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  • 1
    Publication Date: 2016-01-07
    Description: CRISPR-Cas9 nucleases are widely used for genome editing but can induce unwanted off-target mutations. Existing strategies for reducing genome-wide off-target effects of the widely used Streptococcus pyogenes Cas9 (SpCas9) are imperfect, possessing only partial or unproven efficacies and other limitations that constrain their use. Here we describe SpCas9-HF1, a high-fidelity variant harbouring alterations designed to reduce non-specific DNA contacts. SpCas9-HF1 retains on-target activities comparable to wild-type SpCas9 with 〉85% of single-guide RNAs (sgRNAs) tested in human cells. Notably, with sgRNAs targeted to standard non-repetitive sequences, SpCas9-HF1 rendered all or nearly all off-target events undetectable by genome-wide break capture and targeted sequencing methods. Even for atypical, repetitive target sites, the vast majority of off-target mutations induced by wild-type SpCas9 were not detected with SpCas9-HF1. With its exceptional precision, SpCas9-HF1 provides an alternative to wild-type SpCas9 for research and therapeutic applications. More broadly, our results suggest a general strategy for optimizing genome-wide specificities of other CRISPR-RNA-guided nucleases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kleinstiver, Benjamin P -- Pattanayak, Vikram -- Prew, Michelle S -- Tsai, Shengdar Q -- Nguyen, Nhu T -- Zheng, Zongli -- Joung, J Keith -- DP1 GM105378/DP/NCCDPHP CDC HHS/ -- R01 GM088040/GM/NIGMS NIH HHS/ -- R01 GM107427/GM/NIGMS NIH HHS/ -- England -- Nature. 2016 Jan 28;529(7587):490-5. doi: 10.1038/nature16526. Epub 2016 Jan 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA. ; Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA. ; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26735016" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; CRISPR-Associated Proteins/*genetics/*metabolism ; CRISPR-Cas Systems/*physiology ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; DNA/genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Endonucleases/genetics/*metabolism ; *Genetic Engineering ; Genome, Human/*genetics ; Humans ; Mutation ; Protein Binding ; RNA/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; Streptococcus pyogenes/enzymology/genetics ; Substrate Specificity
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  • 2
    Publication Date: 2016-01-21
    Description: Regulatory T (Treg) cells expressing the transcription factor Foxp3 have a pivotal role in maintaining immunological self-tolerance; yet, excessive Treg cell activities suppress anti-tumour immune responses. Compared to the resting Treg (rTreg) cell phenotype in secondary lymphoid organs, Treg cells in non-lymphoid tissues exhibit an activated Treg (aTreg) cell phenotype. However, the function of aTreg cells and whether their generation can be manipulated are largely unexplored. Here we show that the transcription factor Foxo1, previously demonstrated to promote Treg cell suppression of lymphoproliferative diseases, has an unexpected function in inhibiting aTreg-cell-mediated immune tolerance in mice. We find that aTreg cells turned over at a slower rate than rTreg cells, but were not locally maintained in tissues. aTreg cell differentiation was associated with repression of Foxo1-dependent gene transcription, concomitant with reduced Foxo1 expression, cytoplasmic localization and enhanced phosphorylation at the Akt sites. Treg-cell-specific expression of an Akt-insensitive Foxo1 mutant prevented downregulation of lymphoid organ homing molecules, and impeded Treg cell homing to non-lymphoid organs, causing CD8(+) T-cell-mediated autoimmune diseases. Compared to Treg cells from healthy tissues, tumour-infiltrating Treg cells downregulated Foxo1 target genes more substantially. Expression of the Foxo1 mutant at a lower dose was sufficient to deplete tumour-associated Treg cells, activate effector CD8(+) T cells, and inhibit tumour growth without inflicting autoimmunity. Thus, Foxo1 inactivation is essential for the migration of aTreg cells that have a crucial function in suppressing CD8(+) T-cell responses; and the Foxo signalling pathway in Treg cells can be titrated to break tumour immune tolerance preferentially.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Luo, Chong T -- Liao, Will -- Dadi, Saida -- Toure, Ahmed -- Li, Ming O -- P30 CA008748/CA/NCI NIH HHS/ -- R01 AI102888-01A1/AI/NIAID NIH HHS/ -- England -- Nature. 2016 Jan 28;529(7587):532-6. doi: 10.1038/nature16486. Epub 2016 Jan 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA. ; Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA. ; New York Genome Center, New York, New York 10013, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26789248" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autoimmunity/*immunology ; CD8-Positive T-Lymphocytes/*immunology ; Cell Differentiation ; Cell Movement/immunology ; Down-Regulation ; Female ; Forkhead Transcription Factors/biosynthesis/genetics/*metabolism ; Immune Tolerance/*immunology ; Lymphocyte Activation ; Lymphocytes, Tumor-Infiltrating/cytology/immunology/metabolism ; Male ; Mice ; Mutation ; Neoplasms/*immunology ; Phosphorylation ; Signal Transduction/immunology ; T-Lymphocytes, Regulatory/cytology/*immunology/*metabolism ; Transcription, Genetic
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  • 3
    Publication Date: 2016-03-11
    Description: Directional control of tip-growing cells is essential for proper tissue organization and cell-to-cell communication in animals and plants. In the sexual reproduction of flowering plants, the tip growth of the male gametophyte, the pollen tube, is precisely guided by female cues to achieve fertilization. Several female-secreted peptides have recently been identified as species-specific attractants that directly control the direction of pollen tube growth. However, the method by which pollen tubes precisely and promptly respond to the guidance signal from their own species is unknown. Here we show that tip-localized pollen-specific receptor-like kinase 6 (PRK6) with an extracellular leucine-rich repeat domain is an essential receptor for sensing of the LURE1 attractant peptide in Arabidopsis thaliana under semi-in-vivo conditions, and is important for ovule targeting in the pistil. PRK6 interacted with pollen-expressed ROPGEFs (Rho of plant guanine nucleotide-exchange factors), which are important for pollen tube growth through activation of the signalling switch Rho GTPase ROP1 (refs 7, 8). PRK6 conferred responsiveness to AtLURE1 in pollen tubes of the related species Capsella rubella. Furthermore, our genetic and physiological data suggest that PRK6 signalling through ROPGEFs and sensing of AtLURE1 are achieved in cooperation with the other PRK family receptors, PRK1, PRK3 and PRK8. Notably, the tip-focused PRK6 accumulated asymmetrically towards an external AtLURE1 source before reorientation of pollen tube tip growth. These results demonstrate that PRK6 acts as a key membrane receptor for external AtLURE1 attractants, and recruits the core tip-growth machinery, including ROP signalling proteins. This work provides insights into the orchestration of efficient pollen tube growth and species-specific pollen tube attraction by multiple receptors during male-female communication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Takeuchi, Hidenori -- Higashiyama, Tetsuya -- England -- Nature. 2016 Mar 10;531(7593):245-8. doi: 10.1038/nature17413.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan. ; JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan. ; 3Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26961657" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics/*metabolism/physiology ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Capsella/genetics/metabolism/physiology ; GTP-Binding Proteins/metabolism ; Mutation ; Ovule/metabolism ; Phenotype ; Phosphotransferases/chemistry/genetics/*metabolism ; Pollen Tube/genetics/*growth & development/*metabolism ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/genetics/metabolism ; Receptors, Cell Surface/chemistry/genetics/*metabolism ; Reproduction ; *Signal Transduction ; Species Specificity
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  • 4
    Publication Date: 2016-02-11
    Description: Sexual reproduction requires recognition between the male and female gametes. In flowering plants, the immobile sperms are delivered to the ovule-enclosed female gametophyte by guided pollen tube growth. Although the female gametophyte-secreted peptides have been identified to be the chemotactic attractant to the pollen tube, the male receptor(s) is still unknown. Here we identify a cell-surface receptor heteromer, MDIS1-MIK, on the pollen tube that perceives female attractant LURE1 in Arabidopsis thaliana. MDIS1, MIK1 and MIK2 are plasma-membrane-localized receptor-like kinases with extracellular leucine-rich repeats and an intracellular kinase domain. LURE1 specifically binds the extracellular domains of MDIS1, MIK1 and MIK2, whereas mdis1 and mik1 mik2 mutant pollen tubes respond less sensitively to LURE1. Furthermore, LURE1 triggers dimerization of the receptors and activates the kinase activity of MIK1. Importantly, transformation of AtMDIS1 to the sister species Capsella rubella can partially break down the reproductive isolation barrier. Our findings reveal a new mechanism of the male perception of the female attracting signals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Tong -- Liang, Liang -- Xue, Yong -- Jia, Peng-Fei -- Chen, Wei -- Zhang, Meng-Xia -- Wang, Ying-Chun -- Li, Hong-Ju -- Yang, Wei-Cai -- England -- Nature. 2016 Mar 10;531(7593):241-4. doi: 10.1038/nature16975. Epub 2016 Feb 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China. ; University of Chinese Academy of Sciences, Beijing 100049, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26863186" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics/*metabolism/physiology ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Capsella/genetics/metabolism/physiology ; Cell Membrane/metabolism ; Mutation ; Ovule/metabolism ; Phenotype ; Phosphotransferases/chemistry/genetics/*metabolism ; Pollen Tube/genetics/growth & development/metabolism ; Protein Kinases/genetics/metabolism ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Receptors, Cell Surface/chemistry/genetics/*metabolism ; Reproduction ; *Signal Transduction
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  • 5
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    Nature Publishing Group (NPG)
    Publication Date: 2015-06-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2015 Jun 4;522(7554):6. doi: 10.1038/522006a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26040858" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry ; *Public Opinion ; Research Personnel/*ethics/standards ; Retraction of Publication as Topic ; Science/ethics/*standards ; Scientific Misconduct/*statistics & numerical data ; *Trust
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  • 6
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    Nature Publishing Group (NPG)
    Publication Date: 2015-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Yingying -- England -- Nature. 2015 Dec 17;528(7582):S170-3. doi: 10.1038/528S170a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26673023" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Science Disciplines ; Chemistry ; China ; Diffusion of Innovation ; Ecology ; Economic Recession ; Humans ; International Cooperation ; Nobel Prize ; Physics ; Research/economics/manpower/standards/*statistics & numerical data ; Research Personnel/education/standards/supply & distribution ; Time Factors
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  • 7
    Publication Date: 2015-08-19
    Description: Dysfunction of the intramembrane protease gamma-secretase is thought to cause Alzheimer's disease, with most mutations derived from Alzheimer's disease mapping to the catalytic subunit presenilin 1 (PS1). Here we report an atomic structure of human gamma-secretase at 3.4 A resolution, determined by single-particle cryo-electron microscopy. Mutations derived from Alzheimer's disease affect residues at two hotspots in PS1, each located at the centre of a distinct four transmembrane segment (TM) bundle. TM2 and, to a lesser extent, TM6 exhibit considerable flexibility, yielding a plastic active site and adaptable surrounding elements. The active site of PS1 is accessible from the convex side of the TM horseshoe, suggesting considerable conformational changes in nicastrin extracellular domain after substrate recruitment. Component protein APH-1 serves as a scaffold, anchoring the lone transmembrane helix from nicastrin and supporting the flexible conformation of PS1. Ordered phospholipids stabilize the complex inside the membrane. Our structure serves as a molecular basis for mechanistic understanding of gamma-secretase function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568306/" 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/PMC4568306/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bai, Xiao-chen -- Yan, Chuangye -- Yang, Guanghui -- Lu, Peilong -- Ma, Dan -- Sun, Linfeng -- Zhou, Rui -- Scheres, Sjors H W -- Shi, Yigong -- MC_UP_A025_101/Medical Research Council/United Kingdom -- MC_UP_A025_1013/Medical Research Council/United Kingdom -- England -- Nature. 2015 Sep 10;525(7568):212-7. doi: 10.1038/nature14892. Epub 2015 Aug 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. ; Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26280335" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/genetics ; Amyloid Precursor Protein ; Secretases/*chemistry/genetics/metabolism/*ultrastructure ; Binding Sites ; *Cryoelectron Microscopy ; Humans ; Membrane Glycoproteins/*chemistry/metabolism/*ultrastructure ; Models, Molecular ; Mutation ; Presenilin-1/*chemistry/genetics/*ultrastructure ; Protein Structure, Tertiary ; Protein Subunits/chemistry/genetics/metabolism
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  • 8
    Publication Date: 2015-12-10
    Description: Inactivation of the TNFAIP3 gene, encoding the A20 protein, is associated with critical inflammatory diseases including multiple sclerosis, rheumatoid arthritis and Crohn's disease. However, the role of A20 in attenuating inflammatory signalling is unclear owing to paradoxical in vitro and in vivo findings. Here we utilize genetically engineered mice bearing mutations in the A20 ovarian tumour (OTU)-type deubiquitinase domain or in the zinc finger-4 (ZnF4) ubiquitin-binding motif to investigate these discrepancies. We find that phosphorylation of A20 promotes cleavage of Lys63-linked polyubiquitin chains by the OTU domain and enhances ZnF4-mediated substrate ubiquitination. Additionally, levels of linear ubiquitination dictate whether A20-deficient cells die in response to tumour necrosis factor. Mechanistically, linear ubiquitin chains preserve the architecture of the TNFR1 signalling complex by blocking A20-mediated disassembly of Lys63-linked polyubiquitin scaffolds. Collectively, our studies reveal molecular mechanisms whereby A20 deubiquitinase activity and ubiquitin binding, linear ubiquitination, and cellular kinases cooperate to regulate inflammation and cell death.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wertz, Ingrid E -- Newton, Kim -- Seshasayee, Dhaya -- Kusam, Saritha -- Lam, Cynthia -- Zhang, Juan -- Popovych, Nataliya -- Helgason, Elizabeth -- Schoeffler, Allyn -- Jeet, Surinder -- Ramamoorthi, Nandhini -- Kategaya, Lorna -- Newman, Robert J -- Horikawa, Keisuke -- Dugger, Debra -- Sandoval, Wendy -- Mukund, Susmith -- Zindal, Anuradha -- Martin, Flavius -- Quan, Clifford -- Tom, Jeffrey -- Fairbrother, Wayne J -- Townsend, Michael -- Warming, Soren -- DeVoss, Jason -- Liu, Jinfeng -- Dueber, Erin -- Caplazi, Patrick -- Lee, Wyne P -- Goodnow, Christopher C -- Balazs, Mercedesz -- Yu, Kebing -- Kolumam, Ganesh -- Dixit, Vishva M -- England -- Nature. 2015 Dec 17;528(7582):370-5. doi: 10.1038/nature16165. Epub 2015 Dec 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Discovery Oncology, Genentech, South San Francisco, California 94080, USA. ; Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA. ; Physiological Chemistry, Genentech, South San Francisco, California 94080, USA. ; Immunology, Genentech, South San Francisco, California 94080, USA. ; Molecular Biology, Genentech, South San Francisco, California 94080, USA. ; Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia. ; Protein Chemistry, Genentech, South San Francisco, California 94080, USA. ; Structural Biology, Genentech, South San Francisco, California 94080, USA. ; Bioinformatics, Genentech, South San Francisco, California 94080, USA. ; Pathology, Genentech, South San Francisco, California 94080, USA. ; Immunogenomics Laboratory, Immunology Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Sydney, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26649818" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Death ; Cysteine Endopeptidases/chemistry/genetics/*metabolism ; Female ; Inflammation/genetics/*metabolism/pathology ; Intracellular Signaling Peptides and Proteins/chemistry/genetics/*metabolism ; Lysine/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Mutation ; Phosphorylation ; Polyubiquitin/chemistry/metabolism ; Protein Binding ; Protein Kinases/metabolism ; Signal Transduction ; Tumor Necrosis Factor-alpha/metabolism ; Ubiquitin/*chemistry/*metabolism ; Ubiquitination
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  • 9
    Publication Date: 2015-06-18
    Description: Synapse formation is a process tightly controlled in space and time. How gene regulatory mechanisms specify spatial and temporal aspects of synapse formation is not well understood. In the nematode Caenorhabditis elegans, two subtypes of the D-type inhibitory motor neuron (MN) classes, the dorsal D (DD) and ventral D (VD) neurons, extend axons along both the dorsal and ventral nerve cords. The embryonically generated DD motor neurons initially innervate ventral muscles in the first (L1) larval stage and receive their synaptic input from cholinergic motor neurons in the dorsal cord. They rewire by the end of the L1 moult to innervate dorsal muscles and to be innervated by newly formed ventral cholinergic motor neurons. VD motor neurons develop after the L1 moult; they take over the innervation of ventral muscles and receive their synaptic input from dorsal cholinergic motor neurons. We show here that the spatiotemporal control of synaptic wiring of the D-type neurons is controlled by an intersectional transcriptional strategy in which the UNC-30 Pitx-type homeodomain transcription factor acts together, in embryonic and early larval stages, with the temporally controlled LIN-14 transcription factor to prevent premature synapse rewiring of the DD motor neurons and, together with the UNC-55 nuclear hormone receptor, to prevent aberrant VD synaptic wiring in later larval and adult stages. A key effector of this intersectional transcription factor combination is a novel synaptic organizer molecule, the single immunoglobulin domain protein OIG-1. OIG-1 is perisynaptically localized along the synaptic outputs of the D-type motor neurons in a temporally controlled manner and is required for appropriate selection of both pre- and post-synaptic partners.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Howell, Kelly -- White, John G -- Hobert, Oliver -- R01 NS039996/NS/NINDS NIH HHS/ -- R01 NS050266/NS/NINDS NIH HHS/ -- R01NS039996-05/NS/NINDS NIH HHS/ -- R01NS050266-03/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- Medical Research Council/United Kingdom -- England -- Nature. 2015 Jul 2;523(7558):83-7. doi: 10.1038/nature14545. Epub 2015 Jun 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, New York 10032, USA. ; MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26083757" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caenorhabditis elegans/embryology/genetics/growth & development/*physiology ; Caenorhabditis elegans Proteins/genetics/*metabolism ; Gene Expression Regulation ; Homeodomain Proteins/genetics/metabolism ; Motor Neurons/*physiology ; Mutation ; Nerve Tissue Proteins/genetics/*metabolism ; Nuclear Proteins/genetics/metabolism ; Receptors, Cell Surface/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; Synapses/genetics/pathology/physiology ; Transcription Factors/metabolism
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  • 10
    Publication Date: 2015-01-09
    Description: Functional regeneration after nervous system injury requires transected axons to reconnect with their original target tissue. Axonal fusion, a spontaneous regenerative mechanism identified in several species, provides an efficient means of achieving target reconnection as a regrowing axon is able to contact and fuse with its own separated axon fragment, thereby re-establishing the original axonal tract. Here we report a molecular characterization of this process in Caenorhabditis elegans, revealing dynamic changes in the subcellular localization of the EFF-1 fusogen after axotomy, and establishing phosphatidylserine (PS) and the PS receptor (PSR-1) as critical components for axonal fusion. PSR-1 functions cell-autonomously in the regrowing neuron and, instead of acting in its canonical signalling pathway, acts in a parallel phagocytic pathway that includes the transthyretin protein TTR-52, as well as CED-7, NRF-5 and CED-6 (refs 9, 10, 11, 12). We show that TTR-52 binds to PS exposed on the injured axon, and can restore fusion several hours after injury. We propose that PS functions as a 'save-me' signal for the distal fragment, allowing conserved apoptotic cell clearance molecules to function in re-establishing axonal integrity during regeneration of the nervous system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Neumann, Brent -- Coakley, Sean -- Giordano-Santini, Rosina -- Linton, Casey -- Lee, Eui Seung -- Nakagawa, Akihisa -- Xue, Ding -- Hilliard, Massimo A -- GM059083/GM/NIGMS NIH HHS/ -- GM079097/GM/NIGMS NIH HHS/ -- GM088241/GM/NIGMS NIH HHS/ -- P40 OD010440/OD/NIH HHS/ -- R01 NS060129/NS/NINDS NIH HHS/ -- England -- Nature. 2015 Jan 8;517(7533):219-22. doi: 10.1038/nature14102.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CJCADR, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia. ; Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25567286" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/metabolism ; Animals ; Apoptosis/*physiology ; Axons/*metabolism/pathology ; Caenorhabditis elegans/*cytology/*metabolism ; Caenorhabditis elegans Proteins/genetics/*metabolism ; Carrier Proteins/metabolism ; Growth Cones/metabolism ; Membrane Glycoproteins/*metabolism ; Mutation ; Nerve Regeneration/*physiology ; Phagocytes/metabolism ; Phagocytosis ; Phosphatidylserines/metabolism ; Phosphoproteins/metabolism ; Receptors, Cell Surface/metabolism ; Signal Transduction ; Spectrin/genetics/metabolism
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  • 11
    Publication Date: 2015-07-07
    Description: G protein-coupled receptors (GPCRs) allosterically activate heterotrimeric G proteins and trigger GDP release. Given that there are approximately 800 human GPCRs and 16 different Galpha genes, this raises the question of whether a universal allosteric mechanism governs Galpha activation. Here we show that different GPCRs interact with and activate Galpha proteins through a highly conserved mechanism. Comparison of Galpha with the small G protein Ras reveals how the evolution of short segments that undergo disorder-to-order transitions can decouple regions important for allosteric activation from receptor binding specificity. This might explain how the GPCR-Galpha system diversified rapidly, while conserving the allosteric activation mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Flock, Tilman -- Ravarani, Charles N J -- Sun, Dawei -- Venkatakrishnan, A J -- Kayikci, Melis -- Tate, Christopher G -- Veprintsev, Dmitry B -- Babu, M Madan -- MC_U105185859/Medical Research Council/United Kingdom -- MC_U105197215/Medical Research Council/United Kingdom -- England -- Nature. 2015 Aug 13;524(7564):173-9. doi: 10.1038/nature14663. Epub 2015 Jul 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. ; 1] Laboratory of Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland [2] Department of Biology, ETH Zurich, 8039 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26147082" target="_blank"〉PubMed〈/a〉
    Keywords: *Allosteric Regulation ; Animals ; Binding Sites ; Computational Biology ; Conserved Sequence ; Enzyme Activation ; *Evolution, Molecular ; GTP-Binding Protein alpha Subunits/chemistry/genetics/*metabolism ; Genetic Engineering ; Guanosine Diphosphate/metabolism ; Humans ; Models, Molecular ; Mutation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, G-Protein-Coupled/chemistry/*metabolism ; Signal Transduction ; Substrate Specificity ; ras Proteins/chemistry/metabolism
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 12
    Publication Date: 2015-05-20
    Description: Reproduction through sex carries substantial costs, mainly because only half of sexual adults produce offspring. It has been theorized that these costs could be countered if sex allows sexual selection to clear the universal fitness constraint of mutation load. Under sexual selection, competition between (usually) males and mate choice by (usually) females create important intraspecific filters for reproductive success, so that only a subset of males gains paternity. If reproductive success under sexual selection is dependent on individual condition, which is contingent to mutation load, then sexually selected filtering through 'genic capture' could offset the costs of sex because it provides genetic benefits to populations. Here we test this theory experimentally by comparing whether populations with histories of strong versus weak sexual selection purge mutation load and resist extinction differently. After evolving replicate populations of the flour beetle Tribolium castaneum for 6 to 7 years under conditions that differed solely in the strengths of sexual selection, we revealed mutation load using inbreeding. Lineages from populations that had previously experienced strong sexual selection were resilient to extinction and maintained fitness under inbreeding, with some families continuing to survive after 20 generations of sib x sib mating. By contrast, lineages derived from populations that experienced weak or non-existent sexual selection showed rapid fitness declines under inbreeding, and all were extinct after generation 10. Multiple mutations across the genome with individually small effects can be difficult to clear, yet sum to a significant fitness load; our findings reveal that sexual selection reduces this load, improving population viability in the face of genetic stress.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lumley, Alyson J -- Michalczyk, Lukasz -- Kitson, James J N -- Spurgin, Lewis G -- Morrison, Catriona A -- Godwin, Joanne L -- Dickinson, Matthew E -- Martin, Oliver Y -- Emerson, Brent C -- Chapman, Tracey -- Gage, Matthew J G -- England -- Nature. 2015 Jun 25;522(7557):470-3. doi: 10.1038/nature14419. Epub 2015 May 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK. ; Department of Entomology, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387 Krakow, Poland. ; ETH Zurich, Institute of Integrative Biology, D-USYS, Universitatsstrasse 16, CHN J 11, 8092 Zurich, Switzerland. ; Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiologia (IPNA-CSIC), C/Astrofisico Francisco Sanchez 3, 38206 San Cristobal de La Laguna, Santa Cruz de Tenerife, Canary Islands, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25985178" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; *Extinction, Biological ; Female ; Genetic Fitness/genetics/*physiology ; Inbreeding ; Male ; Mating Preference, Animal/*physiology ; Mutation ; Reproduction/genetics ; Selection, Genetic/genetics/physiology ; Tribolium/genetics/*physiology
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 13
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    Nature Publishing Group (NPG)
    Publication Date: 2015-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Meara, Sarah -- England -- Nature. 2015 Dec 17;528(7582):S179-81. doi: 10.1038/528S179a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26673025" target="_blank"〉PubMed〈/a〉
    Keywords: Bibliometrics ; Chemistry ; China ; Cities/*statistics & numerical data ; Personnel Selection ; Research/manpower/organization & administration/*statistics & numerical data
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 14
    Publication Date: 2015-07-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- England -- Nature. 2015 Jul 2;523(7558):13-4. doi: 10.1038/523013a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26135425" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Animals, Genetically Modified ; Gene Knockout Techniques ; Korea ; Meat ; Muscle, Skeletal/*growth & development ; Mutation ; Myostatin/genetics ; Swine
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  • 15
    Publication Date: 2015-08-20
    Description: In the mammalian retina, processes of approximately 70 types of interneurons form specific synapses on roughly 30 types of retinal ganglion cells (RGCs) in a neuropil called the inner plexiform layer. Each RGC type extracts salient features from visual input, which are sent deeper into the brain for further processing. The specificity and stereotypy of synapses formed in the inner plexiform layer account for the feature-detecting ability of RGCs. Here we analyse the development and function of synapses on one mouse RGC type, called the W3B-RGC. These cells have the remarkable property of responding when the timing of the movement of a small object differs from that of the background, but not when they coincide. Such cells, known as local edge detectors or object motion sensors, can distinguish moving objects from a visual scene that is also moving. We show that W3B-RGCs receive strong and selective input from an unusual excitatory amacrine cell type known as VG3-AC (vesicular glutamate transporter 3). Both W3B-RGCs and VG3-ACs express the immunoglobulin superfamily recognition molecule sidekick 2 (Sdk2), and both loss- and gain-of-function studies indicate that Sdk2-dependent homophilic interactions are necessary for the selectivity of the connection. The Sdk2-specified synapse is essential for visual responses of W3B-RGCs: whereas bipolar cells relay visual input directly to most RGCs, the W3B-RGCs receive much of their input indirectly, via the VG3-ACs. This non-canonical circuit introduces a delay into the pathway from photoreceptors in the centre of the receptive field to W3B-RGCs, which could improve their ability to judge the synchrony of local and global motion.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4552609/" 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/PMC4552609/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krishnaswamy, Arjun -- Yamagata, Masahito -- Duan, Xin -- Hong, Y Kate -- Sanes, Joshua R -- EY022073/EY/NEI NIH HHS/ -- F31 NS055488/NS/NINDS NIH HHS/ -- NS029169/NS/NINDS NIH HHS/ -- R01 EY022073/EY/NEI NIH HHS/ -- R37 NS029169/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Aug 27;524(7566):466-70. doi: 10.1038/nature14682. Epub 2015 Aug 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26287463" target="_blank"〉PubMed〈/a〉
    Keywords: Amacrine Cells/cytology/physiology ; Animals ; Female ; Immunoglobulin G/genetics/*metabolism ; Male ; Membrane Proteins/genetics/*metabolism ; Mice ; Motion ; Motion Perception/*physiology ; Mutation ; Retinal Ganglion Cells/*cytology/*physiology ; Synapses/genetics/metabolism ; Visual Pathways/*physiology
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  • 16
    Publication Date: 2015-04-16
    Description: Artemisinins are the cornerstone of anti-malarial drugs. Emergence and spread of resistance to them raises risk of wiping out recent gains achieved in reducing worldwide malaria burden and threatens future malaria control and elimination on a global level. Genome-wide association studies (GWAS) have revealed parasite genetic loci associated with artemisinin resistance. However, there is no consensus on biochemical targets of artemisinin. Whether and how these targets interact with genes identified by GWAS, remains unknown. Here we provide biochemical and cellular evidence that artemisinins are potent inhibitors of Plasmodium falciparum phosphatidylinositol-3-kinase (PfPI3K), revealing an unexpected mechanism of action. In resistant clinical strains, increased PfPI3K was associated with the C580Y mutation in P. falciparum Kelch13 (PfKelch13), a primary marker of artemisinin resistance. Polyubiquitination of PfPI3K and its binding to PfKelch13 were reduced by the PfKelch13 mutation, which limited proteolysis of PfPI3K and thus increased levels of the kinase, as well as its lipid product phosphatidylinositol-3-phosphate (PI3P). We find PI3P levels to be predictive of artemisinin resistance in both clinical and engineered laboratory parasites as well as across non-isogenic strains. Elevated PI3P induced artemisinin resistance in absence of PfKelch13 mutations, but remained responsive to regulation by PfKelch13. Evidence is presented for PI3P-dependent signalling in which transgenic expression of an additional kinase confers resistance. Together these data present PI3P as the key mediator of artemisinin resistance and the sole PfPI3K as an important target for malaria elimination.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417027/" 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/PMC4417027/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mbengue, Alassane -- Bhattacharjee, Souvik -- Pandharkar, Trupti -- Liu, Haining -- Estiu, Guillermina -- Stahelin, Robert V -- Rizk, Shahir S -- Njimoh, Dieudonne L -- Ryan, Yana -- Chotivanich, Kesinee -- Nguon, Chea -- Ghorbal, Mehdi -- Lopez-Rubio, Jose-Juan -- Pfrender, Michael -- Emrich, Scott -- Mohandas, Narla -- Dondorp, Arjen M -- Wiest, Olaf -- Haldar, Kasturi -- AI039071/AI/NIAID NIH HHS/ -- AI081077/AI/NIAID NIH HHS/ -- DK26263/DK/NIDDK NIH HHS/ -- HL069630/HL/NHLBI NIH HHS/ -- HL078826/HL/NHLBI NIH HHS/ -- R01 DK026263/DK/NIDDK NIH HHS/ -- R01 HL069630/HL/NHLBI NIH HHS/ -- R37 DK026263/DK/NIDDK NIH HHS/ -- England -- Nature. 2015 Apr 30;520(7549):683-7. doi: 10.1038/nature14412. Epub 2015 Apr 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA. ; 1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA. ; 1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA [3] Department of Biochemistry &Molecular Biology, Indiana University School of Medicine-South Bend, 143 Raclin-Carmichael Hall, 1234 Notre Dame Avenue, South Bend, Indiana 46617, USA. ; 1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA [3] Departmen of. Biochemistry and Molecular Biology, Faculty of Science University of Buea, P.O. Box 63 Buea, Southwest region, Cameroon. ; Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand. ; National Center for Parasitology, Entomology and Malaria Control, 12302 Phnom Penh, Monivong Blvd, Phnom Penh 12302, Cambodia. ; CNRS 5290/IRD 224/University Montpellier 1&2 ("MiVEGEC"), Montpellier, France. ; Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA. ; Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, Indiana 46556. USA. ; New York Blood Center, New York, New York 10032, USA. ; 1] Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand [2] Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN. UK. ; 1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA [3] Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25874676" target="_blank"〉PubMed〈/a〉
    Keywords: Antimalarials/*pharmacology ; Artemisinins/*pharmacology ; Drug Resistance/*drug effects/genetics ; Genome-Wide Association Study ; Malaria, Falciparum/*drug therapy/*parasitology ; Models, Molecular ; Mutation ; Phosphatidylinositol 3-Kinase/*antagonists & inhibitors/chemistry/metabolism ; Phosphatidylinositol Phosphates/metabolism ; Plasmodium falciparum/*drug effects/*enzymology ; Protozoan Proteins/antagonists & inhibitors/genetics/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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