7,419 research outputs found
Evolution of genes and repeats in the Nimrod superfamily
The recently identified Nimrod superfamily is characterized by the presence of a special type of EGF repeat, the NIM repeat, located right after a typical CCXGY/W amino acid motif. On the basis of structural features, nimrod genes can be divided into three types. The proteins encoded by Draper-type genes have an EMI domain at the N-terminal part and only one copy of the NIM motif, followed by a variable number of EGF-like repeats. The products of Nimrod B-type and Nimrod C-type genes (including the eater gene) have different kinds of N-terminal domains, and lack EGF-like repeats but contain a variable number of NIM repeats. Draper and Nimrod C-type (but not Nimrod B-type) proteins carry a transmembrane domain. Several members of the superfamily were claimed to function as receptors in phagocytosis and/or binding of bacteria, which indicates an important role in the cellular immunity and the elimination of apoptotic cells. In this paper, the evolution of the Nimrod superfamily is studied with various methods on the level of genes and repeats. A hypothesis is presented in which the NIM repeat, along with the EMI domain, emerged by structural reorganizations at the end of an EGF-like repeat chain, suggesting a mechanism for the formation of novel types of repeats. The analyses revealed diverse evolutionary patterns in the sequences containing multiple NIM repeats. Although in the Nimrod B and Nimrod C proteins show characteristics of independent evolution, many internal NIM repeats in Eater sequences seem to have undergone concerted evolution. An analysis of the nimrod genes has been performed using phylogenetic and other methods and an evolutionary scenario of the origin and diversification of the Nimrod superfamily is proposed. Our study presents an intriguing example how the evolution of multigene families may contribute to the complexity of the innate immune response
Molecular characterization of Trichomonas gallinae isolates recovered from the Canadian Maritime provinces’ wild avifauna reveals the presence of the genotype responsible for the European finch trichomonosis epidemic and additional strains
Finch trichomonosis, caused by Trichomonas gallinae, emerged in the Canadian Maritime provinces in 2007 and has since caused ongoing mortality in regional purple finch (Carpodacus purpureus) and American goldfinch (Carduelis tristis) populations. Trichomonas gallinae was isolated from (1) finches and rock pigeons (Columbia livia) submitted for post-mortem or live-captured at bird feeding sites experiencing trichomonosis mortality; (2) bird seed at these same sites; and (3) rock pigeons live-captured at known roosts or humanely killed. Isolates were characterized using internal transcribed spacer (ITS) region and iron hydrogenase (Fe-hyd) gene sequences. Two distinct ITS types were found. Type A was identical to the UK finch epidemic strain and was isolated from finches and a rock pigeon with trichomonosis; apparently healthy rock pigeons and finches; and bird seed at an outbreak site. Type B was obtained from apparently healthy rock pigeons. Fe-hyd sequencing revealed six distinct subtypes. The predominant subtype in both finches and the rock pigeon with trichomonosis was identical to the UK finch epidemic strain A1. Single nucleotide polymorphisms in Fe-hyd sequences suggest there is fine-scale variation amongst isolates and that finch trichomonosis emergence in this region may not have been caused by a single spill-over event
Molecular and morphometric variation in European populations of the articulate brachiopod <i>Terebeatulina retusa</i>
Molecular and morphometric variation within and between population samples of the articulate brachiopod <i>Terebratulina</i> spp., collected in 1985-1987 from a Norwegian fjord, sea lochs and costal sites in western Scotland, the southern English Channel (Brittany) and the western Mediterranean, were measured by the analysis of variation in the lengths of mitochondrial DNA (mtDNA) fragments produced by digestion with nine restriction endonucleases and by multivariate statistical analysis of six selected morphometric parameters. Nucleotide difference within each population sample was high. Nucleotide difference between population samples from the Scottish sites, both those that are tidally contiguous and those that appear to be geographically isolated, were not significantly different from zero. Nucleotide differences between the populations samples from Norway, Brittany, Scotland and the western Mediterranean were also very low. Morphometric analysis confirmed the absence of substantial differentiation
Levels of genetic polymorphism: marker loci versus quantitative traits
Species are the units used to measure ecological diversity and alleles are the units of genetic diversity. Genetic variation within and among species has been documented most extensively using allozyme electrophoresis. This reveals wide differences in genetic variability within, and genetic distances among, species, demonstrating that species are not equivalent units of diversity. The extent to which the pattern observed for allozymes can be used to infer patterns of genetic variation in quantitative traits depends on the forces generating and maintaining variability. Allozyme variation is probably not strictly neutral but, nevertheless, heterozygosity is expected to be influenced by population size and genetic distance will be affected by time since divergence. The same is true for quantitative traits influenced by many genes and under weak stabilizing selection. However, the limited data available suggest that allozyme variability is a poor predictor of genetic variation in quantitative traits within populations. It is a better predictor of general phenotypic divergence and of postzygotic isolation between populations or species, but is only weakly correlated with prezygotic isolation. Studies of grasshopper and planthopper mating signal variation and assortative mating illustrate how these characters evolve independently of general genetic and morphological variation. The role of such traits in prezygotic isolation, and hence speciation, means that they will contribute significantly to the diversity of levels of genetic variation within and among species
Chloroplast microsatellites: measures of genetic diversity and the effect of homoplasy
Chloroplast microsatellites have been widely used in population genetic
studies of conifers in recent years. However, their haplotype configurations
suggest that they could have high levels of homoplasy, thus limiting the power
of these molecular markers. A coalescent-based computer simulation was used to
explore the influence of homoplasy on measures of genetic diversity based on
chloroplast microsatellites. The conditions of the simulation were defined to
fit isolated populations originating from the colonization of one single
haplotype into an area left available after a glacial retreat. Simulated data
were compared with empirical data available from the literature for a species
of Pinus that has expanded north after the Last Glacial Maximum. In the
evaluation of genetic diversity, homoplasy was found to have little influence
on Nei's unbiased haplotype diversity (H(E)) while Goldstein's genetic distance
estimates (D2sh) were much more affected. The effect of the number of
chloroplast microsatellite loci for evaluation of genetic diversity is also
discussed
Hyperbolic Geometry of Complex Networks
We develop a geometric framework to study the structure and function of
complex networks. We assume that hyperbolic geometry underlies these networks,
and we show that with this assumption, heterogeneous degree distributions and
strong clustering in complex networks emerge naturally as simple reflections of
the negative curvature and metric property of the underlying hyperbolic
geometry. Conversely, we show that if a network has some metric structure, and
if the network degree distribution is heterogeneous, then the network has an
effective hyperbolic geometry underneath. We then establish a mapping between
our geometric framework and statistical mechanics of complex networks. This
mapping interprets edges in a network as non-interacting fermions whose
energies are hyperbolic distances between nodes, while the auxiliary fields
coupled to edges are linear functions of these energies or distances. The
geometric network ensemble subsumes the standard configuration model and
classical random graphs as two limiting cases with degenerate geometric
structures. Finally, we show that targeted transport processes without global
topology knowledge, made possible by our geometric framework, are maximally
efficient, according to all efficiency measures, in networks with strongest
heterogeneity and clustering, and that this efficiency is remarkably robust
with respect to even catastrophic disturbances and damages to the network
structure
Genetic characterization of Barbari goats using microsatellite markers
Genetic variation in Barbari goats, a highly prolific breed distributed widely in the northern part of India, known for better milk and meat quality, was studied as a part of genetic characterization and conservation. The genomic DNA from 50 unrelated Barbari goats were amplified via PCR with a panel of 21 microsatellite markers, and resolved through 6 per cent denaturing polyacrylamide gel electrophoresis followed by silver staining. The number of alleles ranged from 4 to 11, with allele sizes ranging from 88 to 220 bp. The distribution of allele frequencies was between 0.0104 and 0.5208. Polymorphism information content varied from 0.5563 to 0.8348. The population was not in Hardy-Weinberg equilibrium for all except two microsatellite loci (ILSTS044 and ILSTS060). The observed heterozygosity ranged from 0.8478 to 1.0000 while the expected heterozygosity ranged from 0.6208 to 0.8509. Based on the results of the present study, there is a good scope for exploiting the genetic variability in the Barbari goats for further improvement of performance
Lossof a chloroplast encoded function could influence species range in kelp
Kelps are important providers and constituents of marine ecological niches, the
coastal kelp forests. Kelp species have differing distribution ranges, but mainly thrive
in temperate and arctic regions. Although the principal factors determining biogeographic
distribution ranges are known, genomics could provide additional answers to
this question.
We sequenced DNA from two Laminaria species with contrasting distribution
ranges, Laminaria digitata and Laminaria solidungula. Laminaria digitata is found in the
Northern Atlantic with a southern boundary in Brittany (France) or Massachusetts
(USA) and a northern boundary in the Arctic, whereas L. solidungula is endemic to the
Arctic only. From the raw reads of DNA, we reconstructed both chloroplast genomes
and annotated them. A concatenated data set of all available brown algae chloroplast
sequences was used for the calculation of a robust phylogeny, and sequence variations
were analyzed.
The two Laminaria chloroplast genomes are collinear to previously analyzed kelp
chloroplast genomes with important exceptions. Rearrangements at the inverted repeat
regions led to the pseudogenization of ycf37 in L. solidungula, a gene possibly
required under high light conditions. This defunct gene might be one of the reasons
why the habitat range of L. solidungula is restricted to lowlight sublittoral sites in the
Arctic. The inheritance pattern of single nucleotide polymorphisms suggests incomplete
lineage sorting of chloroplast genomes in kelp species.
Our analysis of kelp chloroplast genomes shows that not only evolutionary information
could be gleaned from sequence data. Concomitantly, those sequences can
also tell us something about the ecological conditions which are required for species
well‐being
Poisson structures for reduced non-holonomic systems
Borisov, Mamaev and Kilin have recently found certain Poisson structures with
respect to which the reduced and rescaled systems of certain non-holonomic
problems, involving rolling bodies without slipping, become Hamiltonian, the
Hamiltonian function being the reduced energy. We study further the algebraic
origin of these Poisson structures, showing that they are of rank two and
therefore the mentioned rescaling is not necessary. We show that they are
determined, up to a non-vanishing factor function, by the existence of a system
of first-order differential equations providing two integrals of motion. We
generalize the form of that Poisson structures and extend their domain of
definition. We apply the theory to the rolling disk, the Routh's sphere, the
ball rolling on a surface of revolution, and its special case of a ball rolling
inside a cylinder.Comment: 22 page
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