Search results for "Molecular evolution"

An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides

2018

Infection with human BK polyomavirus, a small double-stranded DNA virus, potentially results in severe complications in immunocompromised patients. Here, we describe the in vivo variability and evolution of the BK polyomavirus by deep sequencing. Our data reveal the highest genomic evolutionary rate described in double-stranded DNA viruses, i.e., 10−3–10−5 substitutions per nucleotide site per year. High mutation rates in viruses allow their escape from immune surveillance and adaptation to new hosts. By combining mutational landscapes across viral genomes with in silico prediction of viral peptides, we demonstrate the presence of significantly more coding substitutions within predicted cog…

Comparative cytogenetics of human chromosome 3q21.3 reveals a hot spot for ectopic recombination in hominoid evolution

2004

Fluorescence in situ hybridization mapping of fully integrated human BAC clones to primate chromosomes, combined with precise breakpoint localization by PCR analysis of flow-sorted chromosomes, was used to analyze the evolutionary rearrangements of the human 3q21.3-syntenic region in orangutan, siamang gibbon, and silvered-leaf monkey. Three independent evolutionary breakpoints were localized within a 230-kb segment contained in BACs RP11-93K22 and RP11-77P16. Approximately 200 kb of the human 3q21.3 sequence was not present on the homologous orangutan, siamang, and Old World monkey chromosomes, suggesting a genomic DNA insertion into the breakpoint region in the lineage leading to humans a…

Growth and senescence in the Lowest Metazoa, the porifera: Molecular evolution of apoptotic pathways

1999

Analysis of the Overdispersed Clock in the Short-Term Evolution of Hepatitis C Virus: Using the E1/E2 Gene Sequences to Infer Infection Dates in a Si…

2006

Abstract The assumption of a molecular clock for dating events from sequence information is often frustrated by the presence of heterogeneity among evolutionary rates due, among other factors, to positively selected sites. In this work, our goal is to explore methods to estimate infection dates from sequence analysis. One such method, based on site stripping for clock detection, was proposed to unravel the clocklike molecular evolution in sequences showing high variability of evolutionary rates and in the presence of positive selection. Other alternatives imply accommodating heterogeneity in evolutionary rates at various levels, without eliminating any information from the data. Here we pre…

PARAMETER BOUNDED ESTIMATION FOR QUASISPECIES MODELS OF MOLECULAR EVOLUTION

2006

Abstract The Quasispecies models identification for Evolutionary Dynamics is considered in a worst-case deterministic setting. These models analyze the DNA and RNA evolution or describe the population dynamics of viruses and bacteria. In this paper we identify the Fitness and the Replication Probability parameters of a genetic sequences, subject to a set of stringent constraints to have physical meaning and to guarantee positiveness. The conditional central estimate and the Uncertainty Intervals are determined. The effectiveness of the proposed procedure has been illustrated by means of simulation experiments while tests on real data are under concern.

Comparing diversity patterns in freshwater crustaceans from the Mediterranean area: emerging trends between morphological stasis and molecular evolut…

2013

Isolation and characterization of two T-box genes from sponges, the phylogenetically oldest metazoan taxon

2003

It is now well established that all metazoan phyla derived from one common ancestor, the hypothetical Urmetazoa. Due to the basal position of Porifera (Demospongiae) in the phylogenetic tree of Metazoa, studies on the mechanisms controlling the development of these animals can provide clues on the understanding of the origin of multicellular animals and on how the first organization of the body plan evolved. In this report we describe the isolation and genomic characterization of two T-box genes from the siliceous sponge Suberites domuncula. The phylogenetic analysis classifies one into the subfamily of Brachyury, Sd-Bra, and the second into the Tbx2 subfamily, Sd-Tbx2. Analyses of the Sd-B…

Molecular Evolution and the Phylogenetic Relationships of the African Toad, Bufo danielae PERRET, 1977 (Salientia : Bufonidae)

1980

Abstract Phylogenetic relationships of the African toad Bufo danielae are investigated using a variety of biochemical approaches. Nuclear DNA content was assayed and compared to representatives of three species groups of African Bufo. Cellogel electrophoresis of plasma proteins was performed and patterns of B. danielae compared with those of representatives of the African B. regularis species complex. Finally microcomplement fixation analyses of albumin relationships of B. danielae and African Bufo were carried out. The strengths of the varied approaches for phylogenetic analysis are discussed. B. danielae appears most closely related to B. maculatus and B. pusillus, it being some 5-6 mill…

Molecular Evolution of Defense Pathways in Sponges: Self–Self-recognition and Fight against the Nonself

2016

This article provides an overview of the immune system in poriferans at a tissue, cellular, and molecular level. Despite their simple organization, sponges have developed molecular mechanisms to recognize and resist foreign organisms. They are able to distinguish among food organisms, pathogens, and sponge-associated organisms. Although they lack specialized immune cells, sponges display molecular precursors, which are similar to molecular mediators involved in innate and adaptive immune systems, present in more evolutionarily advanced taxa, as outlined in succeeding articles in the Phylogeny section.

Molecular evolution of the metazoan protein kinase C multigene family

1996

Protein kinases C (PKCs) comprise closely related Ser/Thr kinases, ubiquitously present in animal tissues ; they respond to second messengers, e.g., Ca2+ and/or diacylglycerol, to express their activities. Two PKCs have been sequenced from Geodia cydonium, a member of the lowest multicellular animals, the sponges (Porifera). One sponge G. cydonium PKC, GCPKC1, belongs to the ''novel'' (Ca2+-independent) PKC (nPKC) subfamily while the second one, GCPKC2, has the hall-marks of the ''conventional'' (Ca2+-dependent) PKC (cPKC) subfamily. The alignment of the Ser/Thr catalytic kinase domains, of the predicted aa sequences for these cDNAs with respective segments from previously reported sequence…