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  • Articles  (229)
  • Latest Papers from Table of Contents or Articles in Press  (229)
  • Models, Molecular  (138)
  • Models, Biological  (105)
  • 2005-2009  (229)
  • 2008  (229)
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  • Articles  (229)
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  • Latest Papers from Table of Contents or Articles in Press  (229)
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  • 1
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    Pyruvate kinase M2 is a phosphotyrosine-binding protein (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-03-14
    Description: Growth factors stimulate cells to take up excess nutrients and to use them for anabolic processes. The biochemical mechanism by which this is accomplished is not fully understood but it is initiated by phosphorylation of signalling proteins on tyrosine residues. Using a novel proteomic screen for phosphotyrosine-binding proteins, we have made the observation that an enzyme involved in glycolysis, the human M2 (fetal) isoform of pyruvate kinase (PKM2), binds directly and selectively to tyrosine-phosphorylated peptides. We show that binding of phosphotyrosine peptides to PKM2 results in release of the allosteric activator fructose-1,6-bisphosphate, leading to inhibition of PKM2 enzymatic activity. We also provide evidence that this regulation of PKM2 by phosphotyrosine signalling diverts glucose metabolites from energy production to anabolic processes when cells are stimulated by certain growth factors. Collectively, our results indicate that expression of this phosphotyrosine-binding form of pyruvate kinase is critical for rapid growth in cancer cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Christofk, Heather R -- Vander Heiden, Matthew G -- Wu, Ning -- Asara, John M -- Cantley, Lewis C -- R01 GM056203/GM/NIGMS NIH HHS/ -- T32 CA009172/CA/NCI NIH HHS/ -- England -- Nature. 2008 Mar 13;452(7184):181-6. doi: 10.1038/nature06667.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Systems Biology.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337815" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Site ; Animals ; Catalysis ; Cell Line ; Cell Proliferation/drug effects ; Cells/drug effects/metabolism ; HeLa Cells ; Humans ; Lysine/metabolism ; Models, Molecular ; Peptide Library ; Phosphotyrosine/*metabolism ; Protein Binding ; Proteomics ; Pyruvate Kinase/antagonists & inhibitors/*metabolism ; Substrate Specificity
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  • 2
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    Structural recognition and functional activation of FcgammaR by innate pentraxins (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-11-18
    Description: Pentraxins are a family of ancient innate immune mediators conserved throughout evolution. The classical pentraxins include serum amyloid P component (SAP) and C-reactive protein, which are two of the acute-phase proteins synthesized in response to infection. Both recognize microbial pathogens and activate the classical complement pathway through C1q (refs 3 and 4). More recently, members of the pentraxin family were found to interact with cell-surface Fcgamma receptors (FcgammaR) and activate leukocyte-mediated phagocytosis. Here we describe the structural mechanism for pentraxin's binding to FcgammaR and its functional activation of FcgammaR-mediated phagocytosis and cytokine secretion. The complex structure between human SAP and FcgammaRIIa reveals a diagonally bound receptor on each SAP pentamer with both D1 and D2 domains of the receptor contacting the ridge helices from two SAP subunits. The 1:1 stoichiometry between SAP and FcgammaRIIa infers the requirement for multivalent pathogen binding for receptor aggregation. Mutational and binding studies show that pentraxins are diverse in their binding specificity for FcgammaR isoforms but conserved in their recognition structure. The shared binding site for SAP and IgG results in competition for FcgammaR binding and the inhibition of immune-complex-mediated phagocytosis by soluble pentraxins. These results establish antibody-like functions for pentraxins in the FcgammaR pathway, suggest an evolutionary overlap between the innate and adaptive immune systems, and have new therapeutic implications for autoimmune diseases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688732/" 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/PMC2688732/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Jinghua -- Marnell, Lorraine L -- Marjon, Kristopher D -- Mold, Carolyn -- Du Clos, Terry W -- Sun, Peter D -- R01 AI28358/AI/NIAID NIH HHS/ -- T32 AI007538/AI/NIAID NIH HHS/ -- Z01 AI000853-09/Intramural NIH HHS/ -- England -- Nature. 2008 Dec 18;456(7224):989-92. doi: 10.1038/nature07468. Epub 2008 Nov 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19011614" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Binding, Competitive ; C-Reactive Protein/chemistry/*immunology/*metabolism ; Crystallography, X-Ray ; Cytokines/immunology/secretion ; Humans ; Immunity, Innate/*immunology ; Immunoglobulin G/immunology/metabolism ; Macrophages/cytology/immunology ; Models, Molecular ; Phagocytosis ; Protein Conformation ; Receptors, IgG/chemistry/*immunology/*metabolism ; Serum Amyloid P-Component/chemistry/*immunology/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
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    Structural basis for gibberellin recognition by its receptor GID1 (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-11-28
    Description: Gibberellins (GAs) are phytohormones essential for many developmental processes in plants. A nuclear GA receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1), has a primary structure similar to that of the hormone-sensitive lipases (HSLs). Here we analyse the crystal structure of Oryza sativa GID1 (OsGID1) bound with GA(4) and GA(3) at 1.9 A resolution. The overall structure of both complexes shows an alpha/beta-hydrolase fold similar to that of HSLs except for an amino-terminal lid. The GA-binding pocket corresponds to the substrate-binding site of HSLs. On the basis of the OsGID1 structure, we mutagenized important residues for GA binding and examined their binding activities. Almost all of them showed very little or no activity, confirming that the residues revealed by structural analysis are important for GA binding. The replacement of Ile 133 with Leu or Val-residues corresponding to those of the lycophyte Selaginella moellendorffii GID1s-caused an increase in the binding affinity for GA(34), a 2beta-hydroxylated GA(4). These observations indicate that GID1 originated from HSL and was further modified to have higher affinity and more strict selectivity for bioactive GAs by adapting the amino acids involved in GA binding in the course of plant evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shimada, Asako -- Ueguchi-Tanaka, Miyako -- Nakatsu, Toru -- Nakajima, Masatoshi -- Naoe, Youichi -- Ohmiya, Hiroko -- Kato, Hiroaki -- Matsuoka, Makoto -- England -- Nature. 2008 Nov 27;456(7221):520-3. doi: 10.1038/nature07546.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19037316" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Gibberellins/*chemistry/*metabolism ; Hydrolases/chemistry/metabolism ; Hydroxylation ; Models, Molecular ; Oryza/*chemistry/genetics/metabolism ; Plant Growth Regulators/*chemistry/*metabolism ; Plant Proteins/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Conformation ; Substrate Specificity ; Two-Hybrid System Techniques
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
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    Darwin 200: Great expectations (2008)
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    Publication Date: 2008-11-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2008 Nov 20;456(7220):317-8. doi: 10.1038/456317a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19020598" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Anniversaries and Special Events ; Biodiversity ; *Biological Evolution ; Epidemiology/trends ; Humans ; Models, Biological ; Mutagenesis ; Religion and Science ; Science/*trends ; Selection, Genetic
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  • 5
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    Cancer: Deconstructing oncogenesis (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-06-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Luo, Ji -- Elledge, Stephen J -- England -- Nature. 2008 Jun 19;453(7198):995-6. doi: 10.1038/453995a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18563141" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Transformation, Neoplastic/*genetics ; Colonic Neoplasms/genetics/pathology ; Gene Expression Regulation, Neoplastic ; Genes, p53/genetics ; Genes, ras/genetics ; Humans ; Models, Biological ; Oncogenes/*genetics
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  • 6
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    Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-05-16
    Description: The potential impact of pandemic influenza makes effective measures to limit the spread and morbidity of virus infection a public health priority. Antiviral drugs are seen as essential requirements for control of initial influenza outbreaks caused by a new virus, and in pre-pandemic plans there is a heavy reliance on drug stockpiles. The principal target for these drugs is a virus surface glycoprotein, neuraminidase, which facilitates the release of nascent virus and thus the spread of infection. Oseltamivir (Tamiflu) and zanamivir (Relenza) are two currently used neuraminidase inhibitors that were developed using knowledge of the enzyme structure. It has been proposed that the closer such inhibitors resemble the natural substrate, the less likely they are to select drug-resistant mutant viruses that retain viability. However, there have been reports of drug-resistant mutant selection in vitro and from infected humans. We report here the enzymatic properties and crystal structures of neuraminidase mutants from H5N1-infected patients that explain the molecular basis of resistance. Our results show that these mutants are resistant to oseltamivir but still strongly inhibited by zanamivir owing to an altered hydrophobic pocket in the active site of the enzyme required for oseltamivir binding. Together with recent reports of the viability and pathogenesis of H5N1 (ref. 7) and H1N1 (ref. 8) viruses with neuraminidases carrying these mutations, our results indicate that it would be prudent for pandemic stockpiles of oseltamivir to be augmented by additional antiviral drugs, including zanamivir.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Collins, Patrick J -- Haire, Lesley F -- Lin, Yi Pu -- Liu, Junfeng -- Russell, Rupert J -- Walker, Philip A -- Skehel, John J -- Martin, Stephen R -- Hay, Alan J -- Gamblin, Steven J -- MC_U117512711/Medical Research Council/United Kingdom -- MC_U117512723/Medical Research Council/United Kingdom -- MC_U117570592/Medical Research Council/United Kingdom -- MC_U117584222/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2008 Jun 26;453(7199):1258-61. doi: 10.1038/nature06956. Epub 2008 May 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18480754" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; *Drug Resistance, Viral ; Enzyme Inhibitors/chemistry/metabolism/pharmacology ; Humans ; Influenza A Virus, H1N1 Subtype/drug effects/enzymology/genetics ; Influenza A Virus, H5N1 Subtype/*drug effects/*enzymology/genetics ; Influenza, Human/virology ; Kinetics ; Models, Molecular ; Molecular Conformation ; Mutation/*genetics ; Neuraminidase/antagonists & inhibitors/*chemistry/*genetics/metabolism ; Oseltamivir/chemistry/metabolism/*pharmacology ; Protein Binding ; Zanamivir/pharmacology
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  • 7
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    Structure of the 30S translation initiation complex (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-09-02
    Description: Translation initiation, the rate-limiting step of the universal process of protein synthesis, proceeds through sequential, tightly regulated steps. In bacteria, the correct messenger RNA start site and the reading frame are selected when, with the help of initiation factors IF1, IF2 and IF3, the initiation codon is decoded in the peptidyl site of the 30S ribosomal subunit by the fMet-tRNA(fMet) anticodon. This yields a 30S initiation complex (30SIC) that is an intermediate in the formation of the 70S initiation complex (70SIC) that occurs on joining of the 50S ribosomal subunit to the 30SIC and release of the initiation factors. The localization of IF2 in the 30SIC has proved to be difficult so far using biochemical approaches, but could now be addressed using cryo-electron microscopy and advanced particle separation techniques on the basis of three-dimensional statistical analysis. Here we report the direct visualization of a 30SIC containing mRNA, fMet-tRNA(fMet) and initiation factors IF1 and GTP-bound IF2. We demonstrate that the fMet-tRNA(fMet) is held in a characteristic and precise position and conformation by two interactions that contribute to the formation of a stable complex: one involves the transfer RNA decoding stem which is buried in the 30S peptidyl site, and the other occurs between the carboxy-terminal domain of IF2 and the tRNA acceptor end. The structure provides insights into the mechanism of 70SIC assembly and rationalizes the rapid activation of GTP hydrolysis triggered on 30SIC-50S joining by showing that the GTP-binding domain of IF2 would directly face the GTPase-activated centre of the 50S subunit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simonetti, Angelita -- Marzi, Stefano -- Myasnikov, Alexander G -- Fabbretti, Attilio -- Yusupov, Marat -- Gualerzi, Claudio O -- Klaholz, Bruno P -- England -- Nature. 2008 Sep 18;455(7211):416-20. doi: 10.1038/nature07192. Epub 2008 Aug 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Genetics and of Molecular and Cellular Biology, Department of Structural Biology and Genomics, Illkirch F-67404, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18758445" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; Crystallography, X-Ray ; Guanosine Triphosphate/chemistry/metabolism ; Models, Molecular ; Multiprotein Complexes/*chemistry/genetics/metabolism/*ultrastructure ; *Peptide Chain Initiation, Translational ; Prokaryotic Initiation Factor-1/chemistry/genetics/metabolism/ultrastructure ; Prokaryotic Initiation Factor-2/chemistry/genetics/metabolism/ultrastructure ; Protein Conformation ; RNA, Messenger/chemistry/genetics/metabolism ; RNA, Transfer, Met/chemistry/genetics/metabolism/ultrastructure ; Ribosome Subunits/chemistry/metabolism/ultrastructure ; Ribosomes/chemistry/*metabolism/*ultrastructure ; Thermus thermophilus/*enzymology/genetics/*ultrastructure
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  • 8
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    Systems biology: Reverse engineering the cell (2008)
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    Publication Date: 2008-08-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ingolia, Nicholas T -- Weissman, Jonathan S -- England -- Nature. 2008 Aug 28;454(7208):1059-62. doi: 10.1038/4541059a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18756243" target="_blank"〉PubMed〈/a〉
    Keywords: *Environment ; Galactose/metabolism ; *Gene Expression Regulation, Fungal/drug effects ; Glucose/metabolism/pharmacology ; Metabolic Networks and Pathways/drug effects/*genetics ; Microfluidics ; Models, Biological ; Osmotic Pressure ; RNA Stability/drug effects ; Saccharomyces cerevisiae/classification/drug effects/*genetics/*metabolism ; Systems Biology
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  • 9
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    Preserving cell shape under environmental stress (2008)
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    Publication Date: 2008-02-26
    Description: Maintaining cell shape and tone is crucial for the function and survival of cells and tissues. Mechanotransduction relies on the transformation of minuscule mechanical forces into high-fidelity electrical responses. When mechanoreceptors are stimulated, mechanically sensitive cation channels open and produce an inward transduction current that depolarizes the cell. For this process to operate effectively, the transduction machinery has to retain integrity and remain unfailingly independent of environmental changes. This is particularly challenging for poikilothermic organisms, where changes in temperature in the environment may impact the function of mechanoreceptor neurons. Thus, we wondered how insects whose habitat might quickly vary over several tens of degrees of temperature manage to maintain highly effective mechanical senses. We screened for Drosophila mutants with defective mechanical responses at elevated ambient temperatures, and identified a gene, spam, whose role is to protect the mechanosensory organ from massive cellular deformation caused by heat-induced osmotic imbalance. Here we show that Spam protein forms an extracellular shield that guards mechanosensory neurons from environmental insult. Remarkably, heterologously expressed Spam protein also endowed other cells with superb defence against physically and chemically induced deformation. We studied the mechanical impact of Spam coating and show that spam-coated cells are up to ten times stiffer than uncoated controls. Together, these results help explain how poikilothermic organisms preserve the architecture of critical cells during environmental stress, and illustrate an elegant and simple solution to such challenge.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387185/" 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/PMC2387185/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cook, Boaz -- Hardy, Robert W -- McConnaughey, William B -- Zuker, Charles S -- R01 EY006979/EY/NEI NIH HHS/ -- R01 EY006979-18/EY/NEI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Mar 20;452(7185):361-4. doi: 10.1038/nature06603. Epub 2008 Feb 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Departments of Neurobiology and Neurosciences, University of California at San Diego, La Jolla, California 92093-0649, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18297055" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cell Shape/*drug effects/*physiology ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/*cytology/drug effects/genetics/physiology ; Electrophysiology ; *Environment ; Eye Proteins/genetics/metabolism ; Hot Temperature ; Humidity ; Mechanoreceptors/cytology/physiology ; Mechanotransduction, Cellular/*drug effects/*physiology ; Models, Biological ; Osmotic Pressure ; Stimulation, Chemical ; Stress, Mechanical
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  • 10
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    Computational biochemistry: old enzymes, new tricks (2008)
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    Publication Date: 2008-05-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ghirlanda, Giovanna -- England -- Nature. 2008 May 8;453(7192):164-6. doi: 10.1038/453164a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18464727" target="_blank"〉PubMed〈/a〉
    Keywords: Biochemistry/*methods ; Catalysis ; Computational Biology/*methods ; Directed Molecular Evolution/*methods ; Drug Design ; Drug Evaluation, Preclinical ; Enzymes/*chemistry/*metabolism ; Models, Molecular ; Protein Engineering/*methods
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  • 11
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    High-amplitude fluctuations and alternative dynamical states of midges in Lake Myvatn (2008)
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    Publication Date: 2008-03-07
    Description: Complex dynamics are often shown by simple ecological models and have been clearly demonstrated in laboratory and natural systems. Yet many classes of theoretically possible dynamics are still poorly documented in nature. Here we study long-term time-series data of a midge, Tanytarsus gracilentus (Diptera: Chironomidae), in Lake Myvatn, Iceland. The midge undergoes density fluctuations of almost six orders of magnitude. Rather than regular cycles, however, these fluctuations have irregular periods of 4-7 years, indicating complex dynamics. We fit three consumer-resource models capable of qualitatively distinct dynamics to the data. Of these, the best-fitting model shows alternative dynamical states in the absence of environmental variability; depending on the initial midge densities, the model shows either fluctuations around a fixed point or high-amplitude cycles. This explains the observed complex population dynamics: high-amplitude but irregular fluctuations occur because stochastic variability causes the dynamics to switch between domains of attraction to the alternative states. In the model, the amplitude of fluctuations depends strongly on minute resource subsidies into the midge habitat. These resource subsidies may be sensitive to human-caused changes in the hydrology of the lake, with human impacts such as dredging leading to higher-amplitude fluctuations. Tanytarsus gracilentus is a key component of the Myvatn ecosystem, representing two-thirds of the secondary productivity of the lake and providing vital food resources to fish and to breeding bird populations. Therefore the high-amplitude, irregular fluctuations in midge densities generated by alternative dynamical states dominate much of the ecology of the lake.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ives, Anthony R -- Einarsson, Arni -- Jansen, Vincent A A -- Gardarsson, Arnthor -- England -- Nature. 2008 Mar 6;452(7183):84-7. doi: 10.1038/nature06610.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA. arives@wisc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18322533" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chironomidae/*physiology ; Computer Simulation ; *Ecosystem ; Eukaryota/physiology ; Food ; *Fresh Water ; Iceland ; Models, Biological ; Population Density ; Stochastic Processes
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  • 12
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    Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex (2008)
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    Publication Date: 2008-12-19
    Description: Here we report on a 3.0 A crystal structure of a ternary complex of wild-type Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-nucleotide guide DNA and a 20-nucleotide target RNA containing cleavage-preventing mismatches at the 10-11 step. The seed segment (positions 2 to 8) adopts an A-helical-like Watson-Crick paired duplex, with both ends of the guide strand anchored in the complex. An arginine, inserted between guide-strand bases 10 and 11 in the binary complex, locking it in an inactive conformation, is released on ternary complex formation. The nucleic-acid-binding channel between the PAZ- and PIWI-containing lobes of argonaute widens on formation of a more open ternary complex. The relationship of structure to function was established by determining cleavage activity of ternary complexes containing position-dependent base mismatch, bulge and 2'-O-methyl modifications. Consistent with the geometry of the ternary complex, bulges residing in the seed segments of the target, but not the guide strand, were better accommodated and their complexes were catalytically active.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765400/" 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/PMC2765400/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Yanli -- Juranek, Stefan -- Li, Haitao -- Sheng, Gang -- Tuschl, Thomas -- Patel, Dinshaw J -- R01 AI068776/AI/NIAID NIH HHS/ -- R01 AI068776-02/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Dec 18;456(7224):921-6. doi: 10.1038/nature07666.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19092929" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/genetics/*metabolism ; Base Pair Mismatch ; Base Pairing ; Base Sequence ; Crystallography, X-Ray ; DNA/chemistry/genetics/*metabolism ; Methylation ; Models, Molecular ; Phosphorylation ; Protein Conformation ; RNA/chemistry/genetics/*metabolism ; RNA Interference ; RNA-Induced Silencing Complex/*chemistry/genetics/*metabolism ; Substrate Specificity ; Thermus thermophilus/*chemistry
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    The replisome uses mRNA as a primer after colliding with RNA polymerase (2008)
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    Publication Date: 2008-11-21
    Description: Replication forks are impeded by DNA damage and protein-nucleic acid complexes such as transcribing RNA polymerase. For example, head-on collision of the replisome with RNA polymerase results in replication fork arrest. However, co-directional collision of the replisome with RNA polymerase has little or no effect on fork progression. Here we examine co-directional collisions between a replisome and RNA polymerase in vitro. We show that the Escherichia coli replisome uses the RNA transcript as a primer to continue leading-strand synthesis after the collision with RNA polymerase that is displaced from the DNA. This action results in a discontinuity in the leading strand, yet the replisome remains intact and bound to DNA during the entire process. These findings underscore the notable plasticity by which the replisome operates to circumvent obstacles in its path and may explain why the leading strand is synthesized discontinuously in vivo.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2605185/" 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/PMC2605185/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pomerantz, Richard T -- O'Donnell, Mike -- R01 GM038839/GM/NIGMS NIH HHS/ -- R01 GM038839-21/GM/NIGMS NIH HHS/ -- R37 GM038839/GM/NIGMS NIH HHS/ -- R37 GM038839-20/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Dec 11;456(7223):762-6. doi: 10.1038/nature07527. Epub 2008 Nov 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, New York 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19020502" target="_blank"〉PubMed〈/a〉
    Keywords: DNA Polymerase III/*metabolism ; DNA Replication ; DNA, Bacterial/metabolism ; DNA-Directed RNA Polymerases/*metabolism ; Escherichia coli/genetics/*metabolism ; Models, Molecular ; *Rna ; RNA, Bacterial/*metabolism ; RNA, Messenger/*metabolism
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    Structure of the Tribolium castaneum telomerase catalytic subunit TERT (2008)
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    Publication Date: 2008-09-02
    Description: A common hallmark of human cancers is the overexpression of telomerase, a ribonucleoprotein complex that is responsible for maintaining the length and integrity of chromosome ends. Telomere length deregulation and telomerase activation is an early, and perhaps necessary, step in cancer cell evolution. Here we present the high-resolution structure of the Tribolium castaneum catalytic subunit of telomerase, TERT. The protein consists of three highly conserved domains, organized into a ring-like structure that shares common features with retroviral reverse transcriptases, viral RNA polymerases and B-family DNA polymerases. Domain organization places motifs implicated in substrate binding and catalysis in the interior of the ring, which can accommodate seven to eight bases of double-stranded nucleic acid. Modelling of an RNA-DNA heteroduplex in the interior of this ring demonstrates a perfect fit between the protein and the nucleic acid substrate, and positions the 3'-end of the DNA primer at the active site of the enzyme, providing evidence for the formation of an active telomerase elongation complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gillis, Andrew J -- Schuller, Anthony P -- Skordalakes, Emmanuel -- England -- Nature. 2008 Oct 2;455(7213):633-7. doi: 10.1038/nature07283. Epub 2008 Aug 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gene Expression and Regulation Program, The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18758444" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Binding Sites ; Catalysis ; Catalytic Domain ; Conserved Sequence ; Crystallization ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Nucleotides/metabolism ; Protein Structure, Tertiary ; Telomerase/*chemistry/metabolism ; Tribolium/*enzymology
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    Developmental biology: order in the lung (2008)
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    Publication Date: 2008-06-06
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865228/" 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/PMC2865228/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Warburton, David -- P01 HL060231/HL/NHLBI NIH HHS/ -- P01 HL060231-09/HL/NHLBI NIH HHS/ -- R01 HL044060/HL/NHLBI NIH HHS/ -- R01 HL044977/HL/NHLBI NIH HHS/ -- R01 HL044977-16/HL/NHLBI NIH HHS/ -- England -- Nature. 2008 Jun 5;453(7196):733-5. doi: 10.1038/453733a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18528385" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing ; Animals ; Body Patterning/genetics/*physiology ; Fibroblast Growth Factor 10/metabolism ; Intracellular Signaling Peptides and Proteins ; Lung/*anatomy & histology/*embryology/metabolism ; Membrane Proteins/metabolism ; Mice ; Models, Biological ; Organogenesis/genetics/*physiology ; Receptor, Fibroblast Growth Factor, Type 2/genetics/metabolism
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    The earliest thymic progenitors for T cells possess myeloid lineage potential (2008)
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    Publication Date: 2008-04-11
    Description: There exists controversy over the nature of haematopoietic progenitors of T cells. Most T cells develop in the thymus, but the lineage potential of thymus-colonizing progenitors is unknown. One approach to resolving this question is to determine the lineage potentials of the earliest thymic progenitors (ETPs). Previous work has shown that ETPs possess T and natural killer lymphoid potentials, and rare subsets of ETPs also possess B lymphoid potential, suggesting an origin from lymphoid-restricted progenitor cells. However, whether ETPs also possess myeloid potential is unknown. Here we show that nearly all ETPs in adult mice possess both T and myeloid potential in clonal assays. The existence of progenitors possessing T and myeloid potential within the thymus is incompatible with the current dominant model of haematopoiesis, in which T cells are proposed to arise from lymphoid-. Our results indicate that alternative models for lineage commitment during haematopoiesis must be considered.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bell, J Jeremiah -- Bhandoola, Avinash -- England -- Nature. 2008 Apr 10;452(7188):764-7. doi: 10.1038/nature06840.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18401411" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Cell Lineage ; Cells, Cultured ; Coculture Techniques ; Dendritic Cells/cytology ; Female ; Granulocytes/cytology ; *Hematopoiesis ; Hematopoietic Stem Cells/*cytology/metabolism ; Macrophages/cytology ; Mice ; Models, Biological ; Myeloid Cells/*cytology/metabolism ; Stromal Cells/cytology ; T-Lymphocytes/*cytology/metabolism ; Thymus Gland/*cytology
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    Oligopotent stem cells are distributed throughout the mammalian ocular surface (2008)
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    Publication Date: 2008-10-03
    Description: The integrity of the cornea, the most anterior part of the eye, is indispensable for vision. Forty-five million individuals worldwide are bilaterally blind and another 135 million have severely impaired vision in both eyes because of loss of corneal transparency; treatments range from local medications to corneal transplants, and more recently to stem cell therapy. The corneal epithelium is a squamous epithelium that is constantly renewing, with a vertical turnover of 7 to 14 days in many mammals. Identification of slow cycling cells (label-retaining cells) in the limbus of the mouse has led to the notion that the limbus is the niche for the stem cells responsible for the long-term renewal of the cornea; hence, the corneal epithelium is supposedly renewed by cells generated at and migrating from the limbus, in marked opposition to other squamous epithelia in which each resident stem cell has in charge a limited area of epithelium. Here we show that the corneal epithelium of the mouse can be serially transplanted, is self-maintained and contains oligopotent stem cells with the capacity to generate goblet cells if provided with a conjunctival environment. Furthermore, the entire ocular surface of the pig, including the cornea, contains oligopotent stem cells (holoclones) with the capacity to generate individual colonies of corneal and conjunctival cells. Therefore, the limbus is not the only niche for corneal stem cells and corneal renewal is not different from other squamous epithelia. We propose a model that unifies our observations with the literature and explains why the limbal region is enriched in stem cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Majo, Francois -- Rochat, Ariane -- Nicolas, Michael -- Jaoude, Georges Abou -- Barrandon, Yann -- England -- Nature. 2008 Nov 13;456(7219):250-4. doi: 10.1038/nature07406. Epub 2008 Oct 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Stem Cell Dynamics, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne CH, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18830243" target="_blank"〉PubMed〈/a〉
    Keywords: Adult Stem Cells/*cytology ; Animals ; Cattle ; Cells, Cultured ; Child, Preschool ; Clone Cells ; Corneal Transplantation ; Epithelium, Corneal/*cytology/metabolism ; Female ; Gene Expression Regulation ; Humans ; Infant ; Keratinocytes/cytology/metabolism ; Male ; Mice ; Mice, SCID ; Models, Biological ; Multipotent Stem Cells/*cytology ; Proteins/metabolism ; Rats ; Swine
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    The adaptive significance of temperature-dependent sex determination in a reptile (2008)
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    Publication Date: 2008-01-22
    Description: Understanding the mechanisms that determine an individual's sex remains a primary challenge for evolutionary biology. Chromosome-based systems (genotypic sex determination) that generate roughly equal numbers of sons and daughters accord with theory, but the adaptive significance of environmental sex determination (that is, when embryonic environmental conditions determine offspring sex, ESD) is a major unsolved problem. Theoretical models predict that selection should favour ESD over genotypic sex determination when the developmental environment differentially influences male versus female fitness (that is, the Charnov-Bull model), but empirical evidence for this hypothesis remains elusive in amniote vertebrates--the clade in which ESD is most prevalent. Here we provide the first substantial empirical support for this model by showing that incubation temperatures influence reproductive success of males differently than that of females in a short-lived lizard (Amphibolurus muricatus, Agamidae) with temperature-dependent sex determination. We incubated eggs at a variety of temperatures, and de-confounded sex and incubation temperature by using hormonal manipulations to embryos. We then raised lizards in field enclosures and quantified their lifetime reproductive success. Incubation temperature affected reproductive success differently in males versus females in exactly the way predicted by theory: the fitness of each sex was maximized by the incubation temperature that produces that sex. Our results provide unequivocal empirical support for the Charnov-Bull model for the adaptive significance of temperature-dependent sex determination in amniote vertebrates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Warner, D A -- Shine, R -- England -- Nature. 2008 Jan 31;451(7178):566-8. doi: 10.1038/nature06519. Epub 2008 Jan 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia. dwarner@iastate.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18204437" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization/physiology ; Adaptation, Physiological/*physiology ; Animals ; Body Size ; Fadrozole/pharmacology ; Female ; Lizards/*embryology/*physiology ; Male ; Models, Biological ; Ovum/drug effects/growth & development ; Reproduction/physiology ; Sex Characteristics ; Sex Differentiation/*physiology ; *Temperature
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    Structure of a beta1-adrenergic G-protein-coupled receptor (2008)
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    Publication Date: 2008-07-03
    Description: G-protein-coupled receptors have a major role in transmembrane signalling in most eukaryotes and many are important drug targets. Here we report the 2.7 A resolution crystal structure of a beta(1)-adrenergic receptor in complex with the high-affinity antagonist cyanopindolol. The modified turkey (Meleagris gallopavo) receptor was selected to be in its antagonist conformation and its thermostability improved by earlier limited mutagenesis. The ligand-binding pocket comprises 15 side chains from amino acid residues in 4 transmembrane alpha-helices and extracellular loop 2. This loop defines the entrance of the ligand-binding pocket and is stabilized by two disulphide bonds and a sodium ion. Binding of cyanopindolol to the beta(1)-adrenergic receptor and binding of carazolol to the beta(2)-adrenergic receptor involve similar interactions. A short well-defined helix in cytoplasmic loop 2, not observed in either rhodopsin or the beta(2)-adrenergic receptor, directly interacts by means of a tyrosine with the highly conserved DRY motif at the end of helix 3 that is essential for receptor activation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923055/" 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/PMC2923055/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Warne, Tony -- Serrano-Vega, Maria J -- Baker, Jillian G -- Moukhametzianov, Rouslan -- Edwards, Patricia C -- Henderson, Richard -- Leslie, Andrew G W -- Tate, Christopher G -- Schertler, Gebhard F X -- MC_U105178937/Medical Research Council/United Kingdom -- MC_U105184322/Medical Research Council/United Kingdom -- MC_U105184325/Medical Research Council/United Kingdom -- MC_U105197215/Medical Research Council/United Kingdom -- U.1051.04.020(78937)/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2008 Jul 24;454(7203):486-91. doi: 10.1038/nature07101. Epub 2008 Jun 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18594507" target="_blank"〉PubMed〈/a〉
    Keywords: Adrenergic beta-1 Receptor Agonists ; Adrenergic beta-1 Receptor Antagonists ; Adrenergic beta-Antagonists/chemistry/metabolism ; Amino Acid Motifs ; Animals ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Ligands ; Models, Molecular ; Mutant Proteins/chemistry/genetics/metabolism ; Mutation ; Pindolol/analogs & derivatives/chemistry/metabolism ; Propanolamines/chemistry/metabolism ; Protein Conformation ; Receptors, Adrenergic, beta-1/*chemistry/metabolism ; Thermodynamics ; Turkeys
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    Chaos in a long-term experiment with a plankton community (2008)
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    Publication Date: 2008-02-15
    Description: Mathematical models predict that species interactions such as competition and predation can generate chaos. However, experimental demonstrations of chaos in ecology are scarce, and have been limited to simple laboratory systems with a short duration and artificial species combinations. Here, we present the first experimental demonstration of chaos in a long-term experiment with a complex food web. Our food web was isolated from the Baltic Sea, and consisted of bacteria, several phytoplankton species, herbivorous and predatory zooplankton species, and detritivores. The food web was cultured in a laboratory mesocosm, and sampled twice a week for more than 2,300 days. Despite constant external conditions, the species abundances showed striking fluctuations over several orders of magnitude. These fluctuations displayed a variety of different periodicities, which could be attributed to different species interactions in the food web. The population dynamics were characterized by positive Lyapunov exponents of similar magnitude for each species. Predictability was limited to a time horizon of 15-30 days, only slightly longer than the local weather forecast. Hence, our results demonstrate that species interactions in food webs can generate chaos. This implies that stability is not required for the persistence of complex food webs, and that the long-term prediction of species abundances can be fundamentally impossible.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beninca, Elisa -- Huisman, Jef -- Heerkloss, Reinhard -- Johnk, Klaus D -- Branco, Pedro -- Van Nes, Egbert H -- Scheffer, Marten -- Ellner, Stephen P -- England -- Nature. 2008 Feb 14;451(7180):822-5. doi: 10.1038/nature06512.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Nieuwe Achtergracht 127, 1018 WS Amsterdam, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18273017" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacteria/metabolism ; *Food Chain ; Models, Biological ; *Nonlinear Dynamics ; Oceans and Seas ; Plankton/*metabolism ; Population Dynamics ; Species Specificity ; Time Factors
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    Scaling of the BMP activation gradient in Xenopus embryos (2008)
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    Publication Date: 2008-06-27
    Description: In groundbreaking experiments, Hans Spemann demonstrated that the dorsal part of the amphibian embryo can generate a well-proportioned tadpole, and that a small group of dorsal cells, the 'organizer', can induce a complete and well-proportioned twinned axis when transplanted into a host embryo. Key to organizer function is the localized secretion of inhibitors of bone morphogenetic protein (BMP), which defines a graded BMP activation profile. Although the central proteins involved in shaping this gradient are well characterized, their integrated function, and in particular how pattern scales with size, is not understood. Here we present evidence that in Xenopus, the BMP activity gradient is defined by a 'shuttling-based' mechanism, whereby the BMP ligands are translocated ventrally through their association with the BMP inhibitor Chordin. This shuttling, with feedback repression of the BMP ligand Admp, offers a quantitative explanation to Spemann's observations, and accounts naturally for the scaling of embryo pattern with its size.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ben-Zvi, Danny -- Shilo, Ben-Zion -- Fainsod, Abraham -- Barkai, Naama -- England -- Nature. 2008 Jun 26;453(7199):1205-11. doi: 10.1038/nature07059.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18580943" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Body Patterning ; Body Size ; Bone Morphogenetic Protein 4 ; Bone Morphogenetic Proteins/antagonists & inhibitors/*metabolism ; Embryo, Nonmammalian/embryology/*metabolism ; Glycoproteins/metabolism ; Intercellular Signaling Peptides and Proteins/metabolism ; Ligands ; Models, Biological ; Protein Transport ; Xenopus/*embryology/genetics/metabolism ; Xenopus Proteins/metabolism
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    Microbiology: straight from the gut (2008)
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    Publication Date: 2008-05-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mandavilli, Apoorva -- England -- Nature. 2008 May 29;453(7195):581-2. doi: 10.1038/453581a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18509413" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Defensins/metabolism ; *Ecosystem ; Feces/*microbiology ; Female ; Humans ; Infant, Newborn ; Intestines/*microbiology/*transplantation ; Models, Biological ; Nod2 Signaling Adaptor Protein/genetics/metabolism
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    Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy (2008)
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    Publication Date: 2008-02-29
    Description: A half-century after the determination of the first three-dimensional crystal structure of a protein, more than 40,000 structures ranging from single polypeptides to large assemblies have been reported. The challenge for crystallographers, however, remains the growing of a diffracting crystal. Here we report the 4.5-A resolution structure of a 22-MDa macromolecular assembly, the capsid of the infectious epsilon15 (epsilon15) particle, by single-particle electron cryomicroscopy. From this density map we constructed a complete backbone trace of its major capsid protein, gene product 7 (gp7). The structure reveals a similar protein architecture to that of other tailed double-stranded DNA viruses, even in the absence of detectable sequence similarity. However, the connectivity of the secondary structure elements (topology) in gp7 is unique. Protruding densities are observed around the two-fold axes that cannot be accounted for by gp7. A subsequent proteomic analysis of the whole virus identifies these densities as gp10, a 12-kDa protein. Its structure, location and high binding affinity to the capsid indicate that the gp10 dimer functions as a molecular staple between neighbouring capsomeres to ensure the particle's stability. Beyond epsilon15, this method potentially offers a new approach for modelling the backbone conformations of the protein subunits in other macromolecular assemblies at near-native solution states.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Wen -- Baker, Matthew L -- Jakana, Joanita -- Weigele, Peter R -- King, Jonathan -- Chiu, Wah -- England -- Nature. 2008 Feb 28;451(7182):1130-4. doi: 10.1038/nature06665.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA. jiang12@purdue.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18305544" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophages/*chemistry/genetics/*ultrastructure ; Capsid/*chemistry/*ultrastructure ; Capsid Proteins/chemistry/ultrastructure ; Cryoelectron Microscopy ; DNA Viruses/chemistry/genetics/ultrastructure ; Models, Molecular ; Molecular Conformation ; Salmonella/*virology
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    Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins (2008)
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    Publication Date: 2008-05-27
    Description: Understanding the energetics of molecular interactions is fundamental to all of the central quests of structural biology including structure prediction and design, mapping evolutionary pathways, learning how mutations cause disease, drug design, and relating structure to function. Hydrogen-bonding is widely regarded as an important force in a membrane environment because of the low dielectric constant of membranes and a lack of competition from water. Indeed, polar residue substitutions are the most common disease-causing mutations in membrane proteins. Because of limited structural information and technical challenges, however, there have been few quantitative tests of hydrogen-bond strength in the context of large membrane proteins. Here we show, by using a double-mutant cycle analysis, that the average contribution of eight interhelical side-chain hydrogen-bonding interactions throughout bacteriorhodopsin is only 0.6 kcal mol(-1). In agreement with these experiments, we find that 4% of polar atoms in the non-polar core regions of membrane proteins have no hydrogen-bond partner and the lengths of buried hydrogen bonds in soluble proteins and membrane protein transmembrane regions are statistically identical. Our results indicate that most hydrogen-bond interactions in membrane proteins are only modestly stabilizing. Weak hydrogen-bonding should be reflected in considerations of membrane protein folding, dynamics, design, evolution and function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734483/" 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/PMC2734483/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joh, Nathan Hyunjoong -- Min, Andrew -- Faham, Salem -- Whitelegge, Julian P -- Yang, Duan -- Woods, Virgil L -- Bowie, James U -- R01 CA081000/CA/NCI NIH HHS/ -- R01 CA081000-07/CA/NCI NIH HHS/ -- R01 CA081000-08/CA/NCI NIH HHS/ -- R01 CA081000-09/CA/NCI NIH HHS/ -- R01 GM063919/GM/NIGMS NIH HHS/ -- R01 GM063919-06/GM/NIGMS NIH HHS/ -- R01 GM063919-07/GM/NIGMS NIH HHS/ -- R01 GM063919-08/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Jun 26;453(7199):1266-70. doi: 10.1038/nature06977. Epub 2008 May 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, UCLA-DOE Center for Genomics and Proteomics, Molecular Biology Institute, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18500332" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriorhodopsins/chemistry/genetics/metabolism ; Crystallography, X-Ray ; Deuterium Exchange Measurement ; Hydrogen Bonding ; Membrane Proteins/*chemistry/genetics/*metabolism ; Models, Molecular ; Mutation/genetics ; Protein Folding ; Solubility ; Thermodynamics
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    Evolutionary biology: a first for bats (2008)
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    Publication Date: 2008-02-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Speakman, John -- England -- Nature. 2008 Feb 14;451(7180):774-5. doi: 10.1038/451774a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18270540" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Chiroptera/anatomy & histology/*physiology ; Cochlea/anatomy & histology/physiology ; Darkness ; Echolocation/*physiology ; Extremities/anatomy & histology/physiology ; Flight, Animal/*physiology ; Fossils ; Models, Biological ; Time Factors ; Wyoming
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    Human behaviour: killer instincts (2008)
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    Publication Date: 2008-02-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jones, Dan -- England -- Nature. 2008 Jan 31;451(7178):512-5. doi: 10.1038/451512a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18235473" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Aggression/*physiology/psychology ; Altruism ; Anger/physiology ; Animals ; Antisocial Personality Disorder/physiopathology ; *Biological Evolution ; Conflict (Psychology) ; Female ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Medieval ; *Homicide/history/psychology ; Humans ; Male ; Models, Biological ; Morals ; Pan troglodytes/physiology ; Prefrontal Cortex/anatomy & histology/physiology ; Sex Characteristics ; United Nations ; Violence/psychology ; Warfare
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    Sex determination: some like it hot (and some don't) (2008)
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    Publication Date: 2008-02-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crews, David -- Bull, James J -- England -- Nature. 2008 Jan 31;451(7178):527-8. doi: 10.1038/451527a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18235487" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*physiology ; Animals ; Body Size ; Fadrozole/pharmacology ; Female ; Lizards/*embryology/*physiology ; Male ; Models, Biological ; Ovum/drug effects/growth & development ; Reproduction/physiology ; Sex Characteristics ; Sex Differentiation/*physiology ; *Temperature
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    Ecology: The heart of the wood (2008)
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    Publication Date: 2008-09-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marris, Emma -- England -- Nature. 2008 Sep 18;455(7211):277-80. doi: 10.1038/455277a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18800107" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conservation of Natural Resources/methods ; *Ecosystem ; Human Activities ; Models, Biological ; Nature ; Poland ; Time Factors ; *Trees/physiology
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    Comprehensive genomic characterization defines human glioblastoma genes and core pathways (2008)
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    Publication Date: 2008-09-06
    Description: Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas (TCGA) pilot project aims to assess the value of large-scale multi-dimensional analysis of these molecular characteristics in human cancer and to provide the data rapidly to the research community. Here we report the interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas--the most common type of adult brain cancer--and nucleotide sequence aberrations in 91 of the 206 glioblastomas. This analysis provides new insights into the roles of ERBB2, NF1 and TP53, uncovers frequent mutations of the phosphatidylinositol-3-OH kinase regulatory subunit gene PIK3R1, and provides a network view of the pathways altered in the development of glioblastoma. Furthermore, integration of mutation, DNA methylation and clinical treatment data reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated glioblastomas, an observation with potential clinical implications. Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2671642/" 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/PMC2671642/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cancer Genome Atlas Research Network -- R01 CA099041/CA/NCI NIH HHS/ -- R01 CA099041-05/CA/NCI NIH HHS/ -- T32 GM007753/GM/NIGMS NIH HHS/ -- U24 CA126543-01/CA/NCI NIH HHS/ -- U24 CA126544/CA/NCI NIH HHS/ -- U24 CA126544-01/CA/NCI NIH HHS/ -- U24 CA126546/CA/NCI NIH HHS/ -- U24 CA126546-01/CA/NCI NIH HHS/ -- U24 CA126551-01/CA/NCI NIH HHS/ -- U24 CA126554/CA/NCI NIH HHS/ -- U24 CA126554-01/CA/NCI NIH HHS/ -- U24 CA126561/CA/NCI NIH HHS/ -- U24 CA126561-01/CA/NCI NIH HHS/ -- U24 CA126563/CA/NCI NIH HHS/ -- U24 CA126563-01/CA/NCI NIH HHS/ -- U24CA126543/CA/NCI NIH HHS/ -- U24CA126544/CA/NCI NIH HHS/ -- U24CA126546/CA/NCI NIH HHS/ -- U24CA126551/CA/NCI NIH HHS/ -- U24CA126554/CA/NCI NIH HHS/ -- U24CA126561/CA/NCI NIH HHS/ -- U24CA126563/CA/NCI NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- U54 HG003067-01/HG/NHGRI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- U54 HG003079-05/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- U54 HG003273-01/HG/NHGRI NIH HHS/ -- U54HG003067/HG/NHGRI NIH HHS/ -- U54HG003079/HG/NHGRI NIH HHS/ -- U54HG003273/HG/NHGRI NIH HHS/ -- England -- Nature. 2008 Oct 23;455(7216):1061-8. doi: 10.1038/nature07385. Epub 2008 Sep 4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18772890" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Aged ; Aged, 80 and over ; Brain Neoplasms/*genetics ; DNA Methylation ; DNA Modification Methylases/genetics ; DNA Repair/genetics ; DNA Repair Enzymes/genetics ; Female ; Gene Dosage ; *Gene Expression Regulation, Neoplastic ; Genes, Tumor Suppressor ; Genes, erbB-1/genetics ; Genome, Human/genetics ; *Genomics ; Glioblastoma/*genetics ; Humans ; Male ; Middle Aged ; Models, Molecular ; Mutation/genetics ; Neurofibromin 1/genetics ; Phosphatidylinositol 3-Kinases/genetics ; Protein Structure, Tertiary ; Retrospective Studies ; Signal Transduction/genetics ; Tumor Suppressor Proteins/genetics
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    Structure of the sulphiredoxin-peroxiredoxin complex reveals an essential repair embrace (2008)
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    Publication Date: 2008-01-04
    Description: Typical 2-Cys peroxiredoxins (Prxs) have an important role in regulating hydrogen peroxide-mediated cell signalling. In this process, Prxs can become inactivated through the hyperoxidation of an active site Cys residue to Cys sulphinic acid. The unique repair of this moiety by sulphiredoxin (Srx) restores peroxidase activity and terminates the signal. The hyperoxidized form of Prx exists as a stable decameric structure with each active site buried. Therefore, it is unclear how Srx can access the sulphinic acid moiety. Here we present the 2.6 A crystal structure of the human Srx-PrxI complex. This complex reveals the complete unfolding of the carboxy terminus of Prx, and its unexpected packing onto the backside of Srx away from the Srx active site. Binding studies and activity analyses of site-directed mutants at this interface show that the interaction is required for repair to occur. Moreover, rearrangements in the Prx active site lead to a juxtaposition of the Prx Gly-Gly-Leu-Gly and Srx ATP-binding motifs, providing a structural basis for the first step of the catalytic mechanism. The results also suggest that the observed interactions may represent a common mode for other proteins to bind to Prxs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2646140/" 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/PMC2646140/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jonsson, Thomas J -- Johnson, Lynnette C -- Lowther, W Todd -- R01 GM072866/GM/NIGMS NIH HHS/ -- R01 GM072866-03/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Jan 3;451(7174):98-101. doi: 10.1038/nature06415.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Structural Biology and Department of Biochemistry, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18172504" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites/genetics ; Catalysis ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Multiprotein Complexes/chemistry/genetics/metabolism ; Mutagenesis, Site-Directed ; Oxidation-Reduction ; Oxidoreductases/*chemistry/genetics/*metabolism ; Oxidoreductases Acting on Sulfur Group Donors ; Peroxiredoxins/*chemistry/genetics/*metabolism ; Protein Structure, Quaternary ; Structure-Activity Relationship
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    Language: the language barrier (2008)
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    Publication Date: 2008-05-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marris, Emma -- England -- Nature. 2008 May 22;453(7194):446-8. doi: 10.1038/453446a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497792" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Computer Simulation ; Humans ; *Language ; *Linguistics ; Models, Biological
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    A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing (2008)
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    Publication Date: 2008-02-22
    Description: Messenger-RNA-directed protein synthesis is accomplished by the ribosome. In eubacteria, this complex process is initiated by a specialized transfer RNA charged with formylmethionine (tRNA(fMet)). The amino-terminal formylated methionine of all bacterial nascent polypeptides blocks the reactive amino group to prevent unfavourable side-reactions and to enhance the efficiency of translation initiation. The first enzymatic factor that processes nascent chains is peptide deformylase (PDF); it removes this formyl group as polypeptides emerge from the ribosomal tunnel and before the newly synthesized proteins can adopt their native fold, which may bury the N terminus. Next, the N-terminal methionine is excised by methionine aminopeptidase. Bacterial PDFs are metalloproteases sharing a conserved N-terminal catalytic domain. All Gram-negative bacteria, including Escherichia coli, possess class-1 PDFs characterized by a carboxy-terminal alpha-helical extension. Studies focusing on PDF as a target for antibacterial drugs have not revealed the mechanism of its co-translational mode of action despite indications in early work that it co-purifies with ribosomes. Here we provide biochemical evidence that E. coli PDF interacts directly with the ribosome via its C-terminal extension. Crystallographic analysis of the complex between the ribosome-interacting helix of PDF and the ribosome at 3.7 A resolution reveals that the enzyme orients its active site towards the ribosomal tunnel exit for efficient co-translational processing of emerging nascent chains. Furthermore, we have found that the interaction of PDF with the ribosome enhances cell viability. These results provide the structural basis for understanding the coupling between protein synthesis and enzymatic processing of nascent chains, and offer insights into the interplay of PDF with the ribosome-associated chaperone trigger factor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bingel-Erlenmeyer, Rouven -- Kohler, Rebecca -- Kramer, Gunter -- Sandikci, Arzu -- Antolic, Snjezana -- Maier, Timm -- Schaffitzel, Christiane -- Wiedmann, Brigitte -- Bukau, Bernd -- Ban, Nenad -- England -- Nature. 2008 Mar 6;452(7183):108-11. doi: 10.1038/nature06683. Epub 2008 Feb 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18288106" target="_blank"〉PubMed〈/a〉
    Keywords: Amidohydrolases/*chemistry/deficiency/genetics/*metabolism ; Amino Acid Sequence ; Arabinose/metabolism ; Binding Sites ; Crystallography, X-Ray ; Escherichia coli/*enzymology/genetics/growth & development/metabolism ; Genetic Complementation Test ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; N-Formylmethionine/metabolism ; Peptidylprolyl Isomerase/metabolism ; Protein Binding ; *Protein Biosynthesis ; *Protein Processing, Post-Translational ; Protein Structure, Secondary ; RNA, Transfer, Met/genetics/metabolism ; Ribosome Subunits/chemistry/metabolism ; Ribosomes/*chemistry/*metabolism
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    Structural biology: Serpins' mystery solved (2008)
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    Publication Date: 2008-10-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Whisstock, James C -- Bottomley, Stephen P -- England -- Nature. 2008 Oct 30;455(7217):1189-90. doi: 10.1038/4551189a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18972012" target="_blank"〉PubMed〈/a〉
    Keywords: Amyloid/chemistry/metabolism ; Animals ; Antithrombin III/*chemistry/*metabolism ; Biopolymers/chemistry/metabolism ; Crystallography, X-Ray ; Dimerization ; Humans ; Models, Molecular ; Protein Conformation ; Protein Folding
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    Non-random segregation of sister chromosomes in Escherichia coli (2008)
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    Publication Date: 2008-10-31
    Description: It has long been known that the 5' to 3' polarity of DNA synthesis results in both a leading and lagging strand at all replication forks. Until now, however, there has been no evidence that leading or lagging strands are spatially organized in any way within a cell. Here we show that chromosome segregation in Escherichia coli is not random but is driven in a manner that results in the leading and lagging strands being addressed to particular cellular destinations. These destinations are consistent with the known patterns of chromosome segregation. Our work demonstrates a new level of organization relating to the replication and segregation of the E. coli chromosome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉White, Martin A -- Eykelenboom, John K -- Lopez-Vernaza, Manuel A -- Wilson, Emily -- Leach, David R F -- G0401313/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2008 Oct 30;455(7217):1248-50. doi: 10.1038/nature07282.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18972020" target="_blank"〉PubMed〈/a〉
    Keywords: Cephalexin/pharmacology ; *Chromosome Segregation ; Chromosomes, Bacterial/*genetics/*metabolism ; DNA Replication ; DNA, Bacterial/biosynthesis/genetics ; Deoxyribonucleases/metabolism ; Enzyme Induction/drug effects ; Escherichia coli/*cytology/enzymology/*genetics ; Escherichia coli Proteins/metabolism ; Exonucleases/metabolism ; Models, Biological
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    Crystal structure of the neurotrophin-3 and p75NTR symmetrical complex (2008)
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    Publication Date: 2008-07-04
    Description: Neurotrophins (NTs) are important regulators for the survival, differentiation and maintenance of different peripheral and central neurons. NTs bind to two distinct classes of glycosylated receptor: the p75 neurotrophin receptor (p75(NTR)) and tyrosine kinase receptors (Trks). Whereas p75(NTR) binds to all NTs, the Trk subtypes are specific for each NT. The question of whether NTs stimulate p75(NTR) by inducing receptor homodimerization is still under debate. Here we report the 2.6-A resolution crystal structure of neurotrophin-3 (NT-3) complexed to the ectodomain of glycosylated p75(NTR). In contrast to the previously reported asymmetric complex structure, which contains a dimer of nerve growth factor (NGF) bound to a single ectodomain of deglycosylated p75(NTR) (ref. 3), we show that NT-3 forms a central homodimer around which two glycosylated p75(NTR) molecules bind symmetrically. Symmetrical binding occurs along the NT-3 interfaces, resulting in a 2:2 ligand-receptor cluster. A comparison of the symmetrical and asymmetric structures reveals significant differences in ligand-receptor interactions and p75(NTR) conformations. Biochemical experiments indicate that both NT-3 and NGF bind to p75(NTR) with 2:2 stoichiometry in solution, whereas the 2:1 complexes are the result of artificial deglycosylation. We therefore propose that the symmetrical 2:2 complex reflects a native state of p75(NTR) activation at the cell surface. These results provide a model for NTs-p75(NTR) recognition and signal generation, as well as insights into coordination between p75(NTR) and Trks.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gong, Yong -- Cao, Peng -- Yu, Hong-jun -- Jiang, Tao -- England -- Nature. 2008 Aug 7;454(7205):789-93. doi: 10.1038/nature07089. Epub 2008 Jul 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18596692" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Crystallography, X-Ray ; Dimerization ; Glycosylation ; Humans ; Ligands ; Models, Molecular ; Neurotrophin 3/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Rats ; Receptor, Nerve Growth Factor/*chemistry/genetics/*metabolism ; Spodoptera
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    Identification of a serotonin/glutamate receptor complex implicated in psychosis (2008)
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    Publication Date: 2008-02-26
    Description: The psychosis associated with schizophrenia is characterized by alterations in sensory processing and perception. Some antipsychotic drugs were identified by their high affinity for serotonin 5-HT2A receptors (2AR). Drugs that interact with metabotropic glutamate receptors (mGluR) also have potential for the treatment of schizophrenia. The effects of hallucinogenic drugs, such as psilocybin and lysergic acid diethylamide, require the 2AR and resemble some of the core symptoms of schizophrenia. Here we show that the mGluR2 interacts through specific transmembrane helix domains with the 2AR, a member of an unrelated G-protein-coupled receptor family, to form functional complexes in brain cortex. The 2AR-mGluR2 complex triggers unique cellular responses when targeted by hallucinogenic drugs, and activation of mGluR2 abolishes hallucinogen-specific signalling and behavioural responses. In post-mortem human brain from untreated schizophrenic subjects, the 2AR is upregulated and the mGluR2 is downregulated, a pattern that could predispose to psychosis. These regulatory changes indicate that the 2AR-mGluR2 complex may be involved in the altered cortical processes of schizophrenia, and this complex is therefore a promising new target for the treatment of psychosis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743172/" 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/PMC2743172/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gonzalez-Maeso, Javier -- Ang, Rosalind L -- Yuen, Tony -- Chan, Pokman -- Weisstaub, Noelia V -- Lopez-Gimenez, Juan F -- Zhou, Mingming -- Okawa, Yuuya -- Callado, Luis F -- Milligan, Graeme -- Gingrich, Jay A -- Filizola, Marta -- Meana, J Javier -- Sealfon, Stuart C -- G9811527/Medical Research Council/United Kingdom -- P01 DA012923/DA/NIDA NIH HHS/ -- P01 DA012923-06A10004/DA/NIDA NIH HHS/ -- T32 DA007135/DA/NIDA NIH HHS/ -- T32 DA007135-25S1/DA/NIDA NIH HHS/ -- T32 GM062754/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Mar 6;452(7183):93-7. doi: 10.1038/nature06612. Epub 2008 Feb 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurology, Mount Sinai School of Medicine, New York, New York 10029, USA. javier.maeso@mssm.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18297054" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brain/cytology/metabolism ; Cell Line ; Cells, Cultured ; Down-Regulation ; Hallucinogens/metabolism/pharmacology ; Humans ; Mice ; Models, Molecular ; Multiprotein Complexes/chemistry/genetics/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Psychotic Disorders/drug therapy/genetics/*metabolism ; Receptor, Serotonin, 5-HT2A/analysis/deficiency/genetics/*metabolism ; Receptors, Metabotropic Glutamate/analysis/antagonists & ; inhibitors/genetics/*metabolism ; Schizophrenia/metabolism ; Signal Transduction/drug effects ; Up-Regulation
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    A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA (2008)
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    Publication Date: 2008-07-11
    Description: Structured RNAs embedded in the untranslated regions (UTRs) of messenger RNAs can regulate gene expression. In bacteria, control of a metabolite gene is mediated by the self-cleaving activity of a ribozyme embedded in its 5' UTR. This discovery has raised the question of whether gene-regulating ribozymes also exist in eukaryotic mRNAs. Here we show that highly active hammerhead ribozymes are present in the 3' UTRs of rodent C-type lectin type II (Clec2) genes. Using a hammerhead RNA motif search with relaxed delimitation of the non-conserved regions, we detected ribozyme sequences in which the invariant regions, in contrast to the previously identified continuous hammerheads, occur as two fragments separated by hundreds of nucleotides. Notably, a fragment pair can assemble to form an active hammerhead ribozyme structure between the translation termination and the polyadenylation signals within the 3' UTR. We demonstrate that this hammerhead structure can self-cleave both in vitro and in vivo, and is able to reduce protein expression in mouse cells. These results indicate that an unrecognized mechanism of post-transcriptional gene regulation involving association of discontinuous ribozyme sequences within an mRNA may be modulating the expression of several CLEC2 proteins that function in bone remodelling and the immune response of several mammals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612532/" 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/PMC2612532/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Martick, Monika -- Horan, Lucas H -- Noller, Harry F -- Scott, William G -- R01 AI043393/AI/NIAID NIH HHS/ -- R01 AI043393-09/AI/NIAID NIH HHS/ -- R01 GM087721/GM/NIGMS NIH HHS/ -- R01043393/PHS HHS/ -- England -- Nature. 2008 Aug 14;454(7206):899-902. doi: 10.1038/nature07117. Epub 2008 Jul 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA. mmartick@yahoo.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18615019" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/genetics ; Animals ; Down-Regulation ; Lectins, C-Type/genetics/metabolism ; Mice ; Models, Molecular ; NIH 3T3 Cells ; Nucleic Acid Conformation ; RNA, Catalytic/chemistry/*genetics/metabolism ; RNA, Messenger/chemistry/*genetics/metabolism ; Rats ; Reverse Transcriptase Polymerase Chain Reaction
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    Crystal structure of the lambda repressor and a model for pairwise cooperative operator binding (2008)
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    Publication Date: 2008-04-25
    Description: Bacteriophage lambda has for many years been a model system for understanding mechanisms of gene regulation. A 'genetic switch' enables the phage to transition from lysogenic growth to lytic development when triggered by specific environmental conditions. The key component of the switch is the cI repressor, which binds to two sets of three operator sites on the lambda chromosome that are separated by about 2,400 base pairs (bp). A hallmark of the lambda system is the pairwise cooperativity of repressor binding. In the absence of detailed structural information, it has been difficult to understand fully how repressor molecules establish the cooperativity complex. Here we present the X-ray crystal structure of the intact lambda cI repressor dimer bound to a DNA operator site. The structure of the repressor, determined by multiple isomorphous replacement methods, reveals an unusual overall architecture that allows it to adopt a conformation that appears to facilitate pairwise cooperative binding to adjacent operator sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stayrook, Steven -- Jaru-Ampornpan, Peera -- Ni, Jenny -- Hochschild, Ann -- Lewis, Mitchell -- R01 GM044025/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Apr 24;452(7190):1022-5. doi: 10.1038/nature06831.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 37th and Hamilton Walk, Philadelphia, Pennsylvania 19102-6059, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18432246" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Allosteric Site ; Bacteriophage lambda/*chemistry/genetics ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/*metabolism ; Dimerization ; Models, Biological ; *Models, Molecular ; Operator Regions, Genetic/*genetics ; Protein Conformation ; Repressor Proteins/*chemistry/*metabolism ; Structure-Activity Relationship ; Viral Regulatory and Accessory Proteins/*chemistry/*metabolism
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    HIV/AIDS: virus kept on a leash (2008)
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    Publication Date: 2008-01-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gottlinger, Heinrich G -- England -- Nature. 2008 Jan 24;451(7177):406-8. doi: 10.1038/nature06364.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18200012" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD/chemistry/*metabolism ; Cell Membrane/virology ; GPI-Linked Proteins ; HIV Infections/*metabolism/therapy/*virology ; HIV-1/drug effects/*metabolism ; Herpesvirus 8, Human/enzymology/physiology ; Human Immunodeficiency Virus Proteins/deficiency/genetics/*metabolism ; Humans ; Interferon-alpha/pharmacology ; Membrane Glycoproteins/chemistry/deficiency/*metabolism ; Models, Biological ; Ubiquitin-Protein Ligases/metabolism ; Viral Regulatory and Accessory Proteins/deficiency/genetics/*metabolism
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    Structural biology: It's not all in the family (2008)
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    Publication Date: 2008-08-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kanner, Baruch I -- England -- Nature. 2008 Jul 31;454(7204):593-4. doi: 10.1038/454593a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18668099" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/*metabolism ; Galactose/metabolism ; *Ion Transport ; Models, Molecular ; Protein Structure, Tertiary ; Sodium/metabolism ; Sodium-Glucose Transport Proteins/*chemistry/*metabolism
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    Pharmacology: Unready for action (2008)
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    Publication Date: 2008-08-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Steinbach, Joe Henry -- R01 NS022356/NS/NINDS NIH HHS/ -- England -- Nature. 2008 Aug 7;454(7205):704-5. doi: 10.1038/454704a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18685692" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Drug Partial Agonism ; Humans ; Models, Biological ; Nicotinic Agonists/*pharmacology ; Protein Conformation ; Receptors, Glycine/agonists/chemistry/metabolism ; Receptors, Nicotinic/chemistry/*metabolism
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    Biochemistry: Fit for an enzyme (2008)
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    Publication Date: 2008-08-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kapur, Shiven -- Khosla, Chaitan -- England -- Nature. 2008 Aug 14;454(7206):832-3. doi: 10.1038/454832a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18704072" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/*biosynthesis ; Enzymes/chemistry/*metabolism ; Models, Molecular ; Peptide Synthases/metabolism ; Polyketide Synthases/metabolism ; Protein Interaction Domains and Motifs
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    Linking climate change to lemming cycles (2008)
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    Publication Date: 2008-11-07
    Description: The population cycles of rodents at northern latitudes have puzzled people for centuries, and their impact is manifest throughout the alpine ecosystem. Climate change is known to be able to drive animal population dynamics between stable and cyclic phases, and has been suggested to cause the recent changes in cyclic dynamics of rodents and their predators. But although predator-rodent interactions are commonly argued to be the cause of the Fennoscandian rodent cycles, the role of the environment in the modulation of such dynamics is often poorly understood in natural systems. Hence, quantitative links between climate-driven processes and rodent dynamics have so far been lacking. Here we show that winter weather and snow conditions, together with density dependence in the net population growth rate, account for the observed population dynamics of the rodent community dominated by lemmings (Lemmus lemmus) in an alpine Norwegian core habitat between 1970 and 1997, and predict the observed absence of rodent peak years after 1994. These local rodent dynamics are coherent with alpine bird dynamics both locally and over all of southern Norway, consistent with the influence of large-scale fluctuations in winter conditions. The relationship between commonly available meteorological data and snow conditions indicates that changes in temperature and humidity, and thus conditions in the subnivean space, seem to markedly affect the dynamics of alpine rodents and their linked groups. The pattern of less regular rodent peaks, and corresponding changes in the overall dynamics of the alpine ecosystem, thus seems likely to prevail over a growing area under projected climate change.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kausrud, Kyrre L -- Mysterud, Atle -- Steen, Harald -- Vik, Jon Olav -- Ostbye, Eivind -- Cazelles, Bernard -- Framstad, Erik -- Eikeset, Anne Maria -- Mysterud, Ivar -- Solhoy, Torstein -- Stenseth, Nils Chr -- England -- Nature. 2008 Nov 6;456(7218):93-7. doi: 10.1038/nature07442.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO Box 1066 Blindern, N-0316 Oslo, Norway.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18987742" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arvicolinae/*physiology ; Birds/physiology ; *Ecosystem ; *Greenhouse Effect ; History, 20th Century ; History, 21st Century ; Humidity ; Models, Biological ; Norway ; Population Dynamics ; Seasons ; Snow ; Temperature
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    The genomic and epidemiological dynamics of human influenza A virus (2008)
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    Publication Date: 2008-04-18
    Description: The evolutionary interaction between influenza A virus and the human immune system, manifest as 'antigenic drift' of the viral haemagglutinin, is one of the best described patterns in molecular evolution. However, little is known about the genome-scale evolutionary dynamics of this pathogen. Similarly, how genomic processes relate to global influenza epidemiology, in which the A/H3N2 and A/H1N1 subtypes co-circulate, is poorly understood. Here through an analysis of 1,302 complete viral genomes sampled from temperate populations in both hemispheres, we show that the genomic evolution of influenza A virus is characterized by a complex interplay between frequent reassortment and periodic selective sweeps. The A/H3N2 and A/H1N1 subtypes exhibit different evolutionary dynamics, with diverse lineages circulating in A/H1N1, indicative of weaker antigenic drift. These results suggest a sink-source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir, which we hypothesize to be located in the tropics, to sink populations in temperate regions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441973/" 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/PMC2441973/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rambaut, Andrew -- Pybus, Oliver G -- Nelson, Martha I -- Viboud, Cecile -- Taubenberger, Jeffery K -- Holmes, Edward C -- Z01 AI000996-01/Intramural NIH HHS/ -- England -- Nature. 2008 May 29;453(7195):615-9. doi: 10.1038/nature06945. Epub 2008 Apr 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, UK. a.rambaut@ed.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18418375" target="_blank"〉PubMed〈/a〉
    Keywords: *Evolution, Molecular ; Genetic Drift ; Genetic Variation ; Genome, Viral/*genetics ; Hemagglutinin Glycoproteins, Influenza Virus/genetics ; Humans ; Influenza A Virus, H1N1 Subtype/*genetics/immunology ; Influenza A Virus, H3N2 Subtype/*genetics/immunology ; Influenza, Human/*epidemiology/*virology ; Models, Biological ; Neuraminidase/genetics ; New York/epidemiology ; New Zealand/epidemiology ; Phylogeny ; Reassortant Viruses/genetics/immunology
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    Life without RNase P (2008)
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    Publication Date: 2008-05-03
    Description: The universality of ribonuclease P (RNase P), the ribonucleoprotein essential for transfer RNA (tRNA) 5' maturation, is challenged in the archaeon Nanoarchaeum equitans. Neither extensive computational analysis of the genome nor biochemical tests in cell extracts revealed the existence of this enzyme. Here we show that the conserved placement of its tRNA gene promoters allows the synthesis of leaderless tRNAs, whose presence was verified by the observation of 5' triphosphorylated mature tRNA species. Initiation of tRNA gene transcription requires a purine, which coincides with the finding that tRNAs with a cytosine in position 1 display unusually extended 5' termini with an extra purine residue. These tRNAs were shown to be substrates for their cognate aminoacyl-tRNA synthetases. These findings demonstrate how nature can cope with the loss of the universal and supposedly ancient RNase P through genomic rearrangement at tRNA genes under the pressure of genome condensation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Randau, Lennart -- Schroder, Imke -- Soll, Dieter -- England -- Nature. 2008 May 1;453(7191):120-3. doi: 10.1038/nature06833.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18451863" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acyl-tRNA Synthetases/metabolism ; Aminoacylation ; Base Sequence ; *Evolution, Molecular ; Gene Deletion ; Genes, Archaeal/*genetics ; Models, Biological ; Molecular Sequence Data ; Nanoarchaeota/cytology/enzymology/*genetics ; Phosphorylation ; Promoter Regions, Genetic/*genetics ; RNA, Archaeal/*genetics/metabolism ; RNA, Transfer/*genetics/metabolism ; Ribonuclease P/*deficiency/metabolism ; Substrate Specificity ; Transcription, Genetic/genetics
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    Small-amplitude cycles emerge from stage-structured interactions in Daphnia-algal systems (2008)
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    Publication Date: 2008-10-31
    Description: A long-standing issue in ecology is reconciling the apparent stability of many populations with robust predictions of large-amplitude population cycles from general theory on consumer-resource interactions. Even when consumers are decoupled from dynamic resources, large-amplitude cycles can theoretically emerge from delayed feedback processes found in many consumers. Here we show that resource-dependent mortality and a dynamic developmental delay in consumers produces a new type of small-amplitude cycle that coexists with large-amplitude fluctuations in coupled consumer-resource systems. A distinctive characteristic of the small-amplitude cycles is slow juvenile development for consumers, leading to a developmental delay that is longer than the cycle period. By contrast, the period exceeds the delay in large-amplitude cycles. These theoretical predictions may explain previous empirical results on coexisting attractors found in Daphnia-algal systems. To test this, we used bioassay experiments that measure the growth rates of individuals in populations exhibiting each type of cycle. The results were consistent with predictions. Together, the new theory and experiments establish that two very general features of consumers--a resource-dependent juvenile stage duration and resource-dependent mortality--combine to produce small-amplitude resource-consumer cycles. This phenomenon may contribute to the prevalence of small-amplitude fluctuations in many other consumer-resource populations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McCauley, Edward -- Nelson, William A -- Nisbet, Roger M -- England -- Nature. 2008 Oct 30;455(7217):1240-3. doi: 10.1038/nature07220.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ecology and Evolution Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada. mccauley@ucalgary.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18972019" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Assay ; Daphnia/growth & development/*physiology ; Eukaryota/*physiology ; Female ; *Food Chain ; Models, Biological ; Ovum/physiology
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    Structural basis for the function and inhibition of an influenza virus proton channel (2008)
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    Publication Date: 2008-02-01
    Description: The M2 protein from influenza A virus is a pH-activated proton channel that mediates acidification of the interior of viral particles entrapped in endosomes. M2 is the target of the anti-influenza drugs amantadine and rimantadine; recently, resistance to these drugs in humans, birds and pigs has reached more than 90% (ref. 1). Here we describe the crystal structure of the transmembrane-spanning region of the homotetrameric protein in the presence and absence of the channel-blocking drug amantadine. pH-dependent structural changes occur near a set of conserved His and Trp residues that are involved in proton gating. The drug-binding site is lined by residues that are mutated in amantadine-resistant viruses. Binding of amantadine physically occludes the pore, and might also perturb the pK(a) of the critical His residue. The structure provides a starting point for solving the problem of resistance to M2-channel blockers.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889492/" 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/PMC3889492/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stouffer, Amanda L -- Acharya, Rudresh -- Salom, David -- Levine, Anna S -- Di Costanzo, Luigi -- Soto, Cinque S -- Tereshko, Valentina -- Nanda, Vikas -- Stayrook, Steven -- DeGrado, William F -- R37 GM054616/GM/NIGMS NIH HHS/ -- T32 GM008275/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Jan 31;451(7178):596-9. doi: 10.1038/nature06528.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18235504" target="_blank"〉PubMed〈/a〉
    Keywords: Amantadine/chemistry/metabolism/pharmacology ; Crystallography, X-Ray ; Drug Resistance, Viral/genetics ; Histidine/metabolism ; Hydrogen-Ion Concentration ; Influenza A virus/*chemistry/genetics/metabolism ; Ion Channel Gating/drug effects ; Models, Molecular ; Protein Structure, Quaternary ; Protons ; Structure-Activity Relationship ; Tryptophan/metabolism ; Viral Matrix Proteins/*antagonists & inhibitors/*chemistry/genetics/metabolism
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    X-ray structure of NS1 from a highly pathogenic H5N1 influenza virus (2008)
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    Publication Date: 2008-11-07
    Description: The recent emergence of highly pathogenic avian (H5N1) influenza viruses, their epizootic and panzootic nature, and their association with lethal human infections have raised significant global health concerns. Several studies have underlined the importance of non-structural protein NS1 in the increased pathogenicity and virulence of these strains. NS1, which consists of two domains-a double-stranded RNA (dsRNA) binding domain and the effector domain, separated through a linker-is an antagonist of antiviral type-I interferon response in the host. Here we report the X-ray structure of the full-length NS1 from an H5N1 strain (A/Vietnam/1203/2004) that was associated with 60% of human deaths in an outbreak in Vietnam. Compared to the individually determined structures of the RNA binding domain and the effector domain from non-H5N1 strains, the RNA binding domain within H5N1 NS1 exhibits modest structural changes, while the H5N1 effector domain shows significant alteration, particularly in the dimeric interface. Although both domains in the full-length NS1 individually participate in dimeric interactions, an unexpected finding is that these interactions result in the formation of a chain of NS1 molecules instead of distinct dimeric units. Three such chains in the crystal interact with one another extensively to form a tubular organization of similar dimensions to that observed in the cryo-electron microscopy images of NS1 in the presence of dsRNA. The tubular oligomeric organization of NS1, in which residues implicated in dsRNA binding face a 20-A-wide central tunnel, provides a plausible mechanism for how NS1 sequesters varying lengths of dsRNA, to counter cellular antiviral dsRNA response pathways, while simultaneously interacting with other cellular ligands during an infection.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798118/" 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/PMC2798118/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bornholdt, Zachary A -- Prasad, B V Venkataram -- AI36040/AI/NIAID NIH HHS/ -- R37 AI036040/AI/NIAID NIH HHS/ -- R37 AI036040-21/AI/NIAID NIH HHS/ -- RR002250/RR/NCRR NIH HHS/ -- England -- Nature. 2008 Dec 18;456(7224):985-8. doi: 10.1038/nature07444. Epub 2008 Nov 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18987632" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Humans ; Influenza A Virus, H5N1 Subtype/*chemistry/*pathogenicity ; Influenza, Human/epidemiology/virology ; Models, Molecular ; Protein Multimerization ; Protein Structure, Tertiary ; Vietnam/epidemiology ; Viral Nonstructural Proteins/*chemistry/ultrastructure ; Virulence ; Virulence Factors
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    Mechanism of shape determination in motile cells (2008)
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    Publication Date: 2008-05-24
    Description: The shape of motile cells is determined by many dynamic processes spanning several orders of magnitude in space and time, from local polymerization of actin monomers at subsecond timescales to global, cell-scale geometry that may persist for hours. Understanding the mechanism of shape determination in cells has proved to be extremely challenging due to the numerous components involved and the complexity of their interactions. Here we harness the natural phenotypic variability in a large population of motile epithelial keratocytes from fish (Hypsophrys nicaraguensis) to reveal mechanisms of shape determination. We find that the cells inhabit a low-dimensional, highly correlated spectrum of possible functional states. We further show that a model of actin network treadmilling in an inextensible membrane bag can quantitatively recapitulate this spectrum and predict both cell shape and speed. Our model provides a simple biochemical and biophysical basis for the observed morphology and behaviour of motile cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877812/" 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/PMC2877812/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keren, Kinneret -- Pincus, Zachary -- Allen, Greg M -- Barnhart, Erin L -- Marriott, Gerard -- Mogilner, Alex -- Theriot, Julie A -- U54 GM064346/GM/NIGMS NIH HHS/ -- U54 GM064346-099040/GM/NIGMS NIH HHS/ -- U54 GM64346/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 May 22;453(7194):475-80. doi: 10.1038/nature06952.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Technion- Israel Institute of Technology, Haifa 32000, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497816" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/chemistry/metabolism ; Actins/chemistry/metabolism ; Animals ; Biophysical Phenomena ; Biophysics ; Cell Membrane/chemistry/metabolism ; Cell Movement/*physiology ; Cell Shape/*physiology ; Cells, Cultured ; *Cichlids ; Epithelial Cells/*cytology ; Models, Biological ; Pseudopodia/metabolism ; Time Factors
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Apoptosis: Stabbed in the BAX (2008)
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    Publication Date: 2008-10-25
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242476/" 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/PMC3242476/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, Douglas R -- Chipuk, Jerry E -- F32 CA101444/CA/NCI NIH HHS/ -- R01 AI040646/AI/NIAID NIH HHS/ -- R01 AI040646-14/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Oct 23;455(7216):1047-9. doi: 10.1038/4551047a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18948940" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Apoptosis ; Apoptosis Regulatory Proteins/*metabolism ; BH3 Interacting Domain Death Agonist Protein/metabolism ; Membrane Proteins/*metabolism ; Mitochondrial Membranes/*metabolism ; Models, Molecular ; Permeability ; Protein Binding ; Proto-Oncogene Proteins/*metabolism ; bcl-2-Associated X Protein/chemistry/*metabolism
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    The mode of Hedgehog binding to Ihog homologues is not conserved across different phyla (2008)
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    Publication Date: 2008-09-17
    Description: Hedgehog (Hh) proteins specify tissue pattern in metazoan embryos by forming gradients that emanate from discrete sites of expression and elicit concentration-dependent cellular differentiation or proliferation responses. Cellular responses to Hh and the movement of Hh through tissues are both precisely regulated, and abnormal Hh signalling has been implicated in human birth defects and cancer. Hh signalling is mediated by its amino-terminal domain (HhN), which is dually lipidated and secreted as part of a multivalent lipoprotein particle. Reception of the HhN signal is modulated by several cell-surface proteins on responding cells, including Patched (Ptc), Smoothened (Smo), Ihog (known as CDO or CDON in mammals) and the vertebrate-specific proteins Hip (also known as Hhip) and Gas1 (ref. 11). Drosophila Ihog and its vertebrate homologues CDO and BOC contain multiple immunoglobulin and fibronectin type III (FNIII) repeats, and the first FNIII repeat of Ihog binds Drosophila HhN in a heparin-dependent manner. Surprisingly, pull-down experiments suggest that a mammalian Sonic hedgehog N-terminal domain (ShhN) binds a non-orthologous FNIII repeat of CDO. Here we report biochemical, biophysical and X-ray structural studies of a complex between ShhN and the third FNIII repeat of CDO. We show that the ShhN-CDO interaction is completely unlike the HhN-Ihog interaction and requires calcium, which binds at a previously undetected site on ShhN. This site is conserved in nearly all Hh proteins and is a hotspot for mediating interactions between ShhN and CDO, Ptc, Hip and Gas1. Mutations in vertebrate Hh proteins causing holoprosencephaly and brachydactyly type A1 map to this calcium-binding site and disrupt interactions with these partners.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679680/" 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/PMC2679680/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McLellan, Jason S -- Zheng, Xiaoyan -- Hauk, Glenn -- Ghirlando, Rodolfo -- Beachy, Philip A -- Leahy, Daniel J -- R01 HD055545/HD/NICHD NIH HHS/ -- Z99 DK999999/Intramural NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Oct 16;455(7215):979-83. doi: 10.1038/nature07358. Epub 2008 Sep 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18794898" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Calcium/metabolism ; Cell Adhesion Molecules/chemistry/metabolism ; Cell Cycle Proteins/chemistry/metabolism ; Cell Line ; *Conserved Sequence ; Crystallography, X-Ray ; Drosophila Proteins/*chemistry/*metabolism ; Drosophila melanogaster/chemistry ; Fibronectins/chemistry ; GPI-Linked Proteins ; Hedgehog Proteins/*chemistry/genetics/*metabolism ; Humans ; Immunoglobulin G/chemistry/metabolism ; Membrane Glycoproteins/*chemistry/*metabolism ; Membrane Proteins/chemistry/metabolism ; Mice ; Models, Molecular ; Protein Binding/genetics ; Protein Structure, Tertiary ; Receptors, Cell Surface/*chemistry/*metabolism ; *Sequence Homology, Amino Acid ; Signal Transduction ; Tumor Suppressor Proteins/chemistry/metabolism
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    The coevolution of choosiness and cooperation (2008)
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    Publication Date: 2008-01-11
    Description: Explaining the rise and maintenance of cooperation is central to our understanding of biological systems and human societies. When an individual's cooperativeness is used by other individuals as a choice criterion, there can be competition to be more generous than others, a situation called competitive altruism. The evolution of cooperation between non-relatives can then be driven by a positive feedback between increasing levels of cooperativeness and choosiness. Here we use evolutionary simulations to show that, in a situation where individuals have the opportunity to engage in repeated pairwise interactions, the equilibrium degree of cooperativeness depends critically on the amount of behavioural variation that is being maintained in the population by processes such as mutation. Because our model does not invoke complex mechanisms such as negotiation behaviour, it can be applied to a wide range of species. The results suggest an important role of lifespan in the evolution of cooperation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McNamara, John M -- Barta, Zoltan -- Fromhage, Lutz -- Houston, Alasdair I -- England -- Nature. 2008 Jan 10;451(7175):189-92. doi: 10.1038/nature06455.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Mathematics, University of Bristol, University Walk, Bristol BS8 1TW, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18185587" target="_blank"〉PubMed〈/a〉
    Keywords: Altruism ; Animals ; *Biological Evolution ; Choice Behavior/*physiology ; Competitive Behavior/physiology ; *Cooperative Behavior ; Game Theory ; Humans ; Longevity ; Models, Biological ; Mutagenesis ; Reproduction/genetics/physiology
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    Ecology: Forest air conditioning (2008)
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    Publication Date: 2008-07-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Woodward, F I -- England -- Nature. 2008 Jul 24;454(7203):422-3. doi: 10.1038/454422a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18650910" target="_blank"〉PubMed〈/a〉
    Keywords: Cellulose/chemistry/metabolism ; Humidity ; Models, Biological ; Oxygen Isotopes ; Plant Leaves/*physiology ; *Temperature ; Trees/*physiology
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    Deconstructing voltage sensor function and pharmacology in sodium channels (2008)
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    Publication Date: 2008-11-14
    Description: Voltage-activated sodium (Na(v)) channels are crucial for the generation and propagation of nerve impulses, and as such are widely targeted by toxins and drugs. The four voltage sensors in Na(v) channels have distinct amino acid sequences, raising fundamental questions about their relative contributions to the function and pharmacology of the channel. Here we use four-fold symmetric voltage-activated potassium (K(v)) channels as reporters to examine the contributions of individual S3b-S4 paddle motifs within Na(v) channel voltage sensors to the kinetics of voltage sensor activation and to forming toxin receptors. Our results uncover binding sites for toxins from tarantula and scorpion venom on each of the four paddle motifs in Na(v) channels, and reveal how paddle-specific interactions can be used to reshape Na(v) channel activity. One paddle motif is unique in that it slows voltage sensor activation, and toxins selectively targeting this motif impede Na(v) channel inactivation. This reporter approach and the principles that emerge will be useful in developing new drugs for treating pain and Na(v) channelopathies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2587061/" 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/PMC2587061/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bosmans, Frank -- Martin-Eauclaire, Marie-France -- Swartz, Kenton J -- ZIA NS003017-03/Intramural NIH HHS/ -- England -- Nature. 2008 Nov 13;456(7219):202-8. doi: 10.1038/nature07473.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19005548" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Ion Channel Gating/*drug effects ; Models, Molecular ; Mutagenesis ; Potassium Channels, Voltage-Gated/genetics/metabolism ; Protein Interaction Domains and Motifs/genetics/physiology ; Rats ; Recombinant Fusion Proteins/genetics/metabolism ; Scorpion Venoms/pharmacology ; Sodium Channels/genetics/*metabolism ; Spider Venoms/pharmacology ; Xenopus
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    Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases (2008)
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    Publication Date: 2008-11-07
    Description: Xeroderma pigmentosum is a monogenic disease characterized by hypersensitivity to ultraviolet light. The cells of xeroderma pigmentosum patients are defective in nucleotide excision repair, limiting their capacity to eliminate ultraviolet-induced DNA damage, and resulting in a strong predisposition to develop skin cancers. The use of rare cutting DNA endonucleases-such as homing endonucleases, also known as meganucleases-constitutes one possible strategy for repairing DNA lesions. Homing endonucleases have emerged as highly specific molecular scalpels that recognize and cleave DNA sites, promoting efficient homologous gene targeting through double-strand-break-induced homologous recombination. Here we describe two engineered heterodimeric derivatives of the homing endonuclease I-CreI, produced by a semi-rational approach. These two molecules-Amel3-Amel4 and Ini3-Ini4-cleave DNA from the human XPC gene (xeroderma pigmentosum group C), in vitro and in vivo. Crystal structures of the I-CreI variants complexed with intact and cleaved XPC target DNA suggest that the mechanism of DNA recognition and cleavage by the engineered homing endonucleases is similar to that of the wild-type I-CreI. Furthermore, these derivatives induced high levels of specific gene targeting in mammalian cells while displaying no obvious genotoxicity. Thus, homing endonucleases can be designed to recognize and cleave the DNA sequences of specific genes, opening up new possibilities for genome engineering and gene therapy in xeroderma pigmentosum patients whose illness can be treated ex vivo.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Redondo, Pilar -- Prieto, Jesus -- Munoz, Ines G -- Alibes, Andreu -- Stricher, Francois -- Serrano, Luis -- Cabaniols, Jean-Pierre -- Daboussi, Fayza -- Arnould, Sylvain -- Perez, Christophe -- Duchateau, Philippe -- Paques, Frederic -- Blanco, Francisco J -- Montoya, Guillermo -- England -- Nature. 2008 Nov 6;456(7218):107-11. doi: 10.1038/nature07343.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Macromolecular Crystallography Group, Spanish National Cancer Research Centre (CNIO), c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18987743" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; CHO Cells ; Cell Line ; Cricetinae ; Cricetulus ; Crystallography, X-Ray ; DNA/chemistry/*genetics/*metabolism ; DNA Repair ; DNA Restriction Enzymes/*chemistry/genetics/*metabolism/toxicity ; DNA-Binding Proteins/*genetics ; Enzyme Stability ; *Genetic Engineering ; Humans ; Models, Molecular ; Phosphorylation ; Protein Multimerization ; Substrate Specificity ; Xeroderma Pigmentosum/*genetics
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    Sex ratio adjustment and kin discrimination in malaria parasites (2008)
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    Publication Date: 2008-05-30
    Description: Malaria parasites and related Apicomplexans are the causative agents of the some of the most serious infectious diseases of humans, companion animals, livestock and wildlife. These parasites must undergo sexual reproduction to transmit from vertebrate hosts to vectors, and their sex ratios are consistently female-biased. Sex allocation theory, a cornerstone of evolutionary biology, is remarkably successful at explaining female-biased sex ratios in multicellular taxa, but has proved controversial when applied to malaria parasites. Here we show that, as predicted by theory, sex ratio is an important fitness-determining trait and Plasmodium chabaudi parasites adjust their sex allocation in response to the presence of unrelated conspecifics. This suggests that P. chabaudi parasites use kin discrimination to evaluate the genetic diversity of their infections, and they adjust their behaviour in response to environmental cues. Malaria parasites provide a novel way to test evolutionary theory, and support the generality and power of a darwinian approach.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807728/" 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/PMC3807728/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reece, Sarah E -- Drew, Damien R -- Gardner, Andy -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2008 May 29;453(7195):609-14. doi: 10.1038/nature06954.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological Science, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK. sarah.reece@ed.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18509435" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Cues ; Female ; Fertility/genetics/physiology ; Genetic Variation ; Genotype ; Humans ; Malaria/*parasitology ; Male ; Models, Biological ; Plasmodium chabaudi/genetics/*physiology ; *Sex Ratio
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    Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme (2008)
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    Details
    Publication Date: 2008-06-13
    Description: In modern organisms, protein enzymes are solely responsible for the aminoacylation of transfer RNA. However, the evolution of protein synthesis in the RNA world required RNAs capable of catalysing this reaction. Ribozymes that aminoacylate RNA by using activated amino acids have been discovered through selection in vitro. Flexizyme is a 45-nucleotide ribozyme capable of charging tRNA in trans with various activated l-phenylalanine derivatives. In addition to a more than 10(5) rate enhancement and more than 10(4)-fold discrimination against some non-cognate amino acids, this ribozyme achieves good regioselectivity: of all the hydroxyl groups of a tRNA, it exclusively aminoacylates the terminal 3'-OH. Here we report the 2.8-A resolution structure of flexizyme fused to a substrate RNA. Together with randomization of ribozyme core residues and reselection, this structure shows that very few nucleotides are needed for the aminoacylation of specific tRNAs. Although it primarily recognizes tRNA through base-pairing with the CCA terminus of the tRNA molecule, flexizyme makes numerous local interactions to position the acceptor end of tRNA precisely. A comparison of two crystallographically independent flexizyme conformations, only one of which appears capable of binding activated phenylalanine, suggests that this ribozyme may achieve enhanced specificity by coupling active-site folding to tRNA docking. Such a mechanism would be reminiscent of the mutually induced fit of tRNA and protein employed by some aminoacyl-tRNA synthetases to increase specificity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xiao, Hong -- Murakami, Hiroshi -- Suga, Hiroaki -- Ferre-D'Amare, Adrian R -- England -- Nature. 2008 Jul 17;454(7202):358-61. doi: 10.1038/nature07033. Epub 2008 Jun 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18548004" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acyl-tRNA Synthetases/chemistry/metabolism ; Base Sequence ; Binding Sites ; Escherichia coli/enzymology ; Models, Molecular ; Nucleic Acid Conformation ; Protein Folding ; Protein Structure, Tertiary ; RNA, Catalytic/chemistry/genetics/*metabolism ; RNA, Transfer/chemistry/genetics/*metabolism ; *Transfer RNA Aminoacylation
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    Structure of Epac2 in complex with a cyclic AMP analogue and RAP1B (2008)
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    Publication Date: 2008-07-29
    Description: Epac proteins are activated by binding of the second messenger cAMP and then act as guanine nucleotide exchange factors for Rap proteins. The Epac proteins are involved in the regulation of cell adhesion and insulin secretion. Here we have determined the structure of Epac2 in complex with a cAMP analogue (Sp-cAMPS) and RAP1B by X-ray crystallography and single particle electron microscopy. The structure represents the cAMP activated state of the Epac2 protein with the RAP1B protein trapped in the course of the exchange reaction. Comparison with the inactive conformation reveals that cAMP binding causes conformational changes that allow the cyclic nucleotide binding domain to swing from a position blocking the Rap binding site towards a docking site at the Ras exchange motif domain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rehmann, Holger -- Arias-Palomo, Ernesto -- Hadders, Michael A -- Schwede, Frank -- Llorca, Oscar -- Bos, Johannes L -- England -- Nature. 2008 Sep 4;455(7209):124-7. doi: 10.1038/nature07187. Epub 2008 Jul 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiological Chemistry, Centre for Biomedical Genetics and Cancer Genomics Centre, University Medical Center, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands. h.rehmann@UMCutrecht.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18660803" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Binding Sites ; Carrier Proteins/*chemistry/*metabolism/ultrastructure ; Crystallography, X-Ray ; Cyclic AMP/*analogs & derivatives/chemistry/metabolism ; Enzyme Activation ; Guanine Nucleotide Exchange Factors/*chemistry/*metabolism/ultrastructure ; Humans ; Mice ; Microscopy, Electron ; Models, Molecular ; Protein Binding ; Protein Conformation ; Thionucleotides/*chemistry/*metabolism ; rap GTP-Binding Proteins/chemistry/*metabolism/ultrastructure
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    Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms (2008)
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    Publication Date: 2008-03-07
    Description: Carbonic anhydrase, a zinc enzyme found in organisms from all kingdoms, catalyses the reversible hydration of carbon dioxide and is used for inorganic carbon acquisition by phytoplankton. In the oceans, where zinc is nearly depleted, diatoms use cadmium as a catalytic metal atom in cadmium carbonic anhydrase (CDCA). Here we report the crystal structures of CDCA in four distinct forms: cadmium-bound, zinc-bound, metal-free and acetate-bound. Despite lack of sequence homology, CDCA is a structural mimic of a functional beta-carbonic anhydrase dimer, with striking similarity in the spatial organization of the active site residues. CDCA readily exchanges cadmium and zinc at its active site--an apparently unique adaptation to oceanic life that is explained by a stable opening of the metal coordinating site in the absence of metal. Given the central role of diatoms in exporting carbon to the deep sea, their use of cadmium in an enzyme critical for carbon acquisition establishes a remarkable link between the global cycles of cadmium and carbon.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Yan -- Feng, Liang -- Jeffrey, Philip D -- Shi, Yigong -- Morel, Francois M M -- England -- Nature. 2008 Mar 6;452(7183):56-61. doi: 10.1038/nature06636.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Princeton University, New Jersey 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18322527" target="_blank"〉PubMed〈/a〉
    Keywords: Acetates/metabolism ; Binding Sites ; Cadmium/*metabolism ; Carbonic Anhydrases/*chemistry/*metabolism ; Catalysis ; Crystallography, X-Ray ; Diatoms/*enzymology ; Dimerization ; Kinetics ; Marine Biology ; Models, Molecular ; Molecular Mimicry ; Protein Structure, Secondary ; Seawater/*microbiology ; Zinc/*metabolism
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    Structural biology: Enzyme knocked for a loop (2008)
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    Publication Date: 2008-11-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mellgren, Ronald L -- England -- Nature. 2008 Nov 20;456(7220):337-8. doi: 10.1038/456337a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19020611" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biocatalysis ; Calcium/metabolism ; Calcium-Binding Proteins/*chemistry/*metabolism ; Calpain/*antagonists & inhibitors/chemistry/*metabolism ; *Catalytic Domain ; Crystallography, X-Ray ; Models, Molecular ; Peptide Fragments/chemistry/metabolism ; Protein Binding ; Protein Multimerization ; Rats
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    Being human: Conflict: Altruism's midwife (2008)
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    Publication Date: 2008-11-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bowles, Samuel -- England -- Nature. 2008 Nov 20;456(7220):326-7. doi: 10.1038/456326a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Behavioral Sciences Program at the Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, USA. bowles@santafe.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19020603" target="_blank"〉PubMed〈/a〉
    Keywords: *Altruism ; Animals ; Biological Evolution ; *Conflict (Psychology) ; *Cooperative Behavior ; *Human Characteristics ; Humans ; Models, Biological ; Violence/psychology/statistics & numerical data ; Warfare
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    A systematic look at an old problem (2008)
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    Publication Date: 2008-02-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kirkwood, Thomas B L -- BB/C008200/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2008 Feb 7;451(7179):644-7. doi: 10.1038/451644a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, UK. tom.kirkwood@ncl.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18256658" target="_blank"〉PubMed〈/a〉
    Keywords: Age Distribution ; Aging/*physiology ; Animals ; Caenorhabditis elegans/genetics/physiology ; DNA Damage ; Disease Models, Animal ; Geriatrics/trends ; Health ; Humans ; *Life Expectancy/trends ; Longevity/physiology ; Mice ; Models, Biological ; Neoplasms/epidemiology/pathology ; *Systems Biology ; Werner Syndrome/genetics/pathology
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    Crystal structure of a stable dimer reveals the molecular basis of serpin polymerization (2008)
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    Publication Date: 2008-10-17
    Description: Repeating intermolecular protein association by means of beta-sheet expansion is the mechanism underlying a multitude of diseases including Alzheimer's, Huntington's and Parkinson's and the prion encephalopathies. A family of proteins, known as the serpins, also forms large stable multimers by ordered beta-sheet linkages leading to intracellular accretion and disease. These 'serpinopathies' include early-onset dementia caused by mutations in neuroserpin, liver cirrhosis and emphysema caused by mutations in alpha(1)-antitrypsin (alpha(1)AT), and thrombosis caused by mutations in antithrombin. Serpin structure and function are quite well understood, and the family has therefore become a model system for understanding the beta-sheet expansion disorders collectively known as the conformational diseases. To develop strategies to prevent and reverse these disorders, it is necessary to determine the structural basis of the intermolecular linkage and of the pathogenic monomeric state. Here we report the crystallographic structure of a stable serpin dimer which reveals a domain swap of more than 50 residues, including two long antiparallel beta-strands inserting in the centre of the principal beta-sheet of the neighbouring monomer. This structure explains the extreme stability of serpin polymers, the molecular basis of their rapid propagation, and provides critical new insights into the structural changes which initiate irreversible beta-sheet expansion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yamasaki, Masayuki -- Li, Wei -- Johnson, Daniel J D -- Huntington, James A -- G0801899/Medical Research Council/United Kingdom -- England -- Nature. 2008 Oct 30;455(7217):1255-8. doi: 10.1038/nature07394. Epub 2008 Oct 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Cambridge, Department of Haematology, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18923394" target="_blank"〉PubMed〈/a〉
    Keywords: Antithrombin III/*chemistry/*metabolism ; Biopolymers/chemistry/metabolism ; Crystallography, X-Ray ; Dimerization ; Humans ; Models, Molecular ; Protein Conformation
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    Conformational changes in an ultrafast light-driven enzyme determine catalytic activity (2008)
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    Publication Date: 2008-12-19
    Description: The role of conformational changes in explaining the huge catalytic power of enzymes is currently one of the most challenging questions in biology. Although it is now widely regarded that enzymes modulate reaction rates by means of short- and long-range protein motions, it is almost impossible to distinguish between conformational changes and catalysis. We have solved this problem using the chlorophyll biosynthetic enzyme NADPH:protochlorophyllide (Pchlide) oxidoreductase, which catalyses a unique light-driven reaction involving hydride and proton transfers. Here we report that prior excitation of the enzyme-substrate complex with a laser pulse induces a more favourable conformation of the active site, enabling the coupled hydride and proton transfer reactions to occur. This effect, which is triggered during the Pchlide excited-state lifetime and persists on a long timescale, switches the enzyme into an active state characterized by a high rate and quantum yield of formation of a catalytic intermediate. The corresponding spectral changes in the mid-infrared following the absorption of one photon reveal significant conformational changes in the enzyme, illustrating the importance of flexibility and dynamics in the structure of enzymes for their function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sytina, Olga A -- Heyes, Derren J -- Hunter, C Neil -- Alexandre, Maxime T -- van Stokkum, Ivo H M -- van Grondelle, Rienk -- Groot, Marie Louise -- Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2008 Dec 18;456(7224):1001-4. doi: 10.1038/nature07354.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19092933" target="_blank"〉PubMed〈/a〉
    Keywords: Biocatalysis/radiation effects ; Catalytic Domain/radiation effects ; *Light ; Models, Molecular ; Oxidoreductases Acting on CH-CH Group Donors/chemistry/*metabolism/*radiation ; effects ; Protein Conformation/radiation effects ; Protons ; Structure-Activity Relationship ; Synechocystis/*enzymology ; Time Factors
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    Eocene/Oligocene ocean de-acidification linked to Antarctic glaciation by sea-level fall (2008)
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    Publication Date: 2008-04-25
    Description: One of the most dramatic perturbations to the Earth system during the past 100 million years was the rapid onset of Antarctic glaciation near the Eocene/Oligocene epoch boundary (approximately 34 million years ago). This climate transition was accompanied by a deepening of the calcite compensation depth--the ocean depth at which the rate of calcium carbonate input from surface waters equals the rate of dissolution. Changes in the global carbon cycle, rather than changes in continental configuration, have recently been proposed as the most likely root cause of Antarctic glaciation, but the mechanism linking glaciation to the deepening of calcite compensation depth remains unclear. Here we use a global biogeochemical box model to test competing hypotheses put forward to explain the Eocene/Oligocene transition. We find that, of the candidate hypotheses, only shelf to deep sea carbonate partitioning is capable of explaining the observed changes in both carbon isotope composition and calcium carbonate accumulation at the sea floor. In our simulations, glacioeustatic sea-level fall associated with the growth of Antarctic ice sheets permanently reduces global calcium carbonate accumulation on the continental shelves, leading to an increase in pelagic burial via permanent deepening of the calcite compensation depth. At the same time, fresh limestones are exposed to erosion, thus temporarily increasing global river inputs of dissolved carbonate and increasing seawater delta13C. Our work sheds new light on the mechanisms linking glaciation and ocean acidity change across arguably the most important climate transition of the Cenozoic era.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Merico, Agostino -- Tyrrell, Toby -- Wilson, Paul A -- England -- Nature. 2008 Apr 24;452(7190):979-82. doi: 10.1038/nature06853.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Oceanography Centre, Southampton, European Way, Southampton SO14 3ZH, UK. agostino.merico@gkss.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18432242" target="_blank"〉PubMed〈/a〉
    Keywords: Acids/analysis ; Antarctic Regions ; Atmosphere/chemistry ; Calcium Carbonate/analysis/metabolism ; Carbon/analysis/metabolism ; Carbon Isotopes ; Diatoms/metabolism ; Geologic Sediments/chemistry ; History, Ancient ; Hydrogen-Ion Concentration ; *Ice Cover ; Models, Biological ; Oceans and Seas ; Phytoplankton/metabolism ; Seawater/*analysis/*chemistry ; Time Factors
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    Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA (2008)
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    Publication Date: 2008-04-25
    Description: Escherichia coli AlkB and its human homologues ABH2 and ABH3 repair DNA/RNA base lesions by using a direct oxidative dealkylation mechanism. ABH2 has the primary role of guarding mammalian genomes against 1-meA damage by repairing this lesion in double-stranded DNA (dsDNA), whereas AlkB and ABH3 preferentially repair single-stranded DNA (ssDNA) lesions and can repair damaged bases in RNA. Here we show the first crystal structures of AlkB-dsDNA and ABH2-dsDNA complexes, stabilized by a chemical cross-linking strategy. This study reveals that AlkB uses an unprecedented base-flipping mechanism to access the damaged base: it squeezes together the two bases flanking the flipped-out one to maintain the base stack, explaining the preference of AlkB for repairing ssDNA lesions over dsDNA ones. In addition, the first crystal structure of ABH2, presented here, provides a structural basis for designing inhibitors of this human DNA repair protein.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2587245/" 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/PMC2587245/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Cai-Guang -- Yi, Chengqi -- Duguid, Erica M -- Sullivan, Christopher T -- Jian, Xing -- Rice, Phoebe A -- He, Chuan -- GM071440/GM/NIGMS NIH HHS/ -- R01 GM071440/GM/NIGMS NIH HHS/ -- R01 GM071440-03/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Apr 24;452(7190):961-5. doi: 10.1038/nature06889.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18432238" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/analogs & derivatives/metabolism ; Binding Sites ; Cross-Linking Reagents/chemistry ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA Damage ; DNA Repair ; DNA Repair Enzymes/*chemistry/metabolism ; DNA-Binding Proteins/chemistry/metabolism ; Dioxygenases/*chemistry/*metabolism ; Escherichia coli Proteins/*chemistry/*metabolism ; Humans ; Mixed Function Oxygenases/*chemistry/*metabolism ; Models, Molecular ; Protein Binding ; RNA/*metabolism
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    The branching programme of mouse lung development (2008)
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    Publication Date: 2008-05-09
    Description: Mammalian lungs are branched networks containing thousands to millions of airways arrayed in intricate patterns that are crucial for respiration. How such trees are generated during development, and how the developmental patterning information is encoded, have long fascinated biologists and mathematicians. However, models have been limited by a lack of information on the normal sequence and pattern of branching events. Here we present the complete three-dimensional branching pattern and lineage of the mouse bronchial tree, reconstructed from an analysis of hundreds of developmental intermediates. The branching process is remarkably stereotyped and elegant: the tree is generated by three geometrically simple local modes of branching used in three different orders throughout the lung. We propose that each mode of branching is controlled by a genetically encoded subroutine, a series of local patterning and morphogenesis operations, which are themselves controlled by a more global master routine. We show that this hierarchical and modular programme is genetically tractable, and it is ideally suited to encoding and evolving the complex networks of the lung and other branched organs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892995/" 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/PMC2892995/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Metzger, Ross J -- Klein, Ophir D -- Martin, Gail R -- Krasnow, Mark A -- R01 CA078711/CA/NCI NIH HHS/ -- R01 CA078711-02/CA/NCI NIH HHS/ -- R01 CA078711-03/CA/NCI NIH HHS/ -- R01 CA078711-04/CA/NCI NIH HHS/ -- R01 CA078711-05/CA/NCI NIH HHS/ -- R01 HL075769/HL/NHLBI NIH HHS/ -- R01 HL075769-01/HL/NHLBI NIH HHS/ -- R01 HL075769-02/HL/NHLBI NIH HHS/ -- R01 HL075769-03/HL/NHLBI NIH HHS/ -- R01 HL075769-04/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Jun 5;453(7196):745-50. doi: 10.1038/nature07005. Epub 2008 May 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and HHMI, Stanford University School of Medicine, Stanford, California 94305-5307, USA. ross.metzger@ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18463632" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing ; Animals ; Body Patterning/genetics/*physiology ; Fibroblast Growth Factor 10/metabolism ; Intracellular Signaling Peptides and Proteins ; Lung/*anatomy & histology/cytology/*embryology/metabolism ; Membrane Proteins/metabolism ; Mice ; Models, Biological ; Organogenesis/genetics/*physiology ; Receptor, Fibroblast Growth Factor, Type 2/genetics/metabolism
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    The ion pathway through the opened Na(+),K(+)-ATPase pump (2008)
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    Publication Date: 2008-10-14
    Description: P-type ATPases pump ions across membranes, generating steep electrochemical gradients that are essential for the function of all cells. Access to the ion-binding sites within the pumps alternates between the two sides of the membrane to avoid the dissipation of the gradients that would occur during simultaneous access. In Na(+),K(+)-ATPase pumps treated with the marine agent palytoxin, this strict alternation is disrupted and binding sites are sometimes simultaneously accessible from both sides of the membrane, transforming the pumps into ion channels (see, for example, refs 2, 3). Current recordings in these channels can monitor accessibility of introduced cysteine residues to water-soluble sulphydryl-specific reagents. We found previously that Na(+),K(+) pump-channels open to the extracellular surface through a deep and wide vestibule that emanates from a narrower pathway between transmembrane helices 4 and 6 (TM4 and TM6). Here we report that cysteine scans from TM1 to TM6 reveal a single unbroken cation pathway that traverses palytoxin-bound Na(+),K(+) pump-channels from one side of the membrane to the other. This pathway comprises residues from TM1, TM2, TM4 and TM6, passes through ion-binding site II, and is probably conserved in structurally and evolutionarily related P-type pumps, such as sarcoplasmic- and endoplasmic-reticulum Ca(2+)-ATPases and H(+),K(+)-ATPases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2585603/" 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/PMC2585603/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Takeuchi, Ayako -- Reyes, Nicolas -- Artigas, Pablo -- Gadsby, David C -- R01 HL036783/HL/NHLBI NIH HHS/ -- R01 HL036783-21/HL/NHLBI NIH HHS/ -- England -- Nature. 2008 Nov 20;456(7220):413-6. doi: 10.1038/nature07350. Epub 2008 Oct 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Cardiac/Membrane Physiology, The Rockefeller University, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18849964" target="_blank"〉PubMed〈/a〉
    Keywords: Acrylamides/metabolism/pharmacology ; Animals ; Binding Sites ; Cell Membrane/metabolism ; Conserved Sequence ; Cysteine/genetics/metabolism ; Electric Conductivity ; Ion Transport/drug effects ; Models, Molecular ; Protein Conformation/drug effects ; Sodium-Potassium-Exchanging ATPase/antagonists & ; inhibitors/*chemistry/*metabolism ; Xenopus
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    Structural basis for EGFR ligand sequestration by Argos (2008)
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    Publication Date: 2008-05-27
    Description: Members of the epidermal growth factor receptor (EGFR) or ErbB/HER family and their activating ligands are essential regulators of diverse developmental processes. Inappropriate activation of these receptors is a key feature of many human cancers, and its reversal is an important clinical goal. A natural secreted antagonist of EGFR signalling, called Argos, was identified in Drosophila. We showed previously that Argos functions by directly binding (and sequestering) growth factor ligands that activate EGFR. Here we describe the 1.6-A resolution crystal structure of Argos bound to an EGFR ligand. Contrary to expectations, Argos contains no EGF-like domain. Instead, a trio of closely related domains (resembling a three-finger toxin fold) form a clamp-like structure around the bound EGF ligand. Although structurally unrelated to the receptor, Argos mimics EGFR by using a bipartite binding surface to entrap EGF. The individual Argos domains share unexpected structural similarities with the extracellular ligand-binding regions of transforming growth factor-beta family receptors. The three-domain clamp of Argos also resembles the urokinase-type plasminogen activator (uPA) receptor, which uses a similar mechanism to engulf the EGF-like module of uPA. Our results indicate that undiscovered mammalian counterparts of Argos may exist among other poorly characterized structural homologues. In addition, the structures presented here define requirements for the design of artificial EGF-sequestering proteins that would be valuable anti-cancer therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2526102/" 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/PMC2526102/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Klein, Daryl E -- Stayrook, Steven E -- Shi, Fumin -- Narayan, Kartik -- Lemmon, Mark A -- R01 CA079992/CA/NCI NIH HHS/ -- R01 CA079992-10/CA/NCI NIH HHS/ -- R01 CA125432/CA/NCI NIH HHS/ -- R01 CA125432-01A1/CA/NCI NIH HHS/ -- England -- Nature. 2008 Jun 26;453(7199):1271-5. doi: 10.1038/nature06978. Epub 2008 May 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 809C Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, Pennsylvania 19104-6059, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18500331" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Line ; Crystallography, X-Ray ; Drosophila Proteins/*chemistry/*metabolism ; Drosophila melanogaster/*chemistry/cytology ; Epidermal Growth Factor/*chemistry/*metabolism ; Eye Proteins/*chemistry/*metabolism ; Humans ; Ligands ; Membrane Proteins/*chemistry/*metabolism ; Models, Molecular ; Nerve Tissue Proteins/*chemistry/*metabolism ; Protein Structure, Tertiary ; Receptor, Epidermal Growth Factor/antagonists & inhibitors/chemistry/*metabolism ; Receptors, Transforming Growth Factor beta/chemistry/metabolism ; Spodoptera
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    Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-10-04
    Description: HIV-1 protease processes the Gag and Gag-Pol polyproteins into mature structural and functional proteins, including itself, and is therefore indispensable for viral maturation. The mature protease is active only as a dimer with each subunit contributing catalytic residues. The full-length transframe region protease precursor appears to be monomeric yet undergoes maturation via intramolecular cleavage of a putative precursor dimer, concomitant with the appearance of mature-like catalytic activity. How such intramolecular cleavage can occur when the amino and carboxy termini of the mature protease are part of an intersubunit beta-sheet located distal from the active site is unclear. Here we visualize the early events in N-terminal autoprocessing using an inactive mini-precursor with a four-residue N-terminal extension that mimics the transframe region protease precursor. Using paramagnetic relaxation enhancement, a technique that is exquisitely sensitive to the presence of minor species, we show that the mini-precursor forms highly transient, lowly populated (3-5%) dimeric encounter complexes that involve the mature dimer interface but occupy a wide range of subunit orientations relative to the mature dimer. Furthermore, the occupancy of the mature dimer configuration constitutes a very small fraction of the self-associated species (accounting for the very low enzymatic activity of the protease precursor), and the N-terminal extension makes transient intra- and intersubunit contacts with the substrate binding site and is therefore available for autocleavage when the correct dimer orientation is sampled within the encounter complex ensemble.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798589/" 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/PMC2798589/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tang, Chun -- Louis, John M -- Aniana, Annie -- Suh, Jeong-Yong -- Clore, G Marius -- ZIA DK029023-19/Intramural NIH HHS/ -- England -- Nature. 2008 Oct 2;455(7213):693-6. doi: 10.1038/nature07342.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18833280" target="_blank"〉PubMed〈/a〉
    Keywords: Dimerization ; HIV Protease/*chemistry/genetics/*metabolism ; HIV-1/*enzymology/genetics ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Precursors/*chemistry/genetics/*metabolism ; *Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Spin Labels ; gag Gene Products, Human Immunodeficiency Virus/chemistry/metabolism
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    Structural biology: Modelling collagen diseases (2008)
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    Publication Date: 2008-06-20
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760068/" 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/PMC2760068/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brodsky, Barbara -- Baum, Jean -- R01 GM045302/GM/NIGMS NIH HHS/ -- R01 GM045302-14A2/GM/NIGMS NIH HHS/ -- R01 GM060048/GM/NIGMS NIH HHS/ -- R01 GM060048-29/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Jun 19;453(7198):998-9. doi: 10.1038/453998a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18563144" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Collagen Type I/*chemistry/*genetics/metabolism ; Humans ; Models, Molecular ; Molecular Sequence Data ; Osteogenesis Imperfecta/genetics/metabolism ; Peptides/chemistry/genetics/metabolism ; Structure-Activity Relationship
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    Sae2, Exo1 and Sgs1 collaborate in DNA double-strand break processing (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-09-23
    Description: DNA ends exposed after introduction of double-strand breaks (DSBs) undergo 5'-3' nucleolytic degradation to generate single-stranded DNA, the substrate for binding by the Rad51 protein to initiate homologous recombination. This process is poorly understood in eukaryotes, but several factors have been implicated, including the Mre11 complex (Mre11-Rad50-Xrs2/NBS1), Sae2/CtIP/Ctp1 and Exo1. Here we demonstrate that yeast Exo1 nuclease and Sgs1 helicase function in alternative pathways for DSB processing. Novel, partially resected intermediates accumulate in a double mutant lacking Exo1 and Sgs1, which are poor substrates for homologous recombination. The early processing step that generates partly resected intermediates is dependent on Sae2. When Sae2 is absent, in addition to Exo1 and Sgs1, unprocessed DSBs accumulate and homology-dependent repair fails. These results suggest a two-step mechanism for DSB processing during homologous recombination. First, the Mre11 complex and Sae2 remove a small oligonucleotide(s) from the DNA ends to form an early intermediate. Second, Exo1 and/or Sgs1 rapidly process this intermediate to generate extensive tracts of single-stranded DNA that serve as substrate for Rad51.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3818707/" 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/PMC3818707/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mimitou, Eleni P -- Symington, Lorraine S -- R01 GM041784/GM/NIGMS NIH HHS/ -- R01 GM041784-19/GM/NIGMS NIH HHS/ -- R01 GM041784-20/GM/NIGMS NIH HHS/ -- R01 GM041784-21/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Oct 9;455(7214):770-4. doi: 10.1038/nature07312. Epub 2008 Sep 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, Columbia University Medical Center, 701 West 168th Street, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18806779" target="_blank"〉PubMed〈/a〉
    Keywords: *DNA Breaks, Double-Stranded ; *DNA Repair ; Endodeoxyribonucleases/metabolism ; Endonucleases ; Exodeoxyribonucleases/genetics/*metabolism ; Models, Biological ; Rad51 Recombinase/genetics/metabolism ; RecQ Helicases/genetics/*metabolism ; Recombination, Genetic ; Saccharomyces cerevisiae/*genetics/*metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism
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    Programming biomolecular self-assembly pathways (2008)
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    Publication Date: 2008-01-19
    Description: In nature, self-assembling and disassembling complexes of proteins and nucleic acids bound to a variety of ligands perform intricate and diverse dynamic functions. In contrast, attempts to rationally encode structure and function into synthetic amino acid and nucleic acid sequences have largely focused on engineering molecules that self-assemble into prescribed target structures, rather than on engineering transient system dynamics. To design systems that perform dynamic functions without human intervention, it is necessary to encode within the biopolymer sequences the reaction pathways by which self-assembly occurs. Nucleic acids show promise as a design medium for engineering dynamic functions, including catalytic hybridization, triggered self-assembly and molecular computation. Here, we program diverse molecular self-assembly and disassembly pathways using a 'reaction graph' abstraction to specify complementarity relationships between modular domains in a versatile DNA hairpin motif. Molecular programs are executed for a variety of dynamic functions: catalytic formation of branched junctions, autocatalytic duplex formation by a cross-catalytic circuit, nucleated dendritic growth of a binary molecular 'tree', and autonomous locomotion of a bipedal walker.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yin, Peng -- Choi, Harry M T -- Calvert, Colby R -- Pierce, Niles A -- England -- Nature. 2008 Jan 17;451(7176):318-22. doi: 10.1038/nature06451.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bioengineering, California Institute of Technology, Pasadena, California 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202654" target="_blank"〉PubMed〈/a〉
    Keywords: Biopolymers/chemistry/metabolism ; Catalysis ; *Computer Simulation ; DNA/*chemistry/*metabolism ; DNA, Concatenated/chemistry/metabolism ; Dendrimers/chemistry/metabolism ; Gait ; Kinetics ; Models, Biological ; *Nucleic Acid Conformation ; Stochastic Processes ; Walking
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    Developmental biology: Teeth in double trouble (2008)
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    Publication Date: 2008-10-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koentges, Georgy -- England -- Nature. 2008 Oct 9;455(7214):747-8. doi: 10.1038/455747a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18843358" target="_blank"〉PubMed〈/a〉
    Keywords: Ambystoma mexicanum/*embryology ; Animals ; Ectoderm/*cytology/embryology ; Endoderm/*cytology/embryology ; Epithelium/*embryology ; Models, Biological ; Morphogenesis ; Tooth/*cytology/*embryology
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    Distinct roles of the FliI ATPase and proton motive force in bacterial flagellar protein export (2008)
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    Publication Date: 2008-01-25
    Description: Translocation of many soluble proteins across cell membranes occurs in an ATPase-driven manner. For construction of the bacterial flagellum responsible for motility, most of the components are exported by the flagellar protein export apparatus. The FliI ATPase is required for this export, and its ATPase activity is regulated by FliH; however, it is unclear how the chemical energy derived from ATP hydrolysis is used for the export process. Here we report that flagellar proteins of Salmonella enterica serovar Typhimurium are exported even in the absence of FliI. A fliH fliI double null mutant was weakly motile. Certain mutations in FlhA or FlhB, which form the core of the export gate, substantially improved protein export and motility of the double null mutant. Furthermore, proton motive force was essential for the export process. These results suggest that the FliH-FliI complex facilitates only the initial entry of export substrates into the gate, with the energy of ATP hydrolysis being used to disassemble and release the FliH-FliI complex from the protein about to be exported. The rest of the successive unfolding/translocation process of the substrates is driven by proton motive force.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Minamino, Tohru -- Namba, Keiichi -- England -- Nature. 2008 Jan 24;451(7177):485-8. doi: 10.1038/nature06449.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18216858" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Bacterial Proteins/genetics/*metabolism/secretion ; Carbonyl Cyanide m-Chlorophenyl Hydrazone/pharmacology ; Flagella/chemistry/metabolism/*secretion ; Hydrolysis/drug effects ; Membrane Proteins/genetics/metabolism ; Models, Biological ; Mutant Proteins/genetics/metabolism ; Mutation/genetics ; Protein Transport/drug effects ; Proton-Motive Force/drug effects/*physiology ; Proton-Translocating ATPases/deficiency/genetics/*metabolism ; Salmonella typhimurium/cytology/enzymology/genetics/*metabolism
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    Structural basis for the selectivity of the external thioesterase of the surfactin synthetase (2008)
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    Publication Date: 2008-08-16
    Description: Non-ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) found in bacteria, fungi and plants use two different types of thioesterases for the production of highly active biological compounds. Type I thioesterases (TEI) catalyse the release step from the assembly line of the final product where it is transported from one reaction centre to the next as a thioester linked to a 4'-phosphopantetheine (4'-PP) cofactor that is covalently attached to thiolation (T) domains. The second enzyme involved in the synthesis of these secondary metabolites, the type II thioesterase (TEII), is a crucial repair enzyme for the regeneration of functional 4'-PP cofactors of holo-T domains of NRPS and PKS systems. Mispriming of 4'-PP cofactors by acetyl- and short-chain acyl-residues interrupts the biosynthetic system. This repair reaction is very important, because roughly 80% of CoA, the precursor of the 4'-PP cofactor, is acetylated in bacteria. Here we report the three-dimensional structure of a type II thioesterase from Bacillus subtilis free and in complex with a T domain. Comparison with structures of TEI enzymes shows the basis for substrate selectivity and the different modes of interaction of TEII and TEI enzymes with T domains. Furthermore, we show that the TEII enzyme exists in several conformations of which only one is selected on interaction with its native substrate, a modified holo-T domain.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2854587/" 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/PMC2854587/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koglin, Alexander -- Lohr, Frank -- Bernhard, Frank -- Rogov, Vladimir V -- Frueh, Dominique P -- Strieter, Eric R -- Mofid, Mohammad R -- Guntert, Peter -- Wagner, Gerhard -- Walsh, Christopher T -- Marahiel, Mohamed A -- Dotsch, Volker -- P01 GM047467/GM/NIGMS NIH HHS/ -- P01 GM047467-110009/GM/NIGMS NIH HHS/ -- P01 GM047467-12/GM/NIGMS NIH HHS/ -- P01 GM047467-13/GM/NIGMS NIH HHS/ -- P01 GM047467-14/GM/NIGMS NIH HHS/ -- P01 GM047467-15/GM/NIGMS NIH HHS/ -- P01 GM047467-16/GM/NIGMS NIH HHS/ -- P01 GM047467-160010/GM/NIGMS NIH HHS/ -- P01 GM047467-160012/GM/NIGMS NIH HHS/ -- P01 GM047467-17/GM/NIGMS NIH HHS/ -- P01 GM047467-170012/GM/NIGMS NIH HHS/ -- P41 EB002026/EB/NIBIB NIH HHS/ -- P41 EB002026-29/EB/NIBIB NIH HHS/ -- P41 EB002026-30/EB/NIBIB NIH HHS/ -- P41 EB002026-31/EB/NIBIB NIH HHS/ -- P41 EB002026-32/EB/NIBIB NIH HHS/ -- P41 EB002026-33/EB/NIBIB NIH HHS/ -- R01 AI042738/AI/NIAID NIH HHS/ -- R01 AI042738-09/AI/NIAID NIH HHS/ -- R01 GM020011/GM/NIGMS NIH HHS/ -- R01 GM020011-28/GM/NIGMS NIH HHS/ -- R01 GM020011-29/GM/NIGMS NIH HHS/ -- R01 GM020011-30/GM/NIGMS NIH HHS/ -- R01 GM020011-31/GM/NIGMS NIH HHS/ -- R01 GM020011-32/GM/NIGMS NIH HHS/ -- R01 GM020011-37/GM/NIGMS NIH HHS/ -- R01 GM020011-38/GM/NIGMS NIH HHS/ -- R01 GM049338/GM/NIGMS NIH HHS/ -- R01 GM049338-17/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Aug 14;454(7206):907-11. doi: 10.1038/nature07161.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance and Cluster of Excellence Macromolecular Complexes (CEF), J.W.-Goethe University, 60438 Frankfurt am Main, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18704089" target="_blank"〉PubMed〈/a〉
    Keywords: Bacillus subtilis/*enzymology ; Bacterial Proteins/biosynthesis/*chemistry/*metabolism ; Fatty Acid Synthases/*chemistry/*metabolism ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Peptide Synthases/biosynthesis/*chemistry/*metabolism ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Thiolester Hydrolases/*chemistry/*metabolism
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    Survival variability and population density in fish populations (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-03-21
    Description: To understand the processes that regulate the abundance and persistence of wild populations is a fundamental goal of ecology and a prerequisite for the management of living resources. Variable abundance data, however, make the demonstration of regulation processes challenging. A previously overlooked aspect in understanding how populations are regulated is the possibility that the pattern of variability--its strength as a function of population size--may be more than 'noise', thus revealing much about the characteristics of population regulation. Here we show that patterns in survival variability do provide evidence of regulation through density. Using a large, global compilation of marine, anadromous and freshwater fisheries data, we examine the relationship between the variability of survival and population abundance. The interannual variability in progeny survival increases at low adult abundance in an inversely density-dependent fashion. This pattern is consistent with models in which density dependence enters after the larval stage. The findings are compatible with very simple forms of density dependence: even a linear increase of juvenile mortality with adult density adequately explains the results. The model predictions explain why populations with strong regulation may experience large increases in variability at low densities. Furthermore, the inverse relationship between survival variability and the strength of density dependence has important consequences for fisheries management and recovery, and population persistence or extinction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Minto, Coilin -- Myers, Ransom A -- Blanchard, Wade -- England -- Nature. 2008 Mar 20;452(7185):344-7. doi: 10.1038/nature06605.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4J1, Canada. mintoc@mathstat.dal.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18354480" target="_blank"〉PubMed〈/a〉
    Keywords: Age Distribution ; Aging ; Animals ; Fishes/growth & development/*physiology ; Geography ; Larva/physiology ; Models, Biological ; Oceans and Seas ; Population Density ; Reproduction ; Stochastic Processes ; Survival Rate
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    Structural basis of microtubule severing by the hereditary spastic paraplegia protein spastin (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-01-19
    Description: Spastin, the most common locus for mutations in hereditary spastic paraplegias, and katanin are related microtubule-severing AAA ATPases involved in constructing neuronal and non-centrosomal microtubule arrays and in segregating chromosomes. The mechanism by which spastin and katanin break and destabilize microtubules is unknown, in part owing to the lack of structural information on these enzymes. Here we report the X-ray crystal structure of the Drosophila spastin AAA domain and provide a model for the active spastin hexamer generated using small-angle X-ray scattering combined with atomic docking. The spastin hexamer forms a ring with a prominent central pore and six radiating arms that may dock onto the microtubule. Helices unique to the microtubule-severing AAA ATPases surround the entrances to the pore on either side of the ring, and three highly conserved loops line the pore lumen. Mutagenesis reveals essential roles for these structural elements in the severing reaction. Peptide and antibody inhibition experiments further show that spastin may dismantle microtubules by recognizing specific features in the carboxy-terminal tail of tubulin. Collectively, our data support a model in which spastin pulls the C terminus of tubulin through its central pore, generating a mechanical force that destabilizes tubulin-tubulin interactions within the microtubule lattice. Our work also provides insights into the structural defects in spastin that arise from mutations identified in hereditary spastic paraplegia patients.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882799/" 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/PMC2882799/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roll-Mecak, Antonina -- Vale, Ronald D -- K99 NS057934-01/NS/NINDS NIH HHS/ -- K99 NS057934-02/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Jan 17;451(7176):363-7. doi: 10.1038/nature06482.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202664" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/antagonists & ; inhibitors/*chemistry/*genetics/*metabolism ; Animals ; Drosophila Proteins/antagonists & inhibitors/*chemistry/genetics/*metabolism ; Humans ; Microtubules/chemistry/*metabolism ; Models, Biological ; Models, Molecular ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Scattering, Small Angle ; Spastic Paraplegia, Hereditary/*genetics ; Structure-Activity Relationship ; Substrate Specificity ; Tubulin/chemistry/metabolism ; X-Ray Diffraction
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    Cell biology: Nuclear order out of chaos (2008)
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    Publication Date: 2008-11-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Misteli, Tom -- England -- Nature. 2008 Nov 20;456(7220):333-4. doi: 10.1038/456333a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19020607" target="_blank"〉PubMed〈/a〉
    Keywords: *Cell Compartmentation ; Coiled Bodies/*metabolism ; Models, Biological ; Stochastic Processes
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    3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy (2008)
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    Publication Date: 2008-05-02
    Description: Cytoplasmic polyhedrosis virus (CPV) is unique within the Reoviridae family in having a turreted single-layer capsid contained within polyhedrin inclusion bodies, yet being fully capable of cell entry and endogenous RNA transcription. Biochemical data have shown that the amino-terminal 79 residues of the CPV turret protein (TP) is sufficient to bring CPV or engineered proteins into the polyhedrin matrix for micro-encapsulation. Here we report the three-dimensional structure of CPV at 3.88 A resolution using single-particle cryo-electron microscopy. Our map clearly shows the turns and deep grooves of alpha-helices, the strand separation in beta-sheets, and densities for loops and many bulky side chains; thus permitting atomic model-building effort from cryo-electron microscopy maps. We observed a helix-to-beta-hairpin conformational change between the two conformational states of the capsid shell protein in the region directly interacting with genomic RNA. We have also discovered a messenger RNA release hole coupled with the mRNA capping machinery unique to CPV. Furthermore, we have identified the polyhedrin-binding domain, a structure that has potential in nanobiotechnology applications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746981/" 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/PMC2746981/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Xuekui -- Jin, Lei -- Zhou, Z Hong -- P41 RR002250/RR/NCRR NIH HHS/ -- P41 RR002250-190043/RR/NCRR NIH HHS/ -- P41 RR002250-200043/RR/NCRR NIH HHS/ -- P41 RR002250-217385/RR/NCRR NIH HHS/ -- P41 RR002250-226489/RR/NCRR NIH HHS/ -- R01 AI069015/AI/NIAID NIH HHS/ -- R01 AI069015-01A1/AI/NIAID NIH HHS/ -- R01 AI069015-02/AI/NIAID NIH HHS/ -- R01 AI069015-03/AI/NIAID NIH HHS/ -- R01 GM071940/GM/NIGMS NIH HHS/ -- R01 GM071940-01A2/GM/NIGMS NIH HHS/ -- R01 GM071940-02/GM/NIGMS NIH HHS/ -- R01 GM071940-03/GM/NIGMS NIH HHS/ -- R01 GM071940-04/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 May 15;453(7193):415-9. doi: 10.1038/nature06893. Epub 2008 Apr 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology and Laboratory Medicine, The University of Texas Medical School at Houston, Houston, Texas 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18449192" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bombyx/virology ; Capsid Proteins/chemistry/ultrastructure ; *Cryoelectron Microscopy ; Genome, Viral/physiology ; Larva/virology ; Models, Molecular ; RNA Caps/genetics/metabolism ; RNA Transport ; RNA, Viral/genetics/metabolism ; Reoviridae/chemistry/genetics/metabolism/*ultrastructure
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    Palaeontology: modern life in ancient mats (2008)
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    Publication Date: 2008-03-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tice, Michael M -- England -- Nature. 2008 Mar 6;452(7183):40-1. doi: 10.1038/452040a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18322521" target="_blank"〉PubMed〈/a〉
    Keywords: *Ecosystem ; Fossils ; Geologic Sediments/*chemistry/*microbiology ; *Marine Biology ; Models, Biological ; Oceans and Seas ; Paleontology ; Seawater/*microbiology ; Silicon Dioxide/chemistry ; South Africa ; Time Factors ; Water Movements
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    Structural biology: snapshots of DNA repair (2008)
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    Publication Date: 2008-05-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kowalczykowski, Stephen C -- R01 GM062653/GM/NIGMS NIH HHS/ -- R37 GM062653/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 May 22;453(7194):463-6. doi: 10.1038/453463a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497811" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; DNA/*chemistry/genetics/*metabolism ; *DNA Repair ; Models, Molecular ; Molecular Conformation ; Rec A Recombinases/*chemistry/*metabolism ; *Recombination, Genetic/genetics ; *Sequence Homology, Nucleic Acid
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    Structural analysis of the essential self-cleaving type III secretion proteins EscU and SpaS (2008)
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    Publication Date: 2008-05-03
    Description: During infection by Gram-negative pathogenic bacteria, the type III secretion system (T3SS) is assembled to allow for the direct transmission of bacterial virulence effectors into the host cell. The T3SS system is characterized by a series of prominent multi-component rings in the inner and outer bacterial membranes, as well as a translocation pore in the host cell membrane. These are all connected by a series of polymerized tubes that act as the direct conduit for the T3SS proteins to pass through to the host cell. During assembly of the T3SS, as well as the evolutionarily related flagellar apparatus, a post-translational cleavage event within the inner membrane proteins EscU/FlhB is required to promote a secretion-competent state. These proteins have long been proposed to act as a part of a molecular switch, which would regulate the appropriate chronological secretion of the various T3SS apparatus components during assembly and subsequently the transported virulence effectors. Here we show that a surface type II beta-turn in the Escherichia coli protein EscU undergoes auto-cleavage by a mechanism involving cyclization of a strictly conserved asparagine residue. Structural and in vivo analysis of point and deletion mutations illustrates the subtle conformational effects of auto-cleavage in modulating the molecular features of a highly conserved surface region of EscU, a potential point of interaction with other T3SS components at the inner membrane. In addition, this work provides new structural insight into the distinct conformational requirements for a large class of self-cleaving reactions involving asparagine cyclization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zarivach, Raz -- Deng, Wanyin -- Vuckovic, Marija -- Felise, Heather B -- Nguyen, Hai V -- Miller, Samuel I -- Finlay, B Brett -- Strynadka, Natalie C J -- 5R01 AI030479/AI/NIAID NIH HHS/ -- R01 AI030479/AI/NIAID NIH HHS/ -- U54 AI057141/AI/NIAID NIH HHS/ -- England -- Nature. 2008 May 1;453(7191):124-7. doi: 10.1038/nature06832.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, and the Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18451864" target="_blank"〉PubMed〈/a〉
    Keywords: Asparagine/chemistry/metabolism ; Circular Dichroism ; Crystallography, X-Ray ; Cyclization ; Enteropathogenic Escherichia coli/*chemistry/*metabolism/pathogenicity ; Escherichia coli Proteins/*chemistry/genetics/*metabolism ; Models, Chemical ; Models, Molecular ; Protein Structure, Tertiary ; Salmonella typhimurium/genetics/metabolism ; Virulence Factors/metabolism
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    Crystal structure of the ZP-N domain of ZP3 reveals the core fold of animal egg coats (2008)
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    Publication Date: 2008-12-05
    Description: Species-specific recognition between the egg extracellular matrix (zona pellucida) and sperm is the first, crucial step of mammalian fertilization. Zona pellucida filament components ZP3 and ZP2 act as sperm receptors, and mice lacking either of the corresponding genes produce oocytes without a zona pellucida and are completely infertile. Like their counterparts in the vitelline envelope of non-mammalian eggs and many other secreted eukaryotic proteins, zona pellucida subunits polymerize using a 'zona pellucida (ZP) domain' module, whose conserved amino-terminal part (ZP-N) was suggested to constitute a domain of its own. No atomic structure has been reported for ZP domain proteins, and there is no structural information on any conserved vertebrate protein that is essential for fertilization and directly involved in egg-sperm binding. Here we describe the 2.3 angstrom (A) resolution structure of the ZP-N fragment of mouse primary sperm receptor ZP3. The ZP-N fold defines a new immunoglobulin superfamily subtype with a beta-sheet extension characterized by an E' strand and an invariant tyrosine residue implicated in polymerization. The structure strongly supports the presence of ZP-N repeats within the N-terminal region of ZP2 and other vertebrate zona pellucida/vitelline envelope proteins, with implications for overall egg coat architecture, the post-fertilization block to polyspermy and speciation. Moreover, it provides an important framework for understanding human diseases caused by mutations in ZP domain proteins and developing new methods of non-hormonal contraception.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Monne, Magnus -- Han, Ling -- Schwend, Thomas -- Burendahl, Sofia -- Jovine, Luca -- G0500367/Medical Research Council/United Kingdom -- England -- Nature. 2008 Dec 4;456(7222):653-7. doi: 10.1038/nature07599.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Karolinska Institutet, Department of Biosciences and Nutrition, Halsovagen 7, SE-141 57 Huddinge, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19052627" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; CHO Cells ; Conserved Sequence ; Cricetinae ; Cricetulus ; Crystallization ; Crystallography, X-Ray ; Egg Proteins/*chemistry/genetics/*metabolism ; Female ; Male ; Membrane Glycoproteins/*chemistry/genetics/*metabolism ; Mice ; Models, Molecular ; Molecular Sequence Data ; Ovum/*chemistry/*metabolism ; Peptide Fragments/chemistry/genetics/metabolism ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Cell Surface/*chemistry/genetics/*metabolism ; Repetitive Sequences, Amino Acid ; Spermatozoa/metabolism
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    Science teaching must evolve (2008)
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    Publication Date: 2008-05-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moore, Andrew -- England -- Nature. 2008 May 1;453(7191):31-2. doi: 10.1038/453031a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Science & Society Programme at the European Molecular Biology Organization (EMBO), Meyerhofstrasse 1, D-69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18451837" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Biology/*education/history ; Computational Biology/education ; Curriculum/standards/*trends ; Evolution, Molecular ; History, 20th Century ; History, 21st Century ; Humans ; Internationality ; Models, Biological ; Teaching/history/*standards/*trends
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    Kemp elimination catalysts by computational enzyme design (2008)
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    Publication Date: 2008-03-21
    Description: The design of new enzymes for reactions not catalysed by naturally occurring biocatalysts is a challenge for protein engineering and is a critical test of our understanding of enzyme catalysis. Here we describe the computational design of eight enzymes that use two different catalytic motifs to catalyse the Kemp elimination-a model reaction for proton transfer from carbon-with measured rate enhancements of up to 10(5) and multiple turnovers. Mutational analysis confirms that catalysis depends on the computationally designed active sites, and a high-resolution crystal structure suggests that the designs have close to atomic accuracy. Application of in vitro evolution to enhance the computational designs produced a 〉200-fold increase in k(cat)/K(m) (k(cat)/K(m) of 2,600 M(-1)s(-1) and k(cat)/k(uncat) of 〉10(6)). These results demonstrate the power of combining computational protein design with directed evolution for creating new enzymes, and we anticipate the creation of a wide range of useful new catalysts in the future.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rothlisberger, Daniela -- Khersonsky, Olga -- Wollacott, Andrew M -- Jiang, Lin -- DeChancie, Jason -- Betker, Jamie -- Gallaher, Jasmine L -- Althoff, Eric A -- Zanghellini, Alexandre -- Dym, Orly -- Albeck, Shira -- Houk, Kendall N -- Tawfik, Dan S -- Baker, David -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 May 8;453(7192):190-5. doi: 10.1038/nature06879. Epub 2008 Mar 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18354394" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Motifs ; Binding Sites/genetics ; Catalysis ; Computational Biology ; *Computer Simulation ; Crystallography, X-Ray ; Directed Molecular Evolution/*methods ; Drug Design ; Drug Evaluation, Preclinical ; Enzymes/*chemistry/genetics/*metabolism ; Kinetics ; Models, Chemical ; Models, Molecular ; Protein Engineering/*methods ; Quantum Theory ; Sensitivity and Specificity
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    Structural basis for the regulated protease and chaperone function of DegP (2008)
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    Publication Date: 2008-05-23
    Description: All organisms have to monitor the folding state of cellular proteins precisely. The heat-shock protein DegP is a protein quality control factor in the bacterial envelope that is involved in eliminating misfolded proteins and in the biogenesis of outer-membrane proteins. Here we describe the molecular mechanisms underlying the regulated protease and chaperone function of DegP from Escherichia coli. We show that binding of misfolded proteins transforms hexameric DegP into large, catalytically active 12-meric and 24-meric multimers. A structural analysis of these particles revealed that DegP represents a protein packaging device whose central compartment is adaptable to the size and concentration of substrate. Moreover, the inner cavity serves antagonistic functions. Whereas the encapsulation of folded protomers of outer-membrane proteins is protective and might allow safe transit through the periplasm, misfolded proteins are eliminated in the molecular reaction chamber. Oligomer reassembly and concomitant activation on substrate binding may also be critical in regulating other HtrA proteases implicated in protein-folding diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krojer, Tobias -- Sawa, Justyna -- Schafer, Eva -- Saibil, Helen R -- Ehrmann, Michael -- Clausen, Tim -- 070776/Wellcome Trust/United Kingdom -- 079605/Wellcome Trust/United Kingdom -- BB/C516144/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/C516179/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F010281/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/B/03955/Biotechnology and Biological Sciences Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2008 Jun 12;453(7197):885-90. doi: 10.1038/nature07004. Epub 2008 May 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Research Institute for Molecular Pathology - IMP, Dr Bohrgasse 7, A-1030 Vienna, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18496527" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Outer Membrane ; Proteins/biosynthesis/chemistry/metabolism/ultrastructure ; Cell Membrane/metabolism ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Escherichia coli/*enzymology ; Heat-Shock Proteins/*chemistry/*metabolism/ultrastructure ; Models, Molecular ; Molecular Chaperones/*chemistry/*metabolism/ultrastructure ; Periplasmic Proteins/*chemistry/*metabolism/ultrastructure ; Protein Folding ; Protein Structure, Quaternary ; Serine Endopeptidases/*chemistry/*metabolism/ultrastructure ; Structure-Activity Relationship
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    A fundamental avian wing-stroke provides a new perspective on the evolution of flight (2008)
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    Publication Date: 2008-01-25
    Description: The evolution of avian flight remains one of biology's major controversies, with a long history of functional interpretations of fossil forms given as evidence for either an arboreal or cursorial origin of flight. Despite repeated emphasis on the 'wing-stroke' as a necessary avenue of investigation for addressing the evolution of flight, no empirical data exist on wing-stroke dynamics in an experimental evolutionary context. Here we present the first comparison of wing-stroke kinematics of the primary locomotor modes (descending flight and incline flap-running) that lead to level-flapping flight in juvenile ground birds throughout development. We offer results that are contrary both to popular perception and inferences from other studies. Starting shortly after hatching and continuing through adulthood, ground birds use a wing-stroke confined to a narrow range of less than 20 degrees , when referenced to gravity, that directs aerodynamic forces about 40 degrees above horizontal, permitting a 180 degrees range in the direction of travel. Based on our results, we put forth an ontogenetic-transitional wing hypothesis that posits that the incremental adaptive stages leading to the evolution of avian flight correspond behaviourally and morphologically to transitional stages observed in ontogenetic forms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dial, Kenneth P -- Jackson, Brandon E -- Segre, Paolo -- England -- Nature. 2008 Feb 21;451(7181):985-9. doi: 10.1038/nature06517. Epub 2008 Jan 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Flight Laboratory, Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, Montana 59812, USA. kdial@mso.umt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18216784" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Biomechanical Phenomena ; Flight, Animal/*physiology ; Galliformes/growth & development/*physiology ; Locomotion/physiology ; Models, Biological ; Wings, Animal/*physiology
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    Identification of ALK as a major familial neuroblastoma predisposition gene (2008)
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    Publication Date: 2008-08-30
    Description: Neuroblastoma is a childhood cancer that can be inherited, but the genetic aetiology is largely unknown. Here we show that germline mutations in the anaplastic lymphoma kinase (ALK) gene explain most hereditary neuroblastomas, and that activating mutations can also be somatically acquired. We first identified a significant linkage signal at chromosome bands 2p23-24 using a whole-genome scan in neuroblastoma pedigrees. Resequencing of regional candidate genes identified three separate germline missense mutations in the tyrosine kinase domain of ALK that segregated with the disease in eight separate families. Resequencing in 194 high-risk neuroblastoma samples showed somatically acquired mutations in the tyrosine kinase domain in 12.4% of samples. Nine of the ten mutations map to critical regions of the kinase domain and were predicted, with high probability, to be oncogenic drivers. Mutations resulted in constitutive phosphorylation, and targeted knockdown of ALK messenger RNA resulted in profound inhibition of growth in all cell lines harbouring mutant or amplified ALK, as well as in two out of six wild-type cell lines for ALK. Our results demonstrate that heritable mutations of ALK are the main cause of familial neuroblastoma, and that germline or acquired activation of this cell-surface kinase is a tractable therapeutic target for this lethal paediatric malignancy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672043/" 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/PMC2672043/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mosse, Yael P -- Laudenslager, Marci -- Longo, Luca -- Cole, Kristina A -- Wood, Andrew -- Attiyeh, Edward F -- Laquaglia, Michael J -- Sennett, Rachel -- Lynch, Jill E -- Perri, Patrizia -- Laureys, Genevieve -- Speleman, Frank -- Kim, Cecilia -- Hou, Cuiping -- Hakonarson, Hakon -- Torkamani, Ali -- Schork, Nicholas J -- Brodeur, Garrett M -- Tonini, Gian P -- Rappaport, Eric -- Devoto, Marcella -- Maris, John M -- K08 CA111733/CA/NCI NIH HHS/ -- K08 CA111733-04/CA/NCI NIH HHS/ -- K08-111733/PHS HHS/ -- R01 CA078545/CA/NCI NIH HHS/ -- R01 CA078545-09/CA/NCI NIH HHS/ -- R01 CA124709/CA/NCI NIH HHS/ -- R01-CA78454/CA/NCI NIH HHS/ -- R01-CA87847/CA/NCI NIH HHS/ -- U10 CA098543/CA/NCI NIH HHS/ -- U10 CA098543-06/CA/NCI NIH HHS/ -- England -- Nature. 2008 Oct 16;455(7215):930-5. doi: 10.1038/nature07261. Epub 2008 Aug 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18724359" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Cell Line, Tumor ; Child ; Chromosomes, Human, Pair 2/genetics ; Female ; Gene Dosage ; Gene Expression Regulation, Neoplastic ; Genetic Predisposition to Disease/*genetics ; Germ-Line Mutation/genetics ; Humans ; Male ; Models, Molecular ; Molecular Sequence Data ; Mutation/*genetics ; Neuroblastoma/*enzymology/*genetics ; Pedigree ; Phosphorylation ; Protein Structure, Tertiary ; Protein-Tyrosine Kinases/chemistry/deficiency/*genetics ; Receptor Protein-Tyrosine Kinases
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    Pairs of cooperating cleaner fish provide better service quality than singletons (2008)
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    Publication Date: 2008-10-17
    Description: Service providers may vary service quality depending on whether they work alone or provide the service simultaneously with a partner. The latter case resembles a prisoner's dilemma, in which one provider may try to reap the benefits of the interaction without providing the service. Here we present a game-theory model based on the marginal value theorem, which predicts that as long as the client determines the duration, and the providers cooperate towards mutual gain, service quality will increase in the pair situation. This prediction is consistent with field observations and with an experiment on cleaning mutualism, in which stable male-female pairs of the cleaner wrasse Labroides dimidiatus repeatedly inspect client fish jointly. Cleaners cooperate by eating ectoparasites off clients but actually prefer to cheat and eat client mucus. Because clients often leave in response to such cheating, the benefits of cheating can be gained by only one cleaner during a pair inspection. In both data sets, the increased service quality during pair inspection was mainly due to the smaller females behaving significantly more cooperatively than their larger male partners. In contrast, during solitary inspections, cleaning behaviour was very similar between the sexes. Our study highlights the importance of incorporating interactions between service providers to make more quantitative predictions about cooperation between species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bshary, Redouan -- Grutter, Alexandra S -- Willener, Astrid S T -- Leimar, Olof -- England -- Nature. 2008 Oct 16;455(7215):964-6. doi: 10.1038/nature07184.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Neuchatel, Department of Zoology, Rue Emile-Argand 11 Case postale 158, 2009 Neuchatel, Switzerland. redouan.bshary@unine.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18923522" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Cooperative Behavior ; Feeding Behavior/*physiology ; Female ; Fishes/*physiology ; Game Theory ; Male ; Models, Biological ; Mucus ; *Parasites ; Sex Characteristics ; Swimming/physiology ; *Symbiosis
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    Structure of a complex of the ATPase SecA and the protein-translocation channel (2008)
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    Publication Date: 2008-10-17
    Description: Most proteins are secreted from bacteria by the interaction of the cytoplasmic SecA ATPase with a membrane channel, formed by the heterotrimeric SecY complex. Here we report the crystal structure of SecA bound to the SecY complex, with a maximum resolution of 4.5 angstrom (A), obtained for components from Thermotoga maritima. One copy of SecA in an intermediate state of ATP hydrolysis is bound to one molecule of the SecY complex. Both partners undergo important conformational changes on interaction. The polypeptide-cross-linking domain of SecA makes a large conformational change that could capture the translocation substrate in a 'clamp'. Polypeptide movement through the SecY channel could be achieved by the motion of a 'two-helix finger' of SecA inside the cytoplasmic funnel of SecY, and by the coordinated tightening and widening of SecA's clamp above the SecY pore. SecA binding generates a 'window' at the lateral gate of the SecY channel and it displaces the plug domain, preparing the channel for signal sequence binding and channel opening.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zimmer, Jochen -- Nam, Yunsun -- Rapoport, Tom A -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Oct 16;455(7215):936-43. doi: 10.1038/nature07335.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18923516" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/*metabolism ; Adenosine Triphosphate/metabolism ; Bacillus subtilis/chemistry ; Bacterial Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; Hydrolysis ; Membrane Transport Proteins/*chemistry/*metabolism ; Models, Biological ; Models, Molecular ; Movement ; Multiprotein Complexes/chemistry/metabolism ; Protein Binding ; Protein Conformation ; Protein Sorting Signals/physiology ; Protein Transport ; Structure-Activity Relationship ; Thermotoga maritima/*chemistry
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    Crystal structure of squid rhodopsin (2008)
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    Publication Date: 2008-05-16
    Description: Invertebrate phototransduction uses an inositol-1,4,5-trisphosphate signalling cascade in which photoactivated rhodopsin stimulates a G(q)-type G protein, that is, a class of G protein that stimulates membrane-bound phospholipase Cbeta. The same cascade is used by many G-protein-coupled receptors, indicating that invertebrate rhodopsin is a prototypical member. Here we report the crystal structure of squid (Todarodes pacificus) rhodopsin at 2.5 A resolution. Among seven transmembrane alpha-helices, helices V and VI extend into the cytoplasmic medium and, together with two cytoplasmic helices, they form a rigid protrusion from the membrane surface. This peculiar structure, which is not seen in bovine rhodopsin, seems to be crucial for the recognition of G(q)-type G proteins. The retinal Schiff base forms a hydrogen bond to Asn 87 or Tyr 111; it is far from the putative counterion Glu 180. In the crystal, a tight association is formed between the amino-terminal polypeptides of neighbouring monomers; this intermembrane dimerization may be responsible for the organization of hexagonally packed microvillar membranes in the photoreceptor rhabdom.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murakami, Midori -- Kouyama, Tsutomu -- England -- Nature. 2008 May 15;453(7193):363-7. doi: 10.1038/nature06925.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18480818" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; Decapodiformes/*chemistry ; Dimerization ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Secondary ; Retinaldehyde/metabolism ; Rhodopsin/*chemistry/metabolism ; Schiff Bases ; Vision, Ocular/physiology ; Water/chemistry/metabolism
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    The pathogen protein EspF(U) hijacks actin polymerization using mimicry and multivalency (2008)
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    Publication Date: 2008-07-25
    Description: Enterohaemorrhagic Escherichia coli attaches to the intestine through actin pedestals that are formed when the bacterium injects its protein EspF(U) (also known as TccP) into host cells. EspF(U) potently activates the host WASP (Wiskott-Aldrich syndrome protein) family of actin-nucleating factors, which are normally activated by the GTPase CDC42, among other signalling molecules. Apart from its amino-terminal type III secretion signal, EspF(U) consists of five-and-a-half 47-amino-acid repeats. Here we show that a 17-residue motif within this EspF(U) repeat is sufficient for interaction with N-WASP (also known as WASL). Unlike most pathogen proteins that interface with the cytoskeletal machinery, this motif does not mimic natural upstream activators: instead of mimicking an activated state of CDC42, EspF(U) mimics an autoinhibitory element found within N-WASP. Thus, EspF(U) activates N-WASP by competitively disrupting the autoinhibited state. By mimicking an internal regulatory element and not the natural activator, EspF(U) selectively activates only a precise subset of CDC42-activated processes. Although one repeat is able to stimulate actin polymerization, we show that multiple-repeat fragments have notably increased potency. The activities of these EspF(U) fragments correlate with their ability to coordinate activation of at least two N-WASP proteins. Thus, this pathogen has used a simple autoinhibitory fragment as a component to build a highly effective actin polymerization machine.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749708/" 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/PMC2749708/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sallee, Nathan A -- Rivera, Gonzalo M -- Dueber, John E -- Vasilescu, Dan -- Mullins, R Dyche -- Mayer, Bruce J -- Lim, Wendell A -- PN2 EY016546/EY/NEI NIH HHS/ -- PN2 EY016546-05/EY/NEI NIH HHS/ -- R01 CA082258/CA/NCI NIH HHS/ -- R01 CA082258-10/CA/NCI NIH HHS/ -- R01 GM061010/GM/NIGMS NIH HHS/ -- R01 GM061010-09/GM/NIGMS NIH HHS/ -- R01 GM062583/GM/NIGMS NIH HHS/ -- R01 GM062583-07/GM/NIGMS NIH HHS/ -- U54 RR022232/RR/NCRR NIH HHS/ -- U54 RR022232-03/RR/NCRR NIH HHS/ -- U54 RR022232-03S1/RR/NCRR NIH HHS/ -- England -- Nature. 2008 Aug 21;454(7207):1005-8. doi: 10.1038/nature07170. Epub 2008 Jul 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18650806" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/chemistry/*metabolism ; Amino Acid Sequence ; Animals ; Carrier Proteins/chemistry/*metabolism ; Enterohemorrhagic Escherichia coli/*metabolism/pathogenicity ; Escherichia coli Proteins/chemistry/*metabolism ; Mice ; Models, Molecular ; *Molecular Mimicry ; Molecular Sequence Data ; NIH 3T3 Cells ; Protein Structure, Tertiary ; Repetitive Sequences, Nucleic Acid ; Signal Transduction/physiology ; Wiskott-Aldrich Syndrome Protein, Neuronal/chemistry/metabolism
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    Gibberellin-induced DELLA recognition by the gibberellin receptor GID1 (2008)
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    Publication Date: 2008-11-28
    Description: Gibberellins control a range of growth and developmental processes in higher plants and have been widely used in the agricultural industry. By binding to a nuclear receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1), gibberellins regulate gene expression by promoting degradation of the transcriptional regulator DELLA proteins, including GIBBERELLIN INSENSITIVE (GAI). The precise manner in which GID1 discriminates and becomes activated by bioactive gibberellins for specific binding to DELLA proteins remains unclear. Here we present the crystal structure of a ternary complex of Arabidopsis thaliana GID1A, a bioactive gibberellin and the amino-terminal DELLA domain of GAI. In this complex, GID1A occludes gibberellin in a deep binding pocket covered by its N-terminal helical switch region, which in turn interacts with the DELLA domain containing DELLA, VHYNP and LExLE motifs. Our results establish a structural model of a plant hormone receptor that is distinct from the mechanism of the hormone perception and effector recognition of the known auxin receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murase, Kohji -- Hirano, Yoshinori -- Sun, Tai-ping -- Hakoshima, Toshio -- England -- Nature. 2008 Nov 27;456(7221):459-63. doi: 10.1038/nature07519.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19037309" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Arabidopsis/*chemistry/metabolism ; Arabidopsis Proteins/*chemistry/genetics/*metabolism ; Circular Dichroism ; Crystallography, X-Ray ; Gibberellins/metabolism/*pharmacology ; Models, Biological ; Models, Molecular ; Plant Growth Regulators/metabolism/*pharmacology ; Protein Binding ; Protein Structure, Tertiary/drug effects ; Receptors, Cell Surface/*chemistry/genetics/*metabolism ; Substrate Specificity
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    Could global gardening fix climate change? (2008)
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    Publication Date: 2008-01-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tollefson, Jeff -- England -- Nature. 2008 Jan 10;451(7175):113. doi: 10.1038/451113a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18185549" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/methods/*trends ; Atmosphere/*chemistry ; Bioelectric Energy Sources/trends ; *Biomass ; Carbon Dioxide/*analysis ; *Greenhouse Effect ; Models, Biological
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    Calcium-bound structure of calpain and its mechanism of inhibition by calpastatin (2008)
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    Publication Date: 2008-11-21
    Description: Calpains are non-lysosomal calcium-dependent cysteine proteinases that selectively cleave proteins in response to calcium signals and thereby control cellular functions such as cytoskeletal remodelling, cell cycle progression, gene expression and apoptotic cell death. In mammals, the two best-characterized members of the calpain family, calpain 1 and calpain 2 (micro-calpain and m-calpain, respectively), are ubiquitously expressed. The activity of calpains is tightly controlled by the endogenous inhibitor calpastatin, which is an intrinsically unstructured protein capable of reversibly binding and inhibiting four molecules of calpain, but only in the presence of calcium. To date, the mechanism of inhibition by calpastatin and the basis for its absolute specificity have remained speculative. It was not clear how this unstructured protein inhibits calpains without being cleaved itself, nor was it known how calcium induced changes that facilitated the binding of calpastatin to calpain. Here we report the 2.4-A-resolution crystal structure of the calcium-bound calpain 2 heterodimer bound by one of the four inhibitory domains of calpastatin. Calpastatin is seen to inhibit calpain by occupying both sides of the active site cleft. Although the inhibitor passes through the active site cleft it escapes cleavage in a novel manner by looping out and around the active site cysteine. The inhibitory domain of calpastatin recognizes multiple lower affinity sites present only in the calcium-bound form of the enzyme, resulting in an interaction that is tight, specific and calcium dependent. This crystal structure, and that of a related complex, also reveal the conformational changes that calpain undergoes on binding calcium, which include opening of the active site cleft and movement of the domains relative to each other to produce a more compact enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hanna, Rachel A -- Campbell, Robert L -- Davies, Peter L -- England -- Nature. 2008 Nov 20;456(7220):409-12. doi: 10.1038/nature07451.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19020623" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/*metabolism ; Calcium-Binding Proteins/*chemistry/*metabolism ; Calpain/*antagonists & inhibitors/*chemistry/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Models, Molecular ; Protein Binding ; Protein Multimerization ; Rats ; Structure-Activity Relationship
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    The cranial endoskeleton of Tiktaalik roseae (2008)
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    Publication Date: 2008-10-17
    Description: Among the morphological changes that occurred during the 'fish-to-tetrapod' transition was a marked reorganization of the cranial endoskeleton. Details of this transition, including the sequence of character acquisition, have not been evident from the fossil record. Here we describe the braincase, palatoquadrate and branchial skeleton of Tiktaalik roseae, the Late Devonian sarcopterygian fish most closely related to tetrapods. Although retaining a primitive configuration in many respects, the cranial endoskeleton of T. roseae shares derived features with tetrapods such as a large basal articulation and a flat, horizontally oriented entopterygoid. Other features in T. roseae, like the short, straight hyomandibula, show morphology intermediate between the condition observed in more primitive fish and that observed in tetrapods. The combination of characters in T. roseae helps to resolve the relative timing of modifications in the cranial endoskeleton. The sequence of modifications suggests changes in head mobility and intracranial kinesis that have ramifications for the origin of vertebrate terrestriality.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Downs, Jason P -- Daeschler, Edward B -- Jenkins, Farish A Jr -- Shubin, Neil H -- England -- Nature. 2008 Oct 16;455(7215):925-9. doi: 10.1038/nature07189.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Academy of Natural Sciences of Philadelphia, 1900 Benjamin Franklin Parkway, Philadelphia, Pennsylvania 19103, USA. downs@ansp.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18923515" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Ecosystem ; Fishes/*anatomy & histology/physiology ; *Fossils ; Models, Biological ; Skull/*anatomy & histology/physiology
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    Structural basis for translation termination on the 70S ribosome (2008)
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    Publication Date: 2008-07-04
    Description: At termination of protein synthesis, type I release factors promote hydrolysis of the peptidyl-transfer RNA linkage in response to recognition of a stop codon. Here we describe the crystal structure of the Thermus thermophilus 70S ribosome in complex with the release factor RF1, tRNA and a messenger RNA containing a UAA stop codon, at 3.2 A resolution. The stop codon is recognized in a pocket formed by conserved elements of RF1, including its PxT recognition motif, and 16S ribosomal RNA. The codon and the 30S subunit A site undergo an induced fit that results in stabilization of a conformation of RF1 that promotes its interaction with the peptidyl transferase centre. Unexpectedly, the main-chain amide group of Gln 230 in the universally conserved GGQ motif of the factor is positioned to contribute directly to peptidyl-tRNA hydrolysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laurberg, Martin -- Asahara, Haruichi -- Korostelev, Andrei -- Zhu, Jianyu -- Trakhanov, Sergei -- Noller, Harry F -- England -- Nature. 2008 Aug 14;454(7206):852-7. doi: 10.1038/nature07115. Epub 2008 Jul 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, California 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18596689" target="_blank"〉PubMed〈/a〉
    Keywords: Codon, Terminator/genetics/metabolism ; Crystallography, X-Ray ; Models, Molecular ; *Peptide Chain Termination, Translational ; Peptide Termination Factors/chemistry/metabolism ; Peptidyl Transferases/chemistry/metabolism ; Protein Binding ; Protein Structure, Tertiary ; RNA, Bacterial/metabolism ; RNA, Ribosomal, 23S/chemistry ; RNA, Transfer/chemistry/genetics/metabolism ; Ribosomes/*chemistry/*metabolism ; Thermus thermophilus/*chemistry/metabolism
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    Protein-folding location can regulate manganese-binding versus copper- or zinc-binding (2008)
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    Publication Date: 2008-10-25
    Description: Metals are needed by at least one-quarter of all proteins. Although metallochaperones insert the correct metal into some proteins, they have not been found for the vast majority, and the view is that most metalloproteins acquire their metals directly from cellular pools. However, some metals form more stable complexes with proteins than do others. For instance, as described in the Irving-Williams series, Cu(2+) and Zn(2+) typically form more stable complexes than Mn(2+). Thus it is unclear what cellular mechanisms manage metal acquisition by most nascent proteins. To investigate this question, we identified the most abundant Cu(2+)-protein, CucA (Cu(2+)-cupin A), and the most abundant Mn(2+)-protein, MncA (Mn(2+)-cupin A), in the periplasm of the cyanobacterium Synechocystis PCC 6803. Each of these newly identified proteins binds its respective metal via identical ligands within a cupin fold. Consistent with the Irving-Williams series, MncA only binds Mn(2+) after folding in solutions containing at least a 10(4) times molar excess of Mn(2+) over Cu(2+) or Zn(2+). However once MncA has bound Mn(2+), the metal does not exchange with Cu(2+). MncA and CucA have signal peptides for different export pathways into the periplasm, Tat and Sec respectively. Export by the Tat pathway allows MncA to fold in the cytoplasm, which contains only tightly bound copper or Zn(2+) (refs 10-12) but micromolar Mn(2+) (ref. 13). In contrast, CucA folds in the periplasm to acquire Cu(2+). These results reveal a mechanism whereby the compartment in which a protein folds overrides its binding preference to control its metal content. They explain why the cytoplasm must contain only tightly bound and buffered copper and Zn(2+).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tottey, Steve -- Waldron, Kevin J -- Firbank, Susan J -- Reale, Brian -- Bessant, Conrad -- Sato, Katsuko -- Cheek, Timothy R -- Gray, Joe -- Banfield, Mark J -- Dennison, Christopher -- Robinson, Nigel J -- BB/E001688/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/B/02576/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0500367/Medical Research Council/United Kingdom -- G0600759/Medical Research Council/United Kingdom -- England -- Nature. 2008 Oct 23;455(7216):1138-42. doi: 10.1038/nature07340.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle NE2 4HH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18948958" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/isolation & purification/*metabolism ; Copper/metabolism ; Manganese/metabolism ; Metals, Heavy/*metabolism ; Models, Molecular ; Periplasm/metabolism ; Protein Binding ; *Protein Folding ; Protein Structure, Tertiary ; Synechocystis/metabolism ; Zinc/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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    Integration of growth and specification in chick wing digit-patterning (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-03-21
    Description: In the classical model of chick wing digit-patterning, the polarizing region--a group of cells at the posterior margin of the early bud--produces a morphogen gradient, now known to be based on Sonic hedgehog (Shh), that progressively specifies anteroposterior positional identities in the posterior digit-forming region. Here we add an integral growth component to this model by showing that Shh-dependent proliferation of prospective digit progenitor cells is essential for specifying the complete pattern of digits across the anteroposterior axis. Inhibiting Shh signalling in early wing buds reduced anteroposterior expansion, and posterior digits were lost because all prospective digit precursors formed anterior structures. Inhibiting proliferation also irreversibly reduced anteroposterior expansion, but instead anterior digits were lost because all prospective digit precursors formed posterior structures. When proliferation recovered in such wings, Shh transcription was maintained for longer than normal, suggesting that duration of Shh expression is controlled by a mechanism that measures proliferation. Rescue experiments confirmed that Shh-dependent proliferation controls digit number during a discrete time-window in which Shh-dependent specification normally occurs. Our findings that Shh signalling has dual functions that can be temporally uncoupled have implications for understanding congenital and evolutionary digit reductions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Towers, Matthew -- Mahood, Ruth -- Yin, Yili -- Tickle, Cheryll -- G9806660/Medical Research Council/United Kingdom -- England -- Nature. 2008 Apr 17;452(7189):882-6. doi: 10.1038/nature06718. Epub 2008 Mar 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Cell and Developmental Biology, WTB/MSI Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18354396" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Body Patterning ; Chick Embryo ; Female ; Hedgehog Proteins/metabolism ; Limb Buds/cytology/embryology ; Models, Biological ; Wings, Animal/*anatomy & histology/cytology/*embryology
    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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