4,784 research outputs found
Biology's next revolution
The interpretation of recent environmental genomics data exposes the
far-reaching influence of horizontal gene transfer, and is changing our basic
concepts of organism, species and evolution itself.Comment: Slightly expanded version of invited essay published in Nature. The
most important addition is a complete set of references that could not be
included in the published version due to space limitations and acknowledgment
of the grant that supported our wor
Characterizing Scales of Genetic Recombination and Antibiotic Resistance in Pathogenic Bacteria Using Topological Data Analysis
Pathogenic bacteria present a large disease burden on human health. Control
of these pathogens is hampered by rampant lateral gene transfer, whereby
pathogenic strains may acquire genes conferring resistance to common
antibiotics. Here we introduce tools from topological data analysis to
characterize the frequency and scale of lateral gene transfer in bacteria,
focusing on a set of pathogens of significant public health relevance. As a
case study, we examine the spread of antibiotic resistance in Staphylococcus
aureus. Finally, we consider the possible role of the human microbiome as a
reservoir for antibiotic resistance genes.Comment: 12 pages, 6 figures. To appear in AMT 2014 Special Session on
Advanced Methods of Interactive Data Mining for Personalized Medicin
Identification of Birds through DNA Barcodes
Short DNA sequences from a standardized region of the genome provide a DNA barcode for identifying species. Compiling a public library of DNA barcodes linked to named specimens could provide a new master key for identifying species, one whose power will rise with increased taxon coverage and with faster, cheaper sequencing. Recent work suggests that sequence diversity in a 648-bp region of the mitochondrial gene, cytochrome c oxidase I (COI), might serve as a DNA barcode for the identification of animal species. This study tested the effectiveness of a COI barcode in discriminating bird species, one of the largest and best-studied vertebrate groups. We determined COI barcodes for 260 species of North American birds and found that distinguishing species was generally straightforward. All species had a different COI barcode(s), and the differences between closely related species were, on average, 18 times higher than the differences within species. Our results identified four probable new species of North American birds, suggesting that a global survey will lead to the recognition of many additional bird species. The finding of large COI sequence differences between, as compared to small differences within, species confirms the effectiveness of COI barcodes for the identification of bird species. This result plus those from other groups of animals imply that a standard screening threshold of sequence difference (10Ć average intraspecific difference) could speed the discovery of new animal species. The growing evidence for the effectiveness of DNA barcodes as a basis for species identification supports an international exercise that has recently begun to assemble a comprehensive library of COI sequences linked to named specimens
Optimality Properties of a Proposed Precursor to the Genetic Code
We calculate the optimality of a doublet precursor to the canonical genetic
code with respect to mitigating the effects of point mutations and compare our
results to corresponding ones for the canonical genetic code. We find that the
proposed precursor has much less optimality than that of the canonical code.
Our results render unlikely the notion that the doublet precursor was an
intermediate state in the evolution of the canonical genetic code. These
findings support the notion that code optimality reflects evolutionary
dynamics, and that if such a doublet code originally had a biochemical
significance, it arose before the emergence of translation
The Genetic Code as a Periodic Table: Algebraic Aspects
The systematics of indices of physico-chemical properties of codons and amino
acids across the genetic code are examined. Using a simple numerical labelling
scheme for nucleic acid bases, data can be fitted as low-order polynomials of
the 6 coordinates in the 64-dimensional codon weight space. The work confirms
and extends recent studies by Siemion of amino acid conformational parameters.
The connections between the present work, and recent studies of the genetic
code structure using dynamical symmetry algebras, are pointed out.Comment: 26 pages Latex, 10 figures (4 ps, 6 Tex). Refereed version, small
changes to discussion (conclusion unaltered). Minor alterations to format of
figures and tables. To appear in BioSystem
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