: Miotto YE Key: AD, Value: Department of Crop Science, Agronomy School, Federal University of Rio Grande do Key: Sul, Porto Alegre, Brazil., Value: Key: FAU, Value: Tessele, Carolina Key: AU, Value: Tessele C Key: AD, Value: Department of Crop Science, Agronomy School, Federal University of Rio Grande do Key: Sul, Porto Alegre, Brazil., Value: Key: FAU, Value: Czermainski, Ana Beatriz Costa Key: AU, Value: Czermainski ABC Key: AD, Value: Embrapa Uva e Vinho, Bento Gonçalves, Brazil. Key: FAU, Value: Porto, Diogo Denardi Key: AU, Value: Porto DD Key: AD, Value: Embrapa Uva e Vinho, Bento Gonçalves, Brazil. Key: FAU, Value: Falavigna, Vítor da Silveira Key: AU, Value: Falavigna VDS Key: AD, Value: Embrapa Uva e Vinho, Bento Gonçalves, Brazil. Key: AD, Value: Graduate Program in Cell and Molecular Biology, Centro de Biotecnologia, Federal Key: University of Rio Grande do Sul, Porto Alegre, Brazil., Value: Key: FAU, Value: Sartor, Tiago Key: AU, Value: Sartor T Key: AD, Value: Embrapa Uva e Vinho, Bento Gonçalves, Brazil. Key: AD, Value: Graduate Program in Cell and Molecular Biology, Centro de Biotecnologia, Federal Key: University of Rio Grande do Sul, Porto Alegre, Brazil., Value: Key: FAU, Value: Cattani, Amanda Malvessi Key: AU, Value: Cattani AM Key: AD, Value: Embrapa Uva e Vinho, Bento Gonçalves, Brazil. Key: AD, Value: Graduate Program in Cell and Molecular Biology, Centro de Biotecnologia, Federal Key: University of Rio Grande do Sul, Porto Alegre, Brazil., Value: Key: FAU, Value: Delatorre, Carla Andrea Key: AU, Value: Delatorre CA Key: AD, Value: Department of Crop Science, Agronomy School, Federal University of Rio Grande do Key: Sul, Porto Alegre, Brazil., Value: Key: FAU, Value: de Alencar, Sérgio Amorim Key: AU, Value: de Alencar SA Key: AD, Value: Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Key: Católica de Brasília, Brasília, Brazil., Value: Key: FAU, Value: da Silva-Junior, Orzenil Bonfim Key: AU, Value: da Silva-Junior OB Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil. Key: FAU, Value: Togawa, Roberto Coiti Key: AU, Value: Togawa RC Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil. Key: FAU, Value: Costa, Marcos Mota do Carmo Key: AU, Value: Costa MMDC Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil. Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Department of Cell Biology, Universidade de Brasília, Brasília, Brazil. Key: FAU, Value: Grynberg, Priscila Key: AU, Value: Grynberg P Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil. Key: FAU, Value: de Oliveira, Paulo Ricardo Dias Key: AU, Value: de Oliveira PRD Key: AD, Value: Embrapa Uva e Vinho, Bento Gonçalves, Brazil. Key: FAU, Value: Kvitschal, Marcus Vinícius Key: AU, Value: Kvitschal MV Key: AD, Value: Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina |Epagri | Key: Estação Experimental de Caçador, Caçador, Brazil., Value: Key: FAU, Value: Denardi, Frederico Key: AU, Value: Denardi F Key: AD, Value: Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina |Epagri | Key: Estação Experimental de Caçador, Caçador, Brazil., Value: Key: FAU, Value: Buffon, Vanessa Key: AU, Value: Buffon V Key: AD, Value: Embrapa Uva e Vinho, Bento Gonçalves, Brazil. Key: FAU, Value: Revers, Luís Fernando Key: AU, Value: Revers LF Key: AD, Value: Embrapa Uva e Vinho, Bento Gonçalves, Brazil. Key: AD, Value: Graduate Program in Cell and Molecular Biology, Centro de Biotecnologia, Federal Key: University of Rio Grande do Sul, Porto Alegre, Brazil., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: DEP, Value: 20190307 Key: PL, Value: Switzerland Key: TA, Value: Front Plant Sci Key: JT, Value: Frontiers in plant science Key: JID, Value: 101568200 Key: PMC, Value: PMC6423911 Key: OTO, Value: NOTNLM Key: OT, Value: MdoFLC Key: OT, Value: MdoICE1 Key: OT, Value: MdoPRE1 Key: OT, Value: apple Key: OT, Value: bud dormancy Key: OT, Value: chilling requirement Key: OT, Value: linkage mapping Key: EDAT, Value: 2019/04/02 06:00 Key: MHDA, Value: 2019/04/02 06:01 Key: PMCR, Value: 2019/01/01 Key: CRDT, Value: 2019/04/02 06:00 Key: PHST, Value: 2018/07/16 00:00 [received] Key: PHST, Value: 2019/01/10 00:00 [accepted] Key: PHST, Value: 2019/04/02 06:00 [entrez] Key: PHST, Value: 2019/04/02 06:00 [pubmed] Key: PHST, Value: 2019/04/02 06:01 [medline] Key: PHST, Value: 2019/01/01 00:00 [pmc-release] Key: AID, Value: 10.3389/fpls.2019.00033 [doi] Key: PST, Value: epublish Key: SO, Value: Front Plant Sci. 2019 Mar 7;10:33. doi: 10.3389/fpls.2019.00033. eCollection Key: 2019., Value: Key: PMID, Value: 23663436 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20131030 Key: LR, Value: 20240321 Key: IS, Value: 1471-2164 (Electronic) Key: IS, Value: 1471-2164 (Linking) Key: VI, Value: 14 Key: DP, Value: 2013 May 10 Key: TI, Value: Transcription profile of soybean-root-knot nematode interaction reveals a key Key: role of phythormones in the resistance reaction., Value: Key: PG, Value: 322 Key: LID, Value: 10.1186/1471-2164-14-322 [doi] Key: AB, Value: BACKGROUND: Root-knot nematodes (RKN|Meloidogyne genus) present extensive Key: challenges to soybean crop. The soybean line (PI 595099) is known to be resistant, Value: Key: against specific strains and races of nematode species, thus its differential, Value: Key: gene expression analysis can lead to a comprehensive gene expression profiling in, Value: Key: the incompatible soybean-RKN interaction. Even though many disease resistance, Value: Key: genes have been studied, little has been reported about phytohormone crosstalk on, Value: Key: modulation of ROS signaling during soybean-RKN interaction. RESULTS: Using 454, Value: Key: technology to explore the common aspects of resistance reaction during both, Value: Key: parasitism and resistance phases it was verified that hormone, carbohydrate, Value: Key: metabolism and stress related genes were consistently expressed at high levels in, Value: Key: infected roots as compared to mock control. Most noteworthy genes include those, Value: Key: encoding glycosyltransferases, peroxidases, auxin-responsive proteins and, Value: Key: gibberellin-regulated genes. Our data analysis suggests the key role of, Value: Key: glycosyltransferases, auxins and components of gibberellin signal transduction,, Value: Key: biosynthesis and deactivation pathways in the resistance reaction and their, Value: Key: participation in jasmonate signaling and redox homeostasis in mediating aspects, Value: Key: of plant growth and responses to biotic stress. CONCLUSIONS: Based on this study, Value: Key: we suggest a reasonable model regarding to the complex mechanisms of crosstalk, Value: Key: between plant hormones, mainly gibberellins and auxins, which can be crucial to, Value: Key: modulate the levels of ROS in the resistance reaction to nematode invasion. The, Value: Key: model also includes recent findings concerning to the participation of DELLA-like, Value: Key: proteins and ROS signaling controlling plant immune or stress responses., Value: Key: Furthermore, this study provides a dataset of potential candidate genes involved, Value: Key: in both nematode parasitism and resistance, which can be tested further for their, Value: Key: role in this biological process using functional genomics approaches., Value: Key: FAU, Value: Beneventi, Magda Aparecida Key: AU, Value: Beneventi MA Key: AD, Value: Federal University of Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil. Key: FAU, Value: da Silva, Orzenil Bonfim Jr Key: AU, Value: da Silva OB Jr Key: FAU, Value: de Sá, Maria Eugênia Lisei Key: AU, Value: de Sá ME Key: FAU, Value: Firmino, Alexandre Augusto Pereira Key: AU, Value: Firmino AA Key: FAU, Value: de Amorim, Regina Maria Santos Key: AU, Value: de Amorim RM Key: FAU, Value: Albuquerque, Erika Valéria Saliba Key: AU, Value: Albuquerque EV Key: FAU, Value: da Silva, Maria Cristina Mattar Key: AU, Value: da Silva MC Key: FAU, Value: da Silva, Joseane Padilha Key: AU, Value: da Silva JP Key: FAU, Value: Campos, Magnólia de Araújo Key: AU, Value: Campos Mde A Key: FAU, Value: Lopes, Marcus José Conceição Key: AU, Value: Lopes MJ Key: FAU, Value: Togawa, Roberto Coiti Key: AU, Value: Togawa RC Key: FAU, Value: Pappas, Georgios Joanis Jr Key: AU, Value: Pappas GJ Jr Key: FAU, Value: Grossi-de-Sa, Maria Fatima Key: AU, Value: Grossi-de-Sa MF Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20130510 Key: PL, Value: England Key: TA, Value: BMC Genomics Key: JT, Value: BMC genomics Key: JID, Value: 100965258 Key: RN, Value: 0 (Gibberellins) Key: RN, Value: 0 (Indoleacetic Acids) Key: RN, Value: 0 (Plant Growth Regulators) Key: RN, Value: 0 (Plant Proteins) Key: RN, Value: 0 (RNA, Messenger) Key: SB, Value: IM Key: MH, Value: Animals Key: MH, Value: Disease Resistance/*genetics Key: MH, Value: *Gene Expression Profiling Key: MH, Value: Gibberellins/metabolism Key: MH, Value: *Host-Parasite Interactions Key: MH, Value: Indoleacetic Acids/metabolism Key: MH, Value: Plant Diseases/*parasitology Key: MH, Value: Plant Growth Regulators/genetics/*metabolism Key: MH, Value: Plant Proteins/genetics/metabolism Key: MH, Value: RNA, Messenger/genetics/metabolism Key: MH, Value: Sequence Analysis Key: MH, Value: Glycine max/genetics/immunology/metabolism/*parasitology Key: MH, Value: Stress, Physiological/genetics Key: MH, Value: Transcription, Genetic Key: MH, Value: Tylenchoidea/*physiology Key: PMC, Value: PMC3701510 Key: EDAT, Value: 2013/05/15 06:00 Key: MHDA, Value: 2013/10/31 06:00 Key: PMCR, Value: 2013/05/10 Key: CRDT, Value: 2013/05/14 06:00 Key: PHST, Value: 2013/02/05 00:00 [received] Key: PHST, Value: 2013/05/01 00:00 [accepted] Key: PHST, Value: 2013/05/14 06:00 [entrez] Key: PHST, Value: 2013/05/15 06:00 [pubmed] Key: PHST, Value: 2013/10/31 06:00 [medline] Key: PHST, Value: 2013/05/10 00:00 [pmc-release] Key: AID, Value: 1471-2164-14-322 [pii] Key: AID, Value: 10.1186/1471-2164-14-322 [doi] Key: PST, Value: epublish Key: SO, Value: BMC Genomics. 2013 May 10;14:322. doi: 10.1186/1471-2164-14-322. Key: PMID, Value: 18590545 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20080819 Key: LR, Value: 20240109 Key: IS, Value: 1471-2164 (Electronic) Key: IS, Value: 1471-2164 (Linking) Key: VI, Value: 9 Key: DP, Value: 2008 Jun 30 Key: TI, Value: High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized Key: genome., Value: Key: PG, Value: 312 Key: LID, Value: 10.1186/1471-2164-9-312 [doi] Key: AB, Value: BACKGROUND: Benefits from high-throughput sequencing using 454 pyrosequencing Key: technology may be most apparent for species with high societal or economic value, Value: Key: but few genomic resources. Rapid means of gene sequence and SNP discovery using, Value: Key: this novel sequencing technology provide a set of baseline tools for genome-level, Value: Key: research. However, it is questionable how effective the sequencing of large, Value: Key: numbers of short reads for species with essentially no prior gene sequence, Value: Key: information will support contig assemblies and sequence annotation. RESULTS: With, Value: Key: the purpose of generating the first broad survey of gene sequences in Eucalyptus, Value: Key: grandis, the most widely planted hardwood tree species, we used 454 technology to, Value: Key: sequence and assemble 148 Mbp of expressed sequences (EST). EST sequences were, Value: Key: generated from a normalized cDNA pool comprised of multiple tissues and, Value: Key: genotypes, promoting discovery of homologues to almost half of Arabidopsis genes,, Value: Key: and a comprehensive survey of allelic variation in the transcriptome. By aligning, Value: Key: the sequencing reads from multiple genotypes we detected 23,742 SNPs, 83% of, Value: Key: which were validated in a sample. Genome-wide nucleotide diversity was estimated, Value: Key: for 2,392 contigs using a modified theta (theta) parameter, adapted for measuring, Value: Key: genetic diversity from polymorphisms detected by randomly sequencing a, Value: Key: multi-genotype cDNA pool. Diversity estimates in non-synonymous nucleotides were, Value: Key: on average 4x smaller than in synonymous, suggesting purifying selection., Value: Key: Non-synonymous to synonymous substitutions (Ka/Ks) among 2,001 contigs averaged, Value: Key: 0.30 and was skewed to the right, further supporting that most genes are under, Value: Key: purifying selection. Comparison of these estimates among contigs identified major, Value: Key: functional classes of genes under purifying and diversifying selection in, Value: Key: agreement with previous researches. CONCLUSION: In providing an abundance of, Value: Key: foundational transcript sequences where limited prior genomic information, Value: Key: existed, this work created part of the foundation for the annotation of the E., Value: Key: grandis genome that is being sequenced by the US Department of Energy. In, Value: Key: addition we demonstrated that SNPs sampled in large-scale with 454 pyrosequencing, Value: Key: can be used to detect evolutionary signatures among genes, providing one of the, Value: Key: first genome-wide assessments of nucleotide diversity and Ka/Ks for a non-model, Value: Key: plant species., Value: Key: FAU, Value: Novaes, Evandro Key: AU, Value: Novaes E Key: AD, Value: School of Forest Resources and Conservation, University of Florida, PO Box Key: 110410, Gainesville, USA. evandro@ufl.edu, Value: Key: FAU, Value: Drost, Derek R Key: AU, Value: Drost DR Key: FAU, Value: Farmerie, William G Key: AU, Value: Farmerie WG Key: FAU, Value: Pappas, Georgios J Jr Key: AU, Value: Pappas GJ Jr Key: FAU, Value: Grattapaglia, Dario Key: AU, Value: Grattapaglia D Key: FAU, Value: Sederoff, Ronald R Key: AU, Value: Sederoff RR Key: FAU, Value: Kirst, Matias Key: AU, Value: Kirst M Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20080630 Key: PL, Value: England Key: TA, Value: BMC Genomics Key: JT, Value: BMC genomics Key: JID, Value: 100965258 Key: RN, Value: 0 (DNA, Complementary) Key: SB, Value: IM Key: MH, Value: Alleles Key: MH, Value: DNA, Complementary/biosynthesis Key: MH, Value: Eucalyptus/*genetics Key: MH, Value: *Expressed Sequence Tags Key: MH, Value: Gene Library Key: MH, Value: *Genes, Plant Key: MH, Value: Genetic Variation Key: MH, Value: Haplotypes Key: MH, Value: Polymorphism, Single Nucleotide/*genetics Key: MH, Value: Reproducibility of Results Key: MH, Value: Sequence Analysis, DNA/*methods Key: MH, Value: Software Key: MH, Value: Transcription, Genetic Key: PMC, Value: PMC2483731 Key: EDAT, Value: 2008/07/02 09:00 Key: MHDA, Value: 2008/08/20 09:00 Key: PMCR, Value: 2008/06/30 Key: CRDT, Value: 2008/07/02 09:00 Key: PHST, Value: 2008/02/29 00:00 [received] Key: PHST, Value: 2008/06/30 00:00 [accepted] Key: PHST, Value: 2008/07/02 09:00 [pubmed] Key: PHST, Value: 2008/08/20 09:00 [medline] Key: PHST, Value: 2008/07/02 09:00 [entrez] Key: PHST, Value: 2008/06/30 00:00 [pmc-release] Key: AID, Value: 1471-2164-9-312 [pii] Key: AID, Value: 10.1186/1471-2164-9-312 [doi] Key: PST, Value: epublish Key: SO, Value: BMC Genomics. 2008 Jun 30;9:312. doi: 10.1186/1471-2164-9-312. Key: PMID, Value: 18234080 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20080506 Key: LR, Value: 20211020 Key: IS, Value: 1471-2164 (Electronic) Key: IS, Value: 1471-2164 (Linking) Key: VI, Value: 9 Key: DP, Value: 2008 Jan 30 Key: TI, Value: Insights into the Musa genome: syntenic relationships to rice and between Musa Key: species., Value: Key: PG, Value: 58 Key: LID, Value: 10.1186/1471-2164-9-58 [doi] Key: AB, Value: BACKGROUND: Musa species (Zingiberaceae, Zingiberales) including bananas and Key: plantains are collectively the fourth most important crop in developing, Value: Key: countries. Knowledge concerning Musa genome structure and the origin of distinct, Value: Key: cultivars has greatly increased over the last few years. Until now, however, no, Value: Key: large-scale analyses of Musa genomic sequence have been conducted. This study, Value: Key: compares genomic sequence in two Musa species with orthologous regions in the, Value: Key: rice genome. RESULTS: We produced 1.4 Mb of Musa sequence from 13 BAC clones,, Value: Key: annotated and analyzed them along with 4 previously sequenced BACs. The 443, Value: Key: predicted genes revealed that Zingiberales genes share GC content and, Value: Key: distribution characteristics with eudicot and Poaceae genomes. Comparison with, Value: Key: rice revealed microsynteny regions that have persisted since the divergence of, Value: Key: the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously, Value: Key: hypothesized large-scale duplication event in the common ancestor of major cereal, Value: Key: lineages within the Poaceae was verified. The divergence time distributions for, Value: Key: Musa-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong, Value: Key: evidence for a large-scale duplication event in the Musa lineage after its, Value: Key: divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic, Value: Key: regions from M. acuminata and M. balbisiana revealed highly conserved genome, Value: Key: structure, and indicated that these genomes diverged circa 4.6 Mya. CONCLUSION:, Value: Key: These results point to the utility of comparative analyses between, Value: Key: distantly-related monocot species such as rice and Musa for improving our, Value: Key: understanding of monocot genome evolution. Sequencing the genome of M. acuminata, Value: Key: would provide a strong foundation for comparative genomics in the monocots. In, Value: Key: addition a genome sequence would aid genomic and genetic analyses of cultivated, Value: Key: Musa polyploid genotypes in research aimed at localizing and cloning genes, Value: Key: controlling important agronomic traits for breeding purposes., Value: Key: FAU, Value: Lescot, Magali Key: AU, Value: Lescot M Key: AD, Value: French Agricultural Research Center for International Development, UMR 1096, Key: Avenue Agropolis, TA40/03, FR-34398, Montpellier, Cedex 5, France., Value: Key: magali.lescot@igs.cnrs-mrs.fr, Value: Key: FAU, Value: Piffanelli, Pietro Key: AU, Value: Piffanelli P Key: FAU, Value: Ciampi, Ana Y Key: AU, Value: Ciampi AY Key: FAU, Value: Ruiz, Manuel Key: AU, Value: Ruiz M Key: FAU, Value: Blanc, Guillaume Key: AU, Value: Blanc G Key: FAU, Value: Leebens-Mack, Jim Key: AU, Value: Leebens-Mack J Key: FAU, Value: da Silva, Felipe R Key: AU, Value: da Silva FR Key: FAU, Value: Santos, Candice M R Key: AU, Value: Santos CM Key: FAU, Value: D'Hont, Angélique Key: AU, Value: D'Hont A Key: FAU, Value: Garsmeur, Olivier Key: AU, Value: Garsmeur O Key: FAU, Value: Vilarinhos, Alberto D Key: AU, Value: Vilarinhos AD Key: FAU, Value: Kanamori, Hiroyuki Key: AU, Value: Kanamori H Key: FAU, Value: Matsumoto, Takashi Key: AU, Value: Matsumoto T Key: FAU, Value: Ronning, Catherine M Key: AU, Value: Ronning CM Key: FAU, Value: Cheung, Foo Key: AU, Value: Cheung F Key: FAU, Value: Haas, Brian J Key: AU, Value: Haas BJ Key: FAU, Value: Althoff, Ryan Key: AU, Value: Althoff R Key: FAU, Value: Arbogast, Tammy Key: AU, Value: Arbogast T Key: FAU, Value: Hine, Erin Key: AU, Value: Hine E Key: FAU, Value: Pappas, Georgios J Jr Key: AU, Value: Pappas GJ Jr Key: FAU, Value: Sasaki, Takuji Key: AU, Value: Sasaki T Key: FAU, Value: Souza, Manoel T Jr Key: AU, Value: Souza MT Jr Key: FAU, Value: Miller, Robert N G Key: AU, Value: Miller RN Key: FAU, Value: Glaszmann, Jean-Christophe Key: AU, Value: Glaszmann JC Key: FAU, Value: Town, Christopher D Key: AU, Value: Town CD Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20080130 Key: PL, Value: England Key: TA, Value: BMC Genomics Key: JT, Value: BMC genomics Key: JID, Value: 100965258 Key: RN, Value: 0 (DNA Transposable Elements) Key: RN, Value: 0 (DNA, Complementary) Key: SB, Value: IM Key: MH, Value: Arabidopsis/genetics Key: MH, Value: Base Composition Key: MH, Value: Chromosomes, Artificial, Bacterial Key: MH, Value: DNA Transposable Elements/genetics Key: MH, Value: DNA, Complementary/genetics Key: MH, Value: Evolution, Molecular Key: MH, Value: Expressed Sequence Tags Key: MH, Value: Gene Duplication Key: MH, Value: Genes, Plant/genetics Key: MH, Value: Genome, Plant/*genetics Key: MH, Value: Musa/*classification/enzymology/*genetics Key: MH, Value: Oryza/enzymology/*genetics Key: MH, Value: Polymorphism, Restriction Fragment Length Key: MH, Value: Repetitive Sequences, Nucleic Acid/genetics Key: MH, Value: Sorghum/genetics Key: MH, Value: Species Specificity Key: MH, Value: Synteny/*genetics Key: PMC, Value: PMC2270835 Key: EDAT, Value: 2008/02/01 09:00 Key: MHDA, Value: 2008/05/07 09:00 Key: PMCR, Value: 2008/01/30 Key: CRDT, Value: 2008/02/01 09:00 Key: PHST, Value: 2007/06/11 00:00 [received] Key: PHST, Value: 2008/01/30 00:00 [accepted] Key: PHST, Value: 2008/02/01 09:00 [pubmed] Key: PHST, Value: 2008/05/07 09:00 [medline] Key: PHST, Value: 2008/02/01 09:00 [entrez] Key: PHST, Value: 2008/01/30 00:00 [pmc-release] Key: AID, Value: 1471-2164-9-58 [pii] Key: AID, Value: 10.1186/1471-2164-9-58 [doi] Key: PST, Value: epublish Key: SO, Value: BMC Genomics. 2008 Jan 30;9:58. doi: 10.1186/1471-2164-9-58. Key: PMID, Value: 24635846 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20141217 Key: LR, Value: 20240321 Key: IS, Value: 1471-2164 (Electronic) Key: IS, Value: 1471-2164 (Linking) Key: VI, Value: 15 Key: DP, Value: 2014 Mar 18 Key: TI, Value: Identification of mycoparasitism-related genes against the phytopathogen Key: Sclerotinia sclerotiorum through transcriptome and expression profile analysis in, Value: Key: Trichoderma harzianum., Value: Key: PG, Value: 204 Key: LID, Value: 10.1186/1471-2164-15-204 [doi] Key: AB, Value: BACKGROUND: The species of T. harzianum are well known for their biocontrol Key: activity against plant pathogens. However, few studies have been conducted to, Value: Key: further our understanding of its role as a biological control agent against S., Value: Key: sclerotiorum, a pathogen involved in several crop diseases around the world. In, Value: Key: this study, we have used RNA-seq and quantitative real-time PCR (RT-qPCR), Value: Key: techniques in order to explore changes in T. harzianum gene expression during, Value: Key: growth on cell wall of S. sclerotiorum (SSCW) or glucose. RT-qPCR was also used, Value: Key: to examine genes potentially involved in biocontrol, during confrontation between, Value: Key: T. harzianum and S. sclerotiorum. RESULTS: Data obtained from six RNA-seq, Value: Key: libraries were aligned onto the T. harzianum CBS 226.95 reference genome and, Value: Key: compared after annotation using the Blast2GO suite. A total of 297 differentially, Value: Key: expressed genes were found in mycelia grown for 12, 24 and 36 h under the two, Value: Key: different conditions: supplemented with glucose or SSCW. Functional annotation of, Value: Key: these genes identified diverse biological processes and molecular functions, Value: Key: required during T. harzianum growth on SSCW or glucose. We identified various, Value: Key: genes of biotechnological value encoding proteins with functions such as, Value: Key: transporters, hydrolytic activity, adherence, appressorium development and, Value: Key: pathogenesis. To validate the expression profile, RT-qPCR was performed using 20, Value: Key: randomly chosen genes. RT-qPCR expression profiles were in complete agreement, Value: Key: with the RNA-Seq data for 17 of the genes evaluated. The other three showed, Value: Key: differences at one or two growth times. During the confrontation assay, some, Value: Key: genes were up-regulated during and after contact, as shown in the presence of, Value: Key: SSCW which is commonly used as a model to mimic this interaction. CONCLUSIONS:, Value: Key: The present study is the first initiative to use RNA-seq for identification of, Value: Key: differentially expressed genes in T. harzianum strain TR274, in response to the, Value: Key: phytopathogenic fungus S. sclerotiorum. It provides insights into the mechanisms, Value: Key: of gene expression involved in mycoparasitism of T. harzianum against, Value: Key: S.sclerotiorum. The RNA-seq data presented will facilitate improvement of the, Value: Key: annotation of gene models in the draft T. harzianum genome and provide important, Value: Key: information regarding the transcriptome during this interaction., Value: Key: FAU, Value: Steindorff, Andrei Stecca Key: AU, Value: Steindorff AS Key: FAU, Value: Ramada, Marcelo Henrique Soller Key: AU, Value: Ramada MH Key: FAU, Value: Coelho, Alexandre Siqueira Guedes Key: AU, Value: Coelho AS Key: FAU, Value: Miller, Robert Neil Gerard Key: AU, Value: Miller RN Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: FAU, Value: Ulhoa, Cirano José Key: AU, Value: Ulhoa CJ Key: AD, Value: Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Goiás, Key: Campus Samambaia, Instituto de Ciências Biológicas, CEP 74,090-900 Goiânia, GO,, Value: Key: Brazil. ulhoa@icb.ufg.br., Value: Key: FAU, Value: Noronha, Eliane Ferreira Key: AU, Value: Noronha EF Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: PT, Value: Research Support, U.S. Gov't, Non-P.H.S. Key: DEP, Value: 20140318 Key: PL, Value: England Key: TA, Value: BMC Genomics Key: JT, Value: BMC genomics Key: JID, Value: 100965258 Key: RN, Value: 0 (Fungal Proteins) Key: SB, Value: IM Key: MH, Value: Ascomycota/*genetics Key: MH, Value: Chromosome Mapping Key: MH, Value: Cluster Analysis Key: MH, Value: Fungal Proteins/genetics/metabolism Key: MH, Value: Gene Expression Profiling Key: MH, Value: Gene Library Key: MH, Value: *Genes, Fungal Key: MH, Value: High-Throughput Nucleotide Sequencing Key: MH, Value: Molecular Sequence Annotation Key: MH, Value: Real-Time Polymerase Chain Reaction Key: MH, Value: Sequence Analysis, RNA Key: MH, Value: *Transcriptome Key: MH, Value: Trichoderma/*genetics/growth & development Key: PMC, Value: PMC4004048 Key: EDAT, Value: 2014/03/19 06:00 Key: MHDA, Value: 2014/12/18 06:00 Key: PMCR, Value: 2014/03/18 Key: CRDT, Value: 2014/03/19 06:00 Key: PHST, Value: 2013/11/28 00:00 [received] Key: PHST, Value: 2014/03/06 00:00 [accepted] Key: PHST, Value: 2014/03/19 06:00 [entrez] Key: PHST, Value: 2014/03/19 06:00 [pubmed] Key: PHST, Value: 2014/12/18 06:00 [medline] Key: PHST, Value: 2014/03/18 00:00 [pmc-release] Key: AID, Value: 1471-2164-15-204 [pii] Key: AID, Value: 10.1186/1471-2164-15-204 [doi] Key: PST, Value: epublish Key: SO, Value: BMC Genomics. 2014 Mar 18;15:204. doi: 10.1186/1471-2164-15-204. Key: PMID, Value: 26911872 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20161007 Key: LR, Value: 20240324 Key: IS, Value: 1474-760X (Electronic) Key: IS, Value: 1474-7596 (Print) Key: IS, Value: 1474-7596 (Linking) Key: VI, Value: 17 Key: DP, Value: 2016 Feb 25 Key: TI, Value: Genome and transcriptome analysis of the Mesoamerican common bean and the role of Key: gene duplications in establishing tissue and temporal specialization of genes., Value: Key: PG, Value: 32 Key: LID, Value: 10.1186/s13059-016-0883-6 [doi] Key: LID, Value: 32 Key: AB, Value: BACKGROUND: Legumes are the third largest family of angiosperms and the second Key: most important crop class. Legume genomes have been shaped by extensive, Value: Key: large-scale gene duplications, including an approximately 58 million year old, Value: Key: whole genome duplication shared by most crop legumes. RESULTS: We report the, Value: Key: genome and the transcription atlas of coding and non-coding genes of a, Value: Key: Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a, Value: Key: comprehensive phylogenomics analysis, we assessed the past and recent evolution, Value: Key: of common bean, and traced the diversification of patterns of gene expression, Value: Key: following duplication. We find that successive rounds of gene duplications in, Value: Key: legumes have shaped tissue and developmental expression, leading to increased, Value: Key: levels of specialization in larger gene families. We also find that many long, Value: Key: non-coding RNAs are preferentially expressed in germ-line-related tissues (pods, Value: Key: and seeds), suggesting that they play a significant role in fruit development., Value: Key: Our results also suggest that most bean-specific gene family expansions,, Value: Key: including resistance gene clusters, predate the split of the Mesoamerican and, Value: Key: Andean gene pools. CONCLUSIONS: The genome and transcriptome data herein, Value: Key: generated for a Mesoamerican genotype represent a counterpart to the genomic, Value: Key: resources already available for the Andean gene pool. Altogether, this, Value: Key: information will allow the genetic dissection of the characters involved in the, Value: Key: domestication and adaptation of the crop, and their further implementation in, Value: Key: breeding strategies for this important crop., Value: Key: FAU, Value: Vlasova, Anna Key: AU, Value: Vlasova A Key: AD, Value: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Key: Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain., Value: Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: FAU, Value: Capella-Gutiérrez, Salvador Key: AU, Value: Capella-Gutiérrez S Key: AD, Value: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Key: Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain., Value: Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: AD, Value: Yeast and Basidiomycete Research Group, CBS Fungal Biodiversity Centre, Key: Uppsalalaan 8, 3584 LT, Utrecht, The Netherlands., Value: Key: FAU, Value: Rendón-Anaya, Martha Key: AU, Value: Rendón-Anaya M Key: AD, Value: Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP Key: 36821, Irapuato, Guanajuato, Mexico., Value: Key: FAU, Value: Hernández-Oñate, Miguel Key: AU, Value: Hernández-Oñate M Key: AD, Value: Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP Key: 36821, Irapuato, Guanajuato, Mexico., Value: Key: FAU, Value: Minoche, André E Key: AU, Value: Minoche AE Key: AD, Value: Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW, 2010, Key: Australia., Value: Key: FAU, Value: Erb, Ionas Key: AU, Value: Erb I Key: AD, Value: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Key: Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain., Value: Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: FAU, Value: Câmara, Francisco Key: AU, Value: Câmara F Key: AD, Value: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Key: Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain., Value: Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: FAU, Value: Prieto-Barja, Pablo Key: AU, Value: Prieto-Barja P Key: AD, Value: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Key: Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain., Value: Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: FAU, Value: Corvelo, André Key: AU, Value: Corvelo A Key: AD, Value: New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA. Key: FAU, Value: Sanseverino, Walter Key: AU, Value: Sanseverino W Key: AD, Value: IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Key: Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain., Value: Key: FAU, Value: Westergaard, Gastón Key: AU, Value: Westergaard G Key: AD, Value: Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Key: Argentina., Value: Key: FAU, Value: Dohm, Juliane C Key: AU, Value: Dohm JC Key: AD, Value: Department of Biotechnology, University of Natural Resources and Life Sciences Key: (BOKU), Muthgasse 18, 1190, Vienna, Austria., Value: Key: FAU, Value: Pappas, Georgios J Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Department of Cellular Biology, University of Brasilia, Biological Science Key: Institute, Brasília, DF, 70790-160, Brazil., Value: Key: FAU, Value: Saburido-Alvarez, Soledad Key: AU, Value: Saburido-Alvarez S Key: AD, Value: Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP Key: 36821, Irapuato, Guanajuato, Mexico., Value: Key: FAU, Value: Kedra, Darek Key: AU, Value: Kedra D Key: AD, Value: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Key: Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain., Value: Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: FAU, Value: Gonzalez, Irene Key: AU, Value: Gonzalez I Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: AD, Value: Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Key: Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia,, Value: Key: Spain., Value: Key: FAU, Value: Cozzuto, Luca Key: AU, Value: Cozzuto L Key: AD, Value: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Key: Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain., Value: Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: FAU, Value: Gómez-Garrido, Jessica Key: AU, Value: Gómez-Garrido J Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: AD, Value: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Key: Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain., Value: Key: FAU, Value: Aguilar-Morón, María A Key: AU, Value: Aguilar-Morón MA Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: AD, Value: Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Key: Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia,, Value: Key: Spain., Value: Key: FAU, Value: Andreu, Nuria Key: AU, Value: Andreu N Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: AD, Value: Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Key: Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia,, Value: Key: Spain., Value: Key: FAU, Value: Aguilar, O Mario Key: AU, Value: Aguilar OM Key: AD, Value: Instituto de Biotecnología y Biología Molecular (IBBM), UNLP-CONICET, 1900, La Key: Plata, Argentina., Value: Key: FAU, Value: Garcia-Mas, Jordi Key: AU, Value: Garcia-Mas J Key: AD, Value: IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Key: Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain., Value: Key: FAU, Value: Zehnsdorf, Maik Key: AU, Value: Zehnsdorf M Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: AD, Value: Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Key: Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia,, Value: Key: Spain., Value: Key: FAU, Value: Vázquez, Martín P Key: AU, Value: Vázquez MP Key: AD, Value: Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Key: Argentina., Value: Key: FAU, Value: Delgado-Salinas, Alfonso Key: AU, Value: Delgado-Salinas A Key: AD, Value: Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de Key: México, 04510, Mexico City, Mexico., Value: Key: FAU, Value: Delaye, Luis Key: AU, Value: Delaye L Key: AD, Value: Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav, 36821, Irapuato, Key: Guanajuato, Mexico., Value: Key: FAU, Value: Lowy, Ernesto Key: AU, Value: Lowy E Key: AD, Value: European Molecular Biology Laboratory, European Bioinformatics Institute, Key: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom., Value: Key: FAU, Value: Mentaberry, Alejandro Key: AU, Value: Mentaberry A Key: AD, Value: Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), Key: C1428EGA, Buenos Aires, Argentina., Value: Key: FAU, Value: Vianello-Brondani, Rosana P Key: AU, Value: Vianello-Brondani RP Key: AD, Value: EMBRAPA Rice and Beans, Biotechnology Laboratory, Santo Antônio de Goiás, GO, Key: 75375-000, Brazil., Value: Key: FAU, Value: García, José Luís Key: AU, Value: García JL Key: AD, Value: Environmental Biology Department, Centro de Investigaciones Biológicas, (CSIC), Key: 28040, Madrid, Spain., Value: Key: FAU, Value: Alioto, Tyler Key: AU, Value: Alioto T Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: AD, Value: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Key: Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain., Value: Key: FAU, Value: Sánchez, Federico Key: AU, Value: Sánchez F Key: AD, Value: Depto. de Biología Molecular de Plantas, Instituto Biotecnología, Universidad Key: Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico., Value: Key: FAU, Value: Himmelbauer, Heinz Key: AU, Value: Himmelbauer H Key: AD, Value: Department of Biotechnology, University of Natural Resources and Life Sciences Key: (BOKU), Muthgasse 18, 1190, Vienna, Austria., Value: Key: FAU, Value: Santalla, Marta Key: AU, Value: Santalla M Key: AD, Value: Mision Biológica de Galicia (MBG)-National Spanish Research Council (CSIC), Key: 36080, Pontevedra, Spain., Value: Key: FAU, Value: Notredame, Cedric Key: AU, Value: Notredame C Key: AD, Value: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Key: Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain., Value: Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: FAU, Value: Gabaldón, Toni Key: AU, Value: Gabaldón T Key: AD, Value: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Key: Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain., Value: Key: toni.gabaldon@crg.eu., Value: Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: toni.gabaldon@crg.eu., Value: Key: AD, Value: Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, Key: 08010, Barcelona, Spain. toni.gabaldon@crg.eu., Value: Key: FAU, Value: Herrera-Estrella, Alfredo Key: AU, Value: Herrera-Estrella A Key: AD, Value: Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP Key: 36821, Irapuato, Guanajuato, Mexico. aherrera@langebio.cinvestav.mx., Value: Key: FAU, Value: Guigó, Roderic Key: AU, Value: Guigó R Key: AD, Value: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Key: Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain., Value: Key: roderic.guigo@crg.eu., Value: Key: AD, Value: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. Key: roderic.guigo@crg.eu., Value: Key: AD, Value: IMIM (Hospital del Mar Medical Research Institute), 08003, Barcelona, Spain. Key: roderic.guigo@crg.eu., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20160225 Key: PL, Value: England Key: TA, Value: Genome Biol Key: JT, Value: Genome biology Key: JID, Value: 100960660 Key: RN, Value: 0 (DNA, Plant) Key: SB, Value: IM Key: MH, Value: DNA, Plant/genetics Key: MH, Value: Gene Duplication Key: MH, Value: Gene Expression Profiling Key: MH, Value: *Genome, Plant Key: MH, Value: Genotype Key: MH, Value: Humans Key: MH, Value: Microsatellite Repeats/*genetics Key: MH, Value: Phaseolus/*genetics Key: MH, Value: Phylogeny Key: MH, Value: Seeds/genetics Key: MH, Value: Sequence Analysis, DNA Key: MH, Value: Transcriptome/*genetics Key: PMC, Value: PMC4766624 Key: EDAT, Value: 2016/02/26 06:00 Key: MHDA, Value: 2016/10/08 06:00 Key: PMCR, Value: 2016/02/25 Key: CRDT, Value: 2016/02/26 06:00 Key: PHST, Value: 2015/08/22 00:00 [received] Key: PHST, Value: 2016/01/22 00:00 [accepted] Key: PHST, Value: 2016/02/26 06:00 [entrez] Key: PHST, Value: 2016/02/26 06:00 [pubmed] Key: PHST, Value: 2016/10/08 06:00 [medline] Key: PHST, Value: 2016/02/25 00:00 [pmc-release] Key: AID, Value: 10.1186/s13059-016-0883-6 [pii] Key: AID, Value: 883 [pii] Key: AID, Value: 10.1186/s13059-016-0883-6 [doi] Key: PST, Value: epublish Key: SO, Value: Genome Biol. 2016 Feb 25;17:32. doi: 10.1186/s13059-016-0883-6. Key: PMID, Value: 26714854 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20160928 Key: LR, Value: 20181113 Key: IS, Value: 1471-2164 (Electronic) Key: IS, Value: 1471-2164 (Linking) Key: VI, Value: 16 Key: DP, Value: 2015 Dec 29 Key: TI, Value: Genome-wide discovery and validation of Eucalyptus small RNAs reveals variable Key: patterns of conservation and diversity across species of Myrtaceae., Value: Key: PG, Value: 1113 Key: LID, Value: 10.1186/s12864-015-2322-6 [doi] Key: LID, Value: 1113 Key: AB, Value: BACKGROUND: Micro RNAs are a class of small non coding RNAs of 20-24 nucleotides Key: transcribed as single stranded precursors from MIR gene loci. Initially described, Value: Key: as post-transcriptional regulators involved in development, two decades ago,, Value: Key: miRNAs have been proven to regulate a wide range of processes in plants such as, Value: Key: germination, morphology and responses to biotic and abiotic stress. Despite wide, Value: Key: conservation in plants, a number of miRNAs are lineage specific. We describe the, Value: Key: first genome wide survey of Eucalyptus miRNAs based on high throughput, Value: Key: sequencing. RESULTS: In addition to discovering small RNA sequences, MIR loci, Value: Key: were mapped onto the reference genome and interspecific variability investigated., Value: Key: Sequencing was carried out for the two most world widely planted species, E., Value: Key: grandis and E. globulus. To maximize discovery, E. grandis samples were from, Value: Key: BRASUZ1, the same tree whose genome provided the reference sequence., Value: Key: Interspecific analysis reinforces the variability in small RNA repertoire even, Value: Key: between closely related species. Characterization of Eucalyptus small RNA, Value: Key: sequences showed 95 orthologous to conserved miRNAs and 193 novel miRNAs. In, Value: Key: silico target prediction confirmed 163 novel miRNAs and degradome sequencing, Value: Key: experimentally confirmed several hundred targets. Experimental evidence based on, Value: Key: the exclusive expression of a set of small RNAs across 16 species within, Value: Key: Myrtaceae further highlighted variable patterns of conservation and diversity of, Value: Key: these regulatory elements. CONCLUSIONS: The description of miRNAs in Eucalyptus, Value: Key: contributes to scientific knowledge of this vast genre, which is the most widely, Value: Key: planted hardwood crop in the tropical and subtropical world, adding another, Value: Key: important element to the annotation of Eucalyptus grandis reference genome., Value: Key: FAU, Value: Pappas, Marília de Castro Rodrigues Key: AU, Value: Pappas Mde C Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil. Key: marilia.pappas@embrapa.br., Value: Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Universidade de Brasília, Brasília, DF, Brazil. gpappas@unb.br. Key: FAU, Value: Grattapaglia, Dario Key: AU, Value: Grattapaglia D Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil. Key: dario.grattapaglia@embrapa.br., Value: Key: AD, Value: Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Key: Católica de Brasília, Brasília, DF, Brazil. dario.grattapaglia@embrapa.br., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20151229 Key: PL, Value: England Key: TA, Value: BMC Genomics Key: JT, Value: BMC genomics Key: JID, Value: 100965258 Key: RN, Value: 0 (MicroRNAs) Key: RN, Value: 0 (RNA, Plant) Key: SB, Value: IM Key: MH, Value: Genome, Plant/genetics Key: MH, Value: MicroRNAs/*genetics Key: MH, Value: Myrtaceae/*genetics Key: MH, Value: RNA, Plant/genetics Key: MH, Value: Sequence Analysis, RNA Key: PMC, Value: PMC4696225 Key: EDAT, Value: 2015/12/31 06:00 Key: MHDA, Value: 2016/09/30 06:00 Key: PMCR, Value: 2015/12/29 Key: CRDT, Value: 2015/12/31 06:00 Key: PHST, Value: 2015/06/19 00:00 [received] Key: PHST, Value: 2015/12/15 00:00 [accepted] Key: PHST, Value: 2015/12/31 06:00 [entrez] Key: PHST, Value: 2015/12/31 06:00 [pubmed] Key: PHST, Value: 2016/09/30 06:00 [medline] Key: PHST, Value: 2015/12/29 00:00 [pmc-release] Key: AID, Value: 10.1186/s12864-015-2322-6 [pii] Key: AID, Value: 2322 [pii] Key: AID, Value: 10.1186/s12864-015-2322-6 [doi] Key: PST, Value: epublish Key: SO, Value: BMC Genomics. 2015 Dec 29;16:1113. doi: 10.1186/s12864-015-2322-6. Key: PMID, Value: 27610237 Key: OWN, Value: NLM Key: STAT, Value: PubMed-not-MEDLINE Key: DCOM, Value: 20160909 Key: LR, Value: 20200929 Key: IS, Value: 2662-6810 (Print) Key: IS, Value: 2052-7276 (Electronic) Key: IS, Value: 2052-7276 (Linking) Key: VI, Value: 3 Key: DP, Value: 2016 Key: TI, Value: Transcriptome analyses of the Dof-like gene family in grapevine reveal its Key: involvement in berry, flower and seed development., Value: Key: PG, Value: 16042 Key: LID, Value: 10.1038/hortres.2016.42 [doi] Key: AB, Value: The Dof (DNA-binding with one finger) protein family spans a group of plant Key: transcription factors involved in the regulation of several functions, such as, Value: Key: plant responses to stress, hormones and light, phytochrome signaling and seed, Value: Key: germination. Here we describe the Dof-like gene family in grapevine (Vitis, Value: Key: vinifera L.), which consists of 25 genes coding for Dof. An extensive in silico, Value: Key: characterization of the VviDofL gene family was performed. Additionally, the, Value: Key: expression of the entire gene family was assessed in 54 grapevine tissues and, Value: Key: organs using an integrated approach with microarray (cv Corvina) and real-time, Value: Key: PCR (cv Pinot Noir) analyses. The phylogenetic analysis comparing grapevine, Value: Key: sequences with those of Arabidopsis, tomato, poplar and already described Dof, Value: Key: genes in other species allowed us to identify several duplicated genes. The, Value: Key: diversification of grapevine DofL genes during evolution likely resulted in a, Value: Key: broader range of biological roles. Furthermore, distinct expression patterns were, Value: Key: identified between samples analyzed, corroborating such hypothesis. Our, Value: Key: expression results indicate that several VviDofL genes perform their functional, Value: Key: roles mainly during flower, berry and seed development, highlighting their, Value: Key: importance for grapevine growth and production. The identification of similar, Value: Key: expression profiles between both approaches strongly suggests that these genes, Value: Key: have important regulatory roles that are evolutionally conserved between, Value: Key: grapevine cvs Corvina and Pinot Noir., Value: Key: FAU, Value: da Silva, Danielle Costenaro Key: AU, Value: da Silva DC Key: AD, Value: Graduate Program in Cell and Molecular Biology, Center for Biotechnology, Key: Universidade Federal do Rio Grande do Sul , Porto Alegre, RS 91501-970, Brazil., Value: Key: FAU, Value: da Silveira Falavigna, Vítor Key: AU, Value: da Silveira Falavigna V Key: AD, Value: Graduate Program in Cell and Molecular Biology, Center for Biotechnology, Key: Universidade Federal do Rio Grande do Sul , Porto Alegre, RS 91501-970, Brazil., Value: Key: FAU, Value: Fasoli, Marianna Key: AU, Value: Fasoli M Key: AD, Value: Dipartimento di Biotecnologie, Università degli Studi di Verona , Verona 37134, Key: Italy., Value: Key: FAU, Value: Buffon, Vanessa Key: AU, Value: Buffon V Key: AD, Value: Embrapa Uva e Vinho , Bento Gonçalves, RS 95701-008, Brazil. Key: FAU, Value: Porto, Diogo Denardi Key: AU, Value: Porto DD Key: AD, Value: Embrapa Semiárido , Petrolina, PE 56302-970, Brazil. Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Department of Cell Biology, Universidade de Brasília , Brasília, DF 70910-900, Key: Brazil., Value: Key: FAU, Value: Pezzotti, Mario Key: AU, Value: Pezzotti M Key: AD, Value: Dipartimento di Biotecnologie, Università degli Studi di Verona , Verona 37134, Key: Italy., Value: Key: FAU, Value: Pasquali, Giancarlo Key: AU, Value: Pasquali G Key: AD, Value: Graduate Program in Cell and Molecular Biology, Center for Biotechnology, Key: Universidade Federal do Rio Grande do Sul , Porto Alegre, RS 91501-970, Brazil., Value: Key: FAU, Value: Revers, Luís Fernando Key: AU, Value: Revers LF Key: AD, Value: Embrapa Uva e Vinho , Bento Gonçalves, RS 95701-008, Brazil. Key: LA, Value: eng Key: PT, Value: Journal Article Key: DEP, Value: 20160831 Key: PL, Value: England Key: TA, Value: Hortic Res Key: JT, Value: Horticulture research Key: JID, Value: 101655540 Key: PMC, Value: PMC5005469 Key: EDAT, Value: 2016/09/10 06:00 Key: MHDA, Value: 2016/09/10 06:01 Key: PMCR, Value: 2016/08/31 Key: CRDT, Value: 2016/09/10 06:00 Key: PHST, Value: 2016/06/30 00:00 [received] Key: PHST, Value: 2016/08/08 00:00 [revised] Key: PHST, Value: 2016/08/09 00:00 [accepted] Key: PHST, Value: 2016/09/10 06:00 [entrez] Key: PHST, Value: 2016/09/10 06:00 [pubmed] Key: PHST, Value: 2016/09/10 06:01 [medline] Key: PHST, Value: 2016/08/31 00:00 [pmc-release] Key: AID, Value: hortres201642 [pii] Key: AID, Value: 10.1038/hortres.2016.42 [doi] Key: PST, Value: epublish Key: SO, Value: Hortic Res. 2016 Aug 31;3:16042. doi: 10.1038/hortres.2016.42. eCollection 2016. Key: PMID, Value: 18234103 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20080808 Key: LR, Value: 20240321 Key: IS, Value: 1471-2229 (Electronic) Key: IS, Value: 1471-2229 (Linking) Key: VI, Value: 8 Key: DP, Value: 2008 Jan 30 Key: TI, Value: Analysis of non-TIR NBS-LRR resistance gene analogs in Musa acuminata Colla: Key: isolation, RFLP marker development, and physical mapping., Value: Key: PG, Value: 15 Key: LID, Value: 10.1186/1471-2229-8-15 [doi] Key: AB, Value: BACKGROUND: Many commercial banana varieties lack sources of resistance to pests Key: and diseases, as a consequence of sterility and narrow genetic background., Value: Key: Fertile wild relatives, by contrast, possess greater variability and represent, Value: Key: potential sources of disease resistance genes (R-genes). The largest known family, Value: Key: of plant R-genes encode proteins with nucleotide-binding site (NBS) and, Value: Key: C-terminal leucine-rich repeat (LRR) domains. Conserved motifs in such genes in, Value: Key: diverse plant species offer a means for isolation of candidate genes in banana, Value: Key: which may be involved in plant defence. RESULTS: A computational strategy was, Value: Key: developed for unbiased conserved motif discovery in NBS and LRR domains in, Value: Key: R-genes and homologues in monocotyledonous plant species. Degenerate PCR primers, Value: Key: targeting conserved motifs were tested on the wild cultivar Musa acuminata subsp., Value: Key: burmannicoides, var. Calcutta 4, which is resistant to a number of fungal, Value: Key: pathogens and nematodes. One hundred and seventy four resistance gene analogs, Value: Key: (RGAs) were amplified and assembled into 52 contiguous sequences. Motifs present, Value: Key: were typical of the non-TIR NBS-LRR RGA subfamily. A phylogenetic analysis of, Value: Key: deduced amino-acid sequences for 33 RGAs with contiguous open reading frames, Value: Key: (ORFs), together with RGAs from Arabidopsis thaliana and Oryza sativa, grouped, Value: Key: most Musa RGAs within monocotyledon-specific clades. RFLP-RGA markers were, Value: Key: developed, with 12 displaying distinct polymorphisms in parentals and F1 progeny, Value: Key: of a diploid M. acuminata mapping population. Eighty eight BAC clones were, Value: Key: identified in M. acuminata Calcutta 4, M. acuminata Grande Naine, and M., Value: Key: balbisiana Pisang Klutuk Wulung BAC libraries when hybridized to two RGA probes., Value: Key: Multiple copy RGAs were common within BAC clones, potentially representing, Value: Key: variation reservoirs for evolution of new R-gene specificities. CONCLUSION: This, Value: Key: is the first large scale analysis of NBS-LRR RGAs in M. acuminata Calcutta 4., Value: Key: Contig sequences were deposited in GenBank and assigned numbers ER935972, Value: Key: ER936023. RGA sequences and isolated BACs are a valuable resource for R-gene, Value: Key: discovery, and in future applications will provide insight into the organization, Value: Key: and evolution of NBS-LRR R-genes in the Musa A and B genome. The developed, Value: Key: RFLP-RGA markers are applicable for genetic map development and marker assisted, Value: Key: selection for defined traits such as pest and disease resistance., Value: Key: FAU, Value: Miller, Robert N G Key: AU, Value: Miller RN Key: AD, Value: Postgraduate program in Genomic Science and Biotechnology, Universidade Católica Key: de Brasília, SGAN 916, Módulo B, CEP 70,790-160, Brasília, DF, Brazil., Value: Key: rngmiller@gmail.com., Value: Key: FAU, Value: Bertioli, David J Key: AU, Value: Bertioli DJ Key: FAU, Value: Baurens, Franc C Key: AU, Value: Baurens FC Key: FAU, Value: Santos, Candice M R Key: AU, Value: Santos CM Key: FAU, Value: Alves, Paulo C Key: AU, Value: Alves PC Key: FAU, Value: Martins, Natalia F Key: AU, Value: Martins NF Key: FAU, Value: Togawa, Roberto C Key: AU, Value: Togawa RC Key: FAU, Value: Souza, Manoel T Jr Key: AU, Value: Souza MT Jr Key: FAU, Value: Pappas, Georgios J Jr Key: AU, Value: Pappas GJ Jr Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20080130 Key: PL, Value: England Key: TA, Value: BMC Plant Biol Key: JT, Value: BMC plant biology Key: JID, Value: 100967807 Key: RN, Value: 0 (DNA Primers) Key: SB, Value: IM Key: MH, Value: Bayes Theorem Key: MH, Value: DNA Primers Key: MH, Value: *Genes, Plant Key: MH, Value: Musa/classification/*genetics Key: MH, Value: Phylogeny Key: MH, Value: Polymorphism, Genetic Key: MH, Value: *Polymorphism, Restriction Fragment Length Key: PMC, Value: PMC2262081 Key: EDAT, Value: 2008/02/01 09:00 Key: MHDA, Value: 2008/08/09 09:00 Key: PMCR, Value: 2008/01/30 Key: CRDT, Value: 2008/02/01 09:00 Key: PHST, Value: 2007/07/25 00:00 [received] Key: PHST, Value: 2008/01/30 00:00 [accepted] Key: PHST, Value: 2008/02/01 09:00 [pubmed] Key: PHST, Value: 2008/08/09 09:00 [medline] Key: PHST, Value: 2008/02/01 09:00 [entrez] Key: PHST, Value: 2008/01/30 00:00 [pmc-release] Key: AID, Value: 1471-2229-8-15 [pii] Key: AID, Value: 10.1186/1471-2229-8-15 [doi] Key: PST, Value: epublish Key: SO, Value: BMC Plant Biol. 2008 Jan 30;8:15. doi: 10.1186/1471-2229-8-15. Key: PMID, Value: 22984541 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20130312 Key: LR, Value: 20211021 Key: IS, Value: 1932-6203 (Electronic) Key: IS, Value: 1932-6203 (Linking) Key: VI, Value: 7 Key: IP, Value: 9 Key: DP, Value: 2012 Key: TI, Value: Genomic characterization of DArT markers based on high-density linkage analysis Key: and physical mapping to the Eucalyptus genome., Value: Key: PG, Value: e44684 Key: LID, Value: 10.1371/journal.pone.0044684 [doi] Key: LID, Value: e44684 Key: AB, Value: Diversity Arrays Technology (DArT) provides a robust, high throughput, Key: cost-effective method to query thousands of sequence polymorphisms in a single, Value: Key: assay. Despite the extensive use of this genotyping platform for numerous plant, Value: Key: species, little is known regarding the sequence attributes and genome-wide, Value: Key: distribution of DArT markers. We investigated the genomic properties of the 7,680, Value: Key: DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high, Value: Key: density linkage map and carrying out detailed physical mapping analyses to the, Value: Key: Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT, Value: Key: markers anchored to 210 microsatellites and a framework map, with improved, Value: Key: support for ordering, displayed extensive collinearity with the genome sequence., Value: Key: Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45, Value: Key: linkage mapped but physically unaligned markers to the 11 main Eucalyptus, Value: Key: pseudochromosomes, providing compelling evidence for the quality and completeness, Value: Key: of the current Eucalyptus genome assembly. A highly significant correspondence, Value: Key: was found between the locations of DArT markers and predicted gene models, while, Value: Key: most of the 89 DArT probes unaligned to the genome correspond to sequences likely, Value: Key: absent in E. grandis, consistent with the pan-genomic feature of this, Value: Key: multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical, Value: Key: mapping analyses provide novel data regarding the genomic attributes of DArT, Value: Key: markers in plant genomes in general and for Eucalyptus in particular. DArT, Value: Key: markers preferentially target the gene space and display a largely homogeneous, Value: Key: distribution across the genome, thereby providing superb coverage for mapping and, Value: Key: genome-wide applications in breeding and diversity studies. Data reported on, Value: Key: these ubiquitous properties of DArT markers will be particularly valuable to, Value: Key: researchers working on less-studied crop species who already count on DArT, Value: Key: genotyping arrays but for which no reference genome is yet available to allow, Value: Key: such detailed characterization., Value: Key: FAU, Value: Petroli, César D Key: AU, Value: Petroli CD Key: AD, Value: Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, Brasilia, Key: Brazil., Value: Key: FAU, Value: Sansaloni, Carolina P Key: AU, Value: Sansaloni CP Key: FAU, Value: Carling, Jason Key: AU, Value: Carling J Key: FAU, Value: Steane, Dorothy A Key: AU, Value: Steane DA Key: FAU, Value: Vaillancourt, René E Key: AU, Value: Vaillancourt RE Key: FAU, Value: Myburg, Alexander A Key: AU, Value: Myburg AA Key: FAU, Value: da Silva, Orzenil Bonfim Jr Key: AU, Value: da Silva OB Jr Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: FAU, Value: Kilian, Andrzej Key: AU, Value: Kilian A Key: FAU, Value: Grattapaglia, Dario Key: AU, Value: Grattapaglia D Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20120911 Key: PL, Value: United States Key: TA, Value: PLoS One Key: JT, Value: PloS one Key: JID, Value: 101285081 Key: RN, Value: 0 (DNA, Plant) Key: RN, Value: 0 (Genetic Markers) Key: SB, Value: IM Key: MH, Value: Chromosome Mapping/*methods Key: MH, Value: Chromosomes, Plant Key: MH, Value: Cost-Benefit Analysis Key: MH, Value: DNA, Plant/genetics Key: MH, Value: Eucalyptus/*genetics Key: MH, Value: Genetic Linkage Key: MH, Value: *Genetic Markers Key: MH, Value: Genome, Plant Key: MH, Value: Genomics Key: MH, Value: Genotype Key: MH, Value: Microsatellite Repeats/genetics Key: MH, Value: Models, Genetic Key: MH, Value: Oligonucleotide Array Sequence Analysis/*methods Key: MH, Value: Sequence Analysis, DNA/methods Key: PMC, Value: PMC3439404 Key: COIS, Value: Competing Interests: The authors acknowledge the help and technical support from Key: many employees of Diversity Arrays Technology Pty. Ltd. Two of the authors on, Value: Key: this manuscript, namely Andrzej Kilian and Jason Carling, are employees of, Value: Key: Diversity Arrays Technology Pty Ltd, which offers genome profiling service using, Value: Key: the microarray whose genomic characterization is described in this report. This, Value: Key: fact, however, has not interfered whatsoever with the full, objective,, Value: Key: transparent and unbiased presentation of the research results described in the, Value: Key: manuscript nor alters the authors' adherence to all the PLoS ONE policies on, Value: Key: sharing data and materials., Value: Key: EDAT, Value: 2012/09/18 06:00 Key: MHDA, Value: 2013/03/13 06:00 Key: PMCR, Value: 2012/09/11 Key: CRDT, Value: 2012/09/18 06:00 Key: PHST, Value: 2012/06/01 00:00 [received] Key: PHST, Value: 2012/08/06 00:00 [accepted] Key: PHST, Value: 2012/09/18 06:00 [entrez] Key: PHST, Value: 2012/09/18 06:00 [pubmed] Key: PHST, Value: 2013/03/13 06:00 [medline] Key: PHST, Value: 2012/09/11 00:00 [pmc-release] Key: AID, Value: PONE-D-12-16666 [pii] Key: AID, Value: 10.1371/journal.pone.0044684 [doi] Key: PST, Value: ppublish Key: SO, Value: PLoS One. 2012;7(9):e44684. doi: 10.1371/journal.pone.0044684. Epub 2012 Sep 11. Key: PMID, Value: 21492434 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20110722 Key: LR, Value: 20211020 Key: IS, Value: 1471-2229 (Electronic) Key: IS, Value: 1471-2229 (Linking) Key: VI, Value: 11 Key: DP, Value: 2011 Apr 14 Key: TI, Value: High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: Key: assay success, polymorphism and transferability across species., Value: Key: PG, Value: 65 Key: LID, Value: 10.1186/1471-2229-11-65 [doi] Key: AB, Value: BACKGROUND: High-throughput SNP genotyping has become an essential requirement Key: for molecular breeding and population genomics studies in plant species. Large, Value: Key: scale SNP developments have been reported for several mainstream crops. A growing, Value: Key: interest now exists to expand the speed and resolution of genetic analysis to, Value: Key: outbred species with highly heterozygous genomes. When nucleotide diversity is, Value: Key: high, a refined diagnosis of the target SNP sequence context is needed to convert, Value: Key: queried SNPs into high-quality genotypes using the Golden Gate Genotyping, Value: Key: Technology (GGGT). This issue becomes exacerbated when attempting to transfer, Value: Key: SNPs across species, a scarcely explored topic in plants, and likely to become, Value: Key: significant for population genomics and inter specific breeding applications in, Value: Key: less domesticated and less funded plant genera. RESULTS: We have successfully, Value: Key: developed the first set of 768 SNPs assayed by the GGGT for the highly, Value: Key: heterozygous genome of Eucalyptus from a mixed Sanger/454 database with 1,164,695, Value: Key: ESTs and the preliminary 4.5X draft genome sequence for E. grandis. A systematic, Value: Key: assessment of in silico SNP filtering requirements showed that stringent, Value: Key: constraints on the SNP surrounding sequences have a significant impact on SNP, Value: Key: genotyping performance and polymorphism. SNP assay success was high for the 288, Value: Key: SNPs selected with more rigorous in silico constraints; 93% of them provided high, Value: Key: quality genotype calls and 71% of them were polymorphic in a diverse panel of 96, Value: Key: individuals of five different species.SNP reliability was high across nine, Value: Key: Eucalyptus species belonging to three sections within subgenus Symphomyrtus and, Value: Key: still satisfactory across species of two additional subgenera, although, Value: Key: polymorphism declined as phylogenetic distance increased. CONCLUSIONS: This study, Value: Key: indicates that the GGGT performs well both within and across species of, Value: Key: Eucalyptus notwithstanding its nucleotide diversity ≥ 2%. The development of a, Value: Key: much larger array of informative SNPs across multiple Eucalyptus species is, Value: Key: feasible, although strongly dependent on having a representative and sufficiently, Value: Key: deep collection of sequences from many individuals of each target species. A, Value: Key: higher density SNP platform will be instrumental to undertake genome-wide, Value: Key: phylogenetic and population genomics studies and to implement molecular breeding, Value: Key: by Genomic Selection in Eucalyptus., Value: Key: FAU, Value: Grattapaglia, Dario Key: AU, Value: Grattapaglia D Key: AD, Value: EMBRAPA Genetic Resources and Biotechnology-Estação Parque Biológico, final W5 Key: norte, Brasilia, Brazil. dario@cenargen.embrapa.br, Value: Key: FAU, Value: Silva-Junior, Orzenil B Key: AU, Value: Silva-Junior OB Key: FAU, Value: Kirst, Matias Key: AU, Value: Kirst M Key: FAU, Value: de Lima, Bruno Marco Key: AU, Value: de Lima BM Key: FAU, Value: Faria, Danielle A Key: AU, Value: Faria DA Key: FAU, Value: Pappas, Georgios J Jr Key: AU, Value: Pappas GJ Jr Key: LA, Value: eng Key: PT, Value: Evaluation Study Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20110414 Key: PL, Value: England Key: TA, Value: BMC Plant Biol Key: JT, Value: BMC plant biology Key: JID, Value: 100967807 Key: RN, Value: 0 (Plant Proteins) Key: SB, Value: IM Key: MH, Value: Eucalyptus/classification/*genetics Key: MH, Value: *Genetic Techniques/instrumentation Key: MH, Value: *Genome, Plant Key: MH, Value: Genotype Key: MH, Value: Molecular Sequence Data Key: MH, Value: Phylogeny Key: MH, Value: Plant Proteins/genetics Key: MH, Value: *Polymorphism, Single Nucleotide Key: PMC, Value: PMC3090336 Key: EDAT, Value: 2011/04/16 06:00 Key: MHDA, Value: 2011/07/23 06:00 Key: PMCR, Value: 2011/04/14 Key: CRDT, Value: 2011/04/16 06:00 Key: PHST, Value: 2010/12/21 00:00 [received] Key: PHST, Value: 2011/04/14 00:00 [accepted] Key: PHST, Value: 2011/04/16 06:00 [entrez] Key: PHST, Value: 2011/04/16 06:00 [pubmed] Key: PHST, Value: 2011/07/23 06:00 [medline] Key: PHST, Value: 2011/04/14 00:00 [pmc-release] Key: AID, Value: 1471-2229-11-65 [pii] Key: AID, Value: 10.1186/1471-2229-11-65 [doi] Key: PST, Value: epublish Key: SO, Value: BMC Plant Biol. 2011 Apr 14;11:65. doi: 10.1186/1471-2229-11-65. Key: PMID, Value: 21863554 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20120229 Key: LR, Value: 20181023 Key: IS, Value: 1676-5680 (Electronic) Key: IS, Value: 1676-5680 (Linking) Key: VI, Value: 10 Key: IP, Value: 3 Key: DP, Value: 2011 Key: TI, Value: Identification of genes encoding hypothetical proteins in open-reading frame Key: expressed sequence tags from mammalian stages of Trypanosoma cruzi., Value: Key: PG, Value: 1589-630 Key: LID, Value: 10.4238/vol10-3gmr1140 [doi] Key: AB, Value: Approximately 50% of the predicted protein-coding genes of the Trypanosoma cruzi Key: CL Brener strain are annotated as hypothetical or conserved hypothetical, Value: Key: proteins. To further characterize these genes, we generated 1161 open-reading, Value: Key: frame expressed sequence tags (ORESTES) from the mammalian stages of the VL10, Value: Key: human strain. Sequence clustering resulted in 435 clusters, consisting of 339, Value: Key: singletons and 96 contigs. Significant matches to the T. cruzi predicted gene, Value: Key: database were found for ~94% contigs and ~69% singletons. These included genes, Value: Key: encoding surface proteins, known to be intensely expressed in the parasite, Value: Key: mammalian stages and implicated in host cell invasion and/or immune evasion, Value: Key: mechanisms. Among 151 contigs and singletons with similarity to predicted, Value: Key: hypothetical protein-coding genes and conserved hypothetical protein-coding, Value: Key: genes, 83% showed no match with T. cruzi EST and/or proteome databases. These, Value: Key: ORESTES are the first experimental evidence that the corresponding genes are in, Value: Key: fact transcribed. Sequences with no significant match were searched against, Value: Key: several T. cruzi and National Center for Biotechnology Information non-redundant, Value: Key: sequence databases. The ORESTES analysis indicated that 124 predicted conserved, Value: Key: hypothetical protein-coding genes and 27 predicted hypothetical protein-coding, Value: Key: genes annotated in the CL Brener genome are transcribed in the VL10 mammalian, Value: Key: stages. Six ORESTES annotated as hypothetical protein-coding genes showing no, Value: Key: match to EST and/or proteome databases were confirmed by Northern blot in VL10., Value: Key: The generation of this set of ORESTES complements the T. cruzi genome annotation, Value: Key: and suggests new stage-regulated genes encoding hypothetical proteins., Value: Key: FAU, Value: Martins, C Key: AU, Value: Martins C Key: AD, Value: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Key: Brasil., Value: Key: FAU, Value: Reis-Cunha, J L Key: AU, Value: Reis-Cunha JL Key: FAU, Value: Silva, M N Key: AU, Value: Silva MN Key: FAU, Value: Pereira, E G Key: AU, Value: Pereira EG Key: FAU, Value: Pappas, G J Jr Key: AU, Value: Pappas GJ Jr Key: FAU, Value: Bartholomeu, D C Key: AU, Value: Bartholomeu DC Key: FAU, Value: Zingales, B Key: AU, Value: Zingales B Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: PL, Value: Brazil Key: TA, Value: Genet Mol Res Key: JT, Value: Genetics and molecular research : GMR Key: JID, Value: 101169387 Key: RN, Value: 0 (Protozoan Proteins) Key: SB, Value: IM Key: MH, Value: Animals Key: MH, Value: *Expressed Sequence Tags Key: MH, Value: Genome, Protozoan Key: MH, Value: Humans Key: MH, Value: *Open Reading Frames Key: MH, Value: Protozoan Proteins/*genetics Key: MH, Value: Trypanosoma cruzi/*genetics Key: EDAT, Value: 2011/08/25 06:00 Key: MHDA, Value: 2012/03/01 06:00 Key: CRDT, Value: 2011/08/25 06:00 Key: PHST, Value: 2011/08/25 06:00 [entrez] Key: PHST, Value: 2011/08/25 06:00 [pubmed] Key: PHST, Value: 2012/03/01 06:00 [medline] Key: AID, Value: gmr1140 [pii] Key: AID, Value: 10.4238/vol10-3gmr1140 [doi] Key: PST, Value: ppublish Key: SO, Value: Genet Mol Res. 2011;10(3):1589-630. doi: 10.4238/vol10-3gmr1140. Key: PMID, Value: 15869816 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20050913 Key: LR, Value: 20221207 Key: IS, Value: 0166-6851 (Print) Key: IS, Value: 0166-6851 (Linking) Key: VI, Value: 142 Key: IP, Value: 2 Key: DP, Value: 2005 Aug Key: TI, Value: Expressed sequence tags from the plant trypanosomatid Phytomonas serpens. Key: PG, Value: 149-57 Key: AB, Value: We have generated 2190 expressed sequence tags (ESTs) from a cDNA library of the Key: plant trypanosomatid Phytomonas serpens. Upon processing and clustering the set, Value: Key: of 1893 accepted sequences was reduced to 697 clusters consisting of 452, Value: Key: singletons and 245 contigs. Functional categories were assigned based on BLAST, Value: Key: searches against a database of the eukaryotic orthologous groups of proteins, Value: Key: (KOG). Thirty six percent of the generated sequences showed no hits against the, Value: Key: KOG database and 39.6% presented similarity to the KOG classes corresponding to, Value: Key: translation, ribosomal structure and biogenesis. The most populated cluster, Value: Key: contained 45 ESTs homologous to members of the glucose transporter family. This, Value: Key: fact can be immediately correlated to the reported Phytomonas dependence on, Value: Key: anaerobic glycolytic ATP production due to the lack of cytochrome-mediated, Value: Key: respiratory chain. In this context, not only a number of enzymes of the, Value: Key: glycolytic pathway were identified but also of the Krebs cycle as well as, Value: Key: specific components of the respiratory chain. The data here reported, including a, Value: Key: few hundred unique sequences and the description of tandemly repeated motifs and, Value: Key: putative transcript stability motifs at untranslated mRNA ends, represent an, Value: Key: initial approach to overcome the lack of information on the molecular biology of, Value: Key: this organism., Value: Key: FAU, Value: Pappas, Georgios J Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Genomic Sciences and Biotechnology Program, Universidade Católica de Brasília, Key: Brasília, DF, Brazil., Value: Key: FAU, Value: Benabdellah, Karim Key: AU, Value: Benabdellah K Key: FAU, Value: Zingales, Bianca Key: AU, Value: Zingales B Key: FAU, Value: González, Antonio Key: AU, Value: González A Key: LA, Value: eng Key: SI, Value: GENBANK/CO723750 Key: SI, Value: GENBANK/CO723751 Key: SI, Value: GENBANK/CO723752 Key: SI, Value: GENBANK/CO723753 Key: SI, Value: GENBANK/CO723754 Key: SI, Value: GENBANK/CO723755 Key: SI, Value: GENBANK/CO723756 Key: SI, Value: GENBANK/CO723757 Key: SI, Value: GENBANK/CO723758 Key: SI, Value: GENBANK/CO723759 Key: SI, Value: GENBANK/CO723760 Key: SI, Value: GENBANK/CO723761 Key: SI, Value: GENBANK/CO723762 Key: SI, Value: GENBANK/CO723763 Key: SI, Value: GENBANK/CO723764 Key: SI, Value: GENBANK/CO723765 Key: SI, Value: GENBANK/CO723766 Key: SI, Value: GENBANK/CO723767 Key: SI, Value: GENBANK/CO723768 Key: SI, Value: GENBANK/CO723769 Key: SI, Value: GENBANK/CO723770 Key: SI, Value: GENBANK/CO723771 Key: SI, Value: GENBANK/CO723772 Key: SI, Value: GENBANK/CO723773 Key: SI, Value: GENBANK/CO723774 Key: SI, Value: GENBANK/CO723775 Key: SI, Value: GENBANK/CO723776 Key: SI, Value: GENBANK/CO723777 Key: SI, Value: GENBANK/CO723778 Key: SI, Value: GENBANK/CO723779 Key: SI, Value: GENBANK/CO723780 Key: SI, Value: GENBANK/CO723781 Key: SI, Value: GENBANK/CO723782 Key: SI, Value: GENBANK/CO723783 Key: SI, Value: GENBANK/CO723784 Key: SI, Value: GENBANK/CO723785 Key: SI, Value: GENBANK/CO723786 Key: SI, Value: GENBANK/CO723787 Key: SI, Value: GENBANK/CO723788 Key: SI, Value: GENBANK/CO723789 Key: SI, Value: GENBANK/CO723790 Key: SI, Value: GENBANK/CO723791 Key: SI, Value: GENBANK/CO723792 Key: SI, Value: GENBANK/CO723793 Key: SI, Value: GENBANK/CO723794 Key: SI, Value: GENBANK/CO723795 Key: SI, Value: GENBANK/CO723796 Key: SI, Value: GENBANK/CO723797 Key: SI, Value: GENBANK/CO723798 Key: SI, Value: GENBANK/CO723799 Key: SI, Value: GENBANK/CO723800 Key: SI, Value: GENBANK/CO723801 Key: SI, Value: GENBANK/CO723802 Key: SI, Value: GENBANK/CO723803 Key: SI, Value: GENBANK/CO723804 Key: SI, Value: GENBANK/CO723805 Key: SI, Value: GENBANK/CO723806 Key: SI, Value: GENBANK/CO723807 Key: SI, Value: GENBANK/CO723808 Key: SI, Value: GENBANK/CO723809 Key: SI, Value: GENBANK/CO723810 Key: SI, Value: GENBANK/CO723811 Key: SI, Value: GENBANK/CO723812 Key: SI, Value: GENBANK/CO723813 Key: SI, Value: GENBANK/CO723814 Key: SI, Value: GENBANK/CO723815 Key: SI, Value: GENBANK/CO723816 Key: SI, Value: 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GENBANK/CO724267 Key: SI, Value: GENBANK/CO724268 Key: SI, Value: GENBANK/CO724269 Key: SI, Value: GENBANK/CO724270 Key: SI, Value: GENBANK/CO724271 Key: SI, Value: GENBANK/CO724272 Key: SI, Value: GENBANK/CO724273 Key: SI, Value: GENBANK/CO724274 Key: SI, Value: GENBANK/CO724275 Key: SI, Value: GENBANK/CO724276 Key: SI, Value: GENBANK/CO724277 Key: SI, Value: GENBANK/CO724278 Key: SI, Value: GENBANK/CO724279 Key: SI, Value: GENBANK/CO724280 Key: SI, Value: GENBANK/CO724281 Key: SI, Value: GENBANK/CO724282 Key: SI, Value: GENBANK/CO724283 Key: SI, Value: GENBANK/CO724284 Key: SI, Value: GENBANK/CO724285 Key: SI, Value: GENBANK/CO724286 Key: SI, Value: GENBANK/CO724287 Key: SI, Value: GENBANK/CO724288 Key: SI, Value: GENBANK/CO724289 Key: SI, Value: GENBANK/CO724290 Key: SI, Value: GENBANK/CO724291 Key: SI, Value: GENBANK/CO724292 Key: SI, Value: GENBANK/CO724293 Key: SI, Value: GENBANK/CO724294 Key: SI, Value: GENBANK/CO724295 Key: SI, Value: GENBANK/CO724296 Key: SI, Value: GENBANK/CO724297 Key: SI, Value: GENBANK/CO724298 Key: SI, Value: GENBANK/CO724299 Key: SI, Value: GENBANK/CO724300 Key: SI, Value: GENBANK/CO724301 Key: SI, Value: GENBANK/CO724302 Key: SI, Value: GENBANK/CO724303 Key: SI, Value: GENBANK/CO724304 Key: SI, Value: GENBANK/CO724305 Key: SI, Value: GENBANK/CO724306 Key: SI, Value: GENBANK/CO724307 Key: SI, Value: GENBANK/CO724308 Key: SI, Value: GENBANK/CO724309 Key: SI, Value: GENBANK/CO724310 Key: SI, Value: GENBANK/CO724311 Key: SI, Value: GENBANK/CO724312 Key: SI, Value: GENBANK/CO724313 Key: SI, Value: GENBANK/CO724314 Key: SI, Value: GENBANK/CO724315 Key: SI, Value: GENBANK/CO724316 Key: SI, Value: GENBANK/CO724317 Key: SI, Value: GENBANK/CO724318 Key: SI, Value: GENBANK/CO724319 Key: SI, Value: GENBANK/CO724320 Key: SI, Value: GENBANK/CO724321 Key: SI, Value: GENBANK/CO724322 Key: SI, Value: GENBANK/CO724323 Key: SI, Value: GENBANK/CO724324 Key: SI, Value: GENBANK/CO724325 Key: SI, Value: GENBANK/CO724326 Key: SI, Value: GENBANK/CO724327 Key: SI, Value: GENBANK/CO724328 Key: SI, Value: GENBANK/CO724329 Key: SI, Value: GENBANK/CO724330 Key: SI, Value: GENBANK/CO724331 Key: SI, Value: GENBANK/CO724332 Key: SI, Value: GENBANK/CO724333 Key: SI, Value: GENBANK/CO724334 Key: SI, Value: GENBANK/CO724335 Key: SI, Value: GENBANK/CO724336 Key: SI, Value: GENBANK/CO724337 Key: SI, Value: GENBANK/CO724338 Key: SI, Value: GENBANK/CO724339 Key: SI, Value: GENBANK/CO724340 Key: SI, Value: GENBANK/CO724341 Key: SI, Value: GENBANK/CO724342 Key: SI, Value: GENBANK/CO724343 Key: SI, Value: GENBANK/CO724344 Key: SI, Value: GENBANK/CO724345 Key: SI, Value: GENBANK/CO724346 Key: SI, Value: GENBANK/CO724347 Key: SI, Value: GENBANK/CO724348 Key: SI, Value: GENBANK/CO724349 Key: SI, Value: GENBANK/CO724350 Key: SI, Value: GENBANK/CO724351 Key: SI, Value: GENBANK/CO724352 Key: SI, Value: GENBANK/CO724353 Key: SI, Value: GENBANK/CO724354 Key: SI, Value: GENBANK/CO724355 Key: SI, Value: GENBANK/CO724356 Key: SI, Value: GENBANK/CO724357 Key: SI, Value: GENBANK/CO724358 Key: SI, Value: GENBANK/CO724359 Key: SI, Value: GENBANK/CO724360 Key: SI, Value: GENBANK/CO724361 Key: SI, Value: GENBANK/CO724362 Key: SI, Value: GENBANK/CO724363 Key: SI, Value: GENBANK/CO724364 Key: SI, Value: GENBANK/CO724365 Key: SI, Value: GENBANK/CO724366 Key: SI, Value: GENBANK/CO724367 Key: SI, Value: GENBANK/CO724368 Key: SI, Value: GENBANK/CO724369 Key: SI, Value: GENBANK/CO724370 Key: SI, Value: GENBANK/CO724371 Key: SI, Value: GENBANK/CO724372 Key: SI, Value: GENBANK/CO724373 Key: SI, Value: GENBANK/CO724374 Key: SI, Value: GENBANK/CO724375 Key: SI, Value: GENBANK/CO724376 Key: SI, Value: GENBANK/CO724377 Key: SI, Value: GENBANK/CO724378 Key: SI, Value: GENBANK/CO724379 Key: SI, Value: GENBANK/CO724380 Key: SI, Value: GENBANK/CO724381 Key: SI, Value: GENBANK/CO724382 Key: SI, Value: GENBANK/CO724383 Key: SI, Value: GENBANK/CO724384 Key: SI, Value: GENBANK/CO724385 Key: SI, Value: GENBANK/CO724386 Key: SI, Value: GENBANK/CO724387 Key: SI, Value: GENBANK/CO724388 Key: SI, Value: GENBANK/CO724389 Key: SI, Value: GENBANK/CO724390 Key: SI, Value: GENBANK/CO724391 Key: SI, Value: GENBANK/CO724392 Key: SI, Value: GENBANK/CO724393 Key: SI, Value: GENBANK/CO724394 Key: SI, Value: GENBANK/CO724395 Key: SI, Value: GENBANK/CO724396 Key: SI, Value: GENBANK/CO724397 Key: SI, Value: GENBANK/CO724398 Key: SI, Value: GENBANK/CO724399 Key: SI, Value: GENBANK/CO724400 Key: SI, Value: GENBANK/CO724401 Key: SI, Value: GENBANK/CO724402 Key: SI, Value: GENBANK/CO724403 Key: SI, Value: GENBANK/CO724404 Key: SI, Value: GENBANK/CO724405 Key: SI, Value: GENBANK/CO724406 Key: SI, Value: GENBANK/CO724407 Key: SI, Value: GENBANK/CO724408 Key: SI, Value: GENBANK/CO724409 Key: SI, Value: GENBANK/CO724410 Key: SI, Value: GENBANK/CO724411 Key: SI, Value: GENBANK/CO724412 Key: SI, Value: GENBANK/CO724413 Key: SI, Value: GENBANK/CO724414 Key: SI, Value: GENBANK/CO724415 Key: SI, Value: GENBANK/CO724416 Key: SI, Value: GENBANK/CO724417 Key: SI, Value: GENBANK/CO724418 Key: SI, Value: GENBANK/CO724419 Key: SI, Value: GENBANK/CO724420 Key: SI, Value: GENBANK/CO724421 Key: SI, Value: GENBANK/CO724422 Key: SI, Value: GENBANK/CO724423 Key: SI, Value: GENBANK/CO724424 Key: SI, Value: GENBANK/CO724425 Key: SI, Value: GENBANK/CO724426 Key: SI, Value: GENBANK/CO724427 Key: SI, Value: GENBANK/CO724428 Key: SI, Value: GENBANK/CO724429 Key: SI, Value: GENBANK/CO724430 Key: SI, Value: GENBANK/CO724431 Key: SI, Value: GENBANK/CO724432 Key: SI, Value: GENBANK/CO724433 Key: SI, Value: GENBANK/CO724434 Key: SI, Value: GENBANK/CO724435 Key: SI, Value: GENBANK/CO724436 Key: SI, Value: GENBANK/CO724437 Key: SI, Value: GENBANK/CO724438 Key: SI, Value: GENBANK/CO724439 Key: SI, Value: GENBANK/CO724440 Key: SI, Value: GENBANK/CO724441 Key: SI, Value: GENBANK/CO724442 Key: SI, Value: GENBANK/CO724443 Key: SI, Value: GENBANK/CO724444 Key: SI, Value: GENBANK/CO724445 Key: SI, Value: GENBANK/CO724446 Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20050418 Key: PL, Value: Netherlands Key: TA, Value: Mol Biochem Parasitol Key: JT, Value: Molecular and biochemical parasitology Key: JID, Value: 8006324 Key: RN, Value: 0 (Protozoan Proteins) Key: SB, Value: IM Key: MH, Value: Amino Acid Sequence Key: MH, Value: Animals Key: MH, Value: Base Sequence Key: MH, Value: *Expressed Sequence Tags Key: MH, Value: Gene Library Key: MH, Value: Solanum lycopersicum/*parasitology Key: MH, Value: Molecular Sequence Data Key: MH, Value: Plant Diseases/*parasitology Key: MH, Value: Protozoan Proteins/chemistry/genetics/metabolism Key: MH, Value: Sequence Alignment Key: MH, Value: Sequence Analysis, DNA Key: MH, Value: Trypanosomatina/*genetics/metabolism Key: EDAT, Value: 2005/05/05 09:00 Key: MHDA, Value: 2005/09/15 09:00 Key: CRDT, Value: 2005/05/05 09:00 Key: PHST, Value: 2004/10/21 00:00 [received] Key: PHST, Value: 2005/03/24 00:00 [revised] Key: PHST, Value: 2005/03/31 00:00 [accepted] Key: PHST, Value: 2005/05/05 09:00 [pubmed] Key: PHST, Value: 2005/09/15 09:00 [medline] Key: PHST, Value: 2005/05/05 09:00 [entrez] Key: AID, Value: S0166-6851(05)00115-5 [pii] Key: AID, Value: 10.1016/j.molbiopara.2005.03.017 [doi] Key: PST, Value: ppublish Key: SO, Value: Mol Biochem Parasitol. 2005 Aug;142(2):149-57. doi: Key: 10.1016/j.molbiopara.2005.03.017. Epub 2005 Apr 18., Value: Key: PMID, Value: 26932372 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20170126 Key: LR, Value: 20181113 Key: IS, Value: 1617-4623 (Electronic) Key: IS, Value: 1617-4623 (Linking) Key: VI, Value: 291 Key: IP, Value: 3 Key: DP, Value: 2016 Jun Key: TI, Value: SNP discovery in common bean by restriction-associated DNA (RAD) sequencing for Key: genetic diversity and population structure analysis., Value: Key: PG, Value: 1277-91 Key: LID, Value: 10.1007/s00438-016-1182-3 [doi] Key: AB, Value: Researchers have made great advances into the development and application of Key: genomic approaches for common beans, creating opportunities to driving more real, Value: Key: and applicable strategies for sustainable management of the genetic resource, Value: Key: towards plant breeding. This work provides useful polymorphic single-nucleotide, Value: Key: polymorphisms (SNPs) for high-throughput common bean genotyping developed by RAD, Value: Key: (restriction site-associated DNA) sequencing. The RAD tags were generated from, Value: Key: DNA pooled from 12 common bean genotypes, including breeding lines of different, Value: Key: gene pools and market classes. The aligned sequences identified 23,748 putative, Value: Key: RAD-SNPs, of which 3357 were adequate for genotyping; 1032 RAD-SNPs with the, Value: Key: highest ADT (assay design tool) score are presented in this article. The RAD-SNPs, Value: Key: were structurally annotated in different coding (47.00 %) and non-coding, Value: Key: (53.00 %) sequence components of genes. A subset of 384 RAD-SNPs with broad, Value: Key: genome distribution was used to genotype a diverse panel of 95 common bean, Value: Key: germplasms and revealed a successful amplification rate of 96.6 %, showing 73 %, Value: Key: of polymorphic SNPs within the Andean group and 83 % in the Mesoamerican group. A, Value: Key: slightly increased He (0.161, n = 21) value was estimated for the Andean gene, Value: Key: pool, compared to the Mesoamerican group (0.156, n = 74). For the linkage, Value: Key: disequilibrium (LD) analysis, from a group of 580 SNPs (289 RAD-SNPs and 291, Value: Key: BARC-SNPs) genotyped for the same set of genotypes, 70.2 % were in LD, decreasing, Value: Key: to 0.10 %in the Andean group and 0.77 % in the Mesoamerican group. Haplotype, Value: Key: patterns spanning 310 Mb of the genome (60 %) were characterized in samples from, Value: Key: different origins. However, the haplotype frameworks were under-represented for, Value: Key: the Andean (7.85 %) and Mesoamerican (5.55 %) gene pools separately. In, Value: Key: conclusion, RAD sequencing allowed the discovery of hundreds of useful SNPs for, Value: Key: broad genetic analysis of common bean germplasm. From now, this approach provides, Value: Key: an excellent panel of molecular tools for whole genome analysis, allowing, Value: Key: integrating and better exploring the common bean breeding practices., Value: Key: FAU, Value: Valdisser, Paula Arielle M R Key: AU, Value: Valdisser PA Key: AD, Value: Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Key: Brazil., Value: Key: FAU, Value: Pappas, Georgios J Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Laboratório de Biologia Molecular, Departamento de Biologia Celular, Universidade Key: de Brasília (UnB), Brasilia, DF, Brazil., Value: Key: FAU, Value: de Menezes, Ivandilson P P Key: AU, Value: de Menezes IP Key: AD, Value: Laboratório de Genética e Biologia Molecular, Departamento de Biologia, Instituto Key: Federal Goiano (IF Goiano), Urutaí, GO, Brazil., Value: Key: FAU, Value: Müller, Bárbara S F Key: AU, Value: Müller BS Key: AD, Value: Programa de Pós-Graduação em Biologia Molecular, Universidade de Brasília (UnB), Key: Brasilia, DF, Brazil., Value: Key: FAU, Value: Pereira, Wendell J Key: AU, Value: Pereira WJ Key: AD, Value: Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal de Goiás Key: (UFG), Goiânia, GO, Brazil., Value: Key: FAU, Value: Narciso, Marcelo G Key: AU, Value: Narciso MG Key: AD, Value: Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Key: Brazil., Value: Key: FAU, Value: Brondani, Claudio Key: AU, Value: Brondani C Key: AD, Value: Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Key: Brazil., Value: Key: FAU, Value: Souza, Thiago L P O Key: AU, Value: Souza TL Key: AD, Value: Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Key: Brazil., Value: Key: FAU, Value: Borba, Tereza C O Key: AU, Value: Borba TC Key: AD, Value: Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Key: Brazil., Value: Key: FAU, Value: Vianello, Rosana P Key: AU, Value: Vianello RP Key: AUID, Value: ORCID: 0000-0003-0644-5652 Key: AD, Value: Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Key: Brazil. rosana.vianello@embrapa.br., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: DEP, Value: 20160301 Key: PL, Value: Germany Key: TA, Value: Mol Genet Genomics Key: JT, Value: Molecular genetics and genomics : MGG Key: JID, Value: 101093320 Key: RN, Value: 0 (DNA, Plant) Key: SB, Value: IM Key: MH, Value: Cluster Analysis Key: MH, Value: DNA, Plant/*genetics Key: MH, Value: Evolution, Molecular Key: MH, Value: Genotype Key: MH, Value: Haplotypes Key: MH, Value: Phaseolus/*genetics Key: MH, Value: *Polymorphism, Single Nucleotide Key: MH, Value: Sequence Alignment Key: MH, Value: Sequence Analysis, DNA/*methods Key: OTO, Value: NOTNLM Key: OT, Value: Haplotype blocks Key: OT, Value: Leguminosae Key: OT, Value: Linkage disequilibrium Key: OT, Value: Phaseolus vulgaris Key: OT, Value: SNP discovery Key: EDAT, Value: 2016/03/05 06:00 Key: MHDA, Value: 2017/01/27 06:00 Key: CRDT, Value: 2016/03/03 06:00 Key: PHST, Value: 2015/08/24 00:00 [received] Key: PHST, Value: 2016/02/12 00:00 [accepted] Key: PHST, Value: 2016/03/03 06:00 [entrez] Key: PHST, Value: 2016/03/05 06:00 [pubmed] Key: PHST, Value: 2017/01/27 06:00 [medline] Key: AID, Value: 10.1007/s00438-016-1182-3 [pii] Key: AID, Value: 10.1007/s00438-016-1182-3 [doi] Key: PST, Value: ppublish Key: SO, Value: Mol Genet Genomics. 2016 Jun;291(3):1277-91. doi: 10.1007/s00438-016-1182-3. Epub Key: 2016 Mar 1., Value: Key: PMID, Value: 20231265 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20101005 Key: LR, Value: 20100615 Key: IS, Value: 1465-7333 (Electronic) Key: IS, Value: 0022-1503 (Linking) Key: VI, Value: 101 Key: IP, Value: 4 Key: DP, Value: 2010 Jul-Aug Key: TI, Value: A selected set of EST-derived microsatellites, polymorphic and transferable Key: across 6 species of eucalyptus., Value: Key: PG, Value: 512-20 Key: LID, Value: 10.1093/jhered/esq024 [doi] Key: AB, Value: Species of Eucalyptus are keystone species for ecological studies in their Key: natural ranges and are extensively planted in the tropical and subtropical, Value: Key: regions of the world to supply high-quality woody biomass for various, Value: Key: applications. We report the development of a selected set of 20 dinucleotide and, Value: Key: trinucleotide repeat microsatellites derived from Eucalyptus expressed sequence, Value: Key: tags (ESTs). These microsatellites were selected for full transferability and, Value: Key: homogeneous rate of polymorphism across species. They were evaluated for, Value: Key: individual fingerprinting, parentage testing, and intraspecific population, Value: Key: structure analyses in 6 of the most extensively studied and planted species, Value: Key: worldwide, representing key phylogenetic sections of the largest subgenus, Value: Key: Symphyomyrtus. This set of markers provides exceptional resolution for population, Value: Key: genetics and molecular breeding applications in the genus Eucalyptus. As they, Value: Key: were developed from conserved transcribed regions, the transferability and, Value: Key: polymorphism of these microsatellites will most likely extend to the other 300 or, Value: Key: more species within the same subgenus., Value: Key: FAU, Value: Faria, Danielle A Key: AU, Value: Faria DA Key: AD, Value: Plant Genetics Laboratory, EMBRAPA-Genetic Resources and Biotechnology, PqEB, Key: Brasília, 70770-970 DF, Brazil., Value: Key: FAU, Value: Mamani, Eva Maria Celia Key: AU, Value: Mamani EM Key: FAU, Value: Pappas, Marilia R Key: AU, Value: Pappas MR Key: FAU, Value: Pappas, Georgios Joannis Jr Key: AU, Value: Pappas GJ Jr Key: FAU, Value: Grattapaglia, Dario Key: AU, Value: Grattapaglia D Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20100315 Key: PL, Value: United States Key: TA, Value: J Hered Key: JT, Value: The Journal of heredity Key: JID, Value: 0375373 Key: RN, Value: 0 (DNA, Plant) Key: SB, Value: IM Key: MH, Value: DNA, Plant/metabolism Key: MH, Value: Eucalyptus/*genetics Key: MH, Value: *Expressed Sequence Tags Key: MH, Value: Genetics, Population Key: MH, Value: Genome, Plant Key: MH, Value: Microsatellite Repeats/*genetics Key: MH, Value: *Polymorphism, Genetic Key: MH, Value: Sequence Analysis, DNA Key: MH, Value: Species Specificity Key: EDAT, Value: 2010/03/17 06:00 Key: MHDA, Value: 2010/10/06 06:00 Key: CRDT, Value: 2010/03/17 06:00 Key: PHST, Value: 2010/03/17 06:00 [entrez] Key: PHST, Value: 2010/03/17 06:00 [pubmed] Key: PHST, Value: 2010/10/06 06:00 [medline] Key: AID, Value: esq024 [pii] Key: AID, Value: 10.1093/jhered/esq024 [doi] Key: PST, Value: ppublish Key: SO, Value: J Hered. 2010 Jul-Aug;101(4):512-20. doi: 10.1093/jhered/esq024. Epub 2010 Mar Key: 15., Value: Key: PMID, Value: 20507605 Key: OWN, Value: NLM Key: STAT, Value: PubMed-not-MEDLINE Key: DCOM, Value: 20110714 Key: LR, Value: 20211020 Key: IS, Value: 1756-0500 (Electronic) Key: IS, Value: 1756-0500 (Linking) Key: VI, Value: 3 Key: DP, Value: 2010 May 27 Key: TI, Value: Characterization of novel microsatellite markers in Musa acuminata subsp. Key: burmannicoides, var. Calcutta 4., Value: Key: PG, Value: 148 Key: LID, Value: 10.1186/1756-0500-3-148 [doi] Key: AB, Value: BACKGROUND: Banana is a nutritionally important crop across tropical and Key: sub-tropical countries in sub-Saharan Africa, Central and South America and Asia., Value: Key: Although cultivars have evolved from diploid, triploid and tetraploid wild Asian, Value: Key: species of Musa acuminata (A genome) and Musa balbisiana (B genome), many of, Value: Key: today's commercial cultivars are sterile triploids or diploids, with fruit, Value: Key: developing via parthenocarpy. As a result of restricted genetic variation,, Value: Key: improvement has been limited, resulting in a crop frequently lacking resistance, Value: Key: to pests and disease. Considering the importance of molecular tools to facilitate, Value: Key: development of disease resistant genotypes, the objectives of this study were to, Value: Key: develop polymorphic microsatellite markers from BAC clone sequences for M., Value: Key: acuminata subsp. burmannicoides, var. Calcutta 4. This wild diploid species is, Value: Key: used as a donor cultivar in breeding programs as a source of resistance to, Value: Key: diverse biotic stresses. FINDINGS: Microsatellite sequences were identified from, Value: Key: five Calcutta 4 BAC consensi datasets. Specific primers were designed for 41, Value: Key: loci. Isolated di-nucleotide repeat motifs were the most abundant, followed by, Value: Key: tri-nucleotides. From 33 tested loci, 20 displayed polymorphism when screened, Value: Key: across 21 diploid M. acuminata accessions, contrasting in resistance to Sigatoka, Value: Key: diseases. The number of alleles per SSR locus ranged from two to four, with a, Value: Key: total of 56. Six repeat classes were identified, with di-nucleotides the most, Value: Key: abundant. Expected heterozygosity values for polymorphic markers ranged from 0.31, Value: Key: to 0.75. CONCLUSIONS: This is the first report identifying polymorphic, Value: Key: microsatellite markers from M. acuminata subsp. burmannicoides, var. Calcutta 4, Value: Key: across accessions contrasting in resistance to Sigatoka diseases. These, Value: Key: BAC-derived polymorphic microsatellite markers are a useful resource for banana,, Value: Key: applicable for genetic map development, germplasm characterization, evolutionary, Value: Key: studies and marker assisted selection for traits., Value: Key: FAU, Value: Miller, Robert Ng Key: AU, Value: Miller RN Key: AD, Value: Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Key: Ciências Biológicas, Departamento de Biologia Celular, Asa Norte, Brasília,, Value: Key: Brazil. robertmiller@unb.br., Value: Key: FAU, Value: Passos, Marco An Key: AU, Value: Passos MA Key: FAU, Value: Menezes, Natalia Np Key: AU, Value: Menezes NN Key: FAU, Value: Souza, Manoel T Jr Key: AU, Value: Souza MT Jr Key: FAU, Value: do Carmo Costa, Marcos M Key: AU, Value: do Carmo Costa MM Key: FAU, Value: Rennó Azevedo, Vânia C Key: AU, Value: Rennó Azevedo VC Key: FAU, Value: Amorim, Edson P Key: AU, Value: Amorim EP Key: FAU, Value: Pappas, Georgios J Jr Key: AU, Value: Pappas GJ Jr Key: FAU, Value: Ciampi, Ana Y Key: AU, Value: Ciampi AY Key: LA, Value: eng Key: PT, Value: Journal Article Key: DEP, Value: 20100527 Key: PL, Value: England Key: TA, Value: BMC Res Notes Key: JT, Value: BMC research notes Key: JID, Value: 101462768 Key: PMC, Value: PMC2893197 Key: EDAT, Value: 2010/05/29 06:00 Key: MHDA, Value: 2010/05/29 06:01 Key: PMCR, Value: 2010/05/27 Key: CRDT, Value: 2010/05/29 06:00 Key: PHST, Value: 2009/12/21 00:00 [received] Key: PHST, Value: 2010/05/27 00:00 [accepted] Key: PHST, Value: 2010/05/29 06:00 [entrez] Key: PHST, Value: 2010/05/29 06:00 [pubmed] Key: PHST, Value: 2010/05/29 06:01 [medline] Key: PHST, Value: 2010/05/27 00:00 [pmc-release] Key: AID, Value: 1756-0500-3-148 [pii] Key: AID, Value: 10.1186/1756-0500-3-148 [doi] Key: PST, Value: epublish Key: SO, Value: BMC Res Notes. 2010 May 27;3:148. doi: 10.1186/1756-0500-3-148. Key: PMID, Value: 20388207 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20100705 Key: LR, Value: 20240322 Key: IS, Value: 1471-2229 (Electronic) Key: IS, Value: 1471-2229 (Linking) Key: VI, Value: 10 Key: DP, Value: 2010 Apr 13 Key: TI, Value: A saturated SSR/DArT linkage map of Musa acuminata addressing genome Key: rearrangements among bananas., Value: Key: PG, Value: 65 Key: LID, Value: 10.1186/1471-2229-10-65 [doi] Key: AB, Value: BACKGROUND: The genus Musa is a large species complex which includes cultivars at Key: diploid and triploid levels. These sterile and vegetatively propagated cultivars, Value: Key: are based on the A genome from Musa acuminata, exclusively for sweet bananas such, Value: Key: as Cavendish, or associated with the B genome (Musa balbisiana) in cooking, Value: Key: bananas such as Plantain varieties. In M. acuminata cultivars, structural, Value: Key: heterozygosity is thought to be one of the main causes of sterility, which is, Value: Key: essential for obtaining seedless fruits but hampers breeding. Only partial, Value: Key: genetic maps are presently available due to chromosomal rearrangements within the, Value: Key: parents of the mapping populations. This causes large segregation distortions, Value: Key: inducing pseudo-linkages and difficulties in ordering markers in the linkage, Value: Key: groups. The present study aims at producing a saturated linkage map of M., Value: Key: acuminata, taking into account hypotheses on the structural heterozygosity of the, Value: Key: parents. RESULTS: An F1 progeny of 180 individuals was obtained from a cross, Value: Key: between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang, Value: Key: Lilin' (P. Lilin). Based on the gametic recombination of each parent, two, Value: Key: parental maps composed of SSR and DArT markers were established. A significant, Value: Key: proportion of the markers (21.7%) deviated (p < 0.05) from the expected Mendelian, Value: Key: ratios. These skewed markers were distributed in different linkage groups for, Value: Key: each parent. To solve some complex ordering of the markers on linkage groups, we, Value: Key: associated tools such as tree-like graphic representations, recombination, Value: Key: frequency statistics and cytogenetical studies to identify structural, Value: Key: rearrangements and build parsimonious linkage group order. An illustration of, Value: Key: such an approach is given for the P. Lilin parent. CONCLUSIONS: We propose a, Value: Key: synthetic map with 11 linkage groups containing 489 markers (167 SSRs and 322, Value: Key: DArTs) covering 1197 cM. This first saturated map is proposed as a "reference, Value: Key: Musa map" for further analyses. We also propose two complete parental maps with, Value: Key: interpretations of structural rearrangements localized on the linkage groups. The, Value: Key: structural heterozygosity in P. Lilin is hypothesized to result from a, Value: Key: duplication likely accompanied by an inversion on another chromosome. This paper, Value: Key: also illustrates a methodological approach, transferable to other species, to, Value: Key: investigate the mapping of structural rearrangements and determine their, Value: Key: consequences on marker segregation., Value: Key: FAU, Value: Hippolyte, Isabelle Key: AU, Value: Hippolyte I Key: AD, Value: CIRAD, UR Multiplication Végétative, Av, Agropolis, 34398 Montpellier Cedex 5, Key: France. isabelle.hippolyte@cirad.fr, Value: Key: FAU, Value: Bakry, Frederic Key: AU, Value: Bakry F Key: FAU, Value: Seguin, Marc Key: AU, Value: Seguin M Key: FAU, Value: Gardes, Laetitia Key: AU, Value: Gardes L Key: FAU, Value: Rivallan, Ronan Key: AU, Value: Rivallan R Key: FAU, Value: Risterucci, Ange-Marie Key: AU, Value: Risterucci AM Key: FAU, Value: Jenny, Christophe Key: AU, Value: Jenny C Key: FAU, Value: Perrier, Xavier Key: AU, Value: Perrier X Key: FAU, Value: Carreel, Françoise Key: AU, Value: Carreel F Key: FAU, Value: Argout, Xavier Key: AU, Value: Argout X Key: FAU, Value: Piffanelli, Pietro Key: AU, Value: Piffanelli P Key: FAU, Value: Khan, Imtiaz A Key: AU, Value: Khan IA Key: FAU, Value: Miller, Robert N G Key: AU, Value: Miller RN Key: FAU, Value: Pappas, Georgios J Key: AU, Value: Pappas GJ Key: FAU, Value: Mbéguié-A-Mbéguié, Didier Key: AU, Value: Mbéguié-A-Mbéguié D Key: FAU, Value: Matsumoto, Takashi Key: AU, Value: Matsumoto T Key: FAU, Value: De Bernardinis, Veronique Key: AU, Value: De Bernardinis V Key: FAU, Value: Huttner, Eric Key: AU, Value: Huttner E Key: FAU, Value: Kilian, Andrzej Key: AU, Value: Kilian A Key: FAU, Value: Baurens, Franc-Christophe Key: AU, Value: Baurens FC Key: FAU, Value: D'Hont, Angélique Key: AU, Value: D'Hont A Key: FAU, Value: Cote, François Key: AU, Value: Cote F Key: FAU, Value: Courtois, Brigitte Key: AU, Value: Courtois B Key: FAU, Value: Glaszmann, Jean-Christophe Key: AU, Value: Glaszmann JC Key: LA, Value: eng Key: PT, Value: Journal Article Key: DEP, Value: 20100413 Key: PL, Value: England Key: TA, Value: BMC Plant Biol Key: JT, Value: BMC plant biology Key: JID, Value: 100967807 Key: SB, Value: IM Key: MH, Value: *Chromosome Mapping Key: MH, Value: Chromosome Pairing/genetics Key: MH, Value: Chromosome Segregation/genetics Key: MH, Value: Computer Simulation Key: MH, Value: Crosses, Genetic Key: MH, Value: Gene Rearrangement/*genetics Key: MH, Value: Genome, Plant/*genetics Key: MH, Value: Lod Score Key: MH, Value: Meiosis/genetics Key: MH, Value: Microsatellite Repeats/*genetics Key: MH, Value: Musa/cytology/*genetics Key: MH, Value: Phylogeny Key: MH, Value: Polymorphism, Genetic Key: PMC, Value: PMC2923539 Key: EDAT, Value: 2010/04/15 06:00 Key: MHDA, Value: 2010/07/06 06:00 Key: PMCR, Value: 2010/04/13 Key: CRDT, Value: 2010/04/15 06:00 Key: PHST, Value: 2009/09/18 00:00 [received] Key: PHST, Value: 2010/04/13 00:00 [accepted] Key: PHST, Value: 2010/04/15 06:00 [entrez] Key: PHST, Value: 2010/04/15 06:00 [pubmed] Key: PHST, Value: 2010/07/06 06:00 [medline] Key: PHST, Value: 2010/04/13 00:00 [pmc-release] Key: AID, Value: 1471-2229-10-65 [pii] Key: AID, Value: 10.1186/1471-2229-10-65 [doi] Key: PST, Value: epublish Key: SO, Value: BMC Plant Biol. 2010 Apr 13;10:65. doi: 10.1186/1471-2229-10-65. Key: PMID, Value: 23240072 Key: OWN, Value: NLM Key: STAT, Value: PubMed-not-MEDLINE Key: DCOM, Value: 20121217 Key: LR, Value: 20211021 Key: IS, Value: 2041-2851 (Electronic) Key: VI, Value: 2012 Key: DP, Value: 2012 Key: TI, Value: Development of expressed sequence tag and expressed sequence tag-simple sequence Key: repeat marker resources for Musa acuminata., Value: Key: PG, Value: pls030 Key: LID, Value: 10.1093/aobpla/pls030 [doi] Key: LID, Value: pls030 Key: AB, Value: BACKGROUND AND AIMS: Banana (Musa acuminata) is a crop contributing to global Key: food security. Many varieties lack resistance to biotic stresses, due to, Value: Key: sterility and narrow genetic background. The objective of this study was to, Value: Key: develop an expressed sequence tag (EST) database of transcripts expressed during, Value: Key: compatible and incompatible banana-Mycosphaerella fijiensis (Mf) interactions., Value: Key: Black leaf streak disease (BLSD), caused by Mf, is a destructive disease of, Value: Key: banana. Microsatellite markers were developed as a resource for crop improvement., Value: Key: METHODOLOGY: cDNA libraries were constructed from in vitro-infected leaves from, Value: Key: BLSD-resistant M. acuminata ssp. burmaniccoides Calcutta 4 (MAC4) and susceptible, Value: Key: M. acuminata cv. Cavendish Grande Naine (MACV). Clones were 5'-end Sanger, Value: Key: sequenced, ESTs assembled with TGICL and unigenes annotated using BLAST, Blast2GO, Value: Key: and InterProScan. Mreps was used to screen for simple sequence repeats (SSRs),, Value: Key: with markers evaluated for polymorphism using 20 diploid (AA) M. acuminata, Value: Key: accessions contrasting in resistance to Mycosphaerella leaf spot diseases., Value: Key: PRINCIPAL RESULTS: A total of 9333 high-quality ESTs were obtained for MAC4 and, Value: Key: 3964 for MACV, which assembled into 3995 unigenes. Of these, 2592 displayed, Value: Key: homology to genes encoding proteins with known or putative function, and 266 to, Value: Key: genes encoding proteins with unknown function. Gene ontology (GO) classification, Value: Key: identified 543 GO terms, 2300 unigenes were assigned to EuKaryotic orthologous, Value: Key: group categories and 312 mapped to Kyoto Encyclopedia of Genes and Genomes, Value: Key: pathways. A total of 624 SSR loci were identified, with trinucleotide repeat, Value: Key: motifs the most abundant in MAC4 (54.1 %) and MACV (57.6 %). Polymorphism across, Value: Key: M. acuminata accessions was observed with 75 markers. Alleles per polymorphic, Value: Key: locus ranged from 2 to 8, totalling 289. The polymorphism information content, Value: Key: ranged from 0.08 to 0.81. CONCLUSIONS: This EST collection offers a resource for, Value: Key: studying functional genes, including transcripts expressed in banana-Mf, Value: Key: interactions. Markers are applicable for genetic mapping, diversity, Value: Key: characterization and marker-assisted breeding., Value: Key: FAU, Value: Passos, Marco A N Key: AU, Value: Passos MA Key: AD, Value: Universidade de Brasília , Campus Universitário Darcy Ribeiro , Instituto de Key: Ciências Biológicas , Asa Norte, CEP 70910-900, Brasília, DF , Brazil., Value: Key: FAU, Value: de Oliveira Cruz, Viviane Key: AU, Value: de Oliveira Cruz V Key: FAU, Value: Emediato, Flavia L Key: AU, Value: Emediato FL Key: FAU, Value: de Camargo Teixeira, Cristiane Key: AU, Value: de Camargo Teixeira C Key: FAU, Value: Souza, Manoel T Jr Key: AU, Value: Souza MT Jr Key: FAU, Value: Matsumoto, Takashi Key: AU, Value: Matsumoto T Key: FAU, Value: Rennó Azevedo, Vânia C Key: AU, Value: Rennó Azevedo VC Key: FAU, Value: Ferreira, Claudia F Key: AU, Value: Ferreira CF Key: FAU, Value: Amorim, Edson P Key: AU, Value: Amorim EP Key: FAU, Value: de Alencar Figueiredo, Lucio Flavio Key: AU, Value: de Alencar Figueiredo LF Key: FAU, Value: Martins, Natalia F Key: AU, Value: Martins NF Key: FAU, Value: de Jesus Barbosa Cavalcante, Maria Key: AU, Value: de Jesus Barbosa Cavalcante M Key: FAU, Value: Baurens, Franc-Christophe Key: AU, Value: Baurens FC Key: FAU, Value: da Silva, Orzenil Bonfim Jr Key: AU, Value: da Silva OB Jr Key: FAU, Value: Pappas, Georgios J Jr Key: AU, Value: Pappas GJ Jr Key: FAU, Value: Pignolet, Luc Key: AU, Value: Pignolet L Key: FAU, Value: Abadie, Catherine Key: AU, Value: Abadie C Key: FAU, Value: Ciampi, Ana Y Key: AU, Value: Ciampi AY Key: FAU, Value: Piffanelli, Pietro Key: AU, Value: Piffanelli P Key: FAU, Value: Miller, Robert N G Key: AU, Value: Miller RN Key: LA, Value: eng Key: PT, Value: Journal Article Key: DEP, Value: 20121126 Key: PL, Value: England Key: TA, Value: AoB Plants Key: JT, Value: AoB PLANTS Key: JID, Value: 101539425 Key: PMC, Value: PMC3521319 Key: EDAT, Value: 2012/12/15 06:00 Key: MHDA, Value: 2012/12/15 06:01 Key: PMCR, Value: 2012/01/01 Key: CRDT, Value: 2012/12/15 06:00 Key: PHST, Value: 2012/03/04 00:00 [received] Key: PHST, Value: 2012/09/14 00:00 [accepted] Key: PHST, Value: 2012/12/15 06:00 [entrez] Key: PHST, Value: 2012/12/15 06:00 [pubmed] Key: PHST, Value: 2012/12/15 06:01 [medline] Key: PHST, Value: 2012/01/01 00:00 [pmc-release] Key: AID, Value: pls030 [pii] Key: AID, Value: 10.1093/aobpla/pls030 [doi] Key: PST, Value: ppublish Key: SO, Value: AoB Plants. 2012;2012:pls030. doi: 10.1093/aobpla/pls030. Epub 2012 Nov 26. Key: PMID, Value: 22309312 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20120618 Key: LR, Value: 20210416 Key: IS, Value: 1469-8137 (Electronic) Key: IS, Value: 0028-646X (Linking) Key: VI, Value: 194 Key: IP, Value: 1 Key: DP, Value: 2012 Apr Key: TI, Value: Genomic selection for growth and wood quality in Eucalyptus: capturing the Key: missing heritability and accelerating breeding for complex traits in forest, Value: Key: trees., Value: Key: PG, Value: 116-128 Key: LID, Value: 10.1111/j.1469-8137.2011.04038.x [doi] Key: AB, Value: • Genomic selection (GS) is expected to cause a paradigm shift in tree breeding Key: by improving its speed and efficiency. By fitting all the genome-wide markers, Value: Key: concurrently, GS can capture most of the 'missing heritability' of complex traits, Value: Key: that quantitative trait locus (QTL) and association mapping classically fail to, Value: Key: explain. Experimental support of GS is now required. • The effectiveness of GS, Value: Key: was assessed in two unrelated Eucalyptus breeding populations with contrasting, Value: Key: effective population sizes (N(e) = 11 and 51) genotyped with > 3000 DArT markers., Value: Key: Prediction models were developed for tree circumference and height growth, wood, Value: Key: specific gravity and pulp yield using random regression best linear unbiased, Value: Key: predictor (BLUP). • Accuracies of GS varied between 0.55 and 0.88, matching the, Value: Key: accuracies achieved by conventional phenotypic selection. Substantial proportions, Value: Key: (74-97%) of trait heritability were captured by fitting all genome-wide markers, Value: Key: simultaneously. Genomic regions explaining trait variation largely coincided, Value: Key: between populations, although GS models predicted poorly across populations,, Value: Key: likely as a result of variable patterns of linkage disequilibrium, inconsistent, Value: Key: allelic effects and genotype × environment interaction. • GS brings a new, Value: Key: perspective to the understanding of quantitative trait variation in forest trees, Value: Key: and provides a revolutionary tool for applied tree improvement. Nevertheless, Value: Key: population-specific predictive models will likely drive the initial applications, Value: Key: of GS in forest tree breeding., Value: Key: CI, Value: © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust. Key: FAU, Value: Resende, Marcos D V Key: AU, Value: Resende MDV Key: AD, Value: EMBRAPA Forestry Research, Colombo, PR, 83411-000, Brazil. Key: AD, Value: Universidade Federal de Viçosa |Viçosa MG, 36570-000, Brazil. Key: FAU, Value: Resende, Márcio F R Jr Key: AU, Value: Resende MFR Jr Key: AD, Value: Universidade Federal de Viçosa |Viçosa MG, 36570-000, Brazil. Key: FAU, Value: Sansaloni, Carolina P Key: AU, Value: Sansaloni CP Key: AD, Value: EMBRAPA Genetic Resources and Biotechnology |EPqB, 70770-910, Brasilia, DF, Key: Brazil., Value: Key: AD, Value: Universidade de Brasilia |Campus Darcy Ribeiro Brasília, DF, 70910-900, Brazil. Key: FAU, Value: Petroli, Cesar D Key: AU, Value: Petroli CD Key: AD, Value: EMBRAPA Genetic Resources and Biotechnology |EPqB, 70770-910, Brasilia, DF, Key: Brazil., Value: Key: AD, Value: Universidade de Brasilia |Campus Darcy Ribeiro Brasília, DF, 70910-900, Brazil. Key: FAU, Value: Missiaggia, Alexandre A Key: AU, Value: Missiaggia AA Key: AD, Value: FIBRIA Celulose S.A., Rod. Aracruz/Barra do Riacho, km 25, Aracruz, ES, Key: 29197-900, Brazil., Value: Key: FAU, Value: Aguiar, Aurelio M Key: AU, Value: Aguiar AM Key: AD, Value: FIBRIA Celulose S.A., Rod. Aracruz/Barra do Riacho, km 25, Aracruz, ES, Key: 29197-900, Brazil., Value: Key: FAU, Value: Abad, Jupiter M Key: AU, Value: Abad JM Key: AD, Value: FIBRIA Celulose S.A., Rod. Aracruz/Barra do Riacho, km 25, Aracruz, ES, Key: 29197-900, Brazil., Value: Key: FAU, Value: Takahashi, Elizabete K Key: AU, Value: Takahashi EK Key: AD, Value: CENIBRA Celulose Nipo Brasileira S.A, Belo Oriente, MG, 35196-000, Brazil. Key: FAU, Value: Rosado, Antonio M Key: AU, Value: Rosado AM Key: AD, Value: CENIBRA Celulose Nipo Brasileira S.A, Belo Oriente, MG, 35196-000, Brazil. Key: FAU, Value: Faria, Danielle A Key: AU, Value: Faria DA Key: AD, Value: EMBRAPA Genetic Resources and Biotechnology |EPqB, 70770-910, Brasilia, DF, Key: Brazil., Value: Key: FAU, Value: Pappas, Georgios J Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: EMBRAPA Genetic Resources and Biotechnology |EPqB, 70770-910, Brasilia, DF, Key: Brazil., Value: Key: AD, Value: Universidade Catolica de Brasília|SGAN, 916 modulo B, Brasilia, DF, 70790-160, Key: Brazil., Value: Key: FAU, Value: Kilian, Andrzej Key: AU, Value: Kilian A Key: AD, Value: DArT |Diversity Arrays Technology, POB 7141, Yarralumla, ACT, Australia 2600. Key: FAU, Value: Grattapaglia, Dario Key: AU, Value: Grattapaglia D Key: AD, Value: EMBRAPA Genetic Resources and Biotechnology |EPqB, 70770-910, Brasilia, DF, Key: Brazil., Value: Key: AD, Value: Universidade Catolica de Brasília|SGAN, 916 modulo B, Brasilia, DF, 70790-160, Key: Brazil., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20120206 Key: PL, Value: England Key: TA, Value: New Phytol Key: JT, Value: The New phytologist Key: JID, Value: 9882884 Key: RN, Value: 0 (Genetic Markers) Key: SB, Value: IM Key: MH, Value: *Breeding Key: MH, Value: Eucalyptus/*genetics Key: MH, Value: Genetic Markers Key: MH, Value: Genome, Plant/*genetics Key: MH, Value: Genotype Key: MH, Value: Inheritance Patterns/*genetics Key: MH, Value: Models, Genetic Key: MH, Value: Quantitative Trait, Heritable Key: MH, Value: *Selection, Genetic Key: MH, Value: Trees/*genetics Key: MH, Value: Wood/genetics/*growth & development Key: EDAT, Value: 2012/02/09 06:00 Key: MHDA, Value: 2012/06/19 06:00 Key: CRDT, Value: 2012/02/08 06:00 Key: PHST, Value: 2012/02/08 06:00 [entrez] Key: PHST, Value: 2012/02/09 06:00 [pubmed] Key: PHST, Value: 2012/06/19 06:00 [medline] Key: AID, Value: 10.1111/j.1469-8137.2011.04038.x [doi] Key: PST, Value: ppublish Key: SO, Value: New Phytol. 2012 Apr;194(1):116-128. doi: 10.1111/j.1469-8137.2011.04038.x. Epub Key: 2012 Feb 6., Value: Key: PMID, Value: 18498318 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20080811 Key: LR, Value: 20080618 Key: IS, Value: 1472-765X (Electronic) Key: IS, Value: 0266-8254 (Linking) Key: VI, Value: 47 Key: IP, Value: 1 Key: DP, Value: 2008 Jul Key: TI, Value: Characterization of Aspergillus flavus strains from Brazilian Brazil nuts and Key: cashew by RAPD and ribosomal DNA analysis., Value: Key: PG, Value: 12-8 Key: LID, Value: 10.1111/j.1472-765X.2008.02377.x [doi] Key: AB, Value: AIMS: The aim of this study was to determine the genetic variability in Key: Aspergillus flavus populations from Brazil nut and cashew and develop a, Value: Key: polymerase chain reaction (PCR) detection method. METHODS AND RESULTS:, Value: Key: Chomatography analysis of 48 isolates identified 36 as aflatoxigenic (75%). One, Value: Key: hundred and forty-one DNA bands were generated with 11 random amplified, Value: Key: polymorphic DNA (RAPD) primers and analysed via unweighted pair group analysis,, Value: Key: using arithmetic means (UPGMA). Isolates grouped according to host, with, Value: Key: differentiation of those from A. occidentale also according to geographical, Value: Key: origin. Aspergillus flavus-specific PCR primers ASPITSF2 and ASPITSR3 were, Value: Key: designed from ribosomal DNA internal transcribed spacers (ITS 1 and 2), and an, Value: Key: internal amplification control was developed, to prevent false negative results., Value: Key: Specificity to only A. flavus was confirmed against DNA from additional, Value: Key: aspergilli and other fungi. CONCLUSIONS: RAPD-based characterization, Value: Key: differentiated isolates according to plant host. The PCR primer pair developed, Value: Key: showed specificity to A. flavus, with a detection limit of 10 fg. SIGNIFICANCE, Value: Key: AND IMPACT OF THE STUDY: Genetic variability observed in A. flavus isolates from, Value: Key: two Brazilian agroecosystems suggested reproductive isolation. The PCR detection, Value: Key: method developed for A. flavus represents progress towards multiplex PCR, Value: Key: detection of aflatoxigenic and nonaflatoxigenic strains in Hazard Analysis, Value: Key: Critical Control Point systems., Value: Key: FAU, Value: Midorikawa, G E O Key: AU, Value: Midorikawa GE Key: AD, Value: Postgraduate program in Genomic Science and Biotechnology, Universidade Católica Key: de Brasília, Brasília, DF, Brazil., Value: Key: FAU, Value: Pinheiro, M R R Key: AU, Value: Pinheiro MR Key: FAU, Value: Vidigal, B S Key: AU, Value: Vidigal BS Key: FAU, Value: Arruda, M C Key: AU, Value: Arruda MC Key: FAU, Value: Costa, F F Key: AU, Value: Costa FF Key: FAU, Value: Pappas, G J Jr Key: AU, Value: Pappas GJ Jr Key: FAU, Value: Ribeiro, S G Key: AU, Value: Ribeiro SG Key: FAU, Value: Freire, F Key: AU, Value: Freire F Key: FAU, Value: Miller, R N G Key: AU, Value: Miller RN Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20080521 Key: PL, Value: England Key: TA, Value: Lett Appl Microbiol Key: JT, Value: Letters in applied microbiology Key: JID, Value: 8510094 Key: RN, Value: 0 (Aflatoxins) Key: RN, Value: 0 (DNA, Fungal) Key: RN, Value: 0 (DNA, Ribosomal) Key: SB, Value: IM Key: MH, Value: Aflatoxins/analysis/biosynthesis/genetics Key: MH, Value: Anacardium/microbiology Key: MH, Value: Aspergillus flavus/genetics/*isolation & purification Key: MH, Value: Bertholletia/microbiology Key: MH, Value: Brazil Key: MH, Value: DNA, Fungal/analysis Key: MH, Value: DNA, Ribosomal/*analysis/genetics Key: MH, Value: *Mycological Typing Techniques Key: MH, Value: Random Amplified Polymorphic DNA Technique/*methods Key: EDAT, Value: 2008/05/24 09:00 Key: MHDA, Value: 2008/08/12 09:00 Key: CRDT, Value: 2008/05/24 09:00 Key: PHST, Value: 2008/05/24 09:00 [pubmed] Key: PHST, Value: 2008/08/12 09:00 [medline] Key: PHST, Value: 2008/05/24 09:00 [entrez] Key: AID, Value: LAM2377 [pii] Key: AID, Value: 10.1111/j.1472-765X.2008.02377.x [doi] Key: PST, Value: ppublish Key: SO, Value: Lett Appl Microbiol. 2008 Jul;47(1):12-8. doi: 10.1111/j.1472-765X.2008.02377.x. Key: Epub 2008 May 21., Value: Key: PMID, Value: 18199320 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20080318 Key: LR, Value: 20240314 Key: IS, Value: 1743-422X (Electronic) Key: IS, Value: 1743-422X (Linking) Key: VI, Value: 5 Key: DP, Value: 2008 Jan 16 Key: TI, Value: Genetic variation and recombination of RdRp and HSP 70h genes of Citrus tristeza Key: virus isolates from orange trees showing symptoms of citrus sudden death disease., Value: Key: PG, Value: 9 Key: LID, Value: 10.1186/1743-422X-5-9 [doi] Key: AB, Value: BACKGROUND: Citrus sudden death (CSD), a disease that rapidly kills orange trees, Key: is an emerging threat to the Brazilian citrus industry. Although the causal agent, Value: Key: of CSD has not been definitively determined, based on the disease's distribution, Value: Key: and symptomatology it is suspected that the agent may be a new strain of Citrus, Value: Key: tristeza virus (CTV). CTV genetic variation was therefore assessed in two, Value: Key: Brazilian orange trees displaying CSD symptoms and a third with more conventional, Value: Key: CTV symptoms. RESULTS: A total of 286 RNA-dependent-RNA polymerase (RdRp) and 284, Value: Key: heat shock protein 70 homolog (HSP70h) gene fragments were determined for CTV, Value: Key: variants infecting the three trees. It was discovered that, despite differences, Value: Key: in symptomatology, the trees were all apparently coinfected with similar, Value: Key: populations of divergent CTV variants. While mixed CTV infections are common, the, Value: Key: genetic distance between the most divergent population members observed (24.1%, Value: Key: for RdRp and 11.0% for HSP70h) was far greater than that in previously described, Value: Key: mixed infections. Recombinants of five distinct RdRp lineages and three distinct, Value: Key: HSP70h lineages were easily detectable but respectively accounted for only 5.9, Value: Key: and 11.9% of the RdRp and HSP70h gene fragments analysed and there was no, Value: Key: evidence of an association between particular recombinant mosaics and CSD. Also,, Value: Key: comparisons of CTV population structures indicated that the two most similar CTV, Value: Key: populations were those of one of the trees with CSD and the tree without CSD., Value: Key: CONCLUSION: We suggest that if CTV is the causal agent of CSD, it is most likely, Value: Key: a subtle feature of population structures within mixed infections and not merely, Value: Key: the presence (or absence) of a single CTV variant within these populations that, Value: Key: triggers the disease., Value: Key: FAU, Value: Gomes, Clarissa P C Key: AU, Value: Gomes CP Key: AD, Value: Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Key: Católica de Brasília, SGAN, Quadra 916, Módulo B, Av, W5 Norte, 70,790-160,, Value: Key: Brasília-DF, Brazil. clarissagomes@yahoo.com.br, Value: Key: FAU, Value: Nagata, Tatsuya Key: AU, Value: Nagata T Key: FAU, Value: de Jesus, Waldir C Jr Key: AU, Value: de Jesus WC Jr Key: FAU, Value: Neto, Carlos R Borges Key: AU, Value: Neto CR Key: FAU, Value: Pappas, Georgios J Jr Key: AU, Value: Pappas GJ Jr Key: FAU, Value: Martin, Darren P Key: AU, Value: Martin DP Key: LA, Value: eng Key: GR, Value: WT_/Wellcome Trust/United Kingdom Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: DEP, Value: 20080116 Key: PL, Value: England Key: TA, Value: Virol J Key: JT, Value: Virology journal Key: JID, Value: 101231645 Key: RN, Value: 0 (HSP70 Heat-Shock Proteins) Key: RN, Value: 0 (Viral Proteins) Key: RN, Value: EC 2.7.7.48 (RNA-Dependent RNA Polymerase) Key: SB, Value: IM Key: MH, Value: Brazil Key: MH, Value: Citrus sinensis/*virology Key: MH, Value: Closterovirus/classification/*genetics Key: MH, Value: *Genes, Viral Key: MH, Value: Genetic Variation Key: MH, Value: HSP70 Heat-Shock Proteins/*genetics Key: MH, Value: Plant Diseases/*virology Key: MH, Value: RNA-Dependent RNA Polymerase/*genetics Key: MH, Value: Recombination, Genetic Key: MH, Value: Viral Proteins/*genetics Key: PMC, Value: PMC2244595 Key: EDAT, Value: 2008/01/18 09:00 Key: MHDA, Value: 2008/03/19 09:00 Key: PMCR, Value: 2008/01/16 Key: CRDT, Value: 2008/01/18 09:00 Key: PHST, Value: 2007/12/17 00:00 [received] Key: PHST, Value: 2008/01/16 00:00 [accepted] Key: PHST, Value: 2008/01/18 09:00 [pubmed] Key: PHST, Value: 2008/03/19 09:00 [medline] Key: PHST, Value: 2008/01/18 09:00 [entrez] Key: PHST, Value: 2008/01/16 00:00 [pmc-release] Key: AID, Value: 1743-422X-5-9 [pii] Key: AID, Value: 10.1186/1743-422X-5-9 [doi] Key: PST, Value: epublish Key: SO, Value: Virol J. 2008 Jan 16;5:9. doi: 10.1186/1743-422X-5-9. Key: PMID, Value: 27193516 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20180108 Key: LR, Value: 20231213 Key: IS, Value: 1678-8052 (Electronic) Key: IS, Value: 1519-566X (Linking) Key: VI, Value: 43 Key: IP, Value: 2 Key: DP, Value: 2014 Apr Key: TI, Value: Identification and Expression Profile of Two Putative Odorant-Binding Proteins Key: from the Neotropical Brown Stink Bug, Euschistus heros (Fabricius) (Hemiptera:, Value: Key: Pentatomidae)., Value: Key: PG, Value: 106-14 Key: LID, Value: 10.1007/s13744-013-0187-4 [doi] Key: AB, Value: This work presents the first identification of putative odorant-binding proteins Key: (OBPs) from a member of the Pentatomidae, i.e. the brown stink bug Euschistus, Value: Key: heros (Fabricius), an important pest of soybean in Brazil. Antennae from both, Value: Key: sexes of E. heros adults (12 days old and unmated) were used to construct a cDNA, Value: Key: library, from which two transcripts encoding putative E. heros OBPs (EherOBPs), Value: Key: were identified. The expression levels of EherOBP1 and EherOBP2 were found to be, Value: Key: higher in male antennae than in female and there was difference in expression in, Value: Key: legs, wings, and abdomens of the two sexes. The histolocalization of EherOBP1 and, Value: Key: EherOBP2 transcripts in antennae also showed a sexual dimorphism in the, Value: Key: chemoreception system, with different expression sites in the antennal segments, Value: Key: between males and females, occurring predominantly at the base of the sensillum., Value: Key: The implications of these findings for stink bug chemoreception are discussed., Value: Key: FAU, Value: Farias, L R Key: AU, Value: Farias LR Key: AD, Value: Instituto de Ciências Biológicas, Univ de Brasília, Campus Universitário Darcy Key: Ribeiro, Brasília, DF, Brasil. fariaslr@gmail.com., Value: Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil. Key: fariaslr@gmail.com., Value: Key: FAU, Value: Paula, D P Key: AU, Value: Paula DP Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil. Key: FAU, Value: Zhou, J J Key: AU, Value: Zhou JJ Key: AD, Value: Dept of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Key: UK., Value: Key: FAU, Value: Liu, R Key: AU, Value: Liu R Key: AD, Value: Dept of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Key: UK., Value: Key: FAU, Value: Pappas, G J Jr Key: AU, Value: Pappas GJ Jr Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil. Key: FAU, Value: Moraes, M C B Key: AU, Value: Moraes MC Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil. Key: FAU, Value: Laumann, R A Key: AU, Value: Laumann RA Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil. Key: FAU, Value: Borges, M Key: AU, Value: Borges M Key: AD, Value: Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil. Key: FAU, Value: Birkett, M A Key: AU, Value: Birkett MA Key: AD, Value: Dept of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Key: UK., Value: Key: FAU, Value: Pickett, J A Key: AU, Value: Pickett JA Key: AD, Value: Dept of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Key: UK., Value: Key: FAU, Value: Field, L M Key: AU, Value: Field LM Key: AD, Value: Dept of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Key: UK., Value: Key: FAU, Value: Báo, S N Key: AU, Value: Báo SN Key: AD, Value: Instituto de Ciências Biológicas, Univ de Brasília, Campus Universitário Darcy Key: Ribeiro, Brasília, DF, Brasil., Value: Key: LA, Value: eng Key: PT, Value: Journal Article Key: DEP, Value: 20140306 Key: PL, Value: Netherlands Key: TA, Value: Neotrop Entomol Key: JT, Value: Neotropical entomology Key: JID, Value: 101189728 Key: RN, Value: 0 (Receptors, Odorant) Key: RN, Value: 0 (odorant-binding protein) Key: SB, Value: IM Key: MH, Value: Animals Key: MH, Value: Brazil Key: MH, Value: Female Key: MH, Value: Heteroptera/*chemistry Key: MH, Value: Male Key: MH, Value: Receptors, Odorant/*analysis/metabolism Key: MH, Value: Glycine max Key: OTO, Value: NOTNLM Key: OT, Value: Antennae Key: OT, Value: amphipathic proteins Key: OT, Value: chemoreception Key: OT, Value: olfaction Key: OT, Value: semiochemicals Key: OT, Value: sensillum Key: EDAT, Value: 2014/04/01 00:00 Key: MHDA, Value: 2018/01/09 06:00 Key: CRDT, Value: 2016/05/20 06:00 Key: PHST, Value: 2012/11/26 00:00 [received] Key: PHST, Value: 2013/12/02 00:00 [accepted] Key: PHST, Value: 2016/05/20 06:00 [entrez] Key: PHST, Value: 2014/04/01 00:00 [pubmed] Key: PHST, Value: 2018/01/09 06:00 [medline] Key: AID, Value: 10.1007/s13744-013-0187-4 [pii] Key: AID, Value: 10.1007/s13744-013-0187-4 [doi] Key: PST, Value: ppublish Key: SO, Value: Neotrop Entomol. 2014 Apr;43(2):106-14. doi: 10.1007/s13744-013-0187-4. Epub 2014 Key: Mar 6., Value: Key: PMID, Value: 19449976 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 20090714 Key: LR, Value: 20191210 Key: IS, Value: 1751-8849 (Print) Key: IS, Value: 1751-8849 (Linking) Key: VI, Value: 3 Key: IP, Value: 3 Key: DP, Value: 2009 May Key: TI, Value: Genetic network identification using convex programming. Key: PG, Value: 155-66 Key: LID, Value: 10.1049/iet-syb.2008.0130 [doi] Key: AB, Value: Gene regulatory networks capture interactions between genes and other cell Key: substances, resulting in various models for the fundamental biological process of, Value: Key: transcription and translation. The expression levels of the genes are typically, Value: Key: measured as mRNA concentration in micro-array experiments. In a so-called genetic, Value: Key: perturbation experiment, small perturbations are applied to equilibrium states, Value: Key: and the resulting changes in expression activity are measured. One of the most, Value: Key: important problems in systems biology is to use these data to identify the, Value: Key: interaction pattern between genes in a regulatory network, especially in a large, Value: Key: scale network. The authors develop a novel algorithm for identifying the smallest, Value: Key: genetic network that explains genetic perturbation experimental data. By, Value: Key: construction, our identification algorithm is able to incorporate and respect a, Value: Key: priori knowledge known about the network structure. A priori biological knowledge, Value: Key: is typically qualitative, encoding whether one gene affects another gene or not,, Value: Key: or whether the effect is positive or negative. The method is based on a convex, Value: Key: programming relaxation of the combinatorially hard problem of L(0) minimisation., Value: Key: The authors apply the proposed method to the identification of a subnetwork of, Value: Key: the SOS pathway in Escherichia coli, the segmentation polarity network in, Value: Key: Drosophila melanogaster, and an artificial network for measuring the performance, Value: Key: of the method., Value: Key: FAU, Value: Julius, A Key: AU, Value: Julius A Key: AD, Value: University of Pennsylvania, Department of Electrical and Systems Engineering, Key: USA. agung@seas.upenn.edu, Value: Key: FAU, Value: Zavlanos, M Key: AU, Value: Zavlanos M Key: FAU, Value: Boyd, S Key: AU, Value: Boyd S Key: FAU, Value: Pappas, G J Key: AU, Value: Pappas GJ Key: LA, Value: eng Key: PT, Value: Journal Article Key: PT, Value: Research Support, Non-U.S. Gov't Key: PT, Value: Research Support, U.S. Gov't, Non-P.H.S. Key: PL, Value: England Key: TA, Value: IET Syst Biol Key: JT, Value: IET systems biology Key: JID, Value: 101301198 Key: SB, Value: IM Key: MH, Value: Algorithms Key: MH, Value: Animals Key: MH, Value: Body Patterning/genetics Key: MH, Value: Computer Simulation Key: MH, Value: Drosophila melanogaster/genetics/metabolism Key: MH, Value: Escherichia coli/genetics/metabolism Key: MH, Value: Gene Expression Profiling Key: MH, Value: *Gene Regulatory Networks Key: MH, Value: *Models, Genetic Key: MH, Value: Oligonucleotide Array Sequence Analysis Key: MH, Value: ROC Curve Key: MH, Value: SOS Response, Genetics/genetics Key: MH, Value: Systems Biology/*methods Key: EDAT, Value: 2009/05/20 09:00 Key: MHDA, Value: 2009/07/15 09:00 Key: CRDT, Value: 2009/05/20 09:00 Key: PHST, Value: 2009/05/20 09:00 [entrez] Key: PHST, Value: 2009/05/20 09:00 [pubmed] Key: PHST, Value: 2009/07/15 09:00 [medline] Key: AID, Value: 10.1049/iet-syb.2008.0130 [doi] Key: PST, Value: ppublish Key: SO, Value: IET Syst Biol. 2009 May;3(3):155-66. doi: 10.1049/iet-syb.2008.0130. Key: PMID, Value: 7698012 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 19950504 Key: LR, Value: 20180214 Key: IS, Value: 0301-0171 (Print) Key: IS, Value: 0301-0171 (Linking) Key: VI, Value: 69 Key: IP, Value: 3-4 Key: DP, Value: 1995 Key: TI, Value: Generation and molecular cytogenetic characterization of a radiation-reduction Key: hybrid panel for human chromosome 6., Value: Key: PG, Value: 201-6 Key: AB, Value: A neoR marked chromosome-6 containing hybrid (D113JA) was used to generate a Key: panel of 15 radiation-reduced hybrid cell lines. The panel was constructed by, Value: Key: irradiating microcells isolated from D113JA at 800 or 8000 rads, providing, Value: Key: different levels of chromosome 6 retention. These hybrids have been, Value: Key: systematically analyzed using interspersed repetitive elements, previously, Value: Key: assigned markers for chromosome 6, and fluorescent in situ hybridization (FISH)., Value: Key: As expected, G418 selection has favored the retention of fragments near the, Value: Key: insertion site of the neoR gene (6q16). The panel as constituted provides an, Value: Key: important resource for regional assignment of molecular markers, especially to, Value: Key: regions on 6q., Value: Key: FAU, Value: Pappas, G J Key: AU, Value: Pappas GJ Key: AD, Value: Department of Human Genetics, University of Michigan, Ann Arbor, USA. Key: FAU, Value: Thompson, E Key: AU, Value: Thompson E Key: FAU, Value: Burgess, A Key: AU, Value: Burgess A Key: FAU, Value: Greenwood, A Key: AU, Value: Greenwood A Key: FAU, Value: Trent, J M Key: AU, Value: Trent JM Key: LA, Value: eng Key: PT, Value: Journal Article Key: PL, Value: Switzerland Key: TA, Value: Cytogenet Cell Genet Key: JT, Value: Cytogenetics and cell genetics Key: JID, Value: 0367735 Key: SB, Value: IM Key: MH, Value: Animals Key: MH, Value: Base Sequence Key: MH, Value: CHO Cells Key: MH, Value: Chromosome Mapping Key: MH, Value: *Chromosomes, Human, Pair 6 Key: MH, Value: Cricetinae Key: MH, Value: DNA Fingerprinting Key: MH, Value: Genotype Key: MH, Value: Humans Key: MH, Value: Hybrid Cells/*radiation effects Key: MH, Value: In Situ Hybridization, Fluorescence Key: MH, Value: Molecular Sequence Data Key: MH, Value: Polymerase Chain Reaction Key: EDAT, Value: 1995/01/01 00:00 Key: MHDA, Value: 1995/01/01 00:01 Key: CRDT, Value: 1995/01/01 00:00 Key: PHST, Value: 1995/01/01 00:00 [pubmed] Key: PHST, Value: 1995/01/01 00:01 [medline] Key: PHST, Value: 1995/01/01 00:00 [entrez] Key: AID, Value: 10.1159/000133963 [doi] Key: PST, Value: ppublish Key: SO, Value: Cytogenet Cell Genet. 1995;69(3-4):201-6. doi: 10.1159/000133963. Key: PMID, Value: 7774909 Key: OWN, Value: NLM Key: STAT, Value: MEDLINE Key: DCOM, Value: 19950707 Key: LR, Value: 20190904 Key: IS, Value: 0888-7543 (Print) Key: IS, Value: 0888-7543 (Linking) Key: VI, Value: 25 Key: IP, Value: 1 Key: DP, Value: 1995 Jan 1 Key: TI, Value: Regional assignment by hybrid mapping of 36 expressed sequence tags (ESTs) on Key: human chromosome 6., Value: Key: PG, Value: 124-9 Key: AB, Value: We have determined the regional chromosome assignment of 36 cDNAs from infant Key: brain libraries by assessing the concordant segregation of PCR products using a, Value: Key: human-rodent hybrid mapping panel that subdivides chromosome 6 into 15 regions., Value: Key: These mapped sequences serve as markers for the physical and expression maps of, Value: Key: chromosome 6, as well as candidate genes for various disease loci. Sequence, Value: Key: analysis has identified putative functions and motifs for some of these genes., Value: Key: FAU, Value: Pappas, G J Key: AU, Value: Pappas GJ Key: AD, Value: Department of Human Genetics, University of Michigan, Ann Arbor 48109, USA. Key: FAU, Value: Polymeropoulos, M H Key: AU, Value: Polymeropoulos MH Key: FAU, Value: Boyle, J M Key: AU, Value: Boyle JM Key: FAU, Value: Trent, J M Key: AU, Value: Trent JM Key: LA, Value: eng Key: SI, Value: GENBANK/M61959 Key: SI, Value: GENBANK/M61973 Key: SI, Value: GENBANK/M62068 Key: SI, Value: GENBANK/M62072 Key: SI, Value: GENBANK/M62134 Key: SI, Value: GENBANK/M62157 Key: SI, Value: GENBANK/M62239 Key: SI, Value: GENBANK/M62263 Key: SI, Value: GENBANK/M62284 Key: SI, Value: GENBANK/M78301 Key: SI, Value: GENBANK/M78385 Key: SI, Value: GENBANK/M78509 Key: SI, Value: GENBANK/M78612 Key: SI, Value: GENBANK/M78635 Key: SI, Value: GENBANK/M78685 Key: SI, Value: GENBANK/M78711 Key: SI, Value: GENBANK/M78872 Key: SI, Value: GENBANK/M78981 Key: SI, Value: GENBANK/M78999 Key: SI, Value: GENBANK/M79147 Key: SI, Value: GENBANK/M79183 Key: SI, Value: GENBANK/M79194 Key: SI, Value: GENBANK/M85405 Key: SI, Value: GENBANK/M85639 Key: SI, Value: GENBANK/M85670 Key: SI, Value: GENBANK/M85768 Key: SI, Value: GENBANK/M86009 Key: SI, Value: GENBANK/T03169 Key: SI, Value: GENBANK/T03171 Key: SI, Value: GENBANK/T03273 Key: PT, Value: Comparative Study Key: PT, Value: Journal Article Key: PL, Value: United States Key: TA, Value: Genomics Key: JT, Value: Genomics Key: JID, Value: 8800135 Key: RN, Value: 0 (DNA Primers) Key: RN, Value: 0 (DNA, Complementary) Key: SB, Value: IM Key: MH, Value: Animals Key: MH, Value: Base Sequence Key: MH, Value: Brain/*metabolism Key: MH, Value: Chromosome Mapping Key: MH, Value: *Chromosomes, Human, Pair 6 Key: MH, Value: Cricetinae Key: MH, Value: DNA Primers Key: MH, Value: DNA, Complementary/analysis Key: MH, Value: Gene Library Key: MH, Value: Humans Key: MH, Value: Hybrid Cells Key: MH, Value: Molecular Sequence Data Key: MH, Value: Polymerase Chain Reaction Key: MH, Value: Sequence Homology, Nucleic Acid Key: MH, Value: *Sequence Tagged Sites Key: EDAT, Value: 1995/01/01 00:00 Key: MHDA, Value: 1995/01/01 00:01 Key: CRDT, Value: 1995/01/01 00:00 Key: PHST, Value: 1995/01/01 00:00 [pubmed] Key: PHST, Value: 1995/01/01 00:01 [medline] Key: PHST, Value: 1995/01/01 00:00 [entrez] Key: AID, Value: 0888-7543(95)80117-5 [pii] Key: AID, Value: 10.1016/0888-7543(95)80117-5 [doi] Key: PST, Value: ppublish Key: SO, Value: Genomics. 1995 Jan 1;25(1):124-9. doi: 10.1016/0888-7543(95)80117-5. 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