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Author Robinson, M.S.
Title Forty Years of Clathrin-coated Vesicles Type Journal Article
Year 2015 Publication Abbreviated Journal Traffic
Volume 16 Issue 12 Pages 1210-1238
Keywords JHU, CME, review
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Notes disease information Approved no
Call Number AG @ matthewjvarga @ Serial 46711
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Author Manuel, A.P.; Lambert, J.; Woodside, M.T.
Title Reconstructing folding energy landscapes from splitting probability analysis of single-molecule trajectories Type Journal Article
Year 2015 Publication Abbreviated Journal Proc. Natl. Acad. Sci. U.S.A.
Volume 112 Issue 23 Pages 7183-7188
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Call Number AG @ matthewjvarga @ Serial 46816
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Author Abraham, M.J.; Murtola, T.; Schulz, R.; P\’all, S.\’ard; Smith, J.C.; Hess, B.; Lindahl, E.
Title GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers Type Journal Article
Year 2015 Publication Abbreviated Journal SoftwareX
Volume 1 Issue Pages 19-25
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Call Number AG @ matthewjvarga @ Serial 46956
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Author Olivera-Couto, A.; Salzman, V.; Mailhos, M.; Digman, M. A.; Gratton, E.; Aguilar, P. S.
Title Eisosomes Are Dynamic Plasma Membrane Domains Showing Pil1-Lsp1 Heteroligomer Binding Equilibrium Type Journal Article
Year 2015 Publication Abbreviated Journal Biophysical Journal
Volume 108 Issue 7 Pages 1633-1644
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Notes Times cited: 14 Approved no
Call Number AG @ matthewjvarga @ Serial 46960
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Author Bussi, G.; Branduardi, D.
Title Free-Energy Calculations with Metadynamics: Theory and Practice Type Book Chapter
Year 2015 Publication Reviews in Computational Chemistry: Reviews in Computational Chemistry Volume 28 Abbreviated Journal
Volume Reviews in Computational Chemistry: Reviews in Com Issue Pages 1-49
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Publisher John Wiley & Sons, Inc Place of Publication Hoboken, NJ, USA Editor Libkowitz, K.B.; Abby, L.P.
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ISSN (up) ISBN 9781118889886 Medium
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Notes Times cited: 21 Approved no
Call Number AG @ matthewjvarga @ Serial 46961
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Author Richards, S.; Aziz, N.; Bale, S.; Bick, D.; Das, S.; Gastier-Foster, J.; Grody, W.W.; Hegde, M.; Lyon, E.; Spector, E.; Voelkerding, K.; Rehm, H.L.
Title Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology Type Journal Article
Year 2015 Publication Abbreviated Journal Genetics In Medicine
Volume 17 Issue Pages 405
Keywords guidelines
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Call Number AG @ matthewjvarga @ Serial 47096
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Author Euro, L.; Konovalova, S.; Asin-Cayuela, J.; Tulinius, M.; Griffin, H.; Horvath, R.; Taylor, R.W.; Chinnery, P.F.; Schara, U.; Thorburn, D.R.; Suomalainen, A.; Chihade, J.; Tyynismaa, H.
Title Structural modeling of tissue-specific mitochondrial alanyl-tRNA synthetase (AARS2) defects predicts differential effects on aminoacylation Type Journal Article
Year 2015 Publication Abbreviated Journal Frontiers in Genetics
Volume 6 Issue Pages 21
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Abstract The accuracy of mitochondrial protein synthesis is dependent on the coordinated action of nuclear-encoded mitochondrial aminoacyl-tRNA synthetases (mtARSs) and the mitochondrial DNA-encoded tRNAs. The recent advances in whole-exome sequencing have revealed the importance of the mtARS proteins for mitochondrial pathophysiology since nearly every nuclear gene for mtARS (out of 19) is now recognized as a disease gene for mitochondrial disease. Typically, defects in each mtARS have been identified in one tissue-specific disease, most commonly affecting the brain, or in one syndrome. However, mutations in the AARS2 gene for mitochondrial alanyl-tRNA synthetase (mtAlaRS) have been reported both in patients with infantile-onset cardiomyopathy and in patients with childhood to adulthood-onset leukoencephalopathy. We present here an investigation of the effects of the described mutations on the structure of the synthetase, in an effort to understand the tissue-specific outcomes of the different mutations. The mtAlaRS differs from the other mtARSs because in addition to the aminoacylation domain, it has a conserved editing domain for deacylating tRNAs that have been mischarged with incorrect amino acids. We show that the cardiomyopathy phenotype results from a single allele, causing an amino acid change R592W in the editing domain of AARS2, whereas the leukodystrophy mutations are located in other domains of the synthetase. Nevertheless, our structural analysis predicts that all mutations reduce the aminoacylation activity of the synthetase, because all mtAlaRS domains contribute to tRNA binding for aminoacylation. According to our model, the cardiomyopathy mutations severely compromise aminoacylation whereas partial activity is retained by the mutation combinations found in the leukodystrophy patients. These predictions provide a hypothesis for the molecular basis of the distinct tissue-specific phenotypic outcomes.
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Call Number AG @ matthewjvarga @ Serial 47113
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Author Plattner, N.; Noé, F.
Title Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models Type Journal Article
Year 2015 Publication Abbreviated Journal Nature Communications
Volume 6 Issue Pages 7653
Keywords milestoning,structural biology,flexibility project
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Call Number AG @ matthewjvarga @ Serial 47157
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Author Birch, J. L.
Title A revision of infrageneric classification in Astelia Banks & Sol. ex R.Br. (Asteliaceae) Type Journal Article
Year 2015 Publication PhytoKeys Abbreviated Journal
Volume 52 Issue Pages 105-132
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Abstract Systematic investigations and phylogenetic analyses have indicated that Astelia, as currently circumscribed, is paraphyletic, with Collospermum nested within it. Further, A. subgenus Astelia is polyphyletic, and A. subgenera Asteliopsis and Tricella are paraphyletic, as currently circumscribed. Revision of the subgeneric classification of Astelia is warranted to ensure classification accurately reflects the evolutionary history of these taxa. Collospermum is relegated to synonymy within Astelia. Astelia is dioecious or polygamodioecious, with a superior ovary, anthers dorsi- or basifixed, pistillodes or pistils that have a single short or poorly defined style, a 3 lobed stigma, and fleshy uni- or trilocular fruit with funicular hairs that are poorly to well developed. Astelia subgenus Collospermum (Skottsb.) Birch is described. A key to Astelia sections is provided. Astelia hastata Colenso, A. montana Seem., and A. microsperma Colenso pro parte are resurrected and the new combination A. samoense (Skottsb.) Birch, comb. nov. is made.
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Publisher Pensoft Place of Publication Editor
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Call Number NYBG @ sthackurdeen @ Serial 42161
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Author Pillon, Y.; Lucas, E.; Johansen, J. B.; Sakishima, T.; Hall, B.; Geib, S. M.; Stacy, E. A.
Title An expanded Metrosideros (Myrtaceae) to include Carpolepis and Tepualia based on nuclear genes Type Journal Article
Year 2015 Publication Systematic Botany Abbreviated Journal
Volume 40 Issue 3 Pages 782-790
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Abstract The genus Metrosideros (Myrtaceae) comprises 50-60 species, found largely across the Pacific Islands. The relationships within this genus, including the circumscriptions of the subgenera Mearnsia and Metrosideros and their relationships with the other members of the tribe Metrosidereae, namely the New Caledonian endemic genus Carpolepis and the South American Tepualia, are poorly understood. Phylogenetic analyses were carried out using previously published ITS sequences, covering most species of the tribe, and new sequences of five single-copy nuclear genes on a reduced sampling. The independent and combined analyses of the five nuclear genes using a range of approaches, including Bayesian single-gene, concatenated (MrBayes), concordance (BUCKy) and coalescent (*BEAST) analyses, yielded different topologies, indicating important conflicts among individual gene phylogenetic signals. The deep relationships within the tribe Metrosidereae remain poorly resolved, but our results indicate that the species of Carpolepis and Tepualia are likely nested in the genus Metrosideros. A broad circumscription of the genus Metrosideros is therefore adopted, and the new combinations Metrosideros laurifolia var. demonstrans, Metrosideros tardiflora and Metrosideros vitiensis are here published.
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Call Number NYBG @ sthackurdeen @ Serial 42390
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