ORCID Profile
0000-0002-9646-4322
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Publisher: American Society for Microbiology
Date: 15-04-2017
DOI: 10.1128/JVI.02275-16
Abstract: Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between in idual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification. We reinvestigate whether the structure-based classification for viral coat proteins making icosahedral virus capsids is in fact supported by previously undetected sequence similarity. Since codon choices can influence nascent protein folding cotranslationally, we searched for both amino acid and nucleotide sequence similarity. To demonstrate the sensitivity of the approach, we identify a candidate gene for the pandoravirus capsid protein. We show that the structure-based classification is strongly supported by amino acid and also nucleotide sequence similarities, suggesting that the similarities are due to common descent. The correspondence between structure-based and sequence-based analyses of the same proteins shown here allow them to be used in future analyses of the relationship between linear sequence information and macromolecular function, as well as between linear sequence and protein folds. IMPORTANCE Viral capsids protect nucleic acid genomes, which in turn encode capsid proteins. This tight coupling of protein shell and nucleic acids, together with strong functional constraints on capsid protein folding and architecture, leads to the hypothesis that capsid protein-coding nucleotide sequences may retain signatures of ancient viral evolution. We have been able to show that this is indeed the case, using the major capsid proteins of viruses forming icosahedral capsids. Importantly, we detected similarity at the nucleotide level between capsid protein-coding regions from viruses infecting cells belonging to all three domains of life, reproducing a previously established structure-based classification of icosahedral viral capsids.
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 2014
Publisher: Frontiers Media SA
Date: 14-07-2014
Publisher: Mathematical Society of Japan (Project Euclid)
Date: 25-07-2023
Publisher: Elsevier BV
Date: 06-2015
Publisher: American Physical Society (APS)
Date: 15-12-1990
Publisher: Frontiers Media SA
Date: 25-09-2014
Publisher: European Mathematical Society - EMS - Publishing House GmbH
Date: 08-2009
Publisher: Proceedings of the National Academy of Sciences
Date: 17-11-2015
Abstract: All genes are duplicated by whole-genome duplication (WGD), reverting in number over time, but the actual timing of genome reshaping through gene loss remains poorly understood. We estimated the spatiotemporal loss ersistence pattern of 6,892 gene lineage pairs after the teleost-specific WGD, using careful orthology assignment and a reliable time-calibrated tree. We found that massive gene loss did occur in the first 60 My, mainly due to events involving the simultaneous loss of multiple redundant genes, and the rate of loss then slowed to an approximately constant level for the subsequent 250 My. Similar genomic gene arrangements within teleosts imply that rapid gene loss led to the reshaping of the teleost genomes before their major ergence.
Publisher: Mathematical Institute, Tohoku University
Date: 2007
Publisher: World Scientific Pub Co Pte Lt
Date: 03-1996
Publisher: Informa UK Limited
Date: 2003
Publisher: Springer Science and Business Media LLC
Date: 13-05-2022
DOI: 10.1057/S41599-022-01177-6
Abstract: In this empirical study, we show that the shape of the distribution of relative prices of basic food and drink items has been extraordinarily robust, from ancient Egypt to modern Chile, whether there be peace and economic stability, war, revolution, depression or hyperinflation. The width of the distribution of log prices does not deviate significantly from a specific value, which would appear to be universal. This property of relative prices has not changed over the past three thousand years, wherever there have been food markets, despite great differences in culture, institutions, and the particular food and drink items consumed.
Publisher: Public Library of Science (PLoS)
Date: 12-04-2012
Publisher: American Chemical Society (ACS)
Date: 31-10-2003
DOI: 10.1021/CI034095A
Abstract: The large-scale 3D structure of a protein can be represented by the polygonal curve through the carbon alpha atoms of the protein backbone. We introduce an algorithm for computing the average number of times that a given configuration of crossings on such polygonal curves is seen, the average being taken over all directions in space. Hereby, we introduce a new family of global geometric measures of protein structures, which we compare with the so-called generalized Gauss integrals.
Publisher: Elsevier BV
Date: 07-1990
Publisher: Elsevier BV
Date: 06-1994
Publisher: World Scientific Pub Co Pte Lt
Date: 09-2010
DOI: 10.1142/S0218339010003561
Abstract: We consider a two-patch SI model of integrated pest management with dispersal of both susceptible and infective pests between patches. A biological control, consisting of the periodic release of infective pests and a chemical control, consisting of periodic and impulsive pesticide spraying, are employed in order to maintain the size of the pest population below an economically acceptable level. It is assumed that the spread of the disease which is inflicted on the pest population through the use of the biological control is characterized by a nonlinear force of infection expressed in an abstract form. A sufficient condition for the local stability of the susceptible pest-eradication periodic solution is found using Floquet theory for periodic systems of ordinary differential equations, an analysis of the influence of dispersal between patches being performed for several particular cases. Our numerical simulations indicate that an increase in the amount but not in the frequency of pesticide use may not result in control. We also show that patches which are stable in isolation can be destabilized by dispersal between patches.
Publisher: Springer Science and Business Media LLC
Date: 1995
Publisher: Elsevier BV
Date: 06-2015
DOI: 10.1016/J.JTBI.2015.03.025
Abstract: Genome composition analysis of di-, tri- and tetra-nucleotide frequencies is known to be evolutionarily informative, and useful in metagenomic studies, where binning of raw sequence data is often an important first step. Patterns appearing in genome composition analysis may be due to evolutionary processes or purely mathematical relations. For ex le, the total number of dinucleotides in a sequence is equal to the sum of the in idual totals of the sixteen types of dinucleotide, and this is entirely independent of any assumptions made regarding mutation or selection, or indeed any physical or chemical process. Before any statistical analysis can be attempted, a knowledge of all necessary mathematical relations is required. I show that 25% of di-, tri- and tetra-nucleotide frequencies can be written as simple sums and differences of the remainder. The vast majority of organisms have circular genomes, for which these relations are exact and necessary. In the case of linear molecules, the absolute error is very nearly zero, and does not grow with contiguous sequence length. As a result of the new, necessary relations presented here, the foundations of the statistical analysis of di-, tri- and tetra-nucleotide frequencies, and k-mer analysis in general, need to be revisited.
Publisher: Springer Science and Business Media LLC
Date: 23-11-2000
Publisher: Tokyo Journal of Mathematics
Date: 06-2023
Publisher: Informa UK Limited
Date: 2004
Publisher: Springer Science and Business Media LLC
Date: 08-07-2023
Publisher: American Physical Society (APS)
Date: 15-03-1992
Publisher: Elsevier BV
Date: 1992
Publisher: Informa UK Limited
Date: 2005
Publisher: IOP Publishing
Date: 05-03-1990
Publisher: Birkhäuser Basel
Date: 1998
Publisher: Association for Computing Machinery (ACM)
Date: 02-2003
Abstract: An interactive mathematics textbook presupposes the existence of a language in which it may be written. We approach the specification of such a language from the point of view of what functions it must perform. Special attention needs to be paid to a clear separation of the roles of the author and the reader. We present ex les created with the help of a prototype interactive viewer.
Publisher: American Mathematical Society (AMS)
Date: 27-05-2006
DOI: 10.1090/S0025-5718-06-01924-7
Abstract: Numerical evidence is presented which strongly suggests that “Jacobi’s last geometric statement"—that the conjugate locus from a point has exactly four cusps and the corresponding cut locus consists of only one topological segment—holds for compact real analytic Liouville surfaces diffeomorphic to S 2 S^2 if the Gaussian curvature is everywhere positive and has exactly six critical points, these being two saddles, two global minima, and two global maxima (as is the case for an ellipsoid). Our experiments suggest that this is a sufficient rather than a necessary condition. Furthermore, for compact real analytic Liouville surfaces diffeomorphic to S 2 S^2 upon which the Gaussian curvature can be negative but has exactly six critical points, these being two saddles, two global minima, and two global maxima, it appears that the cut locus is always a subarc of a line given by x 1 = c o n s t x_1=\mathrm {const} or x 2 = c o n s t x_2=\mathrm {const} , where ( x 1 , x 2 ) (x_1,x_2) are canonical coordinates with respect to which the metric has the form ( f 1 ( x 1 ) + f 2 ( x 2 ) ) ( d x 1 2 + d x 2 2 ) (f_1(x_1)+f_2(x_2))(dx_1^2+dx_2^2) . In the case of an ellipsoid, these curves are lines of curvature.
Publisher: Informa UK Limited
Date: 24-04-2014
Location: No location found
No related grants have been discovered for Robert Sinclair.