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Article: Put3 Positively Regulates Proline Utilization in

Tebung, Walters Aji / Omran, Raha Parvizi / Fulton, Debra L / Morschhäuser, Joachim / Whiteway, Malcolm

mSphere

2017 Volume 2, Issue 6

Abstract: The zinc cluster transcription factor Put3 was initially characterized ... ...

Abstract	The zinc cluster transcription factor Put3 was initially characterized in
Language	English
Publishing date	2017-11
Publishing country	United States
Document type	Journal Article
ISSN	2379-5042
ISSN	2379-5042
DOI	10.1128/mSphere.00354-17
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Article ; Online: p38 Mitogen-Activated Protein Kinase Pathway Regulates Genes during Proliferation and Differentiation in Oligodendrocytes.

Haines, Jeffery D / Fulton, Debra L / Richard, Stephane / Almazan, Guillermina

PloS one

2015 Volume 10, Issue 12, Page(s) e0145843

Abstract: We have previously shown that p38 mitogen-activated protein kinase (p38 MAPK) is important for oligodendrocyte (OLG) differentiation and myelination. However, the precise cellular mechanisms by which p38 regulates OLG differentiation remain largely ... ...

Abstract	We have previously shown that p38 mitogen-activated protein kinase (p38 MAPK) is important for oligodendrocyte (OLG) differentiation and myelination. However, the precise cellular mechanisms by which p38 regulates OLG differentiation remain largely unknown. To determine whether p38 functions in part through transcriptional events in regulating OLG identity, we performed microarray analysis on differentiating oligodendrocyte progenitors (OLPs) treated with a p38 inhibitor. Consistent with a role in OLG differentiation, pharmacological inhibition of p38 down-regulated the transcription of genes that are involved in myelin biogenesis, transcriptional control and cell cycle. Proliferation assays showed that OLPs treated with the p38 inhibitor retained a proliferative capacity which could be induced upon application of mitogens demonstrating that after two days of p38-inhibition OLGs remained poised to continue mitosis. Together, our results suggest that the p38 pathway regulates gene transcription which can coordinate OLG differentiation. Our microarray dataset will provide a useful resource for future studies investigating the molecular mechanisms by which p38 regulates oligodendrocyte differentiation and myelination.
MeSH term(s)	Animals ; Biomarkers/metabolism ; Cell Differentiation/drug effects ; Cell Proliferation/drug effects ; Cytokinesis/drug effects ; Gene Expression Regulation/drug effects ; Humans ; Imidazoles/pharmacology ; MAP Kinase Signaling System/drug effects ; Myelin Sheath/genetics ; Oligodendroglia/cytology ; Oligodendroglia/metabolism ; Protein Kinase Inhibitors/pharmacology ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Rats ; Rats, Sprague-Dawley ; S Phase/drug effects ; Transcription, Genetic/drug effects ; p38 Mitogen-Activated Protein Kinases/antagonists & inhibitors ; p38 Mitogen-Activated Protein Kinases/metabolism
Chemical Substances	Biomarkers ; Imidazoles ; Protein Kinase Inhibitors ; RNA, Messenger ; p38 Mitogen-Activated Protein Kinases (EC 2.7.11.24) ; 2-(4-nitrophenyl)-4-(4-fluorophenyl)-5-(4-pyridinyl)-1H-imidazole (GX3Y2V80CV)
Language	English
Publishing date	2015-12-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0145843
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Article ; Online: p38 Mitogen-Activated Protein Kinase Pathway Regulates Genes during Proliferation and Differentiation in Oligodendrocytes.

Jeffery D Haines / Debra L Fulton / Stephane Richard / Guillermina Almazan

PLoS ONE, Vol 10, Iss 12, p e

2015 Volume 0145843

Abstract	We have previously shown that p38 mitogen-activated protein kinase (p38 MAPK) is important for oligodendrocyte (OLG) differentiation and myelination. However, the precise cellular mechanisms by which p38 regulates OLG differentiation remain largely unknown. To determine whether p38 functions in part through transcriptional events in regulating OLG identity, we performed microarray analysis on differentiating oligodendrocyte progenitors (OLPs) treated with a p38 inhibitor. Consistent with a role in OLG differentiation, pharmacological inhibition of p38 down-regulated the transcription of genes that are involved in myelin biogenesis, transcriptional control and cell cycle. Proliferation assays showed that OLPs treated with the p38 inhibitor retained a proliferative capacity which could be induced upon application of mitogens demonstrating that after two days of p38-inhibition OLGs remained poised to continue mitosis. Together, our results suggest that the p38 pathway regulates gene transcription which can coordinate OLG differentiation. Our microarray dataset will provide a useful resource for future studies investigating the molecular mechanisms by which p38 regulates oligodendrocyte differentiation and myelination.
Keywords	Medicine ; R ; Science ; Q
Subject code	500
Language	English
Publishing date	2015-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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Article ; Online: Preparing advanced learners for geriatric team care: A short-term curricular model that works.

Glassburn, Susan L / Westmoreland, Glenda R / Frank, Kathryn I / Fulton, Janet S / Garrison, Emilie / Roth, Sarah / Bo, Na / Tong, Yan / Litzelman, Debra K

Gerontology & geriatrics education

2020 Volume 43, Issue 1, Page(s) 102–118

Abstract: Health outcomes for complex older adults are enhanced by interprofessional collaboration. Funded by a Geriatrics Workforce Enhancement Program (GWEP), an interprofessional team of educators developed a short-term geriatrics experience, including four ... ...

Abstract	Health outcomes for complex older adults are enhanced by interprofessional collaboration. Funded by a Geriatrics Workforce Enhancement Program (GWEP), an interprofessional team of educators developed a short-term geriatrics experience, including four hours of pre-clinical education and 12-20 hours of immersion in team-based care for advanced learners in nursing (n = 70 APN), social work (n = 48 MSW), and medicine (n = 122 medical students). Content focused on five areas: medication management, dementia, depression, falls, and myths about aging. Learners completed pre/post surveys measuring knowledge of geriatrics, attitudes toward geriatric patients and team care, and post-surveys regarding perceptions of the overall clinical experience. Results showed significant improvement in knowledge and attitudes toward older adults and interprofessional (IP) team practice. Qualitative comments reflected increased empathy toward and enthusiasm for working with older adults, valuing IP teams, and a desire for geriatrics content earlier in their respective curricula.
MeSH term(s)	Aged ; Curriculum ; Geriatrics/education ; Humans ; Interprofessional Relations ; Patient Care Team ; Students, Medical ; Workforce
Language	English
Publishing date	2020-07-26
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	605726-3
ISSN	1545-3847 ; 0270-1960
ISSN (online)	1545-3847
ISSN	0270-1960
DOI	10.1080/02701960.2020.1795648
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Article ; Online: Towards resolving the transcription factor network controlling myelin gene expression.

Fulton, Debra L / Denarier, Eric / Friedman, Hana C / Wasserman, Wyeth W / Peterson, Alan C

Nucleic acids research

2011 Volume 39, Issue 18, Page(s) 7974–7991

Abstract: In the central nervous system (CNS), myelin is produced from spirally-wrapped oligodendrocyte plasma membrane and, as exemplified by the debilitating effects of inherited or acquired myelin abnormalities in diseases such as multiple sclerosis, it plays a ...

Abstract	In the central nervous system (CNS), myelin is produced from spirally-wrapped oligodendrocyte plasma membrane and, as exemplified by the debilitating effects of inherited or acquired myelin abnormalities in diseases such as multiple sclerosis, it plays a critical role in nervous system function. Myelin sheath production coincides with rapid up-regulation of numerous genes. The complexity of their subsequent expression patterns, along with recently recognized heterogeneity within the oligodendrocyte lineage, suggest that the regulatory networks controlling such genes drive multiple context-specific transcriptional programs. Conferring this nuanced level of control likely involves a large repertoire of interacting transcription factors (TFs). Here, we combined novel strategies of computational sequence analyses with in vivo functional analysis to establish a TF network model of coordinate myelin-associated gene transcription. Notably, the network model captures regulatory DNA elements and TFs known to regulate oligodendrocyte myelin gene transcription and/or oligodendrocyte development, thereby validating our approach. Further, it links to numerous TFs with previously unsuspected roles in CNS myelination and suggests collaborative relationships amongst both known and novel TFs, thus providing deeper insight into the myelin gene transcriptional network.
MeSH term(s)	Animals ; Base Sequence ; Conserved Sequence ; Enhancer Elements, Genetic ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Regulatory Networks ; Genes, Reporter ; Mice ; Myelin Sheath/genetics ; Myelin Sheath/metabolism ; Neuroglia/metabolism ; Oligodendroglia/metabolism ; Optic Nerve/metabolism ; Promoter Regions, Genetic ; Prosencephalon/metabolism ; Transcription Factors/metabolism
Chemical Substances	Transcription Factors
Language	English
Publishing date	2011-07-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkr326
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Article: TFCat: the curated catalog of mouse and human transcription factors

Fulton, Debra L / Gwenael Badis / Jared C Roach / Rob Sladek / Saravanan Sundararajan / Timothy R Hughes / Wyeth W Wasserman

Genome biology. 2009 Mar., v. 10, no. 3

2009

Abstract: Unravelling regulatory programs governed by transcription factors (TFs) is fundamental to understanding biological systems. TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the ... ...

Abstract	Unravelling regulatory programs governed by transcription factors (TFs) is fundamental to understanding biological systems. TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature. The collection, including proven and homology-based candidate TFs, is annotated within a function-based taxonomy and DNA-binding proteins are organized within a classification system. All data and user-feedback mechanisms are available at the TFCat portal http://www.tfcat.ca .
Keywords	DNA-binding proteins ; humans ; mice ; taxonomy ; transcription factors
Language	English
Dates of publication	2009-03
Size	p. 2179.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/gb-2009-10-3-r29
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Cardiovascular Health Research in the Workplace: A Workshop Report.

Calitz, Chris / Pratt, Charlotte / Pronk, Nicolaas P / Fulton, Janet E / Jinnett, Kimberly / Thorndike, Anne N / Addou, Ebyan / Arena, Ross / Brown, Alison G M / Chang, Chia-Chia / Latts, Lisa / Lerner, Debra / Majors, Michiel / Mancuso, Michelle / Mills, Drew / Sanchez, Eduardo / Goff, David

Journal of the American Heart Association

2021 Volume 10, Issue 17, Page(s) e019016

Abstract: Heart disease and stroke are the first and fifth leading causes of death in the United States, respectively. Employers have a unique opportunity to promote cardiovascular health, because >60% of US adults are employed, and most spend half of their waking ...

Abstract	Heart disease and stroke are the first and fifth leading causes of death in the United States, respectively. Employers have a unique opportunity to promote cardiovascular health, because >60% of US adults are employed, and most spend half of their waking hours at work. Despite the scope of the opportunity, <1 in 5 businesses implement evidence-based, comprehensive workplace health programs, policies, and practices. Integrated, systems-based workplace health approaches that harness data science and technology may have the potential to reach more employees and be cost-effective for employers. To evaluate the role of the workplace in promoting cardiovascular health across the lifespan, the National Heart, Lung, and Blood Institute, the National Institute for Occupational Safety and Health, and the American Heart Association convened a workshop on March 7, 2019, to share best practices, and to discuss current evidence and knowledge gaps, practical application, and dissemination of the evidence, and the need for innovation in workplace health research and practice. This report presents the broad themes discussed at the workshop and considerations for promoting worker cardiovascular health, including opportunities for future research.
MeSH term(s)	American Heart Association ; Health Promotion ; Heart Diseases/epidemiology ; Heart Diseases/prevention & control ; Humans ; Occupational Health ; Stroke/epidemiology ; Stroke/prevention & control ; United States ; Workplace
Language	English
Publishing date	2021-08-28
Publishing country	England
Document type	News ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2653953-6
ISSN	2047-9980 ; 2047-9980
ISSN (online)	2047-9980
ISSN	2047-9980
DOI	10.1161/JAHA.120.019016
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Article ; Online: oPOSSUM: integrated tools for analysis of regulatory motif over-representation.

Ho Sui, Shannan J / Fulton, Debra L / Arenillas, David J / Kwon, Andrew T / Wasserman, Wyeth W

Nucleic acids research

2007 Volume 35, Issue Web Server issue, Page(s) W245–52

Abstract: The identification of over-represented transcription factor binding sites from sets of co-expressed genes provides insights into the mechanisms of regulation for diverse biological contexts. oPOSSUM, an internet-based system for such studies of ... ...

Abstract	The identification of over-represented transcription factor binding sites from sets of co-expressed genes provides insights into the mechanisms of regulation for diverse biological contexts. oPOSSUM, an internet-based system for such studies of regulation, has been improved and expanded in this new release. New features include a worm-specific version for investigating binding sites conserved between Caenorhabditis elegans and C. briggsae, as well as a yeast-specific version for the analysis of co-expressed sets of Saccharomyces cerevisiae genes. The human and mouse applications feature improvements in ortholog mapping, sequence alignments and the delineation of multiple alternative promoters. oPOSSUM2, introduced for the analysis of over-represented combinations of motifs in human and mouse genes, has been integrated with the original oPOSSUM system. Analysis using user-defined background gene sets is now supported. The transcription factor binding site models have been updated to include new profiles from the JASPAR database. oPOSSUM is available at http://www.cisreg.ca/oPOSSUM/
MeSH term(s)	Algorithms ; Animals ; Binding Sites ; Caenorhabditis elegans/genetics ; Computational Biology/methods ; Databases, Nucleic Acid ; Gene Expression Profiling ; Gene Expression Regulation ; Humans ; Internet ; Mice ; NF-kappa B/metabolism ; Promoter Regions, Genetic ; Saccharomyces cerevisiae/genetics ; Transcription Factors/metabolism
Chemical Substances	NF-kappa B ; Transcription Factors
Language	English
Publishing date	2007-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205588-5
ISSN	1362-4962 ; 1746-8272 ; 0305-1048 ; 0261-3166
ISSN (online)	1362-4962 ; 1746-8272
ISSN	0305-1048 ; 0261-3166
DOI	10.1093/nar/gkm427
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Article ; Online: TFCat: the curated catalog of mouse and human transcription factors.

Fulton, Debra L / Sundararajan, Saravanan / Badis, Gwenael / Hughes, Timothy R / Wasserman, Wyeth W / Roach, Jared C / Sladek, Rob

Genome biology

2009 Volume 10, Issue 3, Page(s) R29

Abstract	Unravelling regulatory programs governed by transcription factors (TFs) is fundamental to understanding biological systems. TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature. The collection, including proven and homology-based candidate TFs, is annotated within a function-based taxonomy and DNA-binding proteins are organized within a classification system. All data and user-feedback mechanisms are available at the TFCat portal (http://www.tfcat.ca).
MeSH term(s)	Animals ; DNA/metabolism ; Databases, Protein ; Humans ; Mice ; Protein Binding ; Sequence Homology, Amino Acid ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Transcription Factors ; DNA (9007-49-2)
Language	English
Publishing date	2009-03-12
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/gb-2009-10-3-r29
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Article ; Online: Improving the specificity of high-throughput ortholog prediction.

Fulton, Debra L / Li, Yvonne Y / Laird, Matthew R / Horsman, Benjamin G S / Roche, Fiona M / Brinkman, Fiona S L

BMC bioinformatics

2006 Volume 7, Page(s) 270

Abstract: Background: Orthologs (genes that have diverged after a speciation event) tend to have similar function, and so their prediction has become an important component of comparative genomics and genome annotation. The gold standard phylogenetic analysis ... ...

Abstract	Background: Orthologs (genes that have diverged after a speciation event) tend to have similar function, and so their prediction has become an important component of comparative genomics and genome annotation. The gold standard phylogenetic analysis approach of comparing available organismal phylogeny to gene phylogeny is not easily automated for genome-wide analysis; therefore, ortholog prediction for large genome-scale datasets is typically performed using a reciprocal-best-BLAST-hits (RBH) approach. One problem with RBH is that it will incorrectly predict a paralog as an ortholog when incomplete genome sequences or gene loss is involved. In addition, there is an increasing interest in identifying orthologs most likely to have retained similar function. Results: To address these issues, we present here a high-throughput computational method named Ortholuge that further evaluates previously predicted orthologs (including those predicted using an RBH-based approach) - identifying which orthologs most closely reflect species divergence and may more likely have similar function. Ortholuge analyzes phylogenetic distance ratios involving two comparison species and an outgroup species, noting cases where relative gene divergence is atypical. It also identifies some cases of gene duplication after species divergence. Through simulations of incomplete genome data/gene loss, we show that the vast majority of genes falsely predicted as orthologs by an RBH-based method can be identified. Ortholuge was then used to estimate the number of false-positives (predominantly paralogs) in selected RBH-predicted ortholog datasets, identifying approximately 10% paralogs in a eukaryotic data set (mouse-rat comparison) and 5% in a bacterial data set (Pseudomonas putida - Pseudomonas syringae species comparison). Higher quality (more precise) datasets of orthologs, which we term "ssd-orthologs" (supporting-species-divergence-orthologs), were also constructed. These datasets, as well as Ortholuge software that may be used to characterize other species' datasets, are available at http://www.pathogenomics.ca/ortholuge/ (software under GNU General Public License). Conclusion: The Ortholuge method reported here appears to significantly improve the specificity (precision) of high-throughput ortholog prediction for both bacterial and eukaryotic species. This method, and its associated software, will aid those performing various comparative genomics-based analyses, such as the prediction of conserved regulatory elements upstream of orthologous genes.
MeSH term(s)	Algorithms ; Base Sequence ; Chromosome Mapping/methods ; Conserved Sequence/genetics ; Evolution, Molecular ; Genetic Variation/genetics ; Molecular Sequence Data ; Sensitivity and Specificity ; Sequence Alignment/methods ; Sequence Analysis, DNA/methods ; Sequence Homology, Nucleic Acid
Language	English
Publishing date	2006-05-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/1471-2105-7-270
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