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  • 1
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    Live imaging RNAi screen reveals genes essential for meiosis in mammalian oocytes (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-07-07
    Description: During fertilization, an egg and a sperm fuse to form a new embryo. Eggs develop from oocytes in a process called meiosis. Meiosis in human oocytes is highly error-prone, and defective eggs are the leading cause of pregnancy loss and several genetic disorders such as Down's syndrome. Which genes safeguard accurate progression through meiosis is largely unclear. Here we develop high-content phenotypic screening methods for the systematic identification of mammalian meiotic genes. We targeted 774 genes by RNA interference within follicle-enclosed mouse oocytes to block protein expression from an early stage of oocyte development onwards. We then analysed the function of several genes simultaneously by high-resolution imaging of chromosomes and microtubules in live oocytes and scored each oocyte quantitatively for 50 phenotypes, generating a comprehensive resource of meiotic gene function. The screen generated an unprecedented annotated data set of meiotic progression in 2,241 mammalian oocytes, which allowed us to analyse systematically which defects are linked to abnormal chromosome segregation during meiosis, identifying progression into anaphase with misaligned chromosomes as well as defects in spindle organization as risk factors. This study demonstrates how high-content screens can be performed in oocytes, and allows systematic studies of meiosis in mammals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538867/" 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/PMC4538867/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pfender, Sybille -- Kuznetsov, Vitaliy -- Pasternak, Michal -- Tischer, Thomas -- Santhanam, Balaji -- Schuh, Melina -- 337415/European Research Council/International -- MC_U105185859/Medical Research Council/United Kingdom -- MC_U105192711/Medical Research Council/United Kingdom -- England -- Nature. 2015 Aug 13;524(7564):239-42. doi: 10.1038/nature14568. Epub 2015 Jul 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26147080" target="_blank"〉PubMed〈/a〉
    Keywords: Anaphase/genetics ; Aneuploidy ; Animals ; Chromosome Segregation/genetics ; Chromosomes/genetics/metabolism ; Dual-Specificity Phosphatases/genetics ; Female ; Genomic Instability/genetics ; Male ; Meiosis/*genetics ; Mice ; Microtubule-Associated Proteins/genetics ; Microtubules/genetics/metabolism ; Oocytes/*cytology/*metabolism ; Ovarian Follicle/cytology ; Phenotype ; Protein Biosynthesis ; Protein-Serine-Threonine Kinases/genetics ; *RNA Interference ; Spindle Apparatus/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Independently evolved virulence effectors converge onto hubs in a plant immune system network (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-07-30
    Description: Plants generate effective responses to infection by recognizing both conserved and variable pathogen-encoded molecules. Pathogens deploy virulence effector proteins into host cells, where they interact physically with host proteins to modulate defense. We generated an interaction network of plant-pathogen effectors from two pathogens spanning the eukaryote-eubacteria divergence, three classes of Arabidopsis immune system proteins, and ~8000 other Arabidopsis proteins. We noted convergence of effectors onto highly interconnected host proteins and indirect, rather than direct, connections between effectors and plant immune receptors. We demonstrated plant immune system functions for 15 of 17 tested host proteins that interact with effectors from both pathogens. Thus, pathogens from different kingdoms deploy independently evolved virulence proteins that interact with a limited set of highly connected cellular hubs to facilitate their diverse life-cycle strategies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170753/" 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/PMC3170753/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mukhtar, M Shahid -- Carvunis, Anne-Ruxandra -- Dreze, Matija -- Epple, Petra -- Steinbrenner, Jens -- Moore, Jonathan -- Tasan, Murat -- Galli, Mary -- Hao, Tong -- Nishimura, Marc T -- Pevzner, Samuel J -- Donovan, Susan E -- Ghamsari, Lila -- Santhanam, Balaji -- Romero, Viviana -- Poulin, Matthew M -- Gebreab, Fana -- Gutierrez, Bryan J -- Tam, Stanley -- Monachello, Dario -- Boxem, Mike -- Harbort, Christopher J -- McDonald, Nathan -- Gai, Lantian -- Chen, Huaming -- He, Yijian -- European Union Effectoromics Consortium -- Vandenhaute, Jean -- Roth, Frederick P -- Hill, David E -- Ecker, Joseph R -- Vidal, Marc -- Beynon, Jim -- Braun, Pascal -- Dangl, Jeffery L -- BB/E024815/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G015066/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- E024815/Biotechnology and Biological Sciences Research Council/United Kingdom -- F005806/Biotechnology and Biological Sciences Research Council/United Kingdom -- G015066/Biotechnology and Biological Sciences Research Council/United Kingdom -- GM-066025/GM/NIGMS NIH HHS/ -- P50 HG004233/HG/NHGRI NIH HHS/ -- P50 HG004233-04/HG/NHGRI NIH HHS/ -- P50-HG004233/HG/NHGRI NIH HHS/ -- R01 GM066025/GM/NIGMS NIH HHS/ -- R01 GM066025-07/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Jul 29;333(6042):596-601. doi: 10.1126/science.1203659.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21798943" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics/*immunology/*metabolism/microbiology ; Bacterial Proteins/metabolism ; Evolution, Molecular ; Genes, Plant ; *Host-Pathogen Interactions ; Immunity, Innate ; Oomycetes/pathogenicity ; Plant Diseases/*immunology ; *Plant Immunity ; Protein Interaction Mapping ; Pseudomonas syringae/pathogenicity ; Receptors, Immunologic/*metabolism ; Virulence Factors/*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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  • 3
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    Proto-genes and de novo gene birth (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-06-23
    Description: Novel protein-coding genes can arise either through re-organization of pre-existing genes or de novo. Processes involving re-organization of pre-existing genes, notably after gene duplication, have been extensively described. In contrast, de novo gene birth remains poorly understood, mainly because translation of sequences devoid of genes, or 'non-genic' sequences, is expected to produce insignificant polypeptides rather than proteins with specific biological functions. Here we formalize an evolutionary model according to which functional genes evolve de novo through transitory proto-genes generated by widespread translational activity in non-genic sequences. Testing this model at the genome scale in Saccharomyces cerevisiae, we detect translation of hundreds of short species-specific open reading frames (ORFs) located in non-genic sequences. These translation events seem to provide adaptive potential, as suggested by their differential regulation upon stress and by signatures of retention by natural selection. In line with our model, we establish that S. cerevisiae ORFs can be placed within an evolutionary continuum ranging from non-genic sequences to genes. We identify ~1,900 candidate proto-genes among S. cerevisiae ORFs and find that de novo gene birth from such a reservoir may be more prevalent than sporadic gene duplication. Our work illustrates that evolution exploits seemingly dispensable sequences to generate adaptive functional innovation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3401362/" 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/PMC3401362/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carvunis, Anne-Ruxandra -- Rolland, Thomas -- Wapinski, Ilan -- Calderwood, Michael A -- Yildirim, Muhammed A -- Simonis, Nicolas -- Charloteaux, Benoit -- Hidalgo, Cesar A -- Barbette, Justin -- Santhanam, Balaji -- Brar, Gloria A -- Weissman, Jonathan S -- Regev, Aviv -- Thierry-Mieg, Nicolas -- Cusick, Michael E -- Vidal, Marc -- R01 HG006061/HG/NHGRI NIH HHS/ -- R01-HG006061/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Jul 19;487(7407):370-4. doi: 10.1038/nature11184.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22722833" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Conserved Sequence ; *Evolution, Molecular ; Genes, Fungal/*genetics ; Genetic Variation ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Protein Biosynthesis ; Saccharomyces/classification/*genetics ; Saccharomyces cerevisiae/classification/genetics ; Sequence Alignment
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Nucleocytoplasmic shuttling of a GATA transcription factor functions as a development timer (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-03-22
    Description: Biological oscillations are observed at many levels of cellular organization. In the social amoeba Dictyostelium discoideum, starvation-triggered multicellular development is organized by periodic cyclic adenosine 3',5'-monophosphate (cAMP) waves, which provide both chemoattractant gradients and developmental signals. We report that GtaC, a GATA transcription factor, exhibits rapid nucleocytoplasmic shuttling in response to cAMP waves. This behavior requires coordinated action of a nuclear localization signal and reversible G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptor-mediated phosphorylation. Although both are required for developmental gene expression, receptor occupancy promotes nuclear exit of GtaC, which leads to a transient burst of transcription at each cAMP cycle. We demonstrate that this biological circuit filters out high-frequency signals and counts those admitted, thereby enabling cells to modulate gene expression according to the dynamic pattern of the external stimuli.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4061987/" 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/PMC4061987/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cai, Huaqing -- Katoh-Kurasawa, Mariko -- Muramoto, Tetsuya -- Santhanam, Balaji -- Long, Yu -- Li, Lei -- Ueda, Masahiro -- Iglesias, Pablo A -- Shaulsky, Gad -- Devreotes, Peter N -- GM 28007/GM/NIGMS NIH HHS/ -- GM 34933/GM/NIGMS NIH HHS/ -- HD 039691/HD/NICHD NIH HHS/ -- P01 HD039691/HD/NICHD NIH HHS/ -- R01 GM028007/GM/NIGMS NIH HHS/ -- R01 GM034933/GM/NIGMS NIH HHS/ -- R37 GM028007/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Mar 21;343(6177):1249531. doi: 10.1126/science.1249531.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24653039" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Cell Nucleus/*metabolism ; Cyclic AMP/metabolism/pharmacology ; Cytoplasm/*metabolism ; Dictyostelium/growth & development/*metabolism ; GATA Transcription Factors/chemistry/genetics/*metabolism ; Gene Expression Regulation ; Heterotrimeric GTP-Binding Proteins/metabolism ; Nuclear Localization Signals ; Phosphorylation ; Protozoan Proteins/chemistry/genetics/*metabolism ; Receptors, G-Protein-Coupled/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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  • 5
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    Architecture of human Rag GTPase heterodimers and their complex with mTORC1 (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉The Rag guanosine triphosphatases (GTPases) recruit the master kinase mTORC1 to lysosomes to regulate cell growth and proliferation in response to amino acid availability. The nucleotide state of Rag heterodimers is critical for their association with mTORC1. Our cryo–electron microscopy structure of RagA/RagC in complex with mTORC1 shows the details of RagA/RagC binding to the RAPTOR subunit of mTORC1 and explains why only the RagA〈sub〉GTP〈/sub〉/RagC〈sub〉GDP〈/sub〉 nucleotide state binds mTORC1. Previous kinetic studies suggested that GTP binding to one Rag locks the heterodimer to prevent GTP binding to the other. Our crystal structures and dynamics of RagA/RagC show the mechanism for this locking and explain how oncogenic hotspot mutations disrupt this process. In contrast to allosteric activation by RHEB, Rag heterodimer binding does not change mTORC1 conformation and activates mTORC1 by targeting it to lysosomes.〈/p〉
    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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  • 6
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    Influence of high gas production during thermophilic anaerobic digestion in pilot-scale and lab-scale reactors on survival of the thermotolerant pathogens Clostridium perfringens and Campylobacter jejuni in piggery wastewater (2009)
    Elsevier
    Details
    Publication Date: 2009-07-01
    Print ISSN: 0043-1354
    Electronic ISSN: 1879-2448
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by Elsevier
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  • 7
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    Nonplant/nonfungus eukaryotic terpene synthases [Biochemistry] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-10-26
    Description: Terpenes are structurally diverse natural products involved in many ecological interactions. The pivotal enzymes for terpene biosynthesis, terpene synthases (TPSs), had been described only in plants and fungi in the eukaryotic domain. In this report, we systematically analyzed the genome sequences of a broad range of nonplant/nonfungus eukaryotes and identified...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 8
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    Architecture of eukaryotic mRNA 3'-end processing machinery (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-11-24
    Description: Newly transcribed eukaryotic precursor messenger RNAs (pre-mRNAs) are processed at their 3' ends by the ~1-megadalton multiprotein cleavage and polyadenylation factor (CPF). CPF cleaves pre-mRNAs, adds a polyadenylate tail, and triggers transcription termination, but it is unclear how its various enzymes are coordinated and assembled. Here, we show that the nuclease, polymerase, and phosphatase activities of yeast CPF are organized into three modules. Using electron cryomicroscopy, we determined a 3.5-angstrom-resolution structure of the ~200-kilodalton polymerase module. This revealed four β propellers, in an assembly markedly similar to those of other protein complexes that bind nucleic acid. Combined with in vitro reconstitution experiments, our data show that the polymerase module brings together factors required for specific and efficient polyadenylation, to help coordinate mRNA 3'-end processing.
    Keywords: Biochemistry, Molecular Biology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Structures of closed and open conformations of dimeric human ATM (2017)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2017-05-11
    Description: ATM (ataxia-telangiectasia mutated) is a phosphatidylinositol 3-kinase–related protein kinase (PIKK) best known for its role in DNA damage response. ATM also functions in oxidative stress response, insulin signaling, and neurogenesis. Our electron cryomicroscopy (cryo-EM) suggests that human ATM is in a dynamic equilibrium between closed and open dimers. In the closed state, the PIKK regulatory domain blocks the peptide substrate–binding site, suggesting that this conformation may represent an inactive or basally active enzyme. The active site is held in this closed conformation by interaction with a long helical hairpin in the TRD3 (tetratricopeptide repeats domain 3) domain of the symmetry-related molecule. The open dimer has two protomers with only a limited contact interface, and it lacks the intermolecular interactions that block the peptide-binding site in the closed dimer. This suggests that the open conformation may be more active. The ATM structure shows the detailed topology of the regulator-interacting N-terminal helical solenoid. The ATM conformational dynamics shown by the structures represent an important step in understanding the enzyme regulation.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Hepatitis C virus NS3-4A serine protease inhibitors: SAR of moiety with improved potency (2005)
    Elsevier
    Details
    Publication Date: 2005-10-01
    Print ISSN: 0960-894X
    Electronic ISSN: 1464-3405
    Topics: Chemistry and Pharmacology , Medicine
    Published by Elsevier
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