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  • American Association for the Advancement of Science (AAAS)  (30)
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  • 1
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    Identification of functional elements and regulatory circuits by Drosophila modENCODE (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-12-24
    Description: To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉modENCODE Consortium -- Roy, Sushmita -- Ernst, Jason -- Kharchenko, Peter V -- Kheradpour, Pouya -- Negre, Nicolas -- Eaton, Matthew L -- Landolin, Jane M -- Bristow, Christopher A -- Ma, Lijia -- Lin, Michael F -- Washietl, Stefan -- Arshinoff, Bradley I -- Ay, Ferhat -- Meyer, Patrick E -- Robine, Nicolas -- Washington, Nicole L -- Di Stefano, Luisa -- Berezikov, Eugene -- Brown, Christopher D -- Candeias, Rogerio -- Carlson, Joseph W -- Carr, Adrian -- Jungreis, Irwin -- Marbach, Daniel -- Sealfon, Rachel -- Tolstorukov, Michael Y -- Will, Sebastian -- Alekseyenko, Artyom A -- Artieri, Carlo -- Booth, Benjamin W -- Brooks, Angela N -- Dai, Qi -- Davis, Carrie A -- Duff, Michael O -- Feng, Xin -- Gorchakov, Andrey A -- Gu, Tingting -- Henikoff, Jorja G -- Kapranov, Philipp -- Li, Renhua -- MacAlpine, Heather K -- Malone, John -- Minoda, Aki -- Nordman, Jared -- Okamura, Katsutomo -- Perry, Marc -- Powell, Sara K -- Riddle, Nicole C -- Sakai, Akiko -- Samsonova, Anastasia -- Sandler, Jeremy E -- Schwartz, Yuri B -- Sher, Noa -- Spokony, Rebecca -- Sturgill, David -- van Baren, Marijke -- Wan, Kenneth H -- Yang, Li -- Yu, Charles -- Feingold, Elise -- Good, Peter -- Guyer, Mark -- Lowdon, Rebecca -- Ahmad, Kami -- Andrews, Justen -- Berger, Bonnie -- Brenner, Steven E -- Brent, Michael R -- Cherbas, Lucy -- Elgin, Sarah C R -- Gingeras, Thomas R -- Grossman, Robert -- Hoskins, Roger A -- Kaufman, Thomas C -- Kent, William -- Kuroda, Mitzi I -- Orr-Weaver, Terry -- Perrimon, Norbert -- Pirrotta, Vincenzo -- Posakony, James W -- Ren, Bing -- Russell, Steven -- Cherbas, Peter -- Graveley, Brenton R -- Lewis, Suzanna -- Micklem, Gos -- Oliver, Brian -- Park, Peter J -- Celniker, Susan E -- Henikoff, Steven -- Karpen, Gary H -- Lai, Eric C -- MacAlpine, David M -- Stein, Lincoln D -- White, Kevin P -- Kellis, Manolis -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01HG004037/HG/NHGRI NIH HHS/ -- RC2HG005639/HG/NHGRI NIH HHS/ -- U01 HG004258/HG/NHGRI NIH HHS/ -- U01 HG004271/HG/NHGRI NIH HHS/ -- U01 HG004279/HG/NHGRI NIH HHS/ -- U01HG004258/HG/NHGRI NIH HHS/ -- U01HG004261/HG/NHGRI NIH HHS/ -- U01HG004264/HG/NHGRI NIH HHS/ -- U01HG004271/HG/NHGRI NIH HHS/ -- U01HG004274/HG/NHGRI NIH HHS/ -- U01HG004279/HG/NHGRI NIH HHS/ -- U41HG004269/HG/NHGRI NIH HHS/ -- ZIA DK015600-14/Intramural NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21177974" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; *Chromatin/genetics/metabolism ; Computational Biology/methods ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/*genetics/growth & development/metabolism ; Epigenesis, Genetic ; Gene Expression Regulation ; *Gene Regulatory Networks ; Genes, Insect ; *Genome, Insect ; Genomics/methods ; Histones/metabolism ; *Molecular Sequence Annotation ; Nucleosomes/genetics/metabolism ; Promoter Regions, Genetic ; RNA, Small Untranslated/genetics/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Dysregulated humoral immunity to nontyphoidal Salmonella in HIV-infected African adults (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-04-24
    Description: Nontyphoidal Salmonellae are a major cause of life-threatening bacteremia among HIV-infected individuals. Although cell-mediated immunity controls intracellular infection, antibodies protect against Salmonella bacteremia. We report that high-titer antibodies specific for Salmonella lipopolysaccharide (LPS) are associated with a lack of Salmonella-killing in HIV-infected African adults. Killing was restored by genetically shortening LPS from the target Salmonella or removing LPS-specific antibodies from serum. Complement-mediated killing of Salmonella by healthy serum is shown to be induced specifically by antibodies against outer membrane proteins. This killing is lost when excess antibody against Salmonella LPS is added. Thus, our study indicates that impaired immunity against nontyphoidal Salmonella bacteremia in HIV infection results from excess inhibitory antibodies against Salmonella LPS, whereas serum killing of Salmonella is induced by antibodies against outer membrane proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3772309/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3772309/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉MacLennan, Calman A -- Gilchrist, James J -- Gordon, Melita A -- Cunningham, Adam F -- Cobbold, Mark -- Goodall, Margaret -- Kingsley, Robert A -- van Oosterhout, Joep J G -- Msefula, Chisomo L -- Mandala, Wilson L -- Leyton, Denisse L -- Marshall, Jennifer L -- Gondwe, Esther N -- Bobat, Saeeda -- Lopez-Macias, Constantino -- Doffinger, Rainer -- Henderson, Ian R -- Zijlstra, Eduard E -- Dougan, Gordon -- Drayson, Mark T -- MacLennan, Ian C M -- Molyneux, Malcolm E -- 067321/Wellcome Trust/United Kingdom -- BB/F022778/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0701275/Medical Research Council/United Kingdom -- G108/574/Medical Research Council/United Kingdom -- G8402371/Medical Research Council/United Kingdom -- G9818340/Medical Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2010 Apr 23;328(5977):508-12. doi: 10.1126/science.1180346.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Centre for Immune Regulation and Clinical Immunology Service, Institute of Biomedical Research, School of Immunity and Infection, University of Birmingham, Birmingham, UK. c.maclennan@bham.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20413503" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS-Related Opportunistic Infections/immunology ; Adult ; Animals ; Antibodies, Bacterial/blood/*immunology ; Antibodies, Blocking/blood/*immunology ; Bacteremia/immunology ; Bacterial Outer Membrane Proteins/*immunology ; Complement Activation ; Disease Susceptibility ; HIV Infections/complications/*immunology ; Humans ; Immunoglobulin G/blood/immunology ; Lipopolysaccharides/blood/*immunology ; Malawi ; Mice ; Mutation ; O Antigens/*immunology ; Salmonella Infections/*immunology ; Salmonella typhimurium/genetics/*immunology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    The genetic landscape of a cell (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-01-23
    Description: A genome-scale genetic interaction map was constructed by examining 5.4 million gene-gene pairs for synthetic genetic interactions, generating quantitative genetic interaction profiles for approximately 75% of all genes in the budding yeast, Saccharomyces cerevisiae. A network based on genetic interaction profiles reveals a functional map of the cell in which genes of similar biological processes cluster together in coherent subsets, and highly correlated profiles delineate specific pathways to define gene function. The global network identifies functional cross-connections between all bioprocesses, mapping a cellular wiring diagram of pleiotropy. Genetic interaction degree correlated with a number of different gene attributes, which may be informative about genetic network hubs in other organisms. We also demonstrate that extensive and unbiased mapping of the genetic landscape provides a key for interpretation of chemical-genetic interactions and drug target identification.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Costanzo, Michael -- Baryshnikova, Anastasia -- Bellay, Jeremy -- Kim, Yungil -- Spear, Eric D -- Sevier, Carolyn S -- Ding, Huiming -- Koh, Judice L Y -- Toufighi, Kiana -- Mostafavi, Sara -- Prinz, Jeany -- St Onge, Robert P -- VanderSluis, Benjamin -- Makhnevych, Taras -- Vizeacoumar, Franco J -- Alizadeh, Solmaz -- Bahr, Sondra -- Brost, Renee L -- Chen, Yiqun -- Cokol, Murat -- Deshpande, Raamesh -- Li, Zhijian -- Lin, Zhen-Yuan -- Liang, Wendy -- Marback, Michaela -- Paw, Jadine -- San Luis, Bryan-Joseph -- Shuteriqi, Ermira -- Tong, Amy Hin Yan -- van Dyk, Nydia -- Wallace, Iain M -- Whitney, Joseph A -- Weirauch, Matthew T -- Zhong, Guoqing -- Zhu, Hongwei -- Houry, Walid A -- Brudno, Michael -- Ragibizadeh, Sasan -- Papp, Balazs -- Pal, Csaba -- Roth, Frederick P -- Giaever, Guri -- Nislow, Corey -- Troyanskaya, Olga G -- Bussey, Howard -- Bader, Gary D -- Gingras, Anne-Claude -- Morris, Quaid D -- Kim, Philip M -- Kaiser, Chris A -- Myers, Chad L -- Andrews, Brenda J -- Boone, Charles -- 084314/Wellcome Trust/United Kingdom -- GSP-41567/Canadian Institutes of Health Research/Canada -- R01 HG003224/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2010 Jan 22;327(5964):425-31. doi: 10.1126/science.1180823.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20093466" target="_blank"〉PubMed〈/a〉
    Keywords: Computational Biology ; Gene Duplication ; Gene Expression Regulation, Fungal ; *Gene Regulatory Networks ; Genes, Fungal ; Genetic Fitness ; *Genome, Fungal ; Metabolic Networks and Pathways ; Mutation ; Protein Interaction Mapping ; Saccharomyces cerevisiae/*genetics/*metabolism/physiology ; Saccharomyces cerevisiae Proteins/genetics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Analysis of genetic inheritance in a family quartet by whole-genome sequencing (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-03-12
    Description: We analyzed the whole-genome sequences of a family of four, consisting of two siblings and their parents. Family-based sequencing allowed us to delineate recombination sites precisely, identify 70% of the sequencing errors (resulting in 〉 99.999% accuracy), and identify very rare single-nucleotide polymorphisms. We also directly estimated a human intergeneration mutation rate of approximately 1.1 x 10(-8) per position per haploid genome. Both offspring in this family have two recessive disorders: Miller syndrome, for which the gene was concurrently identified, and primary ciliary dyskinesia, for which causative genes have been previously identified. Family-based genome analysis enabled us to narrow the candidate genes for both of these Mendelian disorders to only four. Our results demonstrate the value of complete genome sequencing in families.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037280/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037280/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roach, Jared C -- Glusman, Gustavo -- Smit, Arian F A -- Huff, Chad D -- Hubley, Robert -- Shannon, Paul T -- Rowen, Lee -- Pant, Krishna P -- Goodman, Nathan -- Bamshad, Michael -- Shendure, Jay -- Drmanac, Radoje -- Jorde, Lynn B -- Hood, Leroy -- Galas, David J -- GM076547/GM/NIGMS NIH HHS/ -- P50 GM076547/GM/NIGMS NIH HHS/ -- P50 GM076547-05/GM/NIGMS NIH HHS/ -- R01 HG002939/HG/NHGRI NIH HHS/ -- R01 HG002939-08/HG/NHGRI NIH HHS/ -- R01GM081083/GM/NIGMS NIH HHS/ -- R01HD048895/HD/NICHD NIH HHS/ -- R01HL094976/HL/NHLBI NIH HHS/ -- RC2HG005608/HG/NHGRI NIH HHS/ -- RZ1HG004749/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2010 Apr 30;328(5978):636-9. doi: 10.1126/science.1186802. Epub 2010 Mar 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Systems Biology, Seattle, WA 98103, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20220176" target="_blank"〉PubMed〈/a〉
    Keywords: Abnormalities, Multiple/*genetics ; Algorithms ; Alleles ; Axonemal Dyneins/genetics ; Ciliary Motility Disorders/*genetics ; Crossing Over, Genetic ; Female ; Genes, Dominant ; Genes, Recessive ; Genetic Association Studies ; *Genome, Human ; Humans ; *Inheritance Patterns ; Limb Deformities, Congenital/genetics ; Male ; Mandibulofacial Dysostosis/genetics ; Mutation ; *Nuclear Family ; Oxidoreductases Acting on CH-CH Group Donors/genetics ; Pedigree ; Polymorphism, Single Nucleotide ; *Sequence Analysis, DNA ; Syndrome
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Plectasin, a fungal defensin, targets the bacterial cell wall precursor Lipid II (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-29
    Description: Host defense peptides such as defensins are components of innate immunity and have retained antibiotic activity throughout evolution. Their activity is thought to be due to amphipathic structures, which enable binding and disruption of microbial cytoplasmic membranes. Contrary to this, we show that plectasin, a fungal defensin, acts by directly binding the bacterial cell-wall precursor Lipid II. A wide range of genetic and biochemical approaches identify cell-wall biosynthesis as the pathway targeted by plectasin. In vitro assays for cell-wall synthesis identified Lipid II as the specific cellular target. Consistently, binding studies confirmed the formation of an equimolar stoichiometric complex between Lipid II and plectasin. Furthermore, key residues in plectasin involved in complex formation were identified using nuclear magnetic resonance spectroscopy and computational modeling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schneider, Tanja -- Kruse, Thomas -- Wimmer, Reinhard -- Wiedemann, Imke -- Sass, Vera -- Pag, Ulrike -- Jansen, Andrea -- Nielsen, Allan K -- Mygind, Per H -- Raventos, Dorotea S -- Neve, Soren -- Ravn, Birthe -- Bonvin, Alexandre M J J -- De Maria, Leonardo -- Andersen, Anders S -- Gammelgaard, Lora K -- Sahl, Hans-Georg -- Kristensen, Hans-Henrik -- New York, N.Y. -- Science. 2010 May 28;328(5982):1168-72. doi: 10.1126/science.1185723.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pharmaceutical Microbiology Section, Institute for Medical Microbiology, Immunology, and Parasitology, University of Bonn, D-53115 Bonn, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20508130" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/pharmacology ; Ascomycota/chemistry ; Bacillus subtilis/drug effects/growth & development/*metabolism/ultrastructure ; Binding Sites ; Cell Membrane/metabolism ; Cell Wall/*metabolism ; Computer Simulation ; Defensins/*metabolism/pharmacology ; Fungal Proteins/*metabolism/pharmacology ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Oligonucleotide Array Sequence Analysis ; Peptides/*metabolism/pharmacology ; Protein Conformation ; Staphylococcus/drug effects/growth & development/*metabolism/ultrastructure ; Uridine Diphosphate N-Acetylmuramic Acid/*analogs & derivatives/metabolism ; Vancomycin/pharmacology
    Print ISSN: 0036-8075
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  • 6
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    Doc2b is a high-affinity Ca2+ sensor for spontaneous neurotransmitter release (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-02-13
    Description: Synaptic vesicle fusion in brain synapses occurs in phases that are either tightly coupled to action potentials (synchronous), immediately following action potentials (asynchronous), or as stochastic events in the absence of action potentials (spontaneous). Synaptotagmin-1, -2, and -9 are vesicle-associated Ca2+ sensors for synchronous release. Here we found that double C2 domain (Doc2) proteins act as Ca2+ sensors to trigger spontaneous release. Although Doc2 proteins are cytosolic, they function analogously to synaptotagmin-1 but with a higher Ca2+ sensitivity. Doc2 proteins bound to N-ethylmaleimide-sensitive factor attachment receptor (SNARE) complexes in competition with synaptotagmin-1. Thus, different classes of multiple C2 domain-containing molecules trigger synchronous versus spontaneous fusion, which suggests a general mechanism for synaptic vesicle fusion triggered by the combined actions of SNAREs and multiple C2 domain-containing proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846320/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846320/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Groffen, Alexander J -- Martens, Sascha -- Diez Arazola, Rocio -- Cornelisse, L Niels -- Lozovaya, Natalia -- de Jong, Arthur P H -- Goriounova, Natalia A -- Habets, Ron L P -- Takai, Yoshimi -- Borst, J Gerard -- Brose, Nils -- McMahon, Harvey T -- Verhage, Matthijs -- MC_U105178795/Medical Research Council/United Kingdom -- U.1051.02.007(78795)/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2010 Mar 26;327(5973):1614-8. doi: 10.1126/science.1183765. Epub 2010 Feb 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Functional Genomics, CNCR, Neuroscience Campus Amsterdam, VU University and VU Medical Center, Amsterdam, 1081 HV, Netherlands. sander.groffen@cncr.vu.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20150444" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials ; Animals ; Binding Sites ; Calcium/*metabolism ; Calcium-Binding Proteins/chemistry/genetics/*metabolism ; Cells, Cultured ; Excitatory Postsynaptic Potentials ; Hippocampus/cytology ; Inhibitory Postsynaptic Potentials ; Membrane Fusion ; Mice ; Mice, Knockout ; Mutant Proteins/genetics/metabolism ; Nerve Tissue Proteins/chemistry/genetics/*metabolism ; Neurons/physiology ; Neurotransmitter Agents/*metabolism ; Patch-Clamp Techniques ; Protein Structure, Tertiary ; Purkinje Cells/physiology ; Rats ; SNARE Proteins/metabolism ; *Synaptic Transmission ; Synaptic Vesicles/*physiology ; Synaptotagmin I/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Heritable individual-specific and allele-specific chromatin signatures in humans (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-03-20
    Description: The extent to which variation in chromatin structure and transcription factor binding may influence gene expression, and thus underlie or contribute to variation in phenotype, is unknown. To address this question, we cataloged both individual-to-individual variation and differences between homologous chromosomes within the same individual (allele-specific variation) in chromatin structure and transcription factor binding in lymphoblastoid cells derived from individuals of geographically diverse ancestry. Ten percent of active chromatin sites were individual-specific; a similar proportion were allele-specific. Both individual-specific and allele-specific sites were commonly transmitted from parent to child, which suggests that they are heritable features of the human genome. Our study shows that heritable chromatin status and transcription factor binding differ as a result of genetic variation and may underlie phenotypic variation in humans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929018/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929018/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McDaniell, Ryan -- Lee, Bum-Kyu -- Song, Lingyun -- Liu, Zheng -- Boyle, Alan P -- Erdos, Michael R -- Scott, Laura J -- Morken, Mario A -- Kucera, Katerina S -- Battenhouse, Anna -- Keefe, Damian -- Collins, Francis S -- Willard, Huntington F -- Lieb, Jason D -- Furey, Terrence S -- Crawford, Gregory E -- Iyer, Vishwanath R -- Birney, Ewan -- U54 HG004563/HG/NHGRI NIH HHS/ -- U54 HG004563-03/HG/NHGRI NIH HHS/ -- Z01 HG000024/HG/NHGRI NIH HHS/ -- Z01 HG000024-13/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Apr 9;328(5975):235-9. doi: 10.1126/science.1184655. Epub 2010 Mar 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20299549" target="_blank"〉PubMed〈/a〉
    Keywords: African Continental Ancestry Group ; *Alleles ; Binding Sites ; Cell Line ; Chromatin/chemistry/*genetics/*metabolism ; Chromatin Immunoprecipitation ; Chromosomes, Human/genetics/metabolism ; Chromosomes, Human, X/genetics/metabolism ; Deoxyribonuclease I/metabolism ; European Continental Ancestry Group ; Female ; *Gene Expression Regulation ; *Genetic Variation ; Humans ; Male ; Nuclear Family ; Polymorphism, Single Nucleotide ; Protein Binding ; Regulatory Elements, Transcriptional ; Repressor Proteins/*metabolism ; Sequence Analysis, DNA ; Transcription Factors/*metabolism ; X Chromosome Inactivation
    Print ISSN: 0036-8075
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  • 8
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    Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-02-20
    Description: Lysine acetylation regulates many eukaryotic cellular processes, but its function in prokaryotes is largely unknown. We demonstrated that central metabolism enzymes in Salmonella were acetylated extensively and differentially in response to different carbon sources, concomitantly with changes in cell growth and metabolic flux. The relative activities of key enzymes controlling the direction of glycolysis versus gluconeogenesis and the branching between citrate cycle and glyoxylate bypass were all regulated by acetylation. This modulation is mainly controlled by a pair of lysine acetyltransferase and deacetylase, whose expressions are coordinated with growth status. Reversible acetylation of metabolic enzymes ensure that cells respond environmental changes via promptly sensing cellular energy status and flexibly altering reaction rates or directions. It represents a metabolic regulatory mechanism conserved from bacteria to mammals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183141/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183141/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Qijun -- Zhang, Yakun -- Yang, Chen -- Xiong, Hui -- Lin, Yan -- Yao, Jun -- Li, Hong -- Xie, Lu -- Zhao, Wei -- Yao, Yufeng -- Ning, Zhi-Bin -- Zeng, Rong -- Xiong, Yue -- Guan, Kun-Liang -- Zhao, Shimin -- Zhao, Guo-Ping -- R01 CA068377/CA/NCI NIH HHS/ -- R01 CA163834/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2010 Feb 19;327(5968):1004-7. doi: 10.1126/science.1179687.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20167787" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Acetyltransferases/chemistry/genetics/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*metabolism ; Citric Acid/*metabolism ; Energy Metabolism ; Enzymes/*metabolism ; Gene Expression Regulation, Bacterial ; *Gluconeogenesis ; Glucose/*metabolism ; Glyceraldehyde-3-Phosphate Dehydrogenases/metabolism ; *Glycolysis ; Group III Histone Deacetylases/genetics/metabolism ; Isocitrate Lyase/metabolism ; Lysine/metabolism ; Metabolic Networks and Pathways ; Multienzyme Complexes/metabolism ; Mutation ; Protein Processing, Post-Translational ; Protein-Serine-Threonine Kinases/metabolism ; Recombinant Proteins/metabolism ; Salmonella typhimurium/enzymology/genetics/growth & development/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Peptidomimetic antibiotics target outer-membrane biogenesis in Pseudomonas aeruginosa (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-02-20
    Description: Antibiotics with new mechanisms of action are urgently required to combat the growing health threat posed by resistant pathogenic microorganisms. We synthesized a family of peptidomimetic antibiotics based on the antimicrobial peptide protegrin I. Several rounds of optimization gave a lead compound that was active in the nanomolar range against Gram-negative Pseudomonas spp., but was largely inactive against other Gram-negative and Gram-positive bacteria. Biochemical and genetic studies showed that the peptidomimetics had a non-membrane-lytic mechanism of action and identified a homolog of the beta-barrel protein LptD (Imp/OstA), which functions in outer-membrane biogenesis, as a cellular target. The peptidomimetic showed potent antimicrobial activity in a mouse septicemia infection model. Drug-resistant strains of Pseudomonas are a serious health problem, so this family of antibiotics may have important therapeutic applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Srinivas, Nityakalyani -- Jetter, Peter -- Ueberbacher, Bernhard J -- Werneburg, Martina -- Zerbe, Katja -- Steinmann, Jessica -- Van der Meijden, Benjamin -- Bernardini, Francesca -- Lederer, Alexander -- Dias, Ricardo L A -- Misson, Pauline E -- Henze, Heiko -- Zumbrunn, Jurg -- Gombert, Frank O -- Obrecht, Daniel -- Hunziker, Peter -- Schauer, Stefan -- Ziegler, Urs -- Kach, Andres -- Eberl, Leo -- Riedel, Kathrin -- DeMarco, Steven J -- Robinson, John A -- New York, N.Y. -- Science. 2010 Feb 19;327(5968):1010-3. doi: 10.1126/science.1182749.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20167788" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anti-Bacterial Agents/chemical synthesis/metabolism/*pharmacology ; Antimicrobial Cationic Peptides/chemistry ; Bacterial Outer Membrane Proteins/chemistry/genetics/*metabolism ; Cell Membrane/*metabolism ; Drug Design ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Lipopolysaccharides/metabolism ; Mice ; Microbial Sensitivity Tests ; Molecular Mimicry ; Mutation ; Peptide Library ; Peptides/chemical synthesis/chemistry/metabolism/*pharmacology ; Protein Structure, Tertiary ; Pseudomonas Infections/drug therapy/microbiology ; Pseudomonas aeruginosa/*drug effects/growth & ; development/*metabolism/ultrastructure ; Sepsis/drug therapy/microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Selection at linked sites shapes heritable phenotypic variation in C. elegans (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-10-16
    Description: Mutation generates the heritable variation that genetic drift and natural selection shape. In classical quantitative genetic models, drift is a function of the effective population size and acts uniformly across traits, whereas mutation and selection act trait-specifically. We identified thousands of quantitative trait loci (QTLs) influencing transcript abundance traits in a cross of two Caenorhabditis elegans strains; although trait-specific mutation and selection explained some of the observed pattern of QTL distribution, the pattern was better explained by trait-independent variation in the intensity of selection on linked sites. Our results suggest that traits in C. elegans exhibit different levels of variation less because of their own attributes than because of differences in the effective population sizes of the genomic regions harboring their underlying loci.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3138179/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3138179/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rockman, Matthew V -- Skrovanek, Sonja S -- Kruglyak, Leonid -- P50 GM071508/GM/NIGMS NIH HHS/ -- P50 GM071508-01/GM/NIGMS NIH HHS/ -- R01 GM089972/GM/NIGMS NIH HHS/ -- R01 GM089972-02/GM/NIGMS NIH HHS/ -- R01 HG004321/HG/NHGRI NIH HHS/ -- R01 HG004321-01/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Oct 15;330(6002):372-6. doi: 10.1126/science.1194208.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Center for Genomics and Systems Biology, New York University, 100 Washington Square East, New York, NY 10003, USA. mrockman@nyu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20947766" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Caenorhabditis elegans/*genetics/physiology ; Chromosome Mapping ; Chromosomes/*genetics ; Crosses, Genetic ; Evolution, Molecular ; Gene Expression ; Genes, Helminth ; *Genetic Variation ; Logistic Models ; Models, Genetic ; Mutation ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Polymorphism, Single Nucleotide ; Population Density ; *Quantitative Trait Loci ; *Quantitative Trait, Heritable ; Recombination, Genetic ; *Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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