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  • 1
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    Phase transitions in the assembly of multivalent signalling proteins (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-03-09
    Description: Cells are organized on length scales ranging from angstrom to micrometres. However, the mechanisms by which angstrom-scale molecular properties are translated to micrometre-scale macroscopic properties are not well understood. Here we show that interactions between diverse synthetic, multivalent macromolecules (including multi-domain proteins and RNA) produce sharp liquid-liquid-demixing phase separations, generating micrometre-sized liquid droplets in aqueous solution. This macroscopic transition corresponds to a molecular transition between small complexes and large, dynamic supramolecular polymers. The concentrations needed for phase transition are directly related to the valency of the interacting species. In the case of the actin-regulatory protein called neural Wiskott-Aldrich syndrome protein (N-WASP) interacting with its established biological partners NCK and phosphorylated nephrin, the phase transition corresponds to a sharp increase in activity towards an actin nucleation factor, the Arp2/3 complex. The transition is governed by the degree of phosphorylation of nephrin, explaining how this property of the system can be controlled to regulatory effect by kinases. The widespread occurrence of multivalent systems suggests that phase transitions may be used to spatially organize and biochemically regulate information throughout biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3343696/" 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/PMC3343696/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Pilong -- Banjade, Sudeep -- Cheng, Hui-Chun -- Kim, Soyeon -- Chen, Baoyu -- Guo, Liang -- Llaguno, Marc -- Hollingsworth, Javoris V -- King, David S -- Banani, Salman F -- Russo, Paul S -- Jiang, Qiu-Xing -- Nixon, B Tracy -- Rosen, Michael K -- P30 CA142543/CA/NCI NIH HHS/ -- P41 GM103622/GM/NIGMS NIH HHS/ -- R01 GM056322/GM/NIGMS NIH HHS/ -- R01 GM056322-13/GM/NIGMS NIH HHS/ -- R01-GM088745/GM/NIGMS NIH HHS/ -- R01-GM56322/GM/NIGMS NIH HHS/ -- RR-08630/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Mar 7;483(7389):336-40. doi: 10.1038/nature10879.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8812, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22398450" target="_blank"〉PubMed〈/a〉
    Keywords: Actin-Related Protein 2-3 Complex/metabolism ; Adaptor Proteins, Signal Transducing/chemistry/metabolism ; Binding Sites ; Biopolymers/chemistry/metabolism ; Fluorescence Recovery After Photobleaching ; HeLa Cells ; Humans ; Ligands ; Membrane Proteins/chemistry/metabolism ; Multiprotein Complexes/*chemistry/*metabolism ; Oncogene Proteins/chemistry/metabolism ; *Phase Transition ; Phosphorylation ; Proline-Rich Protein Domains ; Protein Structure, Quaternary ; Proteins/*chemistry/*metabolism ; *Signal Transduction ; Wiskott-Aldrich Syndrome Protein, Neuronal/chemistry/metabolism ; src Homology Domains
    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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    Antibacterial membrane attack by a pore-forming intestinal C-type lectin (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-11-22
    Description: Human body-surface epithelia coexist in close association with complex bacterial communities and are protected by a variety of antibacterial proteins. C-type lectins of the RegIII family are bactericidal proteins that limit direct contact between bacteria and the intestinal epithelium and thus promote tolerance to the intestinal microbiota. RegIII lectins recognize their bacterial targets by binding peptidoglycan carbohydrate, but the mechanism by which they kill bacteria is unknown. Here we elucidate the mechanistic basis for RegIII bactericidal activity. We show that human RegIIIalpha (also known as HIP/PAP) binds membrane phospholipids and kills bacteria by forming a hexameric membrane-permeabilizing oligomeric pore. We derive a three-dimensional model of the RegIIIalpha pore by docking the RegIIIalpha crystal structure into a cryo-electron microscopic map of the pore complex, and show that the model accords with experimentally determined properties of the pore. Lipopolysaccharide inhibits RegIIIalpha pore-forming activity, explaining why RegIIIalpha is bactericidal for Gram-positive but not Gram-negative bacteria. Our findings identify C-type lectins as mediators of membrane attack in the mucosal immune system, and provide detailed insight into an antibacterial mechanism that promotes mutualism with the resident microbiota.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160023/" 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/PMC4160023/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mukherjee, Sohini -- Zheng, Hui -- Derebe, Mehabaw G -- Callenberg, Keith M -- Partch, Carrie L -- Rollins, Darcy -- Propheter, Daniel C -- Rizo, Josep -- Grabe, Michael -- Jiang, Qiu-Xing -- Hooper, Lora V -- C06 RR30414/RR/NCRR NIH HHS/ -- F32 DK100074/DK/NIDDK NIH HHS/ -- GM093271/GM/NIGMS NIH HHS/ -- R01 DK070855/DK/NIDDK NIH HHS/ -- R01 NS040944/NS/NINDS NIH HHS/ -- R01 NS40944/NS/NINDS NIH HHS/ -- R01GM088745/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Jan 2;505(7481):103-7. doi: 10.1038/nature12729. Epub 2013 Nov 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. ; Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. ; Department of Biological Sciences, University of Pittsburgh, and Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania 15261, USA. ; Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA. ; Department of Biochemistry and Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. ; 1] Department of Biological Sciences, University of Pittsburgh, and Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania 15261, USA [2] Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94143, USA. ; 1] Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA [2]. ; 1] Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA [2] The Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA [3].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24256734" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/chemistry/immunology/*metabolism/pharmacology ; Antigens, Neoplasm/chemistry/immunology/*metabolism ; Biomarkers, Tumor/antagonists & inhibitors/chemistry/immunology/*metabolism ; Cell Membrane Permeability/drug effects ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Gram-Negative Bacteria/drug effects/immunology/metabolism ; Humans ; Immunity, Mucosal/drug effects/immunology ; Intestines/*chemistry/immunology/microbiology ; Lectins, C-Type/antagonists & inhibitors/chemistry/immunology/*metabolism ; Lipopolysaccharides/pharmacology ; Listeria monocytogenes/drug effects/immunology/metabolism ; Microbial Viability/drug effects ; Models, Molecular ; Peptidoglycan/metabolism ; Phospholipids/metabolism ; Porins/antagonists & inhibitors/chemistry/*metabolism ; Symbiosis
    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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  • 3
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    Vibrio effector protein, VopQ, forms a lysosomal gated channel that disrupts host ion homeostasis and autophagic flux (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-06-24
    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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  • 4
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    Voltage sensor ring in a Kv channel in membrane [Biophysics and Computational Biology] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-02-27
    Description: Voltage-gated ion channels support electrochemical activity in cells and are largely responsible for information flow throughout the nervous systems. The voltage sensor domains in these channels sense changes in transmembrane potential and control ion flux across membranes. The X-ray structures of a few voltage-gated ion channels in detergents have been...
    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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  • 5
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    Disruption of the Rice Plastid Ribosomal Protein S20 Leads to Chloroplast Developmental Defects and Seedling Lethality (2013)
    Genetics Society of America (GSA)
    Details
    Publication Date: 2013-10-09
    Description: Plastid ribosomal proteins (PRPs) are essential for ribosome biogenesis, plastid protein biosynthesis, chloroplast differentiation, and early chloroplast development. This study identifies the first rice PRP mutant, asl1 ( albino seedling lethality1 ), which exhibits an albino lethal phenotype at the seedling stage. This albino phenotype was associated with altered chlorophyll (Chl) content and chloroplast development. Map-based cloning revealed that ASL1 encodes PRP S20 (PRPS20), which localizes to the chloroplast. ASL1 showed tissue-specific expression, as it was highly expressed in plumule and young seedlings but expressed at much lower levels in other tissues. In addition, ASL1 expression was regulated by light. The transcript levels of nuclear genes for Chl biosynthesis and chloroplast development were strongly affected in asl1 mutants; transcripts of some plastid genes for photosynthesis were undetectable. Our findings indicate that nuclear-encoded PRPS20 plays an important role in chloroplast development in rice.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 6
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    The paraventricular thalamus is a critical thalamic area for wakefulness (2018)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2018
    Description: 〈p〉Clinical observations indicate that the paramedian region of the thalamus is a critical node for controlling wakefulness. However, the specific nucleus and neural circuitry for this function remain unknown. Using in vivo fiber photometry or multichannel electrophysiological recordings in mice, we found that glutamatergic neurons of the paraventricular thalamus (PVT) exhibited high activities during wakefulness. Suppression of PVT neuronal activity caused a reduction in wakefulness, whereas activation of PVT neurons induced a transition from sleep to wakefulness and an acceleration of emergence from general anesthesia. Moreover, our findings indicate that the PVT–nucleus accumbens projections and hypocretin neurons in the lateral hypothalamus to PVT glutamatergic neurons’ projections are the effector pathways for wakefulness control. These results demonstrate that the PVT is a key wakefulness-controlling nucleus in the thalamus.〈/p〉
    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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  • 7
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    Small activating RNA binds to the genomic target site in a seed-region-dependent manner (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-19
    Description: RNA activation (RNAa) is the upregulation of gene expression by small activating RNAs (saRNAs). In order to investigate the mechanism by which saRNAs act in RNAa, we used the progesterone receptor (PR) gene as a model, established a panel of effective saRNAs and assessed the involvement of the sense and antisense strands of saRNA in RNAa. All active saRNAs had their antisense strand effectively incorporated into Ago2, whereas such consistency did not occur for the sense strand. Using a distal hotspot for saRNA targeting at 1.6-kb upstream from the PR transcription start site, we further established that gene activation mediated by saRNA depended on the complementarity of the 5' region of the antisense strand, and that such activity was largely abolished by mutations in this region of the saRNA. We found markedly reduced RNAa effects when we created mutations in the genomic target site of saRNA PR-1611, thus providing evidence that RNAa depends on the integrity of the DNA target. We further demonstrated that this saRNA bound the target site on promoter DNA. These results demonstrated that saRNAs work via an on-site mechanism by binding to target genomic DNA in a seed-region-dependent manner, reminiscent of miRNA-like target recognition.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    The paraventricular thalamus is a critical thalamic area for wakefulness (2018)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2018-10-26
    Description: Clinical observations indicate that the paramedian region of the thalamus is a critical node for controlling wakefulness. However, the specific nucleus and neural circuitry for this function remain unknown. Using in vivo fiber photometry or multichannel electrophysiological recordings in mice, we found that glutamatergic neurons of the paraventricular thalamus (PVT) exhibited high activities during wakefulness. Suppression of PVT neuronal activity caused a reduction in wakefulness, whereas activation of PVT neurons induced a transition from sleep to wakefulness and an acceleration of emergence from general anesthesia. Moreover, our findings indicate that the PVT–nucleus accumbens projections and hypocretin neurons in the lateral hypothalamus to PVT glutamatergic neurons’ projections are the effector pathways for wakefulness control. These results demonstrate that the PVT is a key wakefulness-controlling nucleus in the thalamus.
    Keywords: Neuroscience
    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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    Vibrio VopQ is a lysosomal gated channel [Microbiology] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-07-10
    Description: Defects in normal autophagic pathways are implicated in numerous human diseases—such as neurodegenerative diseases, cancer, and cardiomyopathy—highlighting the importance of autophagy and its proper regulation. Herein we show that Vibrio parahaemolyticus uses the type III effector VopQ (Vibrio outer protein Q) to alter autophagic flux by manipulating the partitioning of...
    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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  • 10
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    Mechanism of membrane bridging by synaptotagmin-1 [Neuroscience] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-08-21
    Description: Synaptotagmin-1 functions as a Ca2+ sensor in neurotransmitter release through its two C2 domains (the C2A and C2B domain). The ability of synaptotagmin-1 to bridge two membranes is likely crucial for its function, enabling cooperation with the soluble N-ethylmaleimide sensitive factor adaptor protein receptors (SNAREs) in membrane fusion, but two...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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