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  • Articles  (1,001)
  • Models, Molecular  (413)
  • Amino Acid Sequence  (362)
  • Time Factors  (330)
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  • 1
    Publication Date: 2009-12-18
    Description: Avian brood parasites and their hosts provide model systems for investigating links between recognition, learning, and their fitness consequences. One major evolutionary puzzle has continued to capture the attention of naturalists for centuries: why do hosts of brood parasites generally fail to recognize parasitic offspring after they have hatched from the egg, even when the host and parasitic chicks differ to almost comic degrees? One prominent theory to explain this pattern proposes that the costs of mistakenly learning to recognize the wrong offspring make recognition maladaptive. Here we show that American coots, Fulica americana, can recognize and reject parasitic chicks in their brood by using learned cues, despite the fact that the hosts and the brood parasites are of the same species. A series of chick cross-fostering experiments confirm that coots use first-hatched chicks in a brood as referents to learn to recognize their own chicks and then discriminate against later-hatched parasitic chicks in the same brood. When experimentally provided with the wrong reference chicks, coots can be induced to discriminate against their own offspring, confirming that the learning errors proposed by theory can exist. However, learning based on hatching order is reliable in naturally parasitized coot nests because host eggs hatch predictably ahead of parasite eggs. Conversely, a lack of reliable information may help to explain why the evolution of chick recognition is not more common in hosts of most interspecific brood parasites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shizuka, Daizaburo -- Lyon, Bruce E -- England -- Nature. 2010 Jan 14;463(7278):223-6. doi: 10.1038/nature08655. Epub 2009 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA. shizuka@biology.ucsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20016486" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Birds/*parasitology/*physiology ; British Columbia ; Cues ; Discrimination Learning/*physiology ; Feeding Behavior/physiology ; Genetic Fitness ; Nesting Behavior/*physiology ; Ovum/growth & development ; Pattern Recognition, Visual/physiology ; Survival Rate ; Time Factors ; Wetlands
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  • 2
    Publication Date: 2009-12-23
    Description: Reprogramming of somatic cell nuclei to yield induced pluripotent stem (iPS) cells makes possible derivation of patient-specific stem cells for regenerative medicine. However, iPS cell generation is asynchronous and slow (2-3 weeks), the frequency is low (〈0.1%), and DNA demethylation constitutes a bottleneck. To determine regulatory mechanisms involved in reprogramming, we generated interspecies heterokaryons (fused mouse embryonic stem (ES) cells and human fibroblasts) that induce reprogramming synchronously, frequently and fast. Here we show that reprogramming towards pluripotency in single heterokaryons is initiated without cell division or DNA replication, rapidly (1 day) and efficiently (70%). Short interfering RNA (siRNA)-mediated knockdown showed that activation-induced cytidine deaminase (AID, also known as AICDA) is required for promoter demethylation and induction of OCT4 (also known as POU5F1) and NANOG gene expression. AID protein bound silent methylated OCT4 and NANOG promoters in fibroblasts, but not active demethylated promoters in ES cells. These data provide new evidence that mammalian AID is required for active DNA demethylation and initiation of nuclear reprogramming towards pluripotency in human somatic cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906123/" 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/PMC2906123/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhutani, Nidhi -- Brady, Jennifer J -- Damian, Mara -- Sacco, Alessandra -- Corbel, Stephane Y -- Blau, Helen M -- AG009521/AG/NIA NIH HHS/ -- AG024987/AG/NIA NIH HHS/ -- AI007328/AI/NIAID NIH HHS/ -- R01 AG009521/AG/NIA NIH HHS/ -- R01 AG009521-25/AG/NIA NIH HHS/ -- R01 AG024987/AG/NIA NIH HHS/ -- R01 AG024987-05/AG/NIA NIH HHS/ -- T32 AI007328/AI/NIAID NIH HHS/ -- U01 HL100397/HL/NHLBI NIH HHS/ -- England -- Nature. 2010 Feb 25;463(7284):1042-7. doi: 10.1038/nature08752.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Baxter Laboratory for Stem Cell Biology, Institute for Stem Cell Biology and Regenerative Medicine, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305-5175, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20027182" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Division ; Cell Fusion ; Cell Line ; Cells, Cultured ; Cellular Reprogramming/genetics/*physiology ; Chromatin Immunoprecipitation ; Cytidine Deaminase/deficiency/genetics/*metabolism ; DNA/chemistry/genetics/metabolism ; *DNA Methylation ; DNA Replication ; Embryonic Stem Cells/cytology/metabolism ; Fibroblasts/cytology/metabolism ; Gene Expression Regulation ; Gene Knockdown Techniques ; Homeodomain Proteins/genetics ; Humans ; Induced Pluripotent Stem Cells/*cytology/enzymology/*metabolism ; Lung/cytology/embryology ; Mice ; Models, Biological ; Octamer Transcription Factor-3/genetics ; Promoter Regions, Genetic/genetics ; Time Factors
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  • 3
    Publication Date: 2009-12-22
    Description: Broken chromosomes arising from DNA double-strand breaks result from endogenous events such as the production of reactive oxygen species during cellular metabolism, as well as from exogenous sources such as ionizing radiation. Left unrepaired or incorrectly repaired they can lead to genomic changes that may result in cell death or cancer. DNA-dependent protein kinase (DNA-PK), a holoenzyme that comprises the DNA-PK catalytic subunit (DNA-PKcs) and the heterodimer Ku70/Ku80, has a major role in non-homologous end joining-the main pathway in mammals used to repair double-strand breaks. DNA-PKcs is a serine/threonine protein kinase comprising a single polypeptide chain of 4,128 amino acids and belonging to the phosphatidylinositol-3-OH kinase (PI(3)K)-related protein family. DNA-PKcs is involved in the sensing and transmission of DNA damage signals to proteins such as p53, setting off events that lead to cell cycle arrest. It phosphorylates a wide range of substrates in vitro, including Ku70/Ku80, which is translocated along DNA. Here we present the crystal structure of human DNA-PKcs at 6.6 A resolution, in which the overall fold is clearly visible, to our knowledge, for the first time. The many alpha-helical HEAT repeats (helix-turn-helix motifs) facilitate bending and allow the polypeptide chain to fold into a hollow circular structure. The carboxy-terminal kinase domain is located on top of this structure, and a small HEAT repeat domain that probably binds DNA is inside. The structure provides a flexible cradle to promote DNA double-strand-break repair.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811870/" 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/PMC2811870/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sibanda, Bancinyane L -- Chirgadze, Dimitri Y -- Blundell, Tom L -- 079281/Wellcome Trust/United Kingdom -- A3846/Cancer Research UK/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Jan 7;463(7277):118-21. doi: 10.1038/nature08648. Epub 2009 Dec 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Cambridge, Old Addenbrooke's site, 80 Tennis Court Road, Cambridge CB2 1GA, UK. lynn@cryst.bioc.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20023628" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, Nuclear/chemistry ; Catalytic Domain ; Crystallography, X-Ray ; DNA/metabolism ; DNA Breaks, Double-Stranded ; DNA-Activated Protein Kinase/*chemistry/metabolism ; DNA-Binding Proteins/chemistry ; HeLa Cells ; *Helix-Turn-Helix Motifs ; Humans ; Models, Molecular ; Nuclear Proteins/*chemistry/metabolism ; Protein Folding ; Protein Structure, Secondary
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  • 4
    Publication Date: 2009-12-17
    Description: Recent research on changing fears has examined targeting reconsolidation. During reconsolidation, stored information is rendered labile after being retrieved. Pharmacological manipulations at this stage result in an inability to retrieve the memories at later times, suggesting that they are erased or persistently inhibited. Unfortunately, the use of these pharmacological manipulations in humans can be problematic. Here we introduce a non-invasive technique to target the reconsolidation of fear memories in humans. We provide evidence that old fear memories can be updated with non-fearful information provided during the reconsolidation window. As a consequence, fear responses are no longer expressed, an effect that lasted at least a year and was selective only to reactivated memories without affecting others. These findings demonstrate the adaptive role of reconsolidation as a window of opportunity to rewrite emotional memories, and suggest a non-invasive technique that can be used safely in humans to prevent the return of fear.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3640262/" 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/PMC3640262/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schiller, Daniela -- Monfils, Marie-H -- Raio, Candace M -- Johnson, David C -- Ledoux, Joseph E -- Phelps, Elizabeth A -- K05 MH067048/MH/NIMH NIH HHS/ -- P50 MH058911/MH/NIMH NIH HHS/ -- R01 MH038774/MH/NIMH NIH HHS/ -- R01 MH046516/MH/NIMH NIH HHS/ -- R21 MH072279/MH/NIMH NIH HHS/ -- R37 MH038774/MH/NIMH NIH HHS/ -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2010 Jan 7;463(7277):49-53. doi: 10.1038/nature08637. Epub 2009 Dec 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Neural Science, New York University, New York, New York 10003, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010606" target="_blank"〉PubMed〈/a〉
    Keywords: Conditioning, Classical/*physiology ; Cues ; Electrodes ; Electroshock ; Extinction, Psychological/*physiology ; Fear/*physiology/*psychology ; Humans ; Memory/*physiology ; Models, Neurological ; Models, Psychological ; Neuronal Plasticity/*physiology ; Photic Stimulation ; Time Factors
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  • 5
    Publication Date: 2009-01-14
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340503/" 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/PMC4340503/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kelly, Bernard T -- McCoy, Airlie J -- Spate, Kira -- Miller, Sharon E -- Evans, Philip R -- Honing, Stefan -- Owen, David J -- 090909/Wellcome Trust/United Kingdom -- MC_U105178845/Medical Research Council/United Kingdom -- England -- Nature. 2008 Dec 18;456(7224):976-79. doi: 10.1038/nature07422.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19140243" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Protein Complex 2/*chemistry/genetics/*metabolism ; Amino Acid Motifs ; Animals ; Antigens, CD4/*chemistry/*metabolism ; Binding Sites ; Conserved Sequence ; *Endocytosis ; Humans ; Leucine/*metabolism ; Mice ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Subunits/chemistry/genetics/metabolism ; Rats
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  • 6
    Publication Date: 2009-08-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reich, Eugenie Samuel -- England -- Nature. 2009 Aug 20;460(7258):949. doi: 10.1038/460949c.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cambridge, Massachusetts 02139, USA eugenie.reich@gmail.com.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19693062" target="_blank"〉PubMed〈/a〉
    Keywords: Physics ; Risk ; Science/*standards ; *Scientific Misconduct ; *Whistleblowing
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  • 7
    Publication Date: 2009-11-26
    Description: Mutations in the enzyme cytosolic isocitrate dehydrogenase 1 (IDH1) are a common feature of a major subset of primary human brain cancers. These mutations occur at a single amino acid residue of the IDH1 active site, resulting in loss of the enzyme's ability to catalyse conversion of isocitrate to alpha-ketoglutarate. However, only a single copy of the gene is mutated in tumours, raising the possibility that the mutations do not result in a simple loss of function. Here we show that cancer-associated IDH1 mutations result in a new ability of the enzyme to catalyse the NADPH-dependent reduction of alpha-ketoglutarate to R(-)-2-hydroxyglutarate (2HG). Structural studies demonstrate that when arginine 132 is mutated to histidine, residues in the active site are shifted to produce structural changes consistent with reduced oxidative decarboxylation of isocitrate and acquisition of the ability to convert alpha-ketoglutarate to 2HG. Excess accumulation of 2HG has been shown to lead to an elevated risk of malignant brain tumours in patients with inborn errors of 2HG metabolism. Similarly, in human malignant gliomas harbouring IDH1 mutations, we find markedly elevated levels of 2HG. These data demonstrate that the IDH1 mutations result in production of the onco-metabolite 2HG, and indicate that the excess 2HG which accumulates in vivo contributes to the formation and malignant progression of gliomas.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818760/" 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/PMC2818760/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dang, Lenny -- White, David W -- Gross, Stefan -- Bennett, Bryson D -- Bittinger, Mark A -- Driggers, Edward M -- Fantin, Valeria R -- Jang, Hyun Gyung -- Jin, Shengfang -- Keenan, Marie C -- Marks, Kevin M -- Prins, Robert M -- Ward, Patrick S -- Yen, Katharine E -- Liau, Linda M -- Rabinowitz, Joshua D -- Cantley, Lewis C -- Thompson, Craig B -- Vander Heiden, Matthew G -- Su, Shinsan M -- P01 CA104838/CA/NCI NIH HHS/ -- P01 CA104838-05/CA/NCI NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 CA105463/CA/NCI NIH HHS/ -- R01 CA105463-06/CA/NCI NIH HHS/ -- R21 CA128620/CA/NCI NIH HHS/ -- England -- Nature. 2009 Dec 10;462(7274):739-44. doi: 10.1038/nature08617. Epub .〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Agios Pharmaceuticals, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19935646" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/genetics ; Brain Neoplasms/*genetics/*metabolism/pathology ; Catalytic Domain ; Cell Line ; Crystallography, X-Ray ; Disease Progression ; Enzyme Assays ; Glioma/genetics/metabolism/pathology ; Glutarates/*metabolism ; Histidine/genetics/metabolism ; Humans ; Isocitrate Dehydrogenase/*genetics/*metabolism ; Ketoglutaric Acids/metabolism ; Models, Molecular ; Mutant Proteins/*genetics/*metabolism ; Mutation/genetics ; Protein Conformation
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  • 8
    Publication Date: 2009-12-01
    Description: Changes in synaptic connections are considered essential for learning and memory formation. However, it is unknown how neural circuits undergo continuous synaptic changes during learning while maintaining lifelong memories. Here we show, by following postsynaptic dendritic spines over time in the mouse cortex, that learning and novel sensory experience lead to spine formation and elimination by a protracted process. The extent of spine remodelling correlates with behavioural improvement after learning, suggesting a crucial role of synaptic structural plasticity in memory formation. Importantly, a small fraction of new spines induced by novel experience, together with most spines formed early during development and surviving experience-dependent elimination, are preserved and provide a structural basis for memory retention throughout the entire life of an animal. These studies indicate that learning and daily sensory experience leave minute but permanent marks on cortical connections and suggest that lifelong memories are stored in largely stably connected synaptic networks.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724802/" 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/PMC4724802/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Guang -- Pan, Feng -- Gan, Wen-Biao -- R01 NS047325/NS/NINDS NIH HHS/ -- England -- Nature. 2009 Dec 17;462(7275):920-4. doi: 10.1038/nature08577. Epub 2009 Nov 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Neurobiology Program, The Helen and Martin Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, Department of Physiology and Neuroscience, New York University School of Medicine, New York, New York 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19946265" target="_blank"〉PubMed〈/a〉
    Keywords: Aging/physiology ; Animals ; Dendritic Spines/metabolism/*physiology ; Forelimb/physiology ; Memory/*physiology ; Mice ; Motor Cortex/cytology/physiology ; Motor Skills/physiology ; Neuronal Plasticity/physiology ; Pyramidal Cells/metabolism ; Synapses/*metabolism ; Time Factors
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  • 9
    Publication Date: 2009-03-06
    Description: Osmoregulated transporters sense intracellular osmotic pressure and respond to hyperosmotic stress by accumulation of osmolytes to restore normal hydration levels. Here we report the determination of the X-ray structure of a member of the family of betaine/choline/carnitine transporters, the Na(+)-coupled symporter BetP from Corynebacterium glutamicum, which is a highly effective osmoregulated uptake system for glycine betaine. Glycine betaine is bound in a tryptophan box occluded from both sides of the membrane with aromatic side chains lining the transport pathway. BetP has the same overall fold as three unrelated Na(+)-coupled symporters. Whereas these are crystallized in either the outward-facing or the inward-facing conformation, the BetP structure reveals a unique intermediate conformation in the Na(+)-coupled transport cycle. The trimeric architecture of BetP and the break in three-fold symmetry by the osmosensing C-terminal helices suggest a regulatory mechanism of Na(+)-coupled osmolyte transport to counteract osmotic stress.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ressl, Susanne -- Terwisscha van Scheltinga, Anke C -- Vonrhein, Clemens -- Ott, Vera -- Ziegler, Christine -- England -- Nature. 2009 Mar 5;458(7234):47-52. doi: 10.1038/nature07819.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute of Biophysics, Department of Structural Biology, 60438 Frankfurt am Main, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19262666" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/genetics/*metabolism ; Betaine/*metabolism ; Binding Sites ; Carrier Proteins/*chemistry/genetics/*metabolism ; Corynebacterium glutamicum/*chemistry/genetics ; Crystallography, X-Ray ; Ion Transport ; Models, Molecular ; Protein Binding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Sodium/*metabolism ; Structure-Activity Relationship
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  • 10
    Publication Date: 2009-08-21
    Description: A decision is a commitment to a proposition or plan of action based on evidence and the expected costs and benefits associated with the outcome. Progress in a variety of fields has led to a quantitative understanding of the mechanisms that evaluate evidence and reach a decision. Several formalisms propose that a representation of noisy evidence is evaluated against a criterion to produce a decision. Without additional evidence, however, these formalisms fail to explain why a decision-maker would change their mind. Here we extend a model, developed to account for both the timing and the accuracy of the initial decision, to explain subsequent changes of mind. Subjects made decisions about a noisy visual stimulus, which they indicated by moving a handle. Although they received no additional information after initiating their movement, their hand trajectories betrayed a change of mind in some trials. We propose that noisy evidence is accumulated over time until it reaches a criterion level, or bound, which determines the initial decision, and that the brain exploits information that is in the processing pipeline when the initial decision is made to subsequently either reverse or reaffirm the initial decision. The model explains both the frequency of changes of mind as well as their dependence on both task difficulty and whether the initial decision was accurate or erroneous. The theoretical and experimental findings advance the understanding of decision-making to the highly flexible and cognitive acts of vacillation and self-correction.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875179/" 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/PMC2875179/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Resulaj, Arbora -- Kiani, Roozbeh -- Wolpert, Daniel M -- Shadlen, Michael N -- 077730/Wellcome Trust/United Kingdom -- EY11378/EY/NEI NIH HHS/ -- Howard Hughes Medical Institute/ -- Wellcome Trust/United Kingdom -- England -- Nature. 2009 Sep 10;461(7261):263-6. doi: 10.1038/nature08275. Epub 2009 Aug 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computational and Biological Learning Laboratory, Department of Engineering, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19693010" target="_blank"〉PubMed〈/a〉
    Keywords: Computers ; Cues ; Decision Making/*physiology ; Female ; Hand/physiology ; Humans ; Male ; Models, Neurological ; Models, Psychological ; Motion ; Movement ; Photic Stimulation ; Psychomotor Performance ; Reaction Time ; Time Factors
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  • 11
    Publication Date: 2009-11-27
    Description: Protein design provides a rigorous test of our knowledge about proteins and allows the creation of novel enzymes for biotechnological applications. Whereas progress has been made in designing proteins that mimic native proteins structurally, it is more difficult to design functional proteins. In comparison to recent successes in designing non-metalloproteins, it is even more challenging to rationally design metalloproteins that reproduce both the structure and function of native metalloenzymes. This is because protein metal-binding sites are much more varied than non-metal-containing sites, in terms of different metal ion oxidation states, preferred geometry and metal ion ligand donor sets. Because of their variability, it has been difficult to predict metal-binding site properties in silico, as many of the parameters, such as force fields, are ill-defined. Therefore, the successful design of a structural and functional metalloprotein would greatly advance the field of protein design and our understanding of enzymes. Here we report a successful, rational design of a structural and functional model of a metalloprotein, nitric oxide reductase (NOR), by introducing three histidines and one glutamate, predicted as ligands in the active site of NOR, into the distal pocket of myoglobin. A crystal structure of the designed protein confirms that the minimized computer model contains a haem/non-haem Fe(B) centre that is remarkably similar to that in the crystal structure. This designed protein also exhibits NO reduction activity, and so models both the structure and function of NOR, offering insight that the active site glutamate is required for both iron binding and activity. These results show that structural and functional metalloproteins can be rationally designed in silico.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4297211/" 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/PMC4297211/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yeung, Natasha -- Lin, Ying-Wu -- Gao, Yi-Gui -- Zhao, Xuan -- Russell, Brandy S -- Lei, Lanyu -- Miner, Kyle D -- Robinson, Howard -- Lu, Yi -- GM062211/GM/NIGMS NIH HHS/ -- R01 GM062211/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Dec 24;462(7276):1079-82. doi: 10.1038/nature08620. Epub 2009 Nov 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19940850" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallization ; Iron/metabolism ; Models, Molecular ; Myoglobin/chemistry ; Nitric Oxide/metabolism ; Oxidoreductases/*chemical synthesis/*chemistry/metabolism ; Protein Binding ; Protein Structure, Tertiary
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  • 12
    Publication Date: 2009-11-20
    Description: Glutamate transporters are integral membrane proteins that catalyse a thermodynamically uphill uptake of the neurotransmitter glutamate from the synaptic cleft into the cytoplasm of glia and neuronal cells by harnessing the energy of pre-existing electrochemical gradients of ions. Crucial to the reaction is the conformational transition of the transporters between outward and inward facing states, in which the substrate binding sites are accessible from the extracellular space and the cytoplasm, respectively. Here we describe the crystal structure of a double cysteine mutant of a glutamate transporter homologue from Pyrococcus horikoshii, Glt(Ph), which is trapped in the inward facing state by cysteine crosslinking. Together with the previously determined crystal structures of Glt(Ph) in the outward facing state, the structure of the crosslinked mutant allows us to propose a molecular mechanism by which Glt(Ph) and, by analogy, mammalian glutamate transporters mediate sodium-coupled substrate uptake.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2934767/" 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/PMC2934767/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reyes, Nicolas -- Ginter, Christopher -- Boudker, Olga -- R01 NS064357/NS/NINDS NIH HHS/ -- R01 NS064357-01A1/NS/NINDS NIH HHS/ -- England -- Nature. 2009 Dec 17;462(7275):880-5. doi: 10.1038/nature08616. Epub 2009 Nov 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, Box 75, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19924125" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Transport System X-AG/*chemistry/genetics/*metabolism ; Binding Sites ; Biological Transport ; Cross-Linking Reagents ; Crystallography, X-Ray ; Cysteine/genetics/metabolism ; Models, Molecular ; Movement ; Mutant Proteins/chemistry/genetics/metabolism ; Protein Structure, Tertiary ; Pyrococcus horikoshii/*chemistry ; Sodium/metabolism ; Structure-Activity Relationship
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  • 13
    Publication Date: 2009-09-11
    Description: Infectious prion diseases-scrapie of sheep and chronic wasting disease (CWD) of several species in the deer family-are transmitted naturally within affected host populations. Although several possible sources of contagion have been identified in excretions and secretions from symptomatic animals, the biological importance of these sources in sustaining epidemics remains unclear. Here we show that asymptomatic CWD-infected mule deer (Odocoileus hemionus) excrete CWD prions in their faeces long before they develop clinical signs of prion disease. Intracerebral inoculation of irradiated deer faeces into transgenic mice overexpressing cervid prion protein (PrP) revealed infectivity in 14 of 15 faecal samples collected from five deer at 7-11 months before the onset of neurological disease. Although prion concentrations in deer faeces were considerably lower than in brain tissue from the same deer collected at the end of the disease, the estimated total infectious dose excreted in faeces by an infected deer over the disease course may approximate the total contained in a brain. Prolonged faecal prion excretion by infected deer provides a plausible natural mechanism that might explain the high incidence and efficient horizontal transmission of CWD within deer herds, as well as prion transmission among other susceptible cervids.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3186440/" 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/PMC3186440/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tamguney, Gultekin -- Miller, Michael W -- Wolfe, Lisa L -- Sirochman, Tracey M -- Glidden, David V -- Palmer, Christina -- Lemus, Azucena -- DeArmond, Stephen J -- Prusiner, Stanley B -- AG02132/AG/NIA NIH HHS/ -- P01 AG002132/AG/NIA NIH HHS/ -- P01 AG002132-26/AG/NIA NIH HHS/ -- P01 AG002132-29/AG/NIA NIH HHS/ -- England -- Nature. 2009 Sep 24;461(7263):529-32. doi: 10.1038/nature08289. Epub 2009 Sep 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94143 USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19741608" target="_blank"〉PubMed〈/a〉
    Keywords: Administration, Oral ; Animals ; Biological Assay ; Brain/metabolism ; Deer/*metabolism ; Feces/*chemistry ; Injections, Intraventricular ; Mice ; Mice, Transgenic ; PrPSc Proteins/isolation & purification/*metabolism/*pathogenicity/radiation ; effects ; Time Factors ; Wasting Disease, Chronic/*metabolism/*transmission
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  • 14
    Publication Date: 2009-03-20
    Description: Optical activity is the result of chiral molecules interacting differently with left versus right circularly polarized light. Because of this intrinsic link to molecular structure, the determination of optical activity through circular dichroism (CD) spectroscopy has long served as a routine method for obtaining structural information about chemical and biological systems in condensed phases. A recent development is time-resolved CD spectroscopy, which can in principle map the structural changes associated with biomolecular function and thus lead to mechanistic insights into fundamental biological processes. But implementing time-resolved CD measurements is experimentally challenging because CD is a notoriously weak effect (a factor of 10(-4)-10(-6) smaller than absorption). In fact, this problem has so far prevented time-resolved vibrational CD experiments. Here we show that vibrational CD spectroscopy with femtosecond time resolution can be realized when using heterodyned spectral interferometry to detect the phase and amplitude of the infrared optical activity free-induction-decay field in time (much like in a pulsed NMR experiment). We show that we can detect extremely weak signals in the presence of large achiral background contributions, by simultaneously measuring with a femtosecond laser pulse the vibrational CD and optical rotatory dispersion spectra of dissolved chiral limonene molecules. We have so far only targeted molecules in equilibrium, but it would be straightforward to extend the method for the observation of ultrafast structural changes such as those occurring during protein folding or asymmetric chemical reactions. That is, we should now be in a position to produce 'molecular motion pictures' of fundamental molecular processes from a chiral perspective.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rhee, Hanju -- June, Young-Gun -- Lee, Jang-Soo -- Lee, Kyung-Koo -- Ha, Jeong-Hyon -- Kim, Zee Hwan -- Jeon, Seung-Joon -- Cho, Minhaeng -- England -- Nature. 2009 Mar 19;458(7236):310-3. doi: 10.1038/nature07846.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Korea University, Seoul 136-701, Korea.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295604" target="_blank"〉PubMed〈/a〉
    Keywords: Anisotropy ; Circular Dichroism/*methods ; Cyclohexenes/*chemistry ; Stereoisomerism ; Terpenes/*chemistry ; Time Factors ; *Vibration
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  • 15
    Publication Date: 2009-11-20
    Description: The release of fossil fuel CO(2) to the atmosphere by human activity has been implicated as the predominant cause of recent global climate change. The ocean plays a crucial role in mitigating the effects of this perturbation to the climate system, sequestering 20 to 35 per cent of anthropogenic CO(2) emissions. Although much progress has been made in recent years in understanding and quantifying this sink, considerable uncertainties remain as to the distribution of anthropogenic CO(2) in the ocean, its rate of uptake over the industrial era, and the relative roles of the ocean and terrestrial biosphere in anthropogenic CO(2) sequestration. Here we address these questions by presenting an observationally based reconstruction of the spatially resolved, time-dependent history of anthropogenic carbon in the ocean over the industrial era. Our approach is based on the recognition that the transport of tracers in the ocean can be described by a Green's function, which we estimate from tracer data using a maximum entropy deconvolution technique. Our results indicate that ocean uptake of anthropogenic CO(2) has increased sharply since the 1950s, with a small decline in the rate of increase in the last few decades. We estimate the inventory and uptake rate of anthropogenic CO(2) in 2008 at 140 +/- 25 Pg C and 2.3 +/- 0.6 Pg C yr(-1), respectively. We find that the Southern Ocean is the primary conduit by which this CO(2) enters the ocean (contributing over 40 per cent of the anthropogenic CO(2) inventory in the ocean in 2008). Our results also suggest that the terrestrial biosphere was a source of CO(2) until the 1940s, subsequently turning into a sink. Taken over the entire industrial period, and accounting for uncertainties, we estimate that the terrestrial biosphere has been anywhere from neutral to a net source of CO(2), contributing up to half as much CO(2) as has been taken up by the ocean over the same period.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Khatiwala, S -- Primeau, F -- Hall, T -- England -- Nature. 2009 Nov 19;462(7271):346-9. doi: 10.1038/nature08526.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lamont-Doherty Earth Observatory of Columbia University, Palisades, New York 10964, USA. spk@ldeo.columbia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19924213" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Dioxide/*analysis/metabolism ; Humans ; Models, Theoretical ; Oceans and Seas ; Seawater/*chemistry ; Time Factors
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  • 16
    Publication Date: 2009-09-18
    Description: It has been suggested that volatile organic compounds (VOCs) are involved in organic aerosol formation, which in turn affects radiative forcing and climate. The most abundant VOCs emitted by terrestrial vegetation are isoprene and its derivatives, such as monoterpenes and sesquiterpenes. New particle formation in boreal regions is related to monoterpene emissions and causes an estimated negative radiative forcing of about -0.2 to -0.9 W m(-2). The annual variation in aerosol growth rates during particle nucleation events correlates with the seasonality of monoterpene emissions of the local vegetation, with a maximum during summer. The frequency of nucleation events peaks, however, in spring and autumn. Here we present evidence from simulation experiments conducted in a plant chamber that isoprene can significantly inhibit new particle formation. The process leading to the observed decrease in particle number concentration is linked to the high reactivity of isoprene with the hydroxyl radical (OH). The suppression is stronger with higher concentrations of isoprene, but with little dependence on the specific VOC mixture emitted by trees. A parameterization of the observed suppression factor as a function of isoprene concentration suggests that the number of new particles produced depends on the OH concentration and VOCs involved in the production of new particles undergo three to four steps of oxidation by OH. Our measurements simulate conditions that are typical for forested regions and may explain the observed seasonality in the frequency of aerosol nucleation events, with a lower number of nucleation events during summer compared to autumn and spring. Biogenic emissions of isoprene are controlled by temperature and light, and if the relative isoprene abundance of biogenic VOC emissions increases in response to climate change or land use change, the new particle formation potential may decrease, thus damping the aerosol negative radiative forcing effect.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kiendler-Scharr, Astrid -- Wildt, Jurgen -- Dal Maso, Miikka -- Hohaus, Thorsten -- Kleist, Einhard -- Mentel, Thomas F -- Tillmann, Ralf -- Uerlings, Ricarda -- Schurr, Uli -- Wahner, Andreas -- England -- Nature. 2009 Sep 17;461(7262):381-4. doi: 10.1038/nature08292.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut ICG-2, Troposphare. a.kiendler-scharr@fz-juelich.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19759617" target="_blank"〉PubMed〈/a〉
    Keywords: Aerosols/analysis/metabolism ; Air/analysis ; Betula/drug effects/metabolism ; Butadienes/analysis/*pharmacology ; Carbon/analysis ; Environment, Controlled ; Fagus/drug effects/metabolism ; Hemiterpenes/analysis/*pharmacology/*secretion ; Hydroxyl Radical/analysis/metabolism ; Light ; Monoterpenes/metabolism/pharmacology ; Oxidation-Reduction ; Pentanes/analysis/*pharmacology ; Picea/drug effects/metabolism ; Seasons ; Temperature ; Time Factors ; Trees/*drug effects/*metabolism ; Volatile Organic Compounds/analysis/*metabolism
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  • 17
    Publication Date: 2009-02-06
    Description: The heterotrimeric influenza virus polymerase, containing the PA, PB1 and PB2 proteins, catalyses viral RNA replication and transcription in the nucleus of infected cells. PB1 holds the polymerase active site and reportedly harbours endonuclease activity, whereas PB2 is responsible for cap binding. The PA amino terminus is understood to be the major functional part of the PA protein and has been implicated in several roles, including endonuclease and protease activities as well as viral RNA/complementary RNA promoter binding. Here we report the 2.2 angstrom (A) crystal structure of the N-terminal 197 residues of PA, termed PA(N), from an avian influenza H5N1 virus. The PA(N) structure has an alpha/beta architecture and reveals a bound magnesium ion coordinated by a motif similar to the (P)DX(N)(D/E)XK motif characteristic of many endonucleases. Structural comparisons and mutagenesis analysis of the motif identified in PA(N) provide further evidence that PA(N) holds an endonuclease active site. Furthermore, functional analysis with in vivo ribonucleoprotein reconstitution and direct in vitro endonuclease assays strongly suggest that PA(N) holds the endonuclease active site and has critical roles in endonuclease activity of the influenza virus polymerase, rather than PB1. The high conservation of this endonuclease active site among influenza strains indicates that PA(N) is an important target for the design of new anti-influenza therapeutics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yuan, Puwei -- Bartlam, Mark -- Lou, Zhiyong -- Chen, Shoudeng -- Zhou, Jie -- He, Xiaojing -- Lv, Zongyang -- Ge, Ruowen -- Li, Xuemei -- Deng, Tao -- Fodor, Ervin -- Rao, Zihe -- Liu, Yingfang -- G0700848/Medical Research Council/United Kingdom -- England -- Nature. 2009 Apr 16;458(7240):909-13. doi: 10.1038/nature07720. Epub 2009 Feb 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19194458" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds/virology ; Catalytic Domain ; Crystallography, X-Ray ; Endonucleases/*chemistry/genetics/*metabolism ; Influenza A Virus, H5N1 Subtype/*enzymology ; Influenza in Birds/*virology ; Models, Molecular ; Protein Subunits/chemistry/genetics/metabolism ; RNA Replicase/*chemistry/genetics/*metabolism ; Viral Proteins/*chemistry/genetics/*metabolism
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  • 18
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    Nature Publishing Group (NPG)
    Publication Date: 2009-02-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Feb 26;457(7233):1057. doi: 10.1038/4571057a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19242425" target="_blank"〉PubMed〈/a〉
    Keywords: Antarctic Regions ; Arctic Regions ; *Cold Climate ; Ecosystem ; *Environmental Monitoring ; *Internationality ; Research/instrumentation/*trends ; Time Factors
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  • 19
    Publication Date: 2009-05-05
    Description: The proteasome is a protease that controls diverse processes in eukaryotic cells. Its regulatory particle (RP) initiates the degradation of ubiquitin-protein conjugates by unfolding the substrate and translocating it into the proteasome core particle (CP) to be degraded. The RP has 19 subunits, and their pathway of assembly is not understood. Here we show that in the yeast Saccharomyces cerevisiae three proteins are found associated with RP but not with the RP-CP holoenzyme: Nas6, Rpn14 and Hsm3. Mutations in the corresponding genes confer proteasome loss-of-function phenotypes, despite their virtual absence from the holoenzyme. These effects result from deficient RP assembly. Thus, Nas6, Rpn14 and Hsm3 are RP chaperones. The RP contains six ATPases-the Rpt proteins-and each RP chaperone binds to the carboxy-terminal domain of a specific Rpt. We show in an accompanying study that RP assembly is templated through the Rpt C termini, apparently by their insertion into binding pockets in the CP. Thus, RP chaperones may regulate proteasome assembly by directly restricting the accessibility of Rpt C termini to the CP. In addition, competition between the RP chaperones and the CP for Rpt engagement may explain the release of RP chaperones as proteasomes mature.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2727592/" 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/PMC2727592/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roelofs, Jeroen -- Park, Soyeon -- Haas, Wilhelm -- Tian, Geng -- McAllister, Fiona E -- Huo, Ying -- Lee, Byung-Hoon -- Zhang, Fan -- Shi, Yigong -- Gygi, Steven P -- Finley, Daniel -- 5F32GM75737-2/GM/NIGMS NIH HHS/ -- GM043601/GM/NIGMS NIH HHS/ -- GM67945/GM/NIGMS NIH HHS/ -- R37 GM043601/GM/NIGMS NIH HHS/ -- R37 GM043601-19/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Jun 11;459(7248):861-5. doi: 10.1038/nature08063.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉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/19412159" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry/metabolism ; Carrier Proteins/genetics/metabolism ; Conserved Sequence ; Evolution, Molecular ; Holoenzymes/chemistry/metabolism ; Humans ; Models, Molecular ; Molecular Chaperones/genetics/*metabolism ; Mutation ; Phenotype ; Proteasome Endopeptidase Complex/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Proto-Oncogene Proteins/genetics/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Saccharomyces cerevisiae Proteins/genetics/metabolism
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  • 20
    Publication Date: 2009-07-17
    Description: In recent years, strikingly consistent patterns of biodiversity have been identified over space, time, organism type and geographical region. A neutral theory (assuming no environmental selection or organismal interactions) has been shown to predict many patterns of ecological biodiversity. This theory is based on a mechanism by which new species arise similarly to point mutations in a population without sexual reproduction. Here we report the simulation of populations with sexual reproduction, mutation and dispersal. We found simulated time dependence of speciation rates, species-area relationships and species abundance distributions consistent with the behaviours found in nature. From our results, we predict steady speciation rates, more species in one-dimensional environments than two-dimensional environments, three scaling regimes of species-area relationships and lognormal distributions of species abundance with an excess of rare species and a tail that may be approximated by Fisher's logarithmic series. These are consistent with dependences reported for, among others, global birds and flowering plants, marine invertebrate fossils, ray-finned fishes, British birds and moths, North American songbirds, mammal fossils from Kansas and Panamanian shrubs. Quantitative comparisons of specific cases are remarkably successful. Our biodiversity results provide additional evidence that species diversity arises without specific physical barriers. This is similar to heavy traffic flows, where traffic jams can form even without accidents or barriers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉de Aguiar, M A M -- Baranger, M -- Baptestini, E M -- Kaufman, L -- Bar-Yam, Y -- England -- Nature. 2009 Jul 16;460(7253):384-7. doi: 10.1038/nature08168.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉New England Complex Systems Institute, Cambridge, Massachusetts 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19606148" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Disorders of Sex Development ; Extinction, Biological ; *Genetic Speciation ; Genotype ; Haploidy ; Models, Biological ; Mutation/genetics ; Population Dynamics ; Reproduction/genetics/*physiology ; Sexual Behavior, Animal ; Time Factors
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  • 21
    Publication Date: 2009-06-19
    Description: Natural habitats of some microorganisms may fluctuate erratically, whereas others, which are more predictable, offer the opportunity to prepare in advance for the next environmental change. In analogy to classical Pavlovian conditioning, microorganisms may have evolved to anticipate environmental stimuli by adapting to their temporal order of appearance. Here we present evidence for environmental change anticipation in two model microorganisms, Escherichia coli and Saccharomyces cerevisiae. We show that anticipation is an adaptive trait, because pre-exposure to the stimulus that typically appears early in the ecology improves the organism's fitness when encountered with a second stimulus. Additionally, we observe loss of the conditioned response in E. coli strains that were repeatedly exposed in a laboratory evolution experiment only to the first stimulus. Focusing on the molecular level reveals that the natural temporal order of stimuli is embedded in the wiring of the regulatory network-early stimuli pre-induce genes that would be needed for later ones, yet later stimuli only induce genes needed to cope with them. Our work indicates that environmental anticipation is an adaptive trait that was repeatedly selected for during evolution and thus may be ubiquitous in biology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mitchell, Amir -- Romano, Gal H -- Groisman, Bella -- Yona, Avihu -- Dekel, Erez -- Kupiec, Martin -- Dahan, Orna -- Pilpel, Yitzhak -- England -- Nature. 2009 Jul 9;460(7252):220-4. doi: 10.1038/nature08112. Epub 2009 Jun 17.〈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/19536156" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; *Biological Evolution ; Carbohydrate Metabolism ; Carbon/metabolism ; Cell Respiration ; *Environment ; Escherichia coli/genetics/*metabolism ; Fermentation ; Gene Expression Regulation ; Genomics ; Heat-Shock Response/genetics ; Lactose/metabolism ; Maltose/metabolism ; Osmotic Pressure ; Oxidative Stress/genetics ; Saccharomyces cerevisiae/genetics/*metabolism ; Time Factors
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  • 22
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    Nature Publishing Group (NPG)
    Publication Date: 2009-01-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thomson, David J -- England -- Nature. 2009 Jan 22;457(7228):391-2. doi: 10.1038/457391a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158781" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Migration ; Animals ; Carbon Dioxide/analysis ; *Greenhouse Effect ; Human Activities ; Humans ; Models, Theoretical ; *Seasons ; *Temperature ; Time Factors
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  • 23
    Publication Date: 2009-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thompson, Scott M -- Mattison, Hayley A -- R01 MH065488/MH/NIMH NIH HHS/ -- England -- Nature. 2009 Mar 19;458(7236):296-7. doi: 10.1038/458296a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295601" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/metabolism ; Calcium Channels, L-Type/metabolism ; Calcium-Calmodulin-Dependent Protein Kinase Type 2/genetics/*metabolism ; Dendritic Spines/*enzymology/*physiology ; Enzyme Activation ; Fluorescence ; Fluorescence Resonance Energy Transfer ; Glutamic Acid/metabolism ; Humans ; Long-Term Potentiation/*physiology ; Receptors, N-Methyl-D-Aspartate/metabolism ; Synapses/metabolism ; Synaptic Potentials/physiology ; Time Factors
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 24
    Publication Date: 2009-05-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rothschild, Lynn J -- England -- Nature. 2009 May 21;459(7245):335-6. doi: 10.1038/459335a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19458704" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Evolution ; *Earth (Planet) ; History, Ancient ; Hot Temperature ; *Meteoroids ; *Models, Biological ; Moon ; *Origin of Life ; Silicates/analysis ; Sterilization ; Time Factors ; Zirconium/analysis
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  • 25
    Publication Date: 2009-11-13
    Description: Direct inhibition of transcription factor complexes remains a central challenge in the discipline of ligand discovery. In general, these proteins lack surface involutions suitable for high-affinity binding by small molecules. Here we report the design of synthetic, cell-permeable, stabilized alpha-helical peptides that target a critical protein-protein interface in the NOTCH transactivation complex. We demonstrate that direct, high-affinity binding of the hydrocarbon-stapled peptide SAHM1 prevents assembly of the active transcriptional complex. Inappropriate NOTCH activation is directly implicated in the pathogenesis of several disease states, including T-cell acute lymphoblastic leukaemia (T-ALL). The treatment of leukaemic cells with SAHM1 results in genome-wide suppression of NOTCH-activated genes. Direct antagonism of the NOTCH transcriptional program causes potent, NOTCH-specific anti-proliferative effects in cultured cells and in a mouse model of NOTCH1-driven T-ALL.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951323/" 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/PMC2951323/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moellering, Raymond E -- Cornejo, Melanie -- Davis, Tina N -- Del Bianco, Cristina -- Aster, Jon C -- Blacklow, Stephen C -- Kung, Andrew L -- Gilliland, D Gary -- Verdine, Gregory L -- Bradner, James E -- 5T32GM007598/GM/NIGMS NIH HHS/ -- N01-CO-12400/CO/NCI NIH HHS/ -- P01 CA119070/CA/NCI NIH HHS/ -- P01 CA119070-049001/CA/NCI NIH HHS/ -- R01 CA092433/CA/NCI NIH HHS/ -- R01 CA092433-06A2/CA/NCI NIH HHS/ -- R56 CA092433/CA/NCI NIH HHS/ -- R56 CA092433-06A1/CA/NCI NIH HHS/ -- T32 GM007598/GM/NIGMS NIH HHS/ -- T32 GM007598-30/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Nov 12;462(7270):182-8. doi: 10.1038/nature08543.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19907488" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding, Competitive ; Cell Line, Tumor ; Cell Membrane Permeability ; Cell Proliferation/drug effects ; DNA-Binding Proteins/chemistry/metabolism ; Disease Models, Animal ; Drosophila Proteins/chemistry ; Gene Expression Regulation, Neoplastic/drug effects ; Genome/drug effects/genetics ; Humans ; Immunoglobulin J Recombination Signal Sequence-Binding Protein/metabolism ; Mice ; Models, Molecular ; Nuclear Proteins/chemistry ; Peptides/chemical synthesis/chemistry/metabolism/*pharmacology ; Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/drug therapy/genetics/pathology ; Protein Binding/drug effects ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptor, Notch1/*antagonists & inhibitors/chemistry/metabolism ; Signal Transduction/drug effects ; Substrate Specificity ; Transcription Factors/chemistry/metabolism ; Transcriptional Activation/*drug effects
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  • 26
    Publication Date: 2009-10-30
    Description: Enzymes use substrate-binding energy both to promote ground-state association and to stabilize the reaction transition state selectively. The monomeric homing endonuclease I-AniI cleaves with high sequence specificity in the centre of a 20-base-pair (bp) DNA target site, with the amino (N)-terminal domain of the enzyme making extensive binding interactions with the left (-) side of the target site and the similarly structured carboxy (C)-terminal domain interacting with the right (+) side. Here we show that, despite the approximate twofold symmetry of the enzyme-DNA complex, there is almost complete segregation of interactions responsible for substrate binding to the (-) side of the interface and interactions responsible for transition-state stabilization to the (+) side. Although single base-pair substitutions throughout the entire DNA target site reduce catalytic efficiency, mutations in the (-) DNA half-site almost exclusively increase the dissociation constant (K(D)) and the Michaelis constant under single-turnover conditions (K(M)*), and those in the (+) half-site primarily decrease the turnover number (k(cat)*). The reduction of activity produced by mutations on the (-) side, but not mutations on the (+) side, can be suppressed by tethering the substrate to the endonuclease displayed on the surface of yeast. This dramatic asymmetry in the use of enzyme-substrate binding energy for catalysis has direct relevance to the redesign of endonucleases to cleave genomic target sites for gene therapy and other applications. Computationally redesigned enzymes that achieve new specificities on the (-) side do so by modulating K(M)*, whereas redesigns with altered specificities on the (+) side modulate k(cat)*. Our results illustrate how classical enzymology and modern protein design can each inform the other.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771326/" 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/PMC2771326/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thyme, Summer B -- Jarjour, Jordan -- Takeuchi, Ryo -- Havranek, James J -- Ashworth, Justin -- Scharenberg, Andrew M -- Stoddard, Barry L -- Baker, David -- GM084433/GM/NIGMS NIH HHS/ -- R00 RR024107/RR/NCRR NIH HHS/ -- R00 RR024107-03/RR/NCRR NIH HHS/ -- R00 RR024107-04/RR/NCRR NIH HHS/ -- RL1 GM084433/GM/NIGMS NIH HHS/ -- RL1 GM084433-03/GM/NIGMS NIH HHS/ -- RL1CA133832/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Oct 29;461(7268):1300-4. doi: 10.1038/nature08508.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA. sthyme@u.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19865174" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; *Biocatalysis ; Computational Biology ; *Computer Simulation ; DNA/chemistry/metabolism ; Endonucleases/chemistry/*metabolism ; Kinetics ; Models, Molecular ; Protein Binding ; Protein Conformation ; RNA-Directed DNA Polymerase/chemistry/*metabolism ; Saccharomyces cerevisiae/metabolism ; Substrate Specificity ; *Thermodynamics
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  • 27
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2009-09-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ko, Dongwook -- England -- Nature. 2009 Sep 24;461(7263):470. doi: 10.1038/461470b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19779431" target="_blank"〉PubMed〈/a〉
    Keywords: *Communication Barriers ; Congresses as Topic ; *Research Personnel ; *Speech Intelligibility ; Time Factors ; Wit and Humor as Topic
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  • 28
    Publication Date: 2009-12-17
    Description: Mistranslation arising from confusion of serine for alanine by alanyl-tRNA synthetases (AlaRSs) has profound functional consequences. Throughout evolution, two editing checkpoints prevent disease-causing mistranslation from confusing glycine or serine for alanine at the active site of AlaRS. In both bacteria and mice, Ser poses a bigger challenge than Gly. One checkpoint is the AlaRS editing centre, and the other is from widely distributed AlaXps-free-standing, genome-encoded editing proteins that clear Ser-tRNA(Ala). The paradox of misincorporating both a smaller (glycine) and a larger (serine) amino acid suggests a deep conflict for nature-designed AlaRS. Here we show the chemical basis for this conflict. Nine crystal structures, together with kinetic and mutational analysis, provided snapshots of adenylate formation for each amino acid. An inherent dilemma is posed by constraints of a structural design that pins down the alpha-amino group of the bound amino acid by using an acidic residue. This design, dating back more than 3 billion years, creates a serendipitous interaction with the serine OH that is difficult to avoid. Apparently because no better architecture for the recognition of alanine could be found, the serine misactivation problem was solved through free-standing AlaXps, which appeared contemporaneously with early AlaRSs. The results reveal unconventional problems and solutions arising from the historical design of the protein synthesis machinery.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799227/" 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/PMC2799227/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guo, Min -- Chong, Yeeting E -- Shapiro, Ryan -- Beebe, Kirk -- Yang, Xiang-Lei -- Schimmel, Paul -- GM 15539/GM/NIGMS NIH HHS/ -- R01 GM015539/GM/NIGMS NIH HHS/ -- R01 GM015539-43/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Dec 10;462(7274):808-12. doi: 10.1038/nature08612.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010690" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/*metabolism ; Alanine-tRNA Ligase/chemistry/genetics/*metabolism ; Aspartic Acid/genetics/metabolism ; Catalytic Domain ; Crystallization ; Escherichia coli/*enzymology ; Kinetics ; Models, Molecular ; Mutation ; *Protein Biosynthesis ; Protein Conformation ; RNA, Transfer, Ala/metabolism ; Serine/*metabolism ; Structure-Activity Relationship
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  • 29
    Publication Date: 2009-01-17
    Description: Autonomous and self-sustained oscillator circuits mediating the periodic induction of specific target genes are minimal genetic time-keeping devices found in the central and peripheral circadian clocks. They have attracted significant attention because of their intriguing dynamics and their importance in controlling critical repair, metabolic and signalling pathways. The precise molecular mechanism and expression dynamics of this mammalian circadian clock are still not fully understood. Here we describe a synthetic mammalian oscillator based on an auto-regulated sense-antisense transcription control circuit encoding a positive and a time-delayed negative feedback loop, enabling autonomous, self-sustained and tunable oscillatory gene expression. After detailed systems design with experimental analyses and mathematical modelling, we monitored oscillating concentrations of green fluorescent protein with tunable frequency and amplitude by time-lapse microscopy in real time in individual Chinese hamster ovary cells. The synthetic mammalian clock may provide an insight into the dynamics of natural periodic processes and foster advances in the design of prosthetic networks in future gene and cell therapies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tigges, Marcel -- Marquez-Lago, Tatiana T -- Stelling, Jorg -- Fussenegger, Martin -- England -- Nature. 2009 Jan 15;457(7227):309-12. doi: 10.1038/nature07616.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19148099" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Clocks/*physiology ; CHO Cells ; Circadian Rhythm/*physiology ; Cricetinae ; Cricetulus ; Feedback, Physiological ; Fluorescence ; Gene Expression Regulation/*genetics ; Genes, Synthetic/*genetics ; *Genetic Engineering ; Green Fluorescent Proteins/analysis/genetics/metabolism ; Models, Biological ; Reproducibility of Results ; Time Factors ; Transcription, Genetic
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  • 30
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2009-01-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ruth, Thomas -- England -- Nature. 2009 Jan 29;457(7229):536-7. doi: 10.1038/457536a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉TRIUMF, Vancouver, Canada. truth@triumf.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19177112" target="_blank"〉PubMed〈/a〉
    Keywords: Humans ; Internationality ; Netherlands ; Nuclear Medicine/*instrumentation/*methods ; Nuclear Reactors/supply & distribution ; Ontario ; Organotechnetium Compounds/chemical synthesis/supply & distribution ; Positron-Emission Tomography/instrumentation/methods ; Radioisotopes/chemistry/*supply & distribution ; *Radionuclide Imaging ; Time Factors
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  • 31
    Publication Date: 2009-04-17
    Description: Biosynthesis of the DNA base thymine depends on activity of the enzyme thymidylate synthase to catalyse the methylation of the uracil moiety of 2'-deoxyuridine-5'-monophosphate. All known thymidylate synthases rely on an active site residue of the enzyme to activate 2'-deoxyuridine-5'-monophosphate. This functionality has been demonstrated for classical thymidylate synthases, including human thymidylate synthase, and is instrumental in mechanism-based inhibition of these enzymes. Here we report an example of thymidylate biosynthesis that occurs without an enzymatic nucleophile. This unusual biosynthetic pathway occurs in organisms containing the thyX gene, which codes for a flavin-dependent thymidylate synthase (FDTS), and is present in several human pathogens. Our findings indicate that the putative active site nucleophile is not required for FDTS catalysis, and no alternative nucleophilic residues capable of serving this function can be identified. Instead, our findings suggest that a hydride equivalent (that is, a proton and two electrons) is transferred from the reduced flavin cofactor directly to the uracil ring, followed by an isomerization of the intermediate to form the product, 2'-deoxythymidine-5'-monophosphate. These observations indicate a very different chemical cascade than that of classical thymidylate synthases or any other known biological methylation. The findings and chemical mechanism proposed here, together with available structural data, suggest that selective inhibition of FDTSs, with little effect on human thymine biosynthesis, should be feasible. Because several human pathogens depend on FDTS for DNA biosynthesis, its unique mechanism makes it an attractive target for antibiotic drugs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759699/" 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/PMC2759699/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koehn, Eric M -- Fleischmann, Todd -- Conrad, John A -- Palfey, Bruce A -- Lesley, Scott A -- Mathews, Irimpan I -- Kohen, Amnon -- GM08270/GM/NIGMS NIH HHS/ -- R01 GM065368/GM/NIGMS NIH HHS/ -- R01 GM065368-05/GM/NIGMS NIH HHS/ -- R01 GM61087/GM/NIGMS NIH HHS/ -- U54GM074898/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Apr 16;458(7240):919-23. doi: 10.1038/nature07973.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19370033" target="_blank"〉PubMed〈/a〉
    Keywords: Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; Deoxyuracil Nucleotides/chemistry/metabolism ; Deuterium/metabolism ; Electrons ; Flavin-Adenine Dinucleotide/chemistry/metabolism ; Flavins/chemistry/*metabolism ; Helicobacter pylori/enzymology ; Humans ; Magnetic Resonance Spectroscopy ; Methylation ; Models, Molecular ; Mycobacterium tuberculosis/enzymology ; Protons ; Thermotoga maritima/*enzymology/*metabolism ; Thymidine/analogs & derivatives/metabolism ; Thymidine Monophosphate/*biosynthesis ; Thymidylate Synthase/antagonists & inhibitors/*genetics/*metabolism ; Uracil/metabolism
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  • 32
    Publication Date: 2009-02-06
    Description: The influenza virus polymerase, a heterotrimer composed of three subunits, PA, PB1 and PB2, is responsible for replication and transcription of the eight separate segments of the viral RNA genome in the nuclei of infected cells. The polymerase synthesizes viral messenger RNAs using short capped primers derived from cellular transcripts by a unique 'cap-snatching' mechanism. The PB2 subunit binds the 5' cap of host pre-mRNAs, which are subsequently cleaved after 10-13 nucleotides by the viral endonuclease, hitherto thought to reside in the PB2 (ref. 5) or PB1 (ref. 2) subunits. Here we describe biochemical and structural studies showing that the amino-terminal 209 residues of the PA subunit contain the endonuclease active site. We show that this domain has intrinsic RNA and DNA endonuclease activity that is strongly activated by manganese ions, matching observations reported for the endonuclease activity of the intact trimeric polymerase. Furthermore, this activity is inhibited by 2,4-dioxo-4-phenylbutanoic acid, a known inhibitor of the influenza endonuclease. The crystal structure of the domain reveals a structural core closely resembling resolvases and type II restriction endonucleases. The active site comprises a histidine and a cluster of three acidic residues, conserved in all influenza viruses, which bind two manganese ions in a configuration similar to other two-metal-dependent endonucleases. Two active site residues have previously been shown to specifically eliminate the polymerase endonuclease activity when mutated. These results will facilitate the optimisation of endonuclease inhibitors as potential new anti-influenza drugs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dias, Alexandre -- Bouvier, Denis -- Crepin, Thibaut -- McCarthy, Andrew A -- Hart, Darren J -- Baudin, Florence -- Cusack, Stephen -- Ruigrok, Rob W H -- England -- Nature. 2009 Apr 16;458(7240):914-8. doi: 10.1038/nature07745. Epub 2009 Feb 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMR 5233, 6 rue Jules Horowitz, BP181, 38042 Grenoble Cedex 9, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19194459" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Catalytic Domain ; Endonucleases/chemistry/*metabolism ; Enzyme Stability ; Histidine/metabolism ; Humans ; Influenza A Virus, H3N2 Subtype/*enzymology ; Influenza A Virus, H5N1 Subtype/enzymology ; Influenzavirus C/enzymology ; Manganese/metabolism/pharmacology ; Models, Molecular ; Molecular Sequence Data ; Protein Subunits/*chemistry/*metabolism ; RNA Caps/*metabolism ; RNA Replicase/*chemistry/*metabolism ; Viral Proteins/*chemistry/*metabolism
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  • 33
    Publication Date: 2009-08-21
    Description: The dimeric motor protein kinesin-1 converts chemical energy from ATP hydrolysis into mechanical work used to transport cargo along microtubules. Cargo attached to the kinesin stalk moves processively in 8-nm increments as its twin motor domains (heads) carry out an asymmetric, 'hand-over-hand' walk. The extent of individual head interactions with the microtubule during stepping, however, remains controversial. A major experimental limitation has been the lack of a means to monitor the attachment of an individual head to the microtubule during movement, necessitating indirect approaches. Here we report the development of a single-molecule assay that can directly report head binding in a walking kinesin molecule, and show that only a single head is bound to the microtubule between steps at low ATP concentrations. A bead was linked to one of the two kinesin heads by means of a short DNA tether and used to apply rapidly alternating hindering and assisting loads with an optical trap. The time-dependent difference between forwards and backwards displacements of the bead alternated between two discrete values during stepping, corresponding to those intervals when the linked head adopted a bound or an unbound state. The linked head could only rebind the microtubule once ATP had become bound to its partner head.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859689/" 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/PMC2859689/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guydosh, Nicholas R -- Block, Steven M -- GM51453/GM/NIGMS NIH HHS/ -- R01 GM051453/GM/NIGMS NIH HHS/ -- R01 GM051453-15/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Sep 3;461(7260):125-8. doi: 10.1038/nature08259. Epub 2009 Aug 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Program, Stanford University, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19693012" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism/pharmacology ; Animals ; DNA/chemistry/metabolism ; Drosophila melanogaster ; Kinesin/*chemistry/*metabolism ; Microspheres ; Microtubules/*metabolism ; Movement/drug effects ; Optical Tweezers ; Protein Binding/drug effects ; Time Factors
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  • 34
    Publication Date: 2009-12-25
    Description: The clinical efficacy of epidermal growth factor receptor (EGFR) kinase inhibitors in EGFR-mutant non-small-cell lung cancer (NSCLC) is limited by the development of drug-resistance mutations, including the gatekeeper T790M mutation. Strategies targeting EGFR T790M with irreversible inhibitors have had limited success and are associated with toxicity due to concurrent inhibition of wild-type EGFR. All current EGFR inhibitors possess a structurally related quinazoline-based core scaffold and were identified as ATP-competitive inhibitors of wild-type EGFR. Here we identify a covalent pyrimidine EGFR inhibitor by screening an irreversible kinase inhibitor library specifically against EGFR T790M. These agents are 30- to 100-fold more potent against EGFR T790M, and up to 100-fold less potent against wild-type EGFR, than quinazoline-based EGFR inhibitors in vitro. They are also effective in murine models of lung cancer driven by EGFR T790M. Co-crystallization studies reveal a structural basis for the increased potency and mutant selectivity of these agents. These mutant-selective irreversible EGFR kinase inhibitors may be clinically more effective and better tolerated than quinazoline-based inhibitors. Our findings demonstrate that functional pharmacological screens against clinically important mutant kinases represent a powerful strategy to identify new classes of mutant-selective kinase inhibitors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879581/" 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/PMC2879581/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Wenjun -- Ercan, Dalia -- Chen, Liang -- Yun, Cai-Hong -- Li, Danan -- Capelletti, Marzia -- Cortot, Alexis B -- Chirieac, Lucian -- Iacob, Roxana E -- Padera, Robert -- Engen, John R -- Wong, Kwok-Kin -- Eck, Michael J -- Gray, Nathanael S -- Janne, Pasi A -- P50CA090578/CA/NCI NIH HHS/ -- R01 CA122794/CA/NCI NIH HHS/ -- R01 CA130876/CA/NCI NIH HHS/ -- R01 CA130876-02/CA/NCI NIH HHS/ -- R01 CA135257/CA/NCI NIH HHS/ -- R01AG2400401/AG/NIA NIH HHS/ -- R01CA080942/CA/NCI NIH HHS/ -- R01CA11446/CA/NCI NIH HHS/ -- R01CA116020/CA/NCI NIH HHS/ -- R01CA130876-02/CA/NCI NIH HHS/ -- R01CA135257/CA/NCI NIH HHS/ -- R01GM070590/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Dec 24;462(7276):1070-4. doi: 10.1038/nature08622.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20033049" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antineoplastic Agents/chemistry/*pharmacology/toxicity ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Drug Evaluation, Preclinical ; Drug Resistance, Neoplasm/genetics ; Lung/drug effects ; Mice ; Models, Chemical ; Models, Molecular ; Mutation/*genetics ; NIH 3T3 Cells ; Phosphorylation/drug effects ; Protein Kinase Inhibitors/chemistry/*pharmacology/toxicity ; Receptor, Epidermal Growth Factor/*antagonists & inhibitors/*genetics
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  • 35
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    Nature Publishing Group (NPG)
    Publication Date: 2009-05-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2009 May 28;459(7246):490-1. doi: 10.1038/459490a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19478748" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds/virology ; Developing Countries ; *Geography ; Humans ; Influenza A Virus, H1N1 Subtype/genetics/*isolation & purification/*pathogenicity ; Influenza, Human/economics/*epidemiology/prevention & control/*virology ; Population Surveillance ; Reassortant Viruses/genetics/pathogenicity ; Swine/virology ; Time Factors ; *Tropical Climate
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  • 36
    Publication Date: 2009-03-28
    Description: The evolutionary history of osteichthyans (bony fishes plus tetrapods) extends back to the Ludlow epoch of the Silurian period. However, these Silurian forms have been documented exclusively by fragmentary fossils. Here we report the discovery of an exceptionally preserved primitive fish from the Ludlow of Yunnan, China, that represents the oldest near-complete gnathostome (jawed vertebrate). The postcranial skeleton of this fish includes a primitive pectoral girdle and median fin spine as in non-osteichthyan gnathostomes, but a derived macromeric squamation as in crown osteichthyans, and substantiates the unexpected mix of postcranial features in basal sarcopterygians, previously restored from the disarticulated remains of Psarolepis. As the oldest articulated sarcopterygian, the new taxon offers insights into the origin and early divergence of osteichthyans, and indicates that the minimum date for the actinopterygian-sarcopterygian split was no later than 419 million years ago.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhu, Min -- Zhao, Wenjin -- Jia, Liantao -- Lu, Jing -- Qiao, Tuo -- Qu, Qingming -- England -- Nature. 2009 Mar 26;458(7237):469-74. doi: 10.1038/nature07855.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Key Laboratory of Evolutionary Systematics of Vertebrates, Institute of Vertebrate Paleontology and Paleoanthropology (IVPP), Chinese Academy of Sciences, PO Box 643, Beijing 100044, China. zhumin@ivpp.ac.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19325627" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; China ; Fishes/*anatomy & histology/classification ; *Fossils ; Geography ; *Phylogeny ; Time Factors
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  • 37
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    Nature Publishing Group (NPG)
    Publication Date: 2009-05-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2009 May 14;459(7244):144-5. doi: 10.1038/459144a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19444174" target="_blank"〉PubMed〈/a〉
    Keywords: Age Factors ; Aging/immunology ; Disease Outbreaks/prevention & control ; Humans ; Influenza A Virus, H1N1 Subtype/growth & development/*immunology ; Influenza Vaccines/administration & dosage/immunology/standards/*supply & ; distribution ; Influenza, Human/immunology/*prevention & control/*virology ; International Cooperation ; Time Factors ; Vaccines, Attenuated/adverse effects/immunology/*supply & distribution ; Vaccines, Inactivated/administration & dosage/immunology/supply & distribution ; *World Health Organization
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  • 38
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2009-05-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2009 May 7;459(7243):14-5. doi: 10.1038/459014a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19424121" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antiviral Agents/therapeutic use ; Disease Outbreaks/prevention & control/*statistics & numerical data ; Humans ; Influenza A Virus, H1N1 Subtype/*physiology ; Influenza Vaccines ; Influenza, Human/drug therapy/*epidemiology/mortality/prevention & control ; Oseltamivir/therapeutic use ; Time Factors ; Zanamivir/therapeutic use
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  • 39
    Publication Date: 2009-04-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saito, Mak A -- England -- Nature. 2009 Apr 9;458(7239):714-5. doi: 10.1038/458714a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19360074" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/*chemistry ; Cyanobacteria/metabolism ; Euryarchaeota/metabolism ; Geologic Sediments/chemistry ; Nickel/*metabolism ; Oxygen/*chemistry ; Seawater/chemistry ; Time Factors
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  • 40
    Publication Date: 2009-10-02
    Description: A key step in many chromatin-related processes is the recognition of histone post-translational modifications by effector modules such as bromodomains and chromo-like domains of the Royal family. Whereas effector-mediated recognition of single post-translational modifications is well characterized, how the cell achieves combinatorial readout of histones bearing multiple modifications is poorly understood. One mechanism involves multivalent binding by linked effector modules. For example, the tandem bromodomains of human TATA-binding protein-associated factor-1 (TAF1) bind better to a diacetylated histone H4 tail than to monoacetylated tails, a cooperative effect attributed to each bromodomain engaging one acetyl-lysine mark. Here we report a distinct mechanism of combinatorial readout for the mouse TAF1 homologue Brdt, a testis-specific member of the BET protein family. Brdt associates with hyperacetylated histone H4 (ref. 7) and is implicated in the marked chromatin remodelling that follows histone hyperacetylation during spermiogenesis, the stage of spermatogenesis in which post-meiotic germ cells mature into fully differentiated sperm. Notably, we find that a single bromodomain (BD1) of Brdt is responsible for selectively recognizing histone H4 tails bearing two or more acetylation marks. The crystal structure of BD1 bound to a diacetylated H4 tail shows how two acetyl-lysine residues cooperate to interact with one binding pocket. Structure-based mutagenesis that reduces the selectivity of BD1 towards diacetylated tails destabilizes the association of Brdt with acetylated chromatin in vivo. Structural analysis suggests that other chromatin-associated proteins may be capable of a similar mode of ligand recognition, including yeast Bdf1, human TAF1 and human CBP/p300 (also known as CREBBP and EP300, respectively). Our findings describe a new mechanism for the combinatorial readout of histone modifications in which a single effector module engages two marks on a histone tail as a composite binding epitope.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moriniere, Jeanne -- Rousseaux, Sophie -- Steuerwald, Ulrich -- Soler-Lopez, Montserrat -- Curtet, Sandrine -- Vitte, Anne-Laure -- Govin, Jerome -- Gaucher, Jonathan -- Sadoul, Karin -- Hart, Darren J -- Krijgsveld, Jeroen -- Khochbin, Saadi -- Muller, Christoph W -- Petosa, Carlo -- England -- Nature. 2009 Oct 1;461(7264):664-8. doi: 10.1038/nature08397.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, BP 181, 38042 Grenoble Cedex 9, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19794495" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Allosteric Regulation ; Animals ; Binding Sites ; COS Cells ; Cercopithecus aethiops ; Chromatin/chemistry/metabolism ; Crystallography, X-Ray ; Histones/*chemistry/*metabolism ; Lysine/metabolism ; Mice ; Models, Molecular ; Nuclear Proteins/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Substrate Specificity
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  • 41
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    Nature Publishing Group (NPG)
    Publication Date: 2009-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dixon, Nicholas E -- England -- Nature. 2009 Dec 17;462(7275):854-5. doi: 10.1038/462854a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20016583" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T7/enzymology/genetics/*physiology ; DNA Primase/chemistry/*metabolism ; DNA Replication/*physiology ; DNA, Viral/biosynthesis/metabolism ; DNA-Directed DNA Polymerase/chemistry/*metabolism ; *Models, Biological ; Multienzyme Complexes/chemistry/*metabolism ; RNA/biosynthesis ; Time Factors
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  • 42
    Publication Date: 2009-11-06
    Description: Development requires the establishment of precise patterns of gene expression, which are primarily controlled by transcription factors binding to cis-regulatory modules. Although transcription factor occupancy can now be identified at genome-wide scales, decoding this regulatory landscape remains a daunting challenge. Here we used a novel approach to predict spatio-temporal cis-regulatory activity based only on in vivo transcription factor binding and enhancer activity data. We generated a high-resolution atlas of cis-regulatory modules describing their temporal and combinatorial occupancy during Drosophila mesoderm development. The binding profiles of cis-regulatory modules with characterized expression were used to train support vector machines to predict five spatio-temporal expression patterns. In vivo transgenic reporter assays demonstrate the high accuracy of these predictions and reveal an unanticipated plasticity in transcription factor binding leading to similar expression. This data-driven approach does not require previous knowledge of transcription factor sequence affinity, function or expression, making it widely applicable.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zinzen, Robert P -- Girardot, Charles -- Gagneur, Julien -- Braun, Martina -- Furlong, Eileen E M -- England -- Nature. 2009 Nov 5;462(7269):65-70. doi: 10.1038/nature08531.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19890324" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified ; Artificial Intelligence ; Chromatin Immunoprecipitation ; Conserved Sequence/genetics ; Databases, Genetic ; Drosophila melanogaster/*embryology/*genetics ; Enhancer Elements, Genetic/genetics ; *Gene Expression Regulation, Developmental/genetics ; Genes, Reporter/genetics ; Mesoderm/embryology/metabolism ; *Models, Genetic ; Protein Binding ; Time Factors ; Transcription Factors/*metabolism
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  • 43
    Publication Date: 2009-12-18
    Description: With polar temperatures approximately 3-5 degrees C warmer than today, the last interglacial stage (approximately 125 kyr ago) serves as a partial analogue for 1-2 degrees C global warming scenarios. Geological records from several sites indicate that local sea levels during the last interglacial were higher than today, but because local sea levels differ from global sea level, accurately reconstructing past global sea level requires an integrated analysis of globally distributed data sets. Here we present an extensive compilation of local sea level indicators and a statistical approach for estimating global sea level, local sea levels, ice sheet volumes and their associated uncertainties. We find a 95% probability that global sea level peaked at least 6.6 m higher than today during the last interglacial; it is likely (67% probability) to have exceeded 8.0 m but is unlikely (33% probability) to have exceeded 9.4 m. When global sea level was close to its current level (〉or=-10 m), the millennial average rate of global sea level rise is very likely to have exceeded 5.6 m kyr(-1) but is unlikely to have exceeded 9.2 m kyr(-1). Our analysis extends previous last interglacial sea level studies by integrating literature observations within a probabilistic framework that accounts for the physics of sea level change. The results highlight the long-term vulnerability of ice sheets to even relatively low levels of sustained global warming.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kopp, Robert E -- Simons, Frederik J -- Mitrovica, Jerry X -- Maloof, Adam C -- Oppenheimer, Michael -- England -- Nature. 2009 Dec 17;462(7275):863-7. doi: 10.1038/nature08686.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geosciences, Princeton University, Princeton, New Jersey 08544, USA. rkopp@alumni.caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20016591" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Antarctic Regions ; Global Warming/*statistics & numerical data ; Greenhouse Effect ; Greenland ; History, 21st Century ; History, Ancient ; *Ice Cover ; Models, Theoretical ; Oceans and Seas ; *Probability ; Seawater/*analysis ; *Temperature ; Time Factors ; Uncertainty
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  • 44
    Publication Date: 2009-07-22
    Description: Acquired uniparental disomy (aUPD) is a common feature of cancer genomes, leading to loss of heterozygosity. aUPD is associated not only with loss-of-function mutations of tumour suppressor genes, but also with gain-of-function mutations of proto-oncogenes. Here we show unique gain-of-function mutations of the C-CBL (also known as CBL) tumour suppressor that are tightly associated with aUPD of the 11q arm in myeloid neoplasms showing myeloproliferative features. The C-CBL proto-oncogene, a cellular homologue of v-Cbl, encodes an E3 ubiquitin ligase and negatively regulates signal transduction of tyrosine kinases. Homozygous C-CBL mutations were found in most 11q-aUPD-positive myeloid malignancies. Although the C-CBL mutations were oncogenic in NIH3T3 cells, c-Cbl was shown to functionally and genetically act as a tumour suppressor. C-CBL mutants did not have E3 ubiquitin ligase activity, but inhibited that of wild-type C-CBL and CBL-B (also known as CBLB), leading to prolonged activation of tyrosine kinases after cytokine stimulation. c-Cbl(-/-) haematopoietic stem/progenitor cells (HSPCs) showed enhanced sensitivity to a variety of cytokines compared to c-Cbl(+/+) HSPCs, and transduction of C-CBL mutants into c-Cbl(-/-) HSPCs further augmented their sensitivities to a broader spectrum of cytokines, including stem-cell factor (SCF, also known as KITLG), thrombopoietin (TPO, also known as THPO), IL3 and FLT3 ligand (FLT3LG), indicating the presence of a gain-of-function that could not be attributed to a simple loss-of-function. The gain-of-function effects of C-CBL mutants on cytokine sensitivity of HSPCs largely disappeared in a c-Cbl(+/+) background or by co-transduction of wild-type C-CBL, which suggests the pathogenic importance of loss of wild-type C-CBL alleles found in most cases of C-CBL-mutated myeloid neoplasms. Our findings provide a new insight into a role of gain-of-function mutations of a tumour suppressor associated with aUPD in the pathogenesis of some myeloid cancer subsets.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sanada, Masashi -- Suzuki, Takahiro -- Shih, Lee-Yung -- Otsu, Makoto -- Kato, Motohiro -- Yamazaki, Satoshi -- Tamura, Azusa -- Honda, Hiroaki -- Sakata-Yanagimoto, Mamiko -- Kumano, Keiki -- Oda, Hideaki -- Yamagata, Tetsuya -- Takita, Junko -- Gotoh, Noriko -- Nakazaki, Kumi -- Kawamata, Norihiko -- Onodera, Masafumi -- Nobuyoshi, Masaharu -- Hayashi, Yasuhide -- Harada, Hiroshi -- Kurokawa, Mineo -- Chiba, Shigeru -- Mori, Hiraku -- Ozawa, Keiya -- Omine, Mitsuhiro -- Hirai, Hisamaru -- Nakauchi, Hiromitsu -- Koeffler, H Phillip -- Ogawa, Seishi -- 2R01CA026038-30/CA/NCI NIH HHS/ -- England -- Nature. 2009 Aug 13;460(7257):904-8. doi: 10.1038/nature08240. Epub 2009 Jul 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Genomics Project, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19620960" target="_blank"〉PubMed〈/a〉
    Keywords: Allelic Imbalance ; Amino Acid Sequence ; Animals ; Base Sequence ; Chromosomes, Human, Pair 11/genetics ; Female ; *Genes, Tumor Suppressor ; Humans ; Leukemia, Myeloid/*genetics/metabolism/pathology ; Male ; Mice ; Mice, Knockout ; Mice, Nude ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/genetics/*metabolism ; Mutation ; NIH 3T3 Cells ; Neoplasm Transplantation ; Oncogenes/genetics ; Phosphorylation ; Protein Conformation ; Proto-Oncogene Proteins c-cbl/antagonists & ; inhibitors/chemistry/deficiency/*genetics/*metabolism ; Ubiquitination ; Uniparental Disomy/genetics ; ras Proteins/genetics/metabolism
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  • 45
    Publication Date: 2009-10-13
    Description: To initiate gene transcription, RNA polymerase II (Pol II) requires the transcription factor IIB (B). Here we present the crystal structure of the complete Pol II-B complex at 4.3 A resolution, and complementary functional data. The results indicate the mechanism of transcription initiation, including the transition to RNA elongation. Promoter DNA is positioned over the Pol II active centre cleft with the 'B-core' domain that binds the wall at the end of the cleft. DNA is then opened with the help of the 'B-linker' that binds the Pol II rudder and clamp coiled-coil at the edge of the cleft. The DNA template strand slips into the cleft and is scanned for the transcription start site with the help of the 'B-reader' that approaches the active site. Synthesis of the RNA chain and rewinding of upstream DNA displace the B-reader and B-linker, respectively, to trigger B release and elongation complex formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kostrewa, Dirk -- Zeller, Mirijam E -- Armache, Karim-Jean -- Seizl, Martin -- Leike, Kristin -- Thomm, Michael -- Cramer, Patrick -- England -- Nature. 2009 Nov 19;462(7271):323-30. doi: 10.1038/nature08548.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gene Center Munich and Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universitat Munchen, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19820686" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry ; DNA Polymerase II/*chemistry/*metabolism ; Humans ; *Models, Molecular ; Molecular Sequence Data ; Protein Structure, Quaternary ; Saccharomyces cerevisiae/*genetics/*metabolism ; Sequence Alignment ; TATA-Box Binding Protein/chemistry/metabolism ; Transcription Factor TFIIB/*chemistry/*metabolism
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  • 46
    Publication Date: 2009-04-03
    Description: CRM1 (also known as XPO1 and exportin 1) mediates nuclear export of hundreds of proteins through the recognition of the leucine-rich nuclear export signal (LR-NES). Here we present the 2.9 A structure of CRM1 bound to snurportin 1 (SNUPN). Snurportin 1 binds CRM1 in a bipartite manner by means of an amino-terminal LR-NES and its nucleotide-binding domain. The LR-NES is a combined alpha-helical-extended structure that occupies a hydrophobic groove between two CRM1 outer helices. The LR-NES interface explains the consensus hydrophobic pattern, preference for intervening electronegative residues and inhibition by leptomycin B. The second nuclear export signal epitope is a basic surface on the snurportin 1 nucleotide-binding domain, which binds an acidic patch on CRM1 adjacent to the LR-NES site. Multipartite recognition of individually weak nuclear export signal epitopes may be common to CRM1 substrates, enhancing CRM1 binding beyond the generally low affinity LR-NES. Similar energetic construction is also used in multipartite nuclear localization signals to provide broad substrate specificity and rapid evolution in nuclear transport.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3437623/" 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/PMC3437623/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dong, Xiuhua -- Biswas, Anindita -- Suel, Katherine E -- Jackson, Laurie K -- Martinez, Rita -- Gu, Hongmei -- Chook, Yuh Min -- 5-T32-GM008297/GM/NIGMS NIH HHS/ -- R01 GM069909/GM/NIGMS NIH HHS/ -- R01GM069909/GM/NIGMS NIH HHS/ -- R01GM069909-03S1/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Apr 30;458(7242):1136-41. doi: 10.1038/nature07975. Epub 2009 Apr 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park, Dallas, Texas 75390-9041, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19339969" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Crystallography, X-Ray ; Epitopes ; Fatty Acids, Unsaturated/pharmacology ; Humans ; Hydrophobic and Hydrophilic Interactions ; Karyopherins/*chemistry/*metabolism ; Leucine/*metabolism ; Models, Molecular ; Nuclear Export Signals/*physiology ; Protein Binding/drug effects ; Protein Conformation ; Receptors, Cytoplasmic and Nuclear/*chemistry/*metabolism ; Structure-Activity Relationship ; Substrate Specificity ; snRNP Core Proteins/chemistry/metabolism
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  • 47
    Publication Date: 2009-12-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kramer, Gert Jan -- Haigh, Martin -- England -- Nature. 2009 Dec 3;462(7273):568-9. doi: 10.1038/462568a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Shell Global Solutions International, Grasweg 31, 1031 HW Amsterdam, The Netherlands. gertjan.kramer@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19956240" target="_blank"〉PubMed〈/a〉
    Keywords: *Conservation of Energy Resources/legislation & jurisprudence ; *Electric Power Supplies/economics/standards ; Industry/economics/*standards/statistics & numerical data ; Time Factors
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  • 48
    Publication Date: 2009-11-27
    Description: Despite the growing number of atomic-resolution membrane protein structures, direct structural information about proteins in their native membrane environment is scarce. This problem is particularly relevant in the case of the highly charged S1-S4 voltage-sensing domains responsible for nerve impulses, where interactions with the lipid bilayer are critical for the function of voltage-activated ion channels. Here we use neutron diffraction, solid-state nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics simulations to investigate the structure and hydration of bilayer membranes containing S1-S4 voltage-sensing domains. Our results show that voltage sensors adopt transmembrane orientations and cause a modest reshaping of the surrounding lipid bilayer, and that water molecules intimately interact with the protein within the membrane. These structural findings indicate that voltage sensors have evolved to interact with the lipid membrane while keeping energetic and structural perturbations to a minimum, and that water penetrates the membrane, to hydrate charged residues and shape the transmembrane electric field.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784928/" 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/PMC2784928/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krepkiy, Dmitriy -- Mihailescu, Mihaela -- Freites, J Alfredo -- Schow, Eric V -- Worcester, David L -- Gawrisch, Klaus -- Tobias, Douglas J -- White, Stephen H -- Swartz, Kenton J -- GM74737/GM/NIGMS NIH HHS/ -- GM86685/GM/NIGMS NIH HHS/ -- P01 GM086685/GM/NIGMS NIH HHS/ -- R01 GM074637/GM/NIGMS NIH HHS/ -- R01 RR014812/RR/NCRR NIH HHS/ -- ZIA NS002945-13/Intramural NIH HHS/ -- England -- Nature. 2009 Nov 26;462(7272):473-9. doi: 10.1038/nature08542.〈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/19940918" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeal Proteins/chemistry/metabolism ; Circular Dichroism ; Lipid Bilayers/*chemistry/*metabolism ; Membrane Lipids/analysis/chemistry/metabolism ; *Membrane Potentials ; Models, Molecular ; Molecular Dynamics Simulation ; Neutron Diffraction ; Nuclear Magnetic Resonance, Biomolecular ; Potassium Channels, Voltage-Gated/*chemistry/metabolism ; Protein Structure, Tertiary ; Spectrometry, Fluorescence ; Water/*analysis/metabolism
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  • 49
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    Nature Publishing Group (NPG)
    Publication Date: 2009-05-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tollefson, Jeff -- England -- Nature. 2009 May 28;459(7246):492. doi: 10.1038/459493a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19478750" target="_blank"〉PubMed〈/a〉
    Keywords: Air Pollution/*legislation & jurisprudence/*prevention & control ; Conservation of Energy Resources/economics/*legislation & jurisprudence ; *Federal Government ; Green Chemistry Technology/economics/legislation & jurisprudence ; *Greenhouse Effect ; Time Factors ; United States ; Vehicle Emissions/legislation & jurisprudence/prevention & control
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  • 50
    Publication Date: 2009-05-22
    Description: Transmembrane sodium-ion gradients provide energy that can be harnessed by 'secondary transporters' to drive the translocation of solute molecules into a cell. Decades of study have shown that such sodium-coupled transporters are involved in many physiological processes, making them targets for the treatment of numerous diseases. Within the past year, crystal structures of several sodium-coupled transporters from different families have been reported, showing a remarkable structural conservation between functionally unrelated transporters. These atomic-resolution structures are revealing the mechanism of the sodium-coupled transport of solutes across cellular membranes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krishnamurthy, Harini -- Piscitelli, Chayne L -- Gouaux, Eric -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 May 21;459(7245):347-55. doi: 10.1038/nature08143.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Oregon 97239, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19458710" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Humans ; Membrane Transport Proteins/*chemistry/*metabolism ; Models, Molecular ; Protein Conformation ; Sodium/*metabolism
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  • 51
    Publication Date: 2009-04-03
    Description: In the course of synaptic transmission in the brain and periphery, acetylcholine receptors (AChRs) rapidly transduce a chemical signal into an electrical impulse. The speed of transduction is facilitated by rapid ACh association and dissociation, suggesting a binding site relatively non-selective for small cations. Selective transduction has been thought to originate from the ability of ACh, over that of other organic cations, to trigger the subsequent channel-opening step. However, transitions to and from the open state were shown to be similar for agonists with widely different efficacies. By studying mutant AChRs, we show here that the ultimate closed-to-open transition is agonist-independent and preceded by two primed closed states; the first primed state elicits brief openings, whereas the second elicits long-lived openings. Long-lived openings and the associated primed state are detected in the absence and presence of an agonist, and exhibit the same kinetic signatures under both conditions. By covalently locking the agonist-binding sites in the bound conformation, we find that each site initiates a priming step. Thus, a change in binding-site conformation primes the AChR for channel opening in a process that enables selective activation by ACh while maximizing the speed and efficiency of the biological response.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712348/" 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/PMC2712348/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mukhtasimova, Nuriya -- Lee, Won Yong -- Wang, Hai-Long -- Sine, Steven M -- NS031744/NS/NINDS NIH HHS/ -- R01 NS031744/NS/NINDS NIH HHS/ -- R01 NS031744-18/NS/NINDS NIH HHS/ -- England -- Nature. 2009 May 21;459(7245):451-4. doi: 10.1038/nature07923. Epub 2009 Apr 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19339970" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Disulfides/metabolism ; Electric Conductivity ; Humans ; Kinetics ; Models, Molecular ; *Movement ; Nicotinic Agonists/pharmacology ; Patch-Clamp Techniques ; Protein Structure, Tertiary ; Receptors, Nicotinic/*chemistry/genetics/*metabolism ; Synaptic Transmission/physiology ; Torpedo
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  • 52
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    Nature Publishing Group (NPG)
    Publication Date: 2009-10-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hand, Eric -- England -- Nature. 2009 Oct 8;461(7265):708-9. doi: 10.1038/461708a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812644" target="_blank"〉PubMed〈/a〉
    Keywords: California ; *Electrons ; Germany ; Humans ; Japan ; *Lasers ; Photons ; Protein Folding ; Synchrotrons ; Time Factors ; X-Rays
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  • 53
    Publication Date: 2009-02-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tollefson, Jeff -- England -- Nature. 2009 Feb 19;457(7232):942-3. doi: 10.1038/457942b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19225485" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Engineering ; *Federal Government ; Fishes ; *Greenhouse Effect ; History, 20th Century ; History, 21st Century ; Hobbies/history ; Marine Biology ; Physics ; *Research Personnel ; United States ; United States Government Agencies/*organization & administration ; Wine
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  • 54
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    Nature Publishing Group (NPG)
    Publication Date: 2009-10-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kwok, Roberta -- England -- Nature. 2009 Oct 1;461(7264):582-3. doi: 10.1038/461582a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19794468" target="_blank"〉PubMed〈/a〉
    Keywords: Bioelectric Energy Sources/*economics/*trends ; Cellulose/*chemistry/economics/metabolism ; Ethanol/chemistry/*economics/*isolation & purification/metabolism ; Gases/metabolism ; Industry/economics/trends ; Internationality ; Time Factors ; United States ; Zea mays/chemistry
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  • 55
    Publication Date: 2009-02-06
    Description: For a retrovirus such as HIV to be infectious, a properly formed capsid is needed; however, unusually among viruses, retrovirus capsids are highly variable in structure. According to the fullerene conjecture, they are composed of hexamers and pentamers of capsid protein (CA), with the shape of a capsid varying according to how the twelve pentamers are distributed and its size depending on the number of hexamers. Hexamers have been studied in planar and tubular arrays, but the predicted pentamers have not been observed. Here we report cryo-electron microscopic analyses of two in-vitro-assembled capsids of Rous sarcoma virus. Both are icosahedrally symmetric: one is composed of 12 pentamers, and the other of 12 pentamers and 20 hexamers. Fitting of atomic models of the two CA domains into the reconstructions shows three distinct inter-subunit interactions. These observations substantiate the fullerene conjecture, show how pentamers are accommodated at vertices, support the inference that nucleation is a crucial morphologic determinant, and imply that electrostatic interactions govern the differential assembly of pentamers and hexamers.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2721793/" 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/PMC2721793/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cardone, Giovanni -- Purdy, John G -- Cheng, Naiqian -- Craven, Rebecca C -- Steven, Alasdair C -- CA100322/CA/NCI NIH HHS/ -- R01 CA100322/CA/NCI NIH HHS/ -- R01 CA100322-05/CA/NCI NIH HHS/ -- Z01 AR027002-29/Intramural NIH HHS/ -- Z99 AR999999/Intramural NIH HHS/ -- England -- Nature. 2009 Feb 5;457(7230):694-8. doi: 10.1038/nature07724.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Structural Biology, National Institute for Arthritis, Musculoskeletal and Skin Diseases, 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/19194444" target="_blank"〉PubMed〈/a〉
    Keywords: Capsid/chemistry/*metabolism/*ultrastructure ; Capsid Proteins/chemistry/genetics/metabolism/ultrastructure ; Cryoelectron Microscopy ; HIV/chemistry/genetics/ultrastructure ; Models, Molecular ; Mutant Proteins/chemistry/genetics/metabolism/ultrastructure ; Mutation ; Polymorphism, Genetic ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Subunits/chemistry/metabolism ; Rous sarcoma virus/*chemistry/genetics/*ultrastructure ; Static Electricity ; *Virus Assembly
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  • 56
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    Nature Publishing Group (NPG)
    Publication Date: 2009-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbott, Alison -- England -- Nature. 2009 Mar 19;458(7236):264. doi: 10.1038/458264b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295569" target="_blank"〉PubMed〈/a〉
    Keywords: *Brain Mapping ; Compensation and Redress/*legislation & jurisprudence ; *Editorial Policies ; Germany ; Humans ; Peer Review, Research/*ethics/methods ; Periodicals as Topic/*ethics/*legislation & jurisprudence/standards ; Societies, Scientific/*standards ; Time Factors
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  • 57
    Publication Date: 2009-10-23
    Description: Maturation of precursor transfer RNA (pre-tRNA) includes excision of the 5' leader and 3' trailer sequences, removal of introns and addition of the CCA terminus. Nucleotide modifications are incorporated at different stages of tRNA processing, after the RNA molecule adopts the proper conformation. In bacteria, tRNA(Ile2) lysidine synthetase (TilS) modifies cytidine into lysidine (L; 2-lysyl-cytidine) at the first anticodon of tRNA(Ile2) (refs 4-9). This modification switches tRNA(Ile2) from a methionine-specific to an isoleucine-specific tRNA. However, the aminoacylation of tRNA(Ile2) by methionyl-tRNA synthetase (MetRS), before the modification by TilS, might lead to the misincorporation of methionine in response to isoleucine codons. The mechanism used by bacteria to avoid this pitfall is unknown. Here we show that the TilS enzyme specifically recognizes and modifies tRNA(Ile2) in its precursor form, thereby avoiding translation errors. We identified the lysidine modification in pre-tRNA(Ile2) isolated from RNase-E-deficient Escherichia coli and did not detect mature tRNA(Ile2) lacking this modification. Our kinetic analyses revealed that TilS can modify both types of RNA molecule with comparable efficiencies. X-ray crystallography and mutational analyses revealed that TilS specifically recognizes the entire L-shape structure in pre-tRNA(Ile2) through extensive interactions coupled with sequential domain movements. Our results demonstrate how TilS prevents the recognition of tRNA(Ile2) by MetRS and achieves high specificity for its substrate. These two key points form the basis for maintaining the fidelity of isoleucine codon translation in bacteria. Our findings also provide a rationale for the necessity of incorporating specific modifications at the precursor level during tRNA biogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nakanishi, Kotaro -- Bonnefond, Luc -- Kimura, Satoshi -- Suzuki, Tsutomu -- Ishitani, Ryuichiro -- Nureki, Osamu -- England -- Nature. 2009 Oct 22;461(7267):1144-8. doi: 10.1038/nature08474.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 225-8501, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19847269" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acyl-tRNA Synthetases/*chemistry/genetics/*metabolism ; Apoproteins/genetics/metabolism ; Bacillus subtilis ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Base Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Escherichia coli ; Geobacillus ; Kinetics ; Lysine/analogs & derivatives/metabolism ; Mass Spectrometry ; Models, Molecular ; Molecular Sequence Data ; *Protein Biosynthesis ; Pyrimidine Nucleosides/metabolism ; RNA, Transfer, Ile/genetics/metabolism ; Substrate Specificity
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  • 58
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    Nature Publishing Group (NPG)
    Publication Date: 2009-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hand, Eric -- England -- Nature. 2009 Apr 16;458(7240):814-5. doi: 10.1038/458814a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19369994" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/*chemistry ; Carbon Dioxide/*analysis ; *Spacecraft/economics/instrumentation ; Time Factors ; United States ; United States National Aeronautics and Space Administration
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  • 59
    Publication Date: 2009-05-01
    Description: An efficient method for making directed DNA sequence modifications to plant genes (gene targeting) is at present lacking, thereby frustrating efforts to dissect plant gene function and engineer crop plants that better meet the world's burgeoning need for food, fibre and fuel. Zinc-finger nucleases (ZFNs)-enzymes engineered to create DNA double-strand breaks at specific loci-are potent stimulators of gene targeting; for example, they can be used to precisely modify engineered reporter genes in plants. Here we demonstrate high-frequency ZFN-stimulated gene targeting at endogenous plant genes, namely the tobacco acetolactate synthase genes (ALS SuRA and SuRB), for which specific mutations are known to confer resistance to imidazolinone and sulphonylurea herbicides. Herbicide-resistance mutations were introduced into SuR loci by ZFN-mediated gene targeting at frequencies exceeding 2% of transformed cells for mutations as far as 1.3 kilobases from the ZFN cleavage site. More than 40% of recombinant plants had modifications in multiple SuR alleles. The observed high frequency of gene targeting indicates that it is now possible to efficiently make targeted sequence changes in endogenous plant genes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743854/" 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/PMC2743854/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Townsend, Jeffrey A -- Wright, David A -- Winfrey, Ronnie J -- Fu, Fengli -- Maeder, Morgan L -- Joung, J Keith -- Voytas, Daniel F -- DP1 OD006862/OD/NIH HHS/ -- R01 GM069906/GM/NIGMS NIH HHS/ -- R01 GM069906-01A1/GM/NIGMS NIH HHS/ -- R01 GM069906-02/GM/NIGMS NIH HHS/ -- R01 GM069906-02S1/GM/NIGMS NIH HHS/ -- R01 GM069906-03/GM/NIGMS NIH HHS/ -- R01 GM069906-04/GM/NIGMS NIH HHS/ -- R01 GM069906-05/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 May 21;459(7245):442-5. doi: 10.1038/nature07845. Epub 2009 Apr 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Development & Cell Biology, Iowa State University, Ames, Iowa 50011, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19404258" target="_blank"〉PubMed〈/a〉
    Keywords: Acetolactate Synthase/genetics ; Alleles ; Amino Acid Sequence ; Base Sequence ; Deoxyribonucleases/chemistry/genetics/*metabolism ; Food, Genetically Modified ; Gene Targeting/*methods ; Genes, Plant/*genetics ; Herbicide Resistance/genetics ; Herbicides/pharmacology ; Molecular Sequence Data ; Plants, Genetically Modified ; *Protein Engineering ; Recombination, Genetic/genetics ; Tobacco/drug effects/enzymology/*genetics ; Transformation, Genetic ; *Zinc Fingers
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  • 60
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    Nature Publishing Group (NPG)
    Publication Date: 2009-01-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hand, Eric -- England -- Nature. 2009 Jan 22;457(7228):366-7. doi: 10.1038/457366a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158756" target="_blank"〉PubMed〈/a〉
    Keywords: Exobiology/economics/instrumentation/trends ; Extraterrestrial Environment/*chemistry ; Jupiter ; Saturn ; Space Flight/economics/instrumentation/*trends ; Time Factors ; United States ; United States National Aeronautics and Space Administration/economics/trends
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  • 61
    Publication Date: 2009-10-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ladle, Richard J -- Jepson, Paul -- Jennings, Steve -- Malhado, Ana C M -- England -- Nature. 2009 Oct 8;461(7265):723. doi: 10.1038/461723c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812650" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds/*classification ; Conservation of Natural Resources/*methods/trends ; *Extinction, Biological ; Reproducibility of Results ; Species Specificity ; Time Factors
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  • 62
    Publication Date: 2009-05-22
    Description: Lunar rocks and impact melts, lunar and asteroidal meteorites, and an ancient martian meteorite record thermal metamorphic events with ages that group around and/or do not exceed 3.9 Gyr. That such a diverse suite of solar system materials share this feature is interpreted to be the result of a post-primary-accretion cataclysmic spike in the number of impacts commonly referred to as the late heavy bombardment (LHB). Despite its obvious significance to the preservation of crust and the survivability of an emergent biosphere, the thermal effects of this bombardment on the young Earth remain poorly constrained. Here we report numerical models constructed to probe the degree of thermal metamorphism in the crust in the effort to recreate the effect of the LHB on the Earth as a whole; outputs were used to assess habitable volumes of crust for a possible near-surface and subsurface primordial microbial biosphere. Our analysis shows that there is no plausible situation in which the habitable zone was fully sterilized on Earth, at least since the termination of primary accretion of the planets and the postulated impact origin of the Moon. Our results explain the root location of hyperthermophilic bacteria in the phylogenetic tree for 16S small-subunit ribosomal RNA, and bode well for the persistence of microbial biospheres even on planetary bodies strongly reworked by impacts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abramov, Oleg -- Mojzsis, Stephen J -- England -- Nature. 2009 May 21;459(7245):419-22. doi: 10.1038/nature08015.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Colorado, Department of Geological Sciences, 2200 Colorado Avenue, UCB 399, Boulder, Colorado 80309-0399, USA. oleg.abramov@colorado.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19458721" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/genetics/*isolation & purification ; *Earth (Planet) ; Ecosystem ; History, Ancient ; Hot Temperature ; *Meteoroids ; *Models, Biological ; *Moon ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sterilization ; Time Factors
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  • 63
    Publication Date: 2009-11-10
    Description: Direct reprogramming of somatic cells into induced pluripotent stem (iPS) cells can be achieved by overexpression of Oct4, Sox2, Klf4 and c-Myc transcription factors, but only a minority of donor somatic cells can be reprogrammed to pluripotency. Here we demonstrate that reprogramming by these transcription factors is a continuous stochastic process where almost all mouse donor cells eventually give rise to iPS cells on continued growth and transcription factor expression. Additional inhibition of the p53/p21 pathway or overexpression of Lin28 increased the cell division rate and resulted in an accelerated kinetics of iPS cell formation that was directly proportional to the increase in cell proliferation. In contrast, Nanog overexpression accelerated reprogramming in a predominantly cell-division-rate-independent manner. Quantitative analyses define distinct cell-division-rate-dependent and -independent modes for accelerating the stochastic course of reprogramming, and suggest that the number of cell divisions is a key parameter driving epigenetic reprogramming to pluripotency.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789972/" 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/PMC2789972/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hanna, Jacob -- Saha, Krishanu -- Pando, Bernardo -- van Zon, Jeroen -- Lengner, Christopher J -- Creyghton, Menno P -- van Oudenaarden, Alexander -- Jaenisch, Rudolf -- R01 CA087869/CA/NCI NIH HHS/ -- R01 CA087869-09/CA/NCI NIH HHS/ -- R01 HD045022/HD/NICHD NIH HHS/ -- R01 HD045022-06/HD/NICHD NIH HHS/ -- R01-CA087869/CA/NCI NIH HHS/ -- R01-HDO45022/PHS HHS/ -- R37 CA084198/CA/NCI NIH HHS/ -- R37 CA084198-09/CA/NCI NIH HHS/ -- R37-CA084198/CA/NCI NIH HHS/ -- U54CA143874/CA/NCI NIH HHS/ -- England -- Nature. 2009 Dec 3;462(7273):595-601. doi: 10.1038/nature08592. Epub 2009 Nov 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA. Hanna@wi.mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19898493" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Cell Differentiation ; Cell Division ; Cell Line ; *Cellular Reprogramming ; Gene Expression Regulation, Developmental ; Mice ; Mice, SCID ; Models, Biological ; Pluripotent Stem Cells/*cytology/*metabolism ; Time Factors ; Transcription Factors/genetics/metabolism
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  • 64
    Publication Date: 2009-07-10
    Description: Single-walled carbon nanotubes (SWNTs) are a family of molecules that have the same cylindrical shape but different chiralities. Many fundamental studies and technological applications of SWNTs require a population of tubes with identical chirality that current syntheses cannot provide. The SWNT sorting problem-that is, separation of a synthetic mixture of tubes into individual single-chirality components-has attracted considerable attention in recent years. Intense efforts so far have focused largely on, and resulted in solutions for, a weaker version of the sorting problem: metal/semiconductor separation. A systematic and general method to purify each and every single-chirality species of the same electronic type from the synthetic mixture of SWNTs is highly desirable, but the task has proven to be insurmountable to date. Here we report such a method, which allows purification of all 12 major single-chirality semiconducting species from a synthetic mixture, with sufficient yield for both fundamental studies and application development. We have designed an effective search of a DNA library of approximately 10(60) in size, and have identified more than 20 short DNA sequences, each of which recognizes and enables chromatographic purification of a particular nanotube species from the synthetic mixture. Recognition sequences exhibit a periodic purine-pyrimidines pattern, which can undergo hydrogen-bonding to form a two-dimensional sheet, and fold selectively on nanotubes into a well-ordered three-dimensional barrel. We propose that the ordered two-dimensional sheet and three-dimensional barrel provide the structural basis for the observed DNA recognition of SWNTs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tu, Xiaomin -- Manohar, Suresh -- Jagota, Anand -- Zheng, Ming -- England -- Nature. 2009 Jul 9;460(7252):250-3. doi: 10.1038/nature08116.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉DuPont Central Research and Development, Wilmington, Delaware 19880, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19587767" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Chemical Fractionation/*methods ; DNA/*chemistry/genetics ; Gene Library ; Models, Molecular ; Nanotubes, Carbon/*chemistry ; Nucleic Acid Conformation ; Sensitivity and Specificity ; Spectrophotometry ; Substrate Specificity
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  • 65
    Publication Date: 2009-06-12
    Description: Alkyltransferase-like proteins (ATLs) share functional motifs with the cancer chemotherapy target O(6)-alkylguanine-DNA alkyltransferase (AGT) and paradoxically protect cells from the biological effects of DNA alkylation damage, despite lacking the reactive cysteine and alkyltransferase activity of AGT. Here we determine Schizosaccharomyces pombe ATL structures without and with damaged DNA containing the endogenous lesion O(6)-methylguanine or cigarette-smoke-derived O(6)-4-(3-pyridyl)-4-oxobutylguanine. These results reveal non-enzymatic DNA nucleotide flipping plus increased DNA distortion and binding pocket size compared to AGT. Our analysis of lesion-binding site conservation identifies new ATLs in sea anemone and ancestral archaea, indicating that ATL interactions are ancestral to present-day repair pathways in all domains of life. Genetic connections to mammalian XPG (also known as ERCC5) and ERCC1 in S. pombe homologues Rad13 and Swi10 and biochemical interactions with Escherichia coli UvrA and UvrC combined with structural results reveal that ATLs sculpt alkylated DNA to create a genetic and structural intersection of base damage processing with nucleotide excision repair.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2729916/" 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/PMC2729916/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tubbs, Julie L -- Latypov, Vitaly -- Kanugula, Sreenivas -- Butt, Amna -- Melikishvili, Manana -- Kraehenbuehl, Rolf -- Fleck, Oliver -- Marriott, Andrew -- Watson, Amanda J -- Verbeek, Barbara -- McGown, Gail -- Thorncroft, Mary -- Santibanez-Koref, Mauro F -- Millington, Christopher -- Arvai, Andrew S -- Kroeger, Matthew D -- Peterson, Lisa A -- Williams, David M -- Fried, Michael G -- Margison, Geoffrey P -- Pegg, Anthony E -- Tainer, John A -- CA018137/CA/NCI NIH HHS/ -- CA097209/CA/NCI NIH HHS/ -- CA59887/CA/NCI NIH HHS/ -- GM070662/GM/NIGMS NIH HHS/ -- R01 CA059887/CA/NCI NIH HHS/ -- R01 CA059887-12/CA/NCI NIH HHS/ -- R01 CA059887-13/CA/NCI NIH HHS/ -- R01 GM070662/GM/NIGMS NIH HHS/ -- R01 GM070662-01/GM/NIGMS NIH HHS/ -- R01 GM070662-02/GM/NIGMS NIH HHS/ -- R01 GM070662-03/GM/NIGMS NIH HHS/ -- R01 GM070662-04/GM/NIGMS NIH HHS/ -- R01 GM070662-05/GM/NIGMS NIH HHS/ -- R01 GM070662-06/GM/NIGMS NIH HHS/ -- Cancer Research UK/United Kingdom -- England -- Nature. 2009 Jun 11;459(7248):808-13. doi: 10.1038/nature08076.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19516334" target="_blank"〉PubMed〈/a〉
    Keywords: Alkyl and Aryl Transferases/*chemistry/*metabolism ; Alkylation ; Binding Sites ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; *DNA Damage ; *DNA Repair ; Guanine/analogs & derivatives/chemistry/metabolism ; Humans ; Models, Molecular ; Protein Binding ; Protein Conformation
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  • 66
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    Nature Publishing Group (NPG)
    Publication Date: 2009-09-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nelson, Bryn -- England -- Nature. 2009 Sep 10;461(7261):160-3. doi: 10.1038/461160a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19741679" target="_blank"〉PubMed〈/a〉
    Keywords: *Access to Information/legislation & jurisprudence ; Animals ; Archives ; Confidentiality/standards ; Databases, Factual/standards/trends/*utilization ; Human Genome Project ; Humans ; Information Storage and Retrieval/*methods/standards/trends/*utilization ; *Internet/utilization ; Mice ; Periodicals as Topic/standards ; Publishing/standards ; Research/standards ; Research Design ; *Research Personnel/psychology ; Time Factors
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  • 67
    Publication Date: 2009-07-10
    Description: Inhibition of the TOR signalling pathway by genetic or pharmacological intervention extends lifespan in invertebrates, including yeast, nematodes and fruitflies; however, whether inhibition of mTOR signalling can extend lifespan in a mammalian species was unknown. Here we report that rapamycin, an inhibitor of the mTOR pathway, extends median and maximal lifespan of both male and female mice when fed beginning at 600 days of age. On the basis of age at 90% mortality, rapamycin led to an increase of 14% for females and 9% for males. The effect was seen at three independent test sites in genetically heterogeneous mice, chosen to avoid genotype-specific effects on disease susceptibility. Disease patterns of rapamycin-treated mice did not differ from those of control mice. In a separate study, rapamycin fed to mice beginning at 270 days of age also increased survival in both males and females, based on an interim analysis conducted near the median survival point. Rapamycin may extend lifespan by postponing death from cancer, by retarding mechanisms of ageing, or both. To our knowledge, these are the first results to demonstrate a role for mTOR signalling in the regulation of mammalian lifespan, as well as pharmacological extension of lifespan in both genders. These findings have implications for further development of interventions targeting mTOR for the treatment and prevention of age-related diseases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2786175/" 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/PMC2786175/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harrison, David E -- Strong, Randy -- Sharp, Zelton Dave -- Nelson, James F -- Astle, Clinton M -- Flurkey, Kevin -- Nadon, Nancy L -- Wilkinson, J Erby -- Frenkel, Krystyna -- Carter, Christy S -- Pahor, Marco -- Javors, Martin A -- Fernandez, Elizabeth -- Miller, Richard A -- AG022303/AG/NIA NIH HHS/ -- AG022307/AG/NIA NIH HHS/ -- AG022308/AG/NIA NIH HHS/ -- AG025707/AG/NIA NIH HHS/ -- AG13319/AG/NIA NIH HHS/ -- P30 AG013319/AG/NIA NIH HHS/ -- P30 AG013319-119002/AG/NIA NIH HHS/ -- P30 AG013319-129002/AG/NIA NIH HHS/ -- P30 AG013319-139002/AG/NIA NIH HHS/ -- P30 AG013319-149002/AG/NIA NIH HHS/ -- P30 AG025707/AG/NIA NIH HHS/ -- U01 AG022303/AG/NIA NIH HHS/ -- U01 AG022307/AG/NIA NIH HHS/ -- U01 AG022307-01/AG/NIA NIH HHS/ -- U01 AG022307-02/AG/NIA NIH HHS/ -- U01 AG022307-03/AG/NIA NIH HHS/ -- U01 AG022307-04/AG/NIA NIH HHS/ -- U01 AG022307-05/AG/NIA NIH HHS/ -- U01 AG022307-05S1/AG/NIA NIH HHS/ -- U01 AG022308/AG/NIA NIH HHS/ -- England -- Nature. 2009 Jul 16;460(7253):392-5. doi: 10.1038/nature08221. Epub 2009 Jul 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Jackson Laboratory, Bar Harbor, Maine 04609, USA. david.harrison@jax.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19587680" target="_blank"〉PubMed〈/a〉
    Keywords: Administration, Oral ; Aging/*drug effects/genetics/*physiology ; Animals ; Carrier Proteins/antagonists & inhibitors/metabolism ; Diet ; Disease Susceptibility ; Female ; Longevity/*drug effects/*genetics/physiology ; Male ; Mice ; Phosphotransferases (Alcohol Group Acceptor)/antagonists & inhibitors/metabolism ; Sirolimus/*administration & dosage/*pharmacology ; Specific Pathogen-Free Organisms ; Survival Analysis ; TOR Serine-Threonine Kinases ; Time Factors
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  • 68
    Publication Date: 2009-02-20
    Description: Visual working memory provides an essential link between perception and higher cognitive functions, allowing for the active maintenance of information about stimuli no longer in view. Research suggests that sustained activity in higher-order prefrontal, parietal, inferotemporal and lateral occipital areas supports visual maintenance, and may account for the limited capacity of working memory to hold up to 3-4 items. Because higher-order areas lack the visual selectivity of early sensory areas, it has remained unclear how observers can remember specific visual features, such as the precise orientation of a grating, with minimal decay in performance over delays of many seconds. One proposal is that sensory areas serve to maintain fine-tuned feature information, but early visual areas show little to no sustained activity over prolonged delays. Here we show that orientations held in working memory can be decoded from activity patterns in the human visual cortex, even when overall levels of activity are low. Using functional magnetic resonance imaging and pattern classification methods, we found that activity patterns in visual areas V1-V4 could predict which of two oriented gratings was held in memory with mean accuracy levels upwards of 80%, even in participants whose activity fell to baseline levels after a prolonged delay. These orientation-selective activity patterns were sustained throughout the delay period, evident in individual visual areas, and similar to the responses evoked by unattended, task-irrelevant gratings. Our results demonstrate that early visual areas can retain specific information about visual features held in working memory, over periods of many seconds when no physical stimulus is present.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709809/" 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/PMC2709809/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harrison, Stephenie A -- Tong, Frank -- R01 EY017082/EY/NEI NIH HHS/ -- R01 EY017082-01A2/EY/NEI NIH HHS/ -- R01 EY017082-02/EY/NEI NIH HHS/ -- England -- Nature. 2009 Apr 2;458(7238):632-5. doi: 10.1038/nature07832. Epub 2009 Feb 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Psychology Department and Vanderbilt Vision Research Center, Vanderbilt University, Nashville, Tennessee 37240, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19225460" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Humans ; Magnetic Resonance Imaging ; Memory/*physiology ; Models, Neurological ; Photic Stimulation ; Time Factors ; Visual Cortex/*physiology ; Visual Perception/*physiology
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  • 69
    Publication Date: 2009-08-28
    Description: The fruitfly Drosophila melanogaster exhibits a robust and innate olfactory-based avoidance behaviour to CO(2), a component of odour emitted from stressed flies. Specialized neurons in the antenna and a dedicated neuronal circuit in the higher olfactory system mediate CO(2) detection and avoidance. However, fruitflies need to overcome this avoidance response in some environments that contain CO(2) such as ripening fruits and fermenting yeast, which are essential food sources. Very little is known about the molecular and neuronal basis of this unique, context-dependent modification of innate olfactory avoidance behaviour. Here we identify a new class of odorants present in food that directly inhibit CO(2)-sensitive neurons in the antenna. Using an in vivo expression system we establish that the odorants act on the Gr21a/Gr63a CO(2) receptor. The presence of these odorants significantly and specifically reduces CO(2)-mediated avoidance behaviour, as well as avoidance mediated by 'Drosophila stress odour'. We propose a model in which behavioural avoidance to CO(2) is directly influenced by inhibitory interactions of the novel odours with CO(2) receptors. Furthermore, we observe differences in the temporal dynamics of inhibition: the effect of one of these odorants lasts several minutes beyond the initial exposure. Notably, animals that have been briefly pre-exposed to this odorant do not respond to the CO(2) avoidance cue even after the odorant is no longer present. We also show that related odorants are effective inhibitors of the CO(2) response in Culex mosquitoes that transmit West Nile fever and filariasis. Our findings have broader implications in highlighting the important role of inhibitory odorants in olfactory coding, and in their potential to disrupt CO(2)-mediated host-seeking behaviour in disease-carrying insects like mosquitoes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Turner, Stephanie Lynn -- Ray, Anandasankar -- England -- Nature. 2009 Sep 10;461(7261):277-81. doi: 10.1038/nature08295. Epub 2009 Aug 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cellular, Molecular, and Developmental Biology Program, University of California, Riverside, California 92521, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19710651" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Structures/cytology/physiology ; Animals ; Avoidance Learning/*drug effects ; Carbon Dioxide/analysis/*pharmacology ; Cues ; Culex/drug effects/physiology ; Diacetyl/chemistry/pharmacology ; Drosophila Proteins/antagonists & inhibitors/metabolism ; Drosophila melanogaster/*drug effects/*physiology ; Fermentation ; Fruit/*chemistry/growth & development ; Hexanols/chemistry/pharmacology ; Odors/*analysis ; Olfactory Perception/drug effects/physiology ; Olfactory Receptor Neurons/*drug effects/metabolism ; Smell/drug effects/physiology ; Stress, Physiological/physiology ; Time Factors
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  • 70
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    Nature Publishing Group (NPG)
    Publication Date: 2009-01-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chakravarti, Aravinda -- England -- Nature. 2009 Jan 22;457(7228):380-1. doi: 10.1038/457380a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Broadway Research Building, Room 579, 733 North Broadway, Baltimore, Maryland 21205, USA. aravinda@jhmi.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158772" target="_blank"〉PubMed〈/a〉
    Keywords: Africa/ethnology ; Continental Population Groups/*genetics ; *Databases, Genetic ; Emigration and Immigration ; Evolution, Molecular ; Genetics, Population/*trends ; Genome, Human/genetics ; Genomics/*trends ; *Heredity ; Humans ; *Pedigree ; Time Factors
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  • 71
    Publication Date: 2009-09-26
    Description: Reconstructions of atmospheric CO(2) concentrations based on Antarctic ice cores reveal significant changes during the Holocene epoch, but the processes responsible for these changes in CO(2) concentrations have not been unambiguously identified. Distinct characteristics in the carbon isotope signatures of the major carbon reservoirs (ocean, biosphere, sediments and atmosphere) constrain variations in the CO(2) fluxes between those reservoirs. Here we present a highly resolved atmospheric delta(13)C record for the past 11,000 years from measurements on atmospheric CO(2) trapped in an Antarctic ice core. From mass-balance inverse model calculations performed with a simplified carbon cycle model, we show that the decrease in atmospheric CO(2) of about 5 parts per million by volume (p.p.m.v.). The increase in delta(13)C of about 0.25 per thousand during the early Holocene is most probably the result of a combination of carbon uptake of about 290 gigatonnes of carbon by the land biosphere and carbon release from the ocean in response to carbonate compensation of the terrestrial uptake during the termination of the last ice age. The 20 p.p.m.v. increase of atmospheric CO(2) and the small decrease in delta(13)C of about 0.05 per thousand during the later Holocene can mostly be explained by contributions from carbonate compensation of earlier land-biosphere uptake and coral reef formation, with only a minor contribution from a small decrease of the land-biosphere carbon inventory.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Elsig, Joachim -- Schmitt, Jochen -- Leuenberger, Daiana -- Schneider, Robert -- Eyer, Marc -- Leuenberger, Markus -- Joos, Fortunat -- Fischer, Hubertus -- Stocker, Thomas F -- England -- Nature. 2009 Sep 24;461(7263):507-10. doi: 10.1038/nature08393.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Climate and Environmental Physics, Physics Institute, University of Bern, Sidlerstrasse 5, CH-3012 Bern, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19779448" target="_blank"〉PubMed〈/a〉
    Keywords: Air/analysis ; Animals ; Antarctic Regions ; Anthozoa/growth & development/metabolism ; Atmosphere/chemistry ; Carbon/*analysis/*metabolism ; Carbon Dioxide/analysis/*metabolism ; Carbon Isotopes ; Climate ; Ecosystem ; History, Ancient ; Ice Cover/*chemistry ; Time Factors
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  • 72
    Publication Date: 2009-11-20
    Description: Allosteric regulation is used as a very efficient mechanism to control protein activity in most biological processes, including signal transduction, metabolism, catalysis and gene regulation. Allosteric proteins can exist in several conformational states with distinct binding or enzymatic activity. Effectors are considered to function in a purely structural manner by selectively stabilizing a specific conformational state, thereby regulating protein activity. Here we show that allosteric proteins can be regulated predominantly by changes in their structural dynamics. We have used NMR spectroscopy and isothermal titration calorimetry to characterize cyclic AMP (cAMP) binding to the catabolite activator protein (CAP), a transcriptional activator that has been a prototype for understanding effector-mediated allosteric control of protein activity. cAMP switches CAP from the 'off' state (inactive), which binds DNA weakly and non-specifically, to the 'on' state (active), which binds DNA strongly and specifically. In contrast, cAMP binding to a single CAP mutant, CAP-S62F, fails to elicit the active conformation; yet, cAMP binding to CAP-S62F strongly activates the protein for DNA binding. NMR and thermodynamic analyses show that despite the fact that CAP-S62F-cAMP(2) adopts the inactive conformation, its strong binding to DNA is driven by a large conformational entropy originating in enhanced protein motions induced by DNA binding. The results provide strong evidence that changes in protein motions may activate allosteric proteins that are otherwise structurally inactive.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tzeng, Shiou-Ru -- Kalodimos, Charalampos G -- England -- Nature. 2009 Nov 19;462(7271):368-72. doi: 10.1038/nature08560.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19924217" target="_blank"〉PubMed〈/a〉
    Keywords: Cyclic AMP/chemistry/metabolism ; Cyclic AMP Receptor Protein/chemistry/*metabolism ; DNA/metabolism ; *Energy Metabolism ; Escherichia coli/*metabolism ; Escherichia coli Proteins/chemistry/*metabolism ; Models, Molecular ; Protein Binding ; Protein Structure, Tertiary
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  • 73
    Publication Date: 2009-10-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Le Quere, Corinne -- England -- Nature. 2009 Oct 22;461(7267):1031. doi: 10.1038/4611031e.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of East Anglia, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19847222" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Atlantic Ocean ; Decapoda (Crustacea)/*growth & development/*physiology ; *Food Chain ; Larva/growth & development/physiology ; Phytoplankton/*growth & development ; Seawater ; Temperature ; Time Factors
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  • 74
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    Nature Publishing Group (NPG)
    Publication Date: 2009-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vaccaro, Patrick H -- England -- Nature. 2009 Mar 19;458(7236):289-90. doi: 10.1038/458289a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295594" target="_blank"〉PubMed〈/a〉
    Keywords: Anisotropy ; Circular Dichroism/*methods ; Cyclohexenes/*chemistry ; Stereoisomerism ; Terpenes/*chemistry ; Time Factors ; *Vibration
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  • 75
    Publication Date: 2009-03-20
    Description: In the study of complex mammalian behaviours, technological limitations have prevented spatiotemporally precise control over intracellular signalling processes. Here we report the development of a versatile family of genetically encoded optical tools ('optoXRs') that leverage common structure-function relationships among G-protein-coupled receptors (GPCRs) to recruit and control, with high spatiotemporal precision, receptor-initiated biochemical signalling pathways. In particular, we have developed and characterized two optoXRs that selectively recruit distinct, targeted signalling pathways in response to light. The two optoXRs exerted opposing effects on spike firing in nucleus accumbens in vivo, and precisely timed optoXR photostimulation in nucleus accumbens by itself sufficed to drive conditioned place preference in freely moving mice. The optoXR approach allows testing of hypotheses regarding the causal impact of biochemical signalling in behaving mammals, in a targetable and temporally precise manner.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Airan, Raag D -- Thompson, Kimberly R -- Fenno, Lief E -- Bernstein, Hannah -- Deisseroth, Karl -- England -- Nature. 2009 Apr 23;458(7241):1025-9. doi: 10.1038/nature07926. Epub 2009 Mar 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bioengineering, Stanford University, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295515" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cattle ; Cell Line ; Cricetinae ; Cyclic AMP Response Element-Binding Protein/metabolism ; *Genetic Engineering ; Humans ; Intracellular Space/*metabolism/radiation effects ; Mice ; Nucleus Accumbens/cytology/physiology/radiation effects ; Receptors, Adrenergic, alpha-1/genetics/metabolism ; Receptors, Adrenergic, beta-2/genetics/metabolism ; Receptors, G-Protein-Coupled/genetics/*metabolism ; Recombinant Fusion Proteins/genetics/*metabolism ; Reward ; Rhodopsin/genetics/metabolism ; *Signal Transduction/radiation effects ; Structure-Activity Relationship ; Time Factors
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  • 76
    Publication Date: 2009-03-10
    Description: During perceptual decisions, the activity of sensory neurons correlates with a subject's percept, even when the physical stimulus is identical. The origin of this correlation is unknown. Current theory proposes a causal effect of noise in sensory neurons on perceptual decisions, but the correlation could result from different brain states associated with the perceptual choice (a top-down explanation). These two schemes have very different implications for the role of sensory neurons in forming decisions. Here we use white-noise analysis to measure tuning functions of V2 neurons associated with choice and simultaneously measure how the variation in the stimulus affects the subjects' (two macaques) perceptual decisions. In causal models, stronger effects of the stimulus upon decisions, mediated by sensory neurons, are associated with stronger choice-related activity. However, we find that over the time course of the trial these measures change in different directions-at odds with causal models. An analysis of the effect of reward size also supports this conclusion. Finally, we find that choice is associated with changes in neuronal gain that are incompatible with causal models. All three results are readily explained if choice is associated with changes in neuronal gain caused by top-down phenomena that closely resemble attention. We conclude that top-down processes contribute to choice-related activity. Thus, even forming simple sensory decisions involves complex interactions between cognitive processes and sensory neurons.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2917918/" 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/PMC2917918/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nienborg, Hendrikje -- Cumming, Bruce G -- Z99 EY999999/Intramural NIH HHS/ -- ZIA EY000404-08/Intramural NIH HHS/ -- England -- Nature. 2009 May 7;459(7243):89-92. doi: 10.1038/nature07821. Epub 2009 Mar 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Sensorimotor Research, National Eye Institute, National Institutes of Health, 49 Convent Drive, Bethesda, Maryland 20892, USA. hnienb@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19270683" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Behavior, Animal/physiology ; Choice Behavior/physiology ; Decision Making/*physiology ; Macaca mulatta ; Reward ; Sensory Receptor Cells/*physiology ; Time Factors
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  • 77
    Publication Date: 2009-09-01
    Description: The orphan receptor tyrosine kinase ErbB2 (also known as HER2 or Neu) transforms cells when overexpressed, and it is an important therapeutic target in human cancer. Structural studies have suggested that the oncogenic (and ligand-independent) signalling properties of ErbB2 result from the absence of a key intramolecular 'tether' in the extracellular region that autoinhibits other human ErbB receptors, including the epidermal growth factor (EGF) receptor. Although ErbB2 is unique among the four human ErbB receptors, here we show that it is the closest structural relative of the single EGF receptor family member in Drosophila melanogaster (dEGFR). Genetic and biochemical data show that dEGFR is tightly regulated by growth factor ligands, yet a crystal structure shows that it, too, lacks the intramolecular tether seen in human EGFR, ErbB3 and ErbB4. Instead, a distinct set of autoinhibitory interdomain interactions hold unliganded dEGFR in an inactive state. All of these interactions are maintained (and even extended) in ErbB2, arguing against the suggestion that ErbB2 lacks autoinhibition. We therefore suggest that normal and pathogenic ErbB2 signalling may be regulated by ligands in the same way as dEGFR. Our findings have important implications for ErbB2 regulation in human cancer, and for developing therapeutic approaches that target novel aspects of this orphan receptor.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2762480/" 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/PMC2762480/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alvarado, Diego -- Klein, Daryl E -- Lemmon, Mark A -- R01 CA079992/CA/NCI NIH HHS/ -- R01 CA079992-09/CA/NCI NIH HHS/ -- R01 CA079992-10/CA/NCI NIH HHS/ -- R01 CA125432/CA/NCI NIH HHS/ -- R01 CA125432-01A1/CA/NCI NIH HHS/ -- R01 CA125432-02/CA/NCI NIH HHS/ -- R01 CA125432-03/CA/NCI NIH HHS/ -- England -- Nature. 2009 Sep 10;461(7261):287-91. doi: 10.1038/nature08297. Epub 2009 Aug 30.〈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/19718021" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Crystallography, X-Ray ; Drosophila Proteins/*antagonists & inhibitors/chemistry/genetics/*metabolism ; Drosophila melanogaster/chemistry/*metabolism ; Enzyme Activation ; Humans ; Ligands ; Models, Molecular ; Protein Structure, Tertiary ; Receptor, Epidermal Growth Factor/*antagonists & ; inhibitors/chemistry/genetics/*metabolism ; Receptor, ErbB-2/antagonists & inhibitors/*chemistry/*metabolism ; Receptors, Invertebrate Peptide/*antagonists & ; inhibitors/chemistry/genetics/*metabolism ; Scattering, Small Angle ; Solubility ; X-Ray Diffraction
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  • 78
    Publication Date: 2009-05-02
    Description: Global efforts to mitigate climate change are guided by projections of future temperatures. But the eventual equilibrium global mean temperature associated with a given stabilization level of atmospheric greenhouse gas concentrations remains uncertain, complicating the setting of stabilization targets to avoid potentially dangerous levels of global warming. Similar problems apply to the carbon cycle: observations currently provide only a weak constraint on the response to future emissions. Here we use ensemble simulations of simple climate-carbon-cycle models constrained by observations and projections from more comprehensive models to simulate the temperature response to a broad range of carbon dioxide emission pathways. We find that the peak warming caused by a given cumulative carbon dioxide emission is better constrained than the warming response to a stabilization scenario. Furthermore, the relationship between cumulative emissions and peak warming is remarkably insensitive to the emission pathway (timing of emissions or peak emission rate). Hence policy targets based on limiting cumulative emissions of carbon dioxide are likely to be more robust to scientific uncertainty than emission-rate or concentration targets. Total anthropogenic emissions of one trillion tonnes of carbon (3.67 trillion tonnes of CO(2)), about half of which has already been emitted since industrialization began, results in a most likely peak carbon-dioxide-induced warming of 2 degrees C above pre-industrial temperatures, with a 5-95% confidence interval of 1.3-3.9 degrees C.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Allen, Myles R -- Frame, David J -- Huntingford, Chris -- Jones, Chris D -- Lowe, Jason A -- Meinshausen, Malte -- Meinshausen, Nicolai -- England -- Nature. 2009 Apr 30;458(7242):1163-6. doi: 10.1038/nature08019.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, University of Oxford, OX1 3PU, UK. myles.allen@physics.ox.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19407800" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/*chemistry ; Benchmarking ; Carbon/*analysis ; Carbon Dioxide/*analysis ; Computer Simulation ; *Greenhouse Effect ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Human Activities/history ; Industry/history ; *Models, Theoretical ; *Temperature ; Time Factors ; Uncertainty
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  • 79
    Publication Date: 2009-11-13
    Description: Tracing the transient atomic motions that lie at the heart of chemical reactions requires high-resolution multidimensional structural information on the timescale of molecular vibrations, which commonly range from 10 fs to 1 ps. For simple chemical systems, it has been possible to map out in considerable detail the reactive potential-energy surfaces describing atomic motions and resultant reaction dynamics, but such studies remain challenging for complex chemical and biological transformations. A case in point is the green fluorescent protein (GFP) from the jellyfish Aequorea victoria, which is a widely used gene expression marker owing to its efficient bioluminescence. This feature is known to arise from excited-state proton transfer (ESPT), yet the atomistic details of the process are still not fully understood. Here we show that femtosecond stimulated Raman spectroscopy provides sufficiently detailed and time-resolved vibrational spectra of the electronically excited chromophore of GFP to reveal skeletal motions involved in the proton transfer that produces the fluorescent form of the protein. In particular, we observe that the frequencies and intensities of two marker bands, the C-O and C = N stretching modes at opposite ends of the conjugated chromophore, oscillate out of phase with a period of 280 fs; we attribute these oscillations to impulsively excited low-frequency phenoxyl-ring motions, which optimize the geometry of the chromophore for ESPT. Our findings illustrate that femtosecond simulated Raman spectroscopy is a powerful approach to revealing the real-time nuclear dynamics that make up a multidimensional polyatomic reaction coordinate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fang, Chong -- Frontiera, Renee R -- Tran, Rosalie -- Mathies, Richard A -- England -- Nature. 2009 Nov 12;462(7270):200-4. doi: 10.1038/nature08527.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19907490" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Evolution, Molecular ; Green Fluorescent Proteins/*chemistry/genetics/*metabolism ; Models, Molecular ; Movement ; Protons ; Spectrum Analysis, Raman ; Time Factors ; *Vibration
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  • 80
    Publication Date: 2009-07-07
    Description: To reach the mammalian gut, enteric bacteria must pass through the stomach. Many such organisms survive exposure to the harsh gastric environment (pH 1.5-4) by mounting extreme acid-resistance responses, one of which, the arginine-dependent system of Escherichia coli, has been studied at levels of cellular physiology, molecular genetics and protein biochemistry. This multiprotein system keeps the cytoplasm above pH 5 during acid challenge by continually pumping protons out of the cell using the free energy of arginine decarboxylation. At the heart of the process is a 'virtual proton pump' in the inner membrane, called AdiC, that imports L-arginine from the gastric juice and exports its decarboxylation product agmatine. AdiC belongs to the APC superfamily of membrane proteins, which transports amino acids, polyamines and organic cations in a multitude of biological roles, including delivery of arginine for nitric oxide synthesis, facilitation of insulin release from pancreatic beta-cells, and, when inappropriately overexpressed, provisioning of certain fast-growing neoplastic cells with amino acids. High-resolution structures and detailed transport mechanisms of APC transporters are currently unknown. Here we describe a crystal structure of AdiC at 3.2 A resolution. The protein is captured in an outward-open, substrate-free conformation with transmembrane architecture remarkably similar to that seen in four other families of apparently unrelated transport proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745212/" 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/PMC2745212/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fang, Yiling -- Jayaram, Hariharan -- Shane, Tania -- Kolmakova-Partensky, Ludmila -- Wu, Fang -- Williams, Carole -- Xiong, Yong -- Miller, Christopher -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM031768/GM/NIGMS NIH HHS/ -- R01 GM031768-26/GM/NIGMS NIH HHS/ -- R01 GM089688/GM/NIGMS NIH HHS/ -- T32 NS 07292/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Aug 20;460(7258):1040-3. doi: 10.1038/nature08201. Epub 2009 Jul 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19578361" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Transport Systems/*chemistry/metabolism ; Antiporters/*chemistry/metabolism ; Bacterial Proteins/*chemistry ; Crystallography, X-Ray ; Escherichia coli/*chemistry ; Escherichia coli Proteins/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Multigene Family ; Protein Conformation ; Salmonella typhi/*chemistry ; Structural Homology, Protein
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  • 81
    Publication Date: 2009-11-06
    Description: Recent earth science studies have pointed out that massive acceleration of the global nitrogen cycle by anthropogenic addition of bio-available nitrogen has led to a host of environmental problems. Nitrous oxide (N(2)O) is a greenhouse gas that is an intermediate during the biological process known as denitrification. Copper-containing nitrite reductase (CuNIR) is a key enzyme in the process; it produces a precursor for N(2)O by catalysing the one-electron reduction of nitrite (NO2-) to nitric oxide (NO). The reduction step is performed by an efficient electron-transfer reaction with a redox-partner protein. However, details of the mechanism during the electron-transfer reaction are still unknown. Here we show the high-resolution crystal structure of the electron-transfer complex for CuNIR with its cognate cytochrome c as the electron donor. The hydrophobic electron-transfer path is formed at the docking interface by desolvation owing to close contact between the two proteins. Structural analysis of the interface highlights an essential role for the loop region with a hydrophobic patch for protein-protein recognition; it also shows how interface construction allows the variation in atomic components to achieve diverse biological electron transfers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nojiri, Masaki -- Koteishi, Hiroyasu -- Nakagami, Takuya -- Kobayashi, Kazuo -- Inoue, Tsuyoshi -- Yamaguchi, Kazuya -- Suzuki, Shinnichiro -- England -- Nature. 2009 Nov 5;462(7269):117-20. doi: 10.1038/nature08507.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan. nojiri@ch.wani.osaka-u.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19890332" target="_blank"〉PubMed〈/a〉
    Keywords: Achromobacter denitrificans/*enzymology ; Crystallography, X-Ray ; Cytochromes c/chemistry/metabolism ; Electron Transport ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Nitric Oxide/metabolism ; Nitrite Reductases/*chemistry/*metabolism ; Nitrites/metabolism ; Nitrous Oxide/metabolism ; Protein Conformation ; Structure-Activity Relationship
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  • 82
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2009-03-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Van Noorden, Richard -- England -- Nature. 2009 Mar 26;458(7237):391. doi: 10.1038/458391a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19325593" target="_blank"〉PubMed〈/a〉
    Keywords: Financing, Organized/*organization & administration/statistics & numerical data ; Great Britain ; Peer Review, Research/*methods ; Research Personnel/psychology/*statistics & numerical data ; Research Support as Topic/*organization & administration/statistics & numerical ; data ; Time Factors
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  • 83
    Publication Date: 2009-02-03
    Description: Membrane proteins that transport hydrophobic compounds have important roles in multi-drug resistance and can cause a number of diseases, underscoring the importance of protein-mediated transport of hydrophobic compounds. Hydrophobic compounds readily partition into regular membrane lipid bilayers, and their transport through an aqueous protein channel is energetically unfavourable. Alternative transport models involving acquisition from the lipid bilayer by lateral diffusion have been proposed for hydrophobic substrates. So far, all transport proteins for which a lateral diffusion mechanism has been proposed function as efflux pumps. Here we present the first example of a lateral diffusion mechanism for the uptake of hydrophobic substrates by the Escherichia coli outer membrane long-chain fatty acid transporter FadL. A FadL mutant in which a lateral opening in the barrel wall is constricted, but which is otherwise structurally identical to wild-type FadL, does not transport substrates. A crystal structure of FadL from Pseudomonas aeruginosa shows that the opening in the wall of the beta-barrel is conserved and delineates a long, hydrophobic tunnel that could mediate substrate passage from the extracellular environment, through the polar lipopolysaccharide layer and, by means of the lateral opening in the barrel wall, into the lipid bilayer from where the substrate can diffuse into the periplasm. Because FadL homologues are found in pathogenic and biodegrading bacteria, our results have implications for combating bacterial infections and bioremediating xenobiotics in the environment.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2658730/" 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/PMC2658730/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hearn, Elizabeth M -- Patel, Dimki R -- Lepore, Bryan W -- Indic, Mridhu -- van den Berg, Bert -- 1R01GM074824/GM/NIGMS NIH HHS/ -- F32 GM079820-01/GM/NIGMS NIH HHS/ -- F32 GM079820-02/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM074824/GM/NIGMS NIH HHS/ -- R01 GM074824-01/GM/NIGMS NIH HHS/ -- R01 GM074824-02/GM/NIGMS NIH HHS/ -- R01 GM074824-03/GM/NIGMS NIH HHS/ -- R01 GM074824-04/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Mar 19;458(7236):367-70. doi: 10.1038/nature07678. Epub 2009 Feb 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19182779" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Outer Membrane Proteins/*chemistry/genetics/*metabolism ; Cloning, Molecular ; Crystallography, X-Ray ; Diffusion ; Escherichia coli/*chemistry/genetics ; Escherichia coli Proteins/*chemistry/genetics/*metabolism ; Fatty Acid Transport Proteins/*chemistry/genetics/*metabolism ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers/metabolism ; Models, Molecular ; Pseudomonas aeruginosa/*chemistry/genetics
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  • 84
    Publication Date: 2009-08-04
    Description: Polymerization of actin filaments directed by the actin-related protein (Arp)2/3 complex supports many types of cellular movements. However, questions remain regarding the relative contributions of Arp2/3 complex versus other mechanisms of actin filament nucleation to processes such as path finding by neuronal growth cones; this is because of the lack of simple methods to inhibit Arp2/3 complex reversibly in living cells. Here we describe two classes of small molecules that bind to different sites on the Arp2/3 complex and inhibit its ability to nucleate actin filaments. CK-0944636 binds between Arp2 and Arp3, where it appears to block movement of Arp2 and Arp3 into their active conformation. CK-0993548 inserts into the hydrophobic core of Arp3 and alters its conformation. Both classes of compounds inhibit formation of actin filament comet tails by Listeria and podosomes by monocytes. Two inhibitors with different mechanisms of action provide a powerful approach for studying the Arp2/3 complex in living cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780427/" 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/PMC2780427/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nolen, B J -- Tomasevic, N -- Russell, A -- Pierce, D W -- Jia, Z -- McCormick, C D -- Hartman, J -- Sakowicz, R -- Pollard, T D -- F32 GM074374-02/GM/NIGMS NIH HHS/ -- GM-066311/GM/NIGMS NIH HHS/ -- GM074374-02/GM/NIGMS NIH HHS/ -- P01 GM066311/GM/NIGMS NIH HHS/ -- P01 GM066311-01A1/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- England -- Nature. 2009 Aug 20;460(7258):1031-4. doi: 10.1038/nature08231. Epub 2009 Aug 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19648907" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/drug effects/metabolism ; Actin-Related Protein 2/antagonists & inhibitors/chemistry/metabolism ; Actin-Related Protein 2-3 Complex/*antagonists & inhibitors/chemistry/metabolism ; Actin-Related Protein 3/antagonists & inhibitors/chemistry/metabolism ; Actins/chemistry/metabolism ; Animals ; Biopolymers/chemistry/metabolism ; Cattle ; Cell Line ; Crystallography, X-Ray ; Humans ; Hydrophobic and Hydrophilic Interactions ; Indoles/classification/metabolism/pharmacology ; Listeria/physiology ; Models, Molecular ; Monocytes/immunology ; Protein Conformation/drug effects ; Schizosaccharomyces ; Thiazoles/chemistry/classification/metabolism/pharmacology ; Thiophenes/classification/metabolism/pharmacology
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  • 85
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2009-11-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Anthony G -- England -- Nature. 2009 Nov 26;462(7272):420-1. doi: 10.1038/462420a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19940907" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers/*chemistry/*metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Neutron Diffraction ; Potassium Channels, Voltage-Gated/*chemistry/*metabolism ; Protein Structure, Tertiary ; Static Electricity
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  • 86
    Publication Date: 2009-05-29
    Description: The AMP-activated protein kinase (AMPK) is characterized by its ability to bind to AMP, which enables it to adjust enzymatic activity by sensing the cellular energy status and maintain the balance between ATP production and consumption in eukaryotic cells. It also has important roles in the regulation of cell growth and proliferation, and in the establishment and maintenance of cell polarity. These important functions have rendered AMPK an important drug target for obesity, type 2 diabetes and cancer treatments. However, the regulatory mechanism of AMPK activity by AMP binding remains unsolved. Here we report the crystal structures of an unphosphorylated fragment of the AMPK alpha-subunit (KD-AID) from Schizosaccharomyces pombe that contains both the catalytic kinase domain and an autoinhibitory domain (AID), and of a phosphorylated kinase domain from Saccharomyces cerevisiae (Snf1-pKD). The AID binds, from the 'backside', to the hinge region of its kinase domain, forming contacts with both amino-terminal and carboxy-terminal lobes. Structural analyses indicate that AID binding might constrain the mobility of helix alphaC, hence resulting in an autoinhibited KD-AID with much lower kinase activity than that of the kinase domain alone. AMP activates AMPK both allosterically and by inhibiting dephosphorylation. Further in vitro kinetic studies demonstrate that disruption of the KD-AID interface reverses the autoinhibition and these AMPK heterotrimeric mutants no longer respond to the change in AMP concentration. The structural and biochemical data have shown the primary mechanism of AMPK autoinhibition and suggest a conformational switch model for AMPK activation by AMP.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Lei -- Jiao, Zhi-Hao -- Zheng, Li-Sha -- Zhang, Yuan-Yuan -- Xie, Shu-Tao -- Wang, Zhi-Xin -- Wu, Jia-Wei -- England -- Nature. 2009 Jun 25;459(7250):1146-9. doi: 10.1038/nature08075. Epub 2009 May 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MOE Key Laboratory of Bioinformatics, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19474788" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases/*chemistry/*metabolism ; Adenosine Monophosphate/metabolism ; Amino Acid Sequence ; Animals ; *Models, Molecular ; Molecular Sequence Data ; Mutation ; Phosphorylation ; Protein Structure, Tertiary ; Rats ; Saccharomyces cerevisiae/*enzymology ; Schizosaccharomyces/*enzymology ; Sequence Alignment
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  • 87
    Publication Date: 2009-05-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schmidt, Gavin -- Archer, David -- England -- Nature. 2009 Apr 30;458(7242):1117-8. doi: 10.1038/4581117a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19407786" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/*chemistry ; Carbon Dioxide/*analysis ; Ecology/*methods ; Forecasting ; *Greenhouse Effect ; International Cooperation ; *Models, Theoretical ; Probability ; *Temperature ; Time Factors ; Uncertainty
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  • 88
    Publication Date: 2009-07-28
    Description: The discovery of intrinsically photosensitive retinal ganglion cells has overthrown the long-held belief that rods and cones are the exclusive retinal photoreceptors. Intrinsically photosensitive retinal ganglion cells use melanopsin as the photopigment, and mediate non-image-forming visual functions such as circadian photoentrainment. In fish, in situ hybridization studies indicated that melanopsin is present in retinal horizontal cells-lateral association neurons critical for creating the centre-surround receptive fields of visual neurons. This raises the question of whether fish horizontal cells are intrinsically photosensitive. This notion was examined previously in flat-mount roach retina, but all horizontal-cell light response disappeared after synaptic transmission was blocked, making any conclusion difficult to reach. To examine this question directly, we have now recorded from single, acutely dissociated horizontal cells from catfish and goldfish. We found that light induced a response in catfish cone horizontal cells, but not rod horizontal cells, consisting of a modulation of the nifedipine-sensitive, voltage-gated calcium current. The light response was extremely slow, lasting for many minutes. Similar light responses were observed in a high percentage of goldfish horizontal cells. We have cloned two melanopsin genes and one vertebrate ancient (VA) opsin gene from catfish. In situ hybridization indicated that melanopsin, but less likely VA opsin, was expressed in the horizontal-cell layer of catfish retina. This intrinsic light response may serve to modulate, over a long timescale, lateral inhibition mediated by these cells. Thus, at least in some vertebrates, there are retinal non-rod/non-cone photoreceptors involved primarily in image-forming vision.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2737592/" 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/PMC2737592/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheng, Ning -- Tsunenari, Takashi -- Yau, King-Wai -- R01 DC006904/DC/NIDCD NIH HHS/ -- R01 DC006904-01/DC/NIDCD NIH HHS/ -- R01 DC006904-02/DC/NIDCD NIH HHS/ -- R01 DC006904-03/DC/NIDCD NIH HHS/ -- R01 DC006904-04/DC/NIDCD NIH HHS/ -- R01 DC006904-05/DC/NIDCD NIH HHS/ -- R01 EY006837/EY/NEI NIH HHS/ -- R01 EY006837-16A1/EY/NEI NIH HHS/ -- R01 EY006837-17/EY/NEI NIH HHS/ -- R01 EY006837-18/EY/NEI NIH HHS/ -- R01 EY006837-19/EY/NEI NIH HHS/ -- R01 EY006837-20A1/EY/NEI NIH HHS/ -- R01 EY006837-21/EY/NEI NIH HHS/ -- R01 EY006837-22/EY/NEI NIH HHS/ -- R01 EY014596/EY/NEI NIH HHS/ -- R01 EY014596-01/EY/NEI NIH HHS/ -- R01 EY014596-02/EY/NEI NIH HHS/ -- R01 EY014596-03/EY/NEI NIH HHS/ -- R01 EY014596-04/EY/NEI NIH HHS/ -- R01 EY014596-05/EY/NEI NIH HHS/ -- R01 EY014596-06/EY/NEI NIH HHS/ -- R01 EY014596-07/EY/NEI NIH HHS/ -- R01 EY014596-07S1/EY/NEI NIH HHS/ -- R37 EY006837/EY/NEI NIH HHS/ -- R37 EY006837-13/EY/NEI NIH HHS/ -- R37 EY006837-14/EY/NEI NIH HHS/ -- R37 EY006837-15/EY/NEI NIH HHS/ -- R37 EY006837-15S1/EY/NEI NIH HHS/ -- England -- Nature. 2009 Aug 13;460(7257):899-903. doi: 10.1038/nature08175. Epub 2009 Jul 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. chengn2@mail.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19633653" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/metabolism ; *Catfishes ; Cloning, Molecular ; Electric Conductivity ; Fish Proteins/genetics/metabolism ; Gene Expression Profiling ; *Goldfish ; Ion Channel Gating/drug effects/radiation effects ; *Light ; Molecular Sequence Data ; Nifedipine/pharmacology ; Opsins/genetics ; RNA, Messenger/analysis/genetics ; Retinal Cone Photoreceptor Cells/cytology/drug effects/radiation effects ; Retinal Horizontal Cells/drug effects/*radiation effects ; Retinal Rod Photoreceptor Cells/cytology ; Rod Opsins/genetics/metabolism ; Time Factors
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  • 89
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2009-08-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nosengo, Nicola -- England -- Nature. 2009 Aug 27;460(7259):1076-8. doi: 10.1038/4601076a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19713909" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; Behavior ; Biological Evolution ; Child ; Child, Preschool ; *Computer Simulation ; European Union ; Exploratory Behavior ; Goals ; Humans ; Infant ; Infant, Newborn ; Language ; *Learning ; Robotics/*methods ; Speech ; *Thinking ; Time Factors
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  • 90
    Publication Date: 2009-09-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vasquez, Valeria -- Perozo, Eduardo -- England -- Nature. 2009 Sep 3;461(7260):47-9. doi: 10.1038/461047a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19727188" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; Ion Channel Gating/*physiology ; Ion Channels/*chemistry/*metabolism ; Models, Biological ; Models, Molecular ; Mycobacterium tuberculosis/chemistry ; Pressure ; Protein Structure, Quaternary ; Staphylococcus aureus/*chemistry
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  • 91
    Publication Date: 2009-01-02
    Description: Pyrrolysine (Pyl), the 22nd natural amino acid, is genetically encoded by UAG and inserted into proteins by the unique suppressor tRNA(Pyl) (ref. 1). The Methanosarcinaceae produce Pyl and express Pyl-containing methyltransferases that allow growth on methylamines. Homologous methyltransferases and the Pyl biosynthetic and coding machinery are also found in two bacterial species. Pyl coding is maintained by pyrrolysyl-tRNA synthetase (PylRS), which catalyses the formation of Pyl-tRNA(Pyl) (refs 4, 5). Pyl is not a recent addition to the genetic code. PylRS was already present in the last universal common ancestor; it then persisted in organisms that utilize methylamines as energy sources. Recent protein engineering efforts added non-canonical amino acids to the genetic code. This technology relies on the directed evolution of an 'orthogonal' tRNA synthetase-tRNA pair in which an engineered aminoacyl-tRNA synthetase (aaRS) specifically and exclusively acylates the orthogonal tRNA with a non-canonical amino acid. For Pyl the natural evolutionary process developed such a system some 3 billion years ago. When transformed into Escherichia coli, Methanosarcina barkeri PylRS and tRNA(Pyl) function as an orthogonal pair in vivo. Here we show that Desulfitobacterium hafniense PylRS-tRNA(Pyl) is an orthogonal pair in vitro and in vivo, and present the crystal structure of this orthogonal pair. The ancient emergence of PylRS-tRNA(Pyl) allowed the evolution of unique structural features in both the protein and the tRNA. These structural elements manifest an intricate, specialized aaRS-tRNA interaction surface that is highly distinct from those observed in any other known aaRS-tRNA complex; it is this general property that underlies the molecular basis of orthogonality.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648862/" 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/PMC2648862/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nozawa, Kayo -- O'Donoghue, Patrick -- Gundllapalli, Sarath -- Araiso, Yuhei -- Ishitani, Ryuichiro -- Umehara, Takuya -- Soll, Dieter -- Nureki, Osamu -- R01 GM022854/GM/NIGMS NIH HHS/ -- R01 GM022854-33/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Feb 26;457(7233):1163-7. doi: 10.1038/nature07611. Epub 2008 Dec 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19118381" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acyl-tRNA Synthetases/*chemistry/genetics/*metabolism ; Aminoacylation ; Crystallography, X-Ray ; Desulfitobacterium/*enzymology/genetics ; Escherichia coli/genetics ; Lysine/*analogs & derivatives/biosynthesis/genetics/metabolism ; Methanosarcina barkeri/enzymology/genetics ; Models, Molecular ; RNA, Transfer, Amino Acid-Specific/genetics/metabolism ; Structural Homology, Protein
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  • 92
    Publication Date: 2009-02-20
    Description: The complement system is an essential component of the innate and acquired immune system, and consists of a series of proteolytic cascades that are initiated by the presence of microorganisms. In health, activation of complement is precisely controlled through membrane-bound and soluble plasma-regulatory proteins including complement factor H (fH; ref. 2), a 155 kDa protein composed of 20 domains (termed complement control protein repeats). Many pathogens have evolved the ability to avoid immune-killing by recruiting host complement regulators and several pathogens have adapted to avoid complement-mediated killing by sequestering fH to their surface. Here we present the structure of a complement regulator in complex with its pathogen surface-protein ligand. This reveals how the important human pathogen Neisseria meningitidis subverts immune responses by mimicking the host, using protein instead of charged-carbohydrate chemistry to recruit the host complement regulator, fH. The structure also indicates the molecular basis of the host-specificity of the interaction between fH and the meningococcus, and informs attempts to develop novel therapeutics and vaccines.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2670278/" 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/PMC2670278/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schneider, Muriel C -- Prosser, Beverly E -- Caesar, Joseph J E -- Kugelberg, Elisabeth -- Li, Su -- Zhang, Qian -- Quoraishi, Sadik -- Lovett, Janet E -- Deane, Janet E -- Sim, Robert B -- Roversi, Pietro -- Johnson, Steven -- Tang, Christoph M -- Lea, Susan M -- 083599/Wellcome Trust/United Kingdom -- G0400775/Medical Research Council/United Kingdom -- G0400775(71657)/Medical Research Council/United Kingdom -- G0500367/Medical Research Council/United Kingdom -- G0601195/Medical Research Council/United Kingdom -- G0601195(79743)/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2009 Apr 16;458(7240):890-3. doi: 10.1038/nature07769. Epub 2009 Feb 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Molecular Microbiology and Infection, Imperial College, London SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19225461" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, Bacterial/*chemistry/*metabolism ; Bacterial Proteins/*chemistry/*metabolism ; Binding Sites ; Carbohydrates/*chemistry ; Complement Factor H/*chemistry/immunology/*metabolism ; Crystallography, X-Ray ; Ligands ; Models, Molecular ; *Molecular Mimicry ; Neisseria meningitidis/chemistry/immunology/*metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; Protein Conformation ; Structure-Activity Relationship ; Substrate Specificity
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  • 93
    Publication Date: 2009-03-20
    Description: Calcium/calmodulin-dependent kinase II (CaMKII) plays a central part in long-term potentiation (LTP), which underlies some forms of learning and memory. Here we monitored the spatiotemporal dynamics of CaMKII activation in individual dendritic spines during LTP using two-photon fluorescence lifetime imaging microscopy, in combination with two-photon glutamate uncaging. Induction of LTP and associated spine enlargement in single spines triggered transient ( approximately 1 min) CaMKII activation restricted to the stimulated spines. CaMKII in spines was specifically activated by NMDA receptors and L-type voltage-sensitive calcium channels, presumably by nanodomain Ca(2+) near the channels, in response to glutamate uncaging and depolarization, respectively. The high degree of compartmentalization and channel specificity of CaMKII signalling allow stimuli-specific spatiotemporal patterns of CaMKII signalling and may be important for synapse-specificity of synaptic plasticity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2719773/" 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/PMC2719773/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Seok-Jin R -- Escobedo-Lozoya, Yasmin -- Szatmari, Erzsebet M -- Yasuda, Ryohei -- AS1398/Autism Speaks/ -- R01 MH080047/MH/NIMH NIH HHS/ -- R01 MH080047-01/MH/NIMH NIH HHS/ -- R01 MH080047-02/MH/NIMH NIH HHS/ -- R01MH08004/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Mar 19;458(7236):299-304. doi: 10.1038/nature07842.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Duke University Medical Center, Durham, North Carolina 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19295602" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/antagonists & inhibitors/metabolism ; Calcium Channels, L-Type/metabolism ; Calcium-Calmodulin-Dependent Protein Kinase Type 2/genetics/*metabolism ; Cell Line ; Cells, Cultured ; Chelating Agents/pharmacology ; Dendritic Spines/*enzymology/*physiology ; Enzyme Activation/drug effects ; Fluorescence ; Fluorescence Resonance Energy Transfer ; Glutamic Acid/metabolism ; Hippocampus/cytology ; Humans ; Kinetics ; Long-Term Potentiation/*physiology ; Photons ; Rats ; Receptors, N-Methyl-D-Aspartate/metabolism ; Synapses/metabolism ; Synaptic Potentials/physiology ; Time Factors
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  • 94
    Publication Date: 2009-08-08
    Description: The detection of methane on Mars has revived the possibility of past or extant life on this planet, despite the fact that an abiogenic origin is thought to be equally plausible. An intriguing aspect of the recent observations of methane on Mars is that methane concentrations appear to be locally enhanced and change with the seasons. However, methane has a photochemical lifetime of several centuries, and is therefore expected to have a spatially uniform distribution on the planet. Here we use a global climate model of Mars with coupled chemistry to examine the implications of the recently observed variations of Martian methane for our understanding of the chemistry of methane. We find that photochemistry as currently understood does not produce measurable variations in methane concentrations, even in the case of a current, local and episodic methane release. In contrast, we find that the condensation-sublimation cycle of Mars' carbon dioxide atmosphere can generate large-scale methane variations differing from those observed. In order to reproduce local methane enhancements similar to those recently reported, we show that an atmospheric lifetime of less than 200 days is necessary, even if a local source of methane is only active around the time of the observation itself. This implies an unidentified methane loss process that is 600 times faster than predicted by standard photochemistry. The existence of such a fast loss in the Martian atmosphere is difficult to reconcile with the observed distribution of other trace gas species. In the case of a destruction mechanism only active at the surface of Mars, destruction of methane must occur with an even shorter timescale of the order of approximately 1 hour to explain the observations. If recent observations of spatial and temporal variations of methane are confirmed, this would suggest an extraordinarily harsh environment for the survival of organics on the planet.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lefevre, Franck -- Forget, Francois -- England -- Nature. 2009 Aug 6;460(7256):720-3. doi: 10.1038/nature08228.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉LATMOS, UPMC Universite Paris 06, CNRS, Paris 75005, France. franck.lefevre@upmc.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19661912" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Carbon Dioxide/analysis ; Climate ; Electrochemistry ; Exobiology ; Extraterrestrial Environment/*chemistry ; *Mars ; Methane/*analysis ; Models, Chemical ; Photochemistry ; Time Factors
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  • 95
    Publication Date: 2009-01-23
    Description: Actin plays crucial parts in cell motility through a dynamic process driven by polymerization and depolymerization, that is, the globular (G) to fibrous (F) actin transition. Although our knowledge about the actin-based cellular functions and the molecules that regulate the G- to F-actin transition is growing, the structural aspects of the transition remain enigmatic. We created a model of F-actin using X-ray fibre diffraction intensities obtained from well oriented sols of rabbit skeletal muscle F-actin to 3.3 A in the radial direction and 5.6 A along the equator. Here we show that the G- to F-actin conformational transition is a simple relative rotation of the two major domains by about 20 degrees. As a result of the domain rotation, the actin molecule in the filament is flat. The flat form is essential for the formation of stable, helical F-actin. Our F-actin structure model provides the basis for understanding actin polymerization as well as its molecular interactions with actin-binding proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oda, Toshiro -- Iwasa, Mitsusada -- Aihara, Tomoki -- Maeda, Yuichiro -- Narita, Akihiro -- England -- Nature. 2009 Jan 22;457(7228):441-5. doi: 10.1038/nature07685.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉X-ray Structural Analysis Research Team, RIKEN SPring-8 Center, RIKEN Harima Institute, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan. toda@spring8.or.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158791" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/*chemistry/*metabolism ; Animals ; Biopolymers/chemistry/metabolism ; Cell Movement ; Glutamine/metabolism ; Hydrolysis ; Magnetics ; Models, Molecular ; Muscle Contraction ; Muscle, Skeletal/chemistry ; Protein Structure, Quaternary ; Protein Subunits/chemistry/metabolism ; Rabbits ; X-Ray Diffraction
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  • 96
    Publication Date: 2009-10-23
    Description: Millions of people regularly obtain insufficient sleep. Given the effect of sleep deprivation on our lives, understanding the cellular and molecular pathways affected by sleep deprivation is clearly of social and clinical importance. One of the major effects of sleep deprivation on the brain is to produce memory deficits in learning models that are dependent on the hippocampus. Here we have identified a molecular mechanism by which brief sleep deprivation alters hippocampal function. Sleep deprivation selectively impaired 3', 5'-cyclic AMP (cAMP)- and protein kinase A (PKA)-dependent forms of synaptic plasticity in the mouse hippocampus, reduced cAMP signalling, and increased activity and protein levels of phosphodiesterase 4 (PDE4), an enzyme that degrades cAMP. Treatment of mice with phosphodiesterase inhibitors rescued the sleep-deprivation-induced deficits in cAMP signalling, synaptic plasticity and hippocampus-dependent memory. These findings demonstrate that brief sleep deprivation disrupts hippocampal function by interfering with cAMP signalling through increased PDE4 activity. Thus, drugs that enhance cAMP signalling may provide a new therapeutic approach to counteract the cognitive effects of sleep deprivation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783639/" 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/PMC2783639/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vecsey, Christopher G -- Baillie, George S -- Jaganath, Devan -- Havekes, Robbert -- Daniels, Andrew -- Wimmer, Mathieu -- Huang, Ted -- Brown, Kim M -- Li, Xiang-Yao -- Descalzi, Giannina -- Kim, Susan S -- Chen, Tao -- Shang, Yu-Ze -- Zhuo, Min -- Houslay, Miles D -- Abel, Ted -- 84256/Canadian Institutes of Health Research/Canada -- AG017628/AG/NIA NIH HHS/ -- G0600765/Medical Research Council/United Kingdom -- GM07517/GM/NIGMS NIH HHS/ -- HL060287/HL/NHLBI NIH HHS/ -- HL07953/HL/NHLBI NIH HHS/ -- P01 AG017628/AG/NIA NIH HHS/ -- P01 AG017628-080006/AG/NIA NIH HHS/ -- P50 HL060287/HL/NHLBI NIH HHS/ -- P50 HL060287-100006/HL/NHLBI NIH HHS/ -- England -- Nature. 2009 Oct 22;461(7267):1122-5. doi: 10.1038/nature08488.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19847264" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Colforsin/pharmacology ; Cyclic AMP/*metabolism ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Cyclic Nucleotide Phosphodiesterases, Type 4/metabolism ; Hippocampus/drug effects/enzymology/*metabolism/physiology ; Long-Term Potentiation/drug effects ; Male ; Memory/drug effects/physiology ; Mice ; Mice, Inbred C57BL ; Neuronal Plasticity ; Phosphodiesterase 4 Inhibitors ; Rolipram/pharmacology ; *Second Messenger Systems/drug effects ; Sleep Deprivation/*physiopathology ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 97
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    Nature Publishing Group (NPG)
    Publication Date: 2009-06-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leigh Mascarelli, Amanda -- England -- Nature. 2009 Jun 11;459(7248):770-3. doi: 10.1038/459770a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19516316" target="_blank"〉PubMed〈/a〉
    Keywords: Altitude ; Archaea/isolation & purification/*metabolism ; Atlantic Ocean ; Bacteria/isolation & purification/*metabolism ; *Environment ; Exobiology/trends ; Geologic Sediments/*microbiology ; Methane/metabolism ; Origin of Life ; *Soil Microbiology ; South Africa ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 98
    Publication Date: 2009-12-04
    Description: External climate forcings-such as long-term changes in solar insolation-generate different climate responses in tropical and high latitude regions. Documenting the spatial and temporal variability of past climates is therefore critical for understanding how such forcings are translated into regional climate variability. In contrast to the data-rich middle and high latitudes, high-quality climate-proxy records from equatorial regions are relatively few, especially from regions experiencing the bimodal seasonal rainfall distribution associated with twice-annual passage of the Intertropical Convergence Zone. Here we present a continuous and well-resolved climate-proxy record of hydrological variability during the past 25,000 years from equatorial East Africa. Our results, based on complementary evidence from seismic-reflection stratigraphy and organic biomarker molecules in the sediment record of Lake Challa near Mount Kilimanjaro, reveal that monsoon rainfall in this region varied at half-precessional ( approximately 11,500-year) intervals in phase with orbitally controlled insolation forcing. The southeasterly and northeasterly monsoons that advect moisture from the western Indian Ocean were strengthened in alternation when the inter-hemispheric insolation gradient was at a maximum; dry conditions prevailed when neither monsoon was intensified and modest local March or September insolation weakened the rain season that followed. On sub-millennial timescales, the temporal pattern of hydrological change on the East African Equator bears clear high-northern-latitude signatures, but on the orbital timescale it mainly responded to low-latitude insolation forcing. Predominance of low-latitude climate processes in this monsoon region can be attributed to the low-latitude position of its continental regions of surface air flow convergence, and its relative isolation from the Atlantic Ocean, where prominent meridional overturning circulation more tightly couples low-latitude climate regimes to high-latitude boundary conditions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Verschuren, Dirk -- Sinninghe Damste, Jaap S -- Moernaut, Jasper -- Kristen, Iris -- Blaauw, Maarten -- Fagot, Maureen -- Haug, Gerald H -- CHALLACEA project members -- England -- Nature. 2009 Dec 3;462(7273):637-41. doi: 10.1038/nature08520.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Limnology Unit, Department of Biology, Ghent University, Ledeganckstraat 35, 9000 Gent, Belgium. dirk.verschuren@UGent.be〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19956257" target="_blank"〉PubMed〈/a〉
    Keywords: Africa, Eastern ; Climate Change ; Geologic Sediments/*chemistry ; *Rain ; *Seasons ; Time Factors ; *Tropical Climate
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 99
    Publication Date: 2009-12-25
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3873764/" 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/PMC3873764/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Christie, Peter J -- R01 GM048746/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Dec 24;462(7276):992-4. doi: 10.1038/462992b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20033031" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/chemistry/*metabolism ; Conjugation, Genetic/*physiology ; DNA, Bacterial/*metabolism ; Escherichia coli Proteins/*chemistry/*metabolism ; Models, Molecular ; Protein Structure, Quaternary
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 100
    Publication Date: 2009-06-26
    Description: Myogenic potential, survival and expansion of mammalian muscle progenitors depend on the myogenic determinants Pax3 and Pax7 embryonically, and Pax7 alone perinatally. Several in vitro studies support the critical role of Pax7 in these functions of adult muscle stem cells (satellite cells), but a formal demonstration has been lacking in vivo. Here we show, through the application of inducible Cre/loxP lineage tracing and conditional gene inactivation to the tibialis anterior muscle regeneration paradigm, that, unexpectedly, when Pax7 is inactivated in adult mice, mutant satellite cells are not compromised in muscle regeneration, they can proliferate and reoccupy the sublaminal satellite niche, and they are able to support further regenerative processes. Dual adult inactivation of Pax3 and Pax7 also results in normal muscle regeneration. Multiple time points of gene inactivation reveal that Pax7 is only required up to the juvenile period when progenitor cells make the transition into quiescence. Furthermore, we demonstrate a cell-intrinsic difference between neonatal progenitor and adult satellite cells in their Pax7-dependency. Our finding of an age-dependent change in the genetic requirement for muscle stem cells cautions against inferring adult stem-cell biology from embryonic studies, and has direct implications for the use of stem cells from hosts of different ages in transplantation-based therapy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2767162/" 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/PMC2767162/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lepper, Christoph -- Conway, Simon J -- Fan, Chen-Ming -- R01 HL060714/HL/NHLBI NIH HHS/ -- R01 HL060714-02/HL/NHLBI NIH HHS/ -- R01 HL060714-11/HL/NHLBI NIH HHS/ -- England -- Nature. 2009 Jul 30;460(7255):627-31. doi: 10.1038/nature08209.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Embryology, Carnegie Institution, 3520 San Martin Drive, Baltimore, Maryland 21218, USA. lepper@ciwemb.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19554048" target="_blank"〉PubMed〈/a〉
    Keywords: Aging ; Animals ; Cell Proliferation ; Cells, Cultured ; Gene Expression Regulation, Developmental ; Mice ; Muscle, Skeletal/cytology/growth & development ; Mutation ; PAX7 Transcription Factor/metabolism ; Paired Box Transcription Factors/metabolism ; Regeneration/genetics/*physiology ; Satellite Cells, Skeletal Muscle/*cytology/drug effects/*physiology ; Selective Estrogen Receptor Modulators/pharmacology ; Stem Cells/*cytology/drug effects/*physiology ; Tamoxifen/pharmacology ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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