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PubMed1998

Antigenic variants of J subgroup avian leukosis virus: sequence analysis reveals multiple changes in the env gene.

HPRS-103, the prototype of avian leukosis virus (ALV) subgroup J, was isolated in 1989 from meat-type chickens from commercial flocks where it induces myelocytic myeloid leukosis (ML). The HPRS-103 env gene differs considerably from other ALV subgroups but shows high identity (75-97%) to env-like sequences of the different members of the EAV family of endogenous avian retroviruses. Recently, we have isolated several viruses related to HPRS-103 from cases of ML. Although these isolates showed properties of ALV subgroup J, the majority of them resisted neutralization by HPRS-103-specific serum, suggesting antigenic variation. The nucleotide sequence of the env gene of the variant viruses showed several substitutions resulting in amino acid changes especially clustered in the variable regions hr1, hr2 and vr3. Analysis of the data suggests that selection pressure, probably from the immune response, is driving the antigenic variation among the isolates. Phylogenetic analysis of the sequences showed the evolutionary relationships of the isolates with HPRS-103 and the EAV family of endogenous avian retroviruses. The epidemiological significance of the antigenic variation and the emergence of variant viruses are discussed.

Amino Acid Sequence↗
PubMed1994

Non-congruent relationships between variation in emm gene sequences and the population genetic structure of group A streptococci.

To examine the molecular population genetics of the M protein family of Streptococcus pyogenes (group A Streptococcus), the 5' regions of polymerase chain reaction-amplified emm products from 79 M serotypes were sequenced and the phylogeny was compared to estimates of overall genetic relationships among strains determined by multilocus enzyme electrophoresis. Although the 5' emm sequences from several strains designated as distinct M types were identical or almost identical, the overall pattern is characterized by very extensive variation. The composition of distinct emm sequence clusters generally parallels the ability of strains to express serum opacity factor and in some cases historical associations of certain M types with acute rheumatic fever, but not with M types classified as nephritogenic. For many strains there is a lack of congruency between variation in 5' emm sequences and estimates of overall chromosomal relationships, which is undoubtedly due to horizontal transfer and recombination of emm sequences. The results of these studies provide insights into the nature and extent of emm sequence variation and describe how this variation 'maps' onto the population genetic structure of extant S. pyogenes lineages. The complexity of emm sequence and streptococcal cell lineage relationships revealed by this analysis has significant implications for understanding evolutionary events generating strain diversity and the epidemiology of S. pyogenes diseases.

Amino Acid Sequence↗
PubMed2000

Assessing infestation risk by vectors. Spatial and temporal distribution of African ticks at the scale of a landscape.

Control of major livestock diseases in the tropics, such as theileriosis or trypanosomosis, is still largely based on the control of their vectors. Understanding the distribution of vectors, such as ticks and tsetse flies, is needed in order to improve the efficiency and economical viability of control operations. Technical improvements such as remote sensing and global information systems have allowed valuable improvements for the prediction of large-scale vector distribution (continental to national), but trying to make these predictions at the scale of a landscape is facing other challenges. At this scale, an analysis of host/vector interactions with an evolutionary point of view is useful. A study was undertaken on a mixed game/cattle ranch in Zimbabwe during which we monitored variations in the abundance and spatial distribution of the immature free stages of Rhipicephalus appendiculatus/R. zambeziensis and R. e. evertsi, two major groups of tick species in Southern Africa. We found two contrasting distributions in relation to contact between tick larvae. The ungulate-host R. e. evertsi appeared to be unpredictable, whereas R. appendiculatus/R. zambeziensis were predictable in time and space, but associated with key-resources for ungulates (water and forage resources). The consequences of such distributions are discussed in terms of vector control.

Africa, Southern↗
PubMed2025

TRB proteins in moss reveal their evolutionarily conserved roles in plant development and telomere maintenance.

Telomere repeat binding (TRB) proteins are plant-specific proteins with a unique domain structure distinct from telomerebinding proteins in animals and yeast. While extensively studied in seed plants, their role in early-diverging plant lineages remains largely unexplored. Here, we investigate TRB proteins in a model moss, Physcomitrium patens, to assess their evolutionary conservation and functional significance. Functional analysis using single knockout mutants revealed that individual PpTRB genes are essential for normal development, with mutants exhibiting defects in the two-dimensional (protonemal) stage, and more prominently, in the formation of three-dimensional (gametophore) structures. Some double mutants displayed telomere shortening, a phenotype also observed in TRB-deficient seed plants, indicating a conserved role for TRBs in telomere maintenance. Transcriptome profiling of TRB mutants revealed altered expression of genes associated with transcriptional regulation and stimulus response in protonema. Subcellular localization studies across various plant cell types confirmed that PpTRBs, like their seed plant counterparts, localize prevalently to the plant nucleus and mutually interact. In bryophytes, TRBs form a monophyletic group that mirrors the species phylogeny, whereas in seed plants, TRBs have diversified into two distinct monophyletic groups. Our findings provide the first comprehensive characterization of TRB proteins in non-vascular plants and demonstrate their conserved roles in telomere maintenance, with additional implications for plant development and gene regulation across land plant lineages.

Bryopsida↗
PubMed2001

Nonequilibrium diversity dynamics of the Lesser Antillean avifauna.

MacArthur and Wilson's model of island diversity predicts an increase in the number of species until colonization and extinction are balanced at a long-term steady state. We appraise this model on an evolutionary time scale by molecular phylogenetic analysis of the colonization of the Lesser Antilles by small land birds. The pattern of accumulation of species with time, estimated by genetic divergence between island and source lineages, rejects a homogeneous model of colonization and extinction. Rather, our results suggest an abrupt, roughly 10-fold increase in colonization rate or a 90% mass extinction event 0.55 to 0.75 million years ago.

Animals↗
PubMed1998

Genetic variability among group A and group B respiratory syncytial viruses in a children's hospital.

Respiratory syncytial (RS) viruses isolated over three epidemic periods in a children's hospital in the United States were analyzed. The viruses (n = 174) were characterized as to major antigenic group (group A or B) by a PCR-based assay. Group A RS viruses were dominant the first 2 years, followed by a year with group B dominance (ratios of group A to group B viruses for epidemic periods, 56/4 for 1993-1994, 42/3 for 1994-1995, and 19/50 for 1995-1996). Genetic variability within the groups was assessed by restriction fragment analysis of PCR products; 79 isolates were also analyzed by nucleotide sequence determination of a variable region of the glycoprotein G gene. Among the group A RS virus isolates, this G-protein variable region had amino acid differences of as great as 38%. The G-protein amino acids of the group A viruses differed by up to 31% from the G-protein amino acids of a prototype (A2) group A virus. Among the group B RS virus G proteins, amino acid differences were as great as 14%. The G-protein amino acids of the group B viruses differed by up to 27% from the G-protein amino acids of a prototype (18537) group B virus. The group A and group B RS viruses demonstrated genetic variability between years and within individual years. Phylogenetic analysis revealed that there were multiple evolutionary lineages among both the group A and group B viruses. Among the recent group B isolates, variability was less than that seen for the group A viruses. However, comparisons to prototype strains revealed that the group B RS viruses may vary more extensively than was observed over the 3 years studied in the present investigation.

Amino Acid Sequence↗
PubMed2002

Mapping epigenetic quantitative trait loci (QTL) altering a developmental trajectory.

Genetic variation in a quantitative trait that changes with age is important to both evolutionary biologists and breeders. A traditional analysis of the dynamics of genetic variation is based on the genetic variance-covariance matrix among different ages estimated from a quantitative genetic model. Such an analysis, however, cannot reveal the mechanistic basis of the genetic variation for a growth trait during ontogeny. Age-specific genetic variance at time t conditional on the causal genetic effect at time t - 1 implies the generation of episodes of new genetic variation arising during the interval t - 1 to t. In the present paper, the conditional genetic variance estimated from Zhu's (1995) conditional model was partitioned into its underlying individual quantitative trait loci (QTL) using molecular markers in an F2 progeny of poplars (Populus trichocarpa and Populus deltoides). These QTL, defined as epigenetic QTL, govern the alterations of growth trajectory in a population. Three epigenetic QTL were detected to contribute significantly to variation in growth trajectory during the period from the establishment year to the subsequent year in the field. It is suggested that the activation and expression of epigenetic QTL are influenced by the developmental status of trees and the environment in which they are grown.

Analysis of Variance↗
PubMed1999

Brain size is not correlated with forelimb dexterity in fissiped carnivores (Carnivora): A comparative test of the principle of proper mass.

To test the hypothesis that brain size and forelimb dexterity are positively correlated, the relative brain size of 41 species of fissiped (terrestrial) carnivores (Order: Carnivora) was examined with respect to their forelimb use during feeding. With the use of a newly derived dexterity index, the forelimb dexterity executed by each of the species was calculated as a single, continuous variable which was then regressed against the residuals of brain size. To account for confounding effects of phylogenetic inertia, the analysis was performed with independent contrasts analysis using a speciational model of evolutionary change (i.e. equal branch lengths). The results suggest that relative brain size and isocortex size are not correlated with the dexterity of the proximal or distal segments or a combination of the two (total forelimb dexterity). The presence of species with widely different brain sizes and similar dexterities, and vice versa, suggests that an increase in the amount of neural substrate might not be necessary for the production of finely coordinated forelimb movements. It is suggested that this outcome is representative of the plasticity of both mammalian brain size and behavior and that variations in brain size and forelimb dexterity could be linked to disparate ecological and phylogenetic factors which act in concert to promote or constrain neural development and behavior in different species.

Animals↗
PubMed2004

PASS2: an automated database of protein alignments organised as structural superfamilies.

BACKGROUND: The functional selection and three-dimensional structural constraints of proteins in nature often relates to the retention of significant sequence similarity between proteins of similar fold and function despite poor sequence identity. Organization of structure-based sequence alignments for distantly related proteins, provides a map of the conserved and critical regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The Protein Alignment organised as Structural Superfamily (PASS2) database represents continuously updated, structural alignments for evolutionary related, sequentially distant proteins. DESCRIPTION: An automated and updated version of PASS2 is, in direct correspondence with SCOP 1.63, consisting of sequences having identity below 40% among themselves. Protein domains have been grouped into 628 multi-member superfamilies and 566 single member superfamilies. Structure-based sequence alignments for the superfamilies have been obtained using COMPARER, while initial equivalencies have been derived from a preliminary superposition using LSQMAN or STAMP 4.0. The final sequence alignments have been annotated for structural features using JOY4.0. The database is supplemented with sequence relatives belonging to different genomes, conserved spatially interacting and structural motifs, probabilistic hidden markov models of superfamilies based on the alignments and useful links to other databases. Probabilistic models and sensitive position specific profiles obtained from reliable superfamily alignments aid annotation of remote homologues and are useful tools in structural and functional genomics. PASS2 presents the phylogeny of its members both based on sequence and structural dissimilarities. Clustering of members allows us to understand diversification of the family members. The search engine has been improved for simpler browsing of the database. CONCLUSIONS: The database resolves alignments among the structural domains consisting of evolutionarily diverged set of sequences. Availability of reliable sequence alignments of distantly related proteins despite poor sequence identity and single-member superfamilies permit better sampling of structures in libraries for fold recognition of new sequences and for the understanding of protein structure-function relationships of individual superfamilies. PASS2 is accessible at http://www.ncbs.res.in/~faculty/mini/campass/pass2.html

Amino Acid Sequence↗
PubMed2004

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction.

BACKGROUND: RNA secondary structure prediction methods based on probabilistic modeling can be developed using stochastic context-free grammars (SCFGs). Such methods can readily combine different sources of information that can be expressed probabilistically, such as an evolutionary model of comparative RNA sequence analysis and a biophysical model of structure plausibility. However, the number of free parameters in an integrated model for consensus RNA structure prediction can become untenable if the underlying SCFG design is too complex. Thus a key question is, what small, simple SCFG designs perform best for RNA secondary structure prediction? RESULTS: Nine different small SCFGs were implemented to explore the tradeoffs between model complexity and prediction accuracy. Each model was tested for single sequence structure prediction accuracy on a benchmark set of RNA secondary structures. CONCLUSIONS: Four SCFG designs had prediction accuracies near the performance of current energy minimization programs. One of these designs, introduced by Knudsen and Hein in their PFOLD algorithm, has only 21 free parameters and is significantly simpler than the others.

Computational Biology↗
PubMed2004

Nonconcerted evolution of histone 3 genes in a liverwort, Conocephalum conicum.

To estimate the extent of genetic variation at the DNA level, the histone 3 (H3) genes were sequenced from single individual each from the three cryptic species recognized based on allozyme analyses, YFS, J and T types of Conocephalum conicum and two closely related species, C. japonicum and Marchantia polymorpha. Although the H3 genes are known to be highly conserved, the nucleotide diversities were 0.128, 0.109, 0.108, 0.049 and 0.034. These values are 30 to 100 times higher than that in Drosophila melanogaster (0.001). Besides, there were considerable differences in the position, length and number of introns among the loci of H3 genes. The observed high level of nucleotide diversities was explained by the fixation of many random mutations, and non-concerted evolution that resulted from low rates of unequal crossing-over and gene conversion probably due to the dispersed structure of H3 genes on genome in this species. The non-concerted evolutionary pattern was established by the analysis of phylogenetic tree and divergence rates. This study confirmed previous results suggesting that natural populations of liverwort maintains high extent of variation at DNA level.

Base Sequence↗
PubMedDate not supplied

Evolutionary origins of the mammalian apolipoproteinB RNA editing enzyme, apobec-1: structural homology inferred from analysis of a cloned chicken small intestinal cytidine deaminase.

Mammalian apolipoproteinB (apoB) RNA editing is a site-specific deamination reaction that mediates the C to U conversion responsible for apoB48 production in the mammalian small intestine. This process is not detected in chicken apoB RNA. Mammalian apoB RNA editing is mediated by a multicomponent enzyme complex that includes a single catalytic subunit, apobec-1. In order to examine the evolution of apobec-1, we have cloned and characterized an orthologous cytidine deaminase cDNA isolated from chicken small intestine. Northern blot analysis revealed expression restricted to the small intestine, colon and lung but not the liver or other tissues. The cDNA encodes a single 31 kDa protein with features reminiscent of other cytidine deaminases and with approximately 39% overall homology to rat apobec-1. The recombinant protein is a cytidine deaminase with activity on a monomeric substrate that was found to be zinc-dependent. However, no RNA editing activity was detectable towards cytidine nucleotides presented in the context of an optimally configured mammalian apoB RNA template. These studies provide information concerning the evolution of the apoB RNA editing machinery and indicate that a chicken small intestinal cytidine deaminase with homology to apobec-1 demonstrates no activity on an RNA substrate.

APOBEC-1 Deaminase↗
PubMed1990

DNA analysis in the diagnosis of infection and in the speciation of nematode parasites.

DNA analysis is playing an increasingly important role in characterising and classifying nematode parasites. Though less emphasis has been placed on utilising DNA elements to study nematodes of veterinary importance, correct diagnosis is, nevertheless, critical to proper treatment and control. The genus Trichinella presents a particularly interesting problem since the level of classification within this genus remains unclear. Herein we discuss the application of DNA analysis to the diagnosis and speciation of the parasitic nematode Trichinella spiralis, where the study of cloned repetitive DNA elements and ribosomal RNA genes has led to significant advances in the understanding of the species-level systematics of this nematode. Despite advances in the recognition of multiple gene pools within the genus Trichinella, their taxonomic level is still uncertain because of insufficient knowledge regarding intraspecific variation within this genus. The utility of mitochondrial DNA and ribosomal DNA sequence analysis in studying the phylogeny and evolutionary history of parasites within this genus is also discussed.

Animals↗
PubMed2001

Virtual anthropology: the digital evolution in anthropological sciences.

The discovery and explanation of differences among organisms is a major concern for evolutionary and systematic biologists. In physical anthropology, the discrimination of taxa and the qualitative and quantitative description of ontogenetic or evolutionary change require, of course, the analysis of morphological features. Since the 1960s, a remarkable amount of fossil material was excavated, some of it still awaiting a detailed first analysis, some of it requiring re-examination by more developed methods. While the fossil record grew continuously, a revolution in anthropological research took place with advances in computer technology in the 1980s: a handful of innovative researchers working in specialized anthropology laboratories or medical departments developed the methodological inventory needed to extract critical information from subjects in vivo and from fossilized remains. A considerable part of this information is preserved in the physically heretofore inaccessible interior of anatomical structures. Virtual Anthropology (VA) is a means of making them visible and measurable. Thus, VA also allows access to 'hidden' landmarks; in addition, the large number of semilandmarks accessible on the form enhances the power of Geometric Morphometrics analysis. Furthermore, the density information in volume data allows manipulations such as segmentation, impossible with the real, physical object. Moreover, metric body measurements generally, and cranial measurements specifically, are also an important source of information for the analysis of the ontogenetic development of the skeletal system, and--last but not least--for clinical use (e.g., operation planning, operation simulation, prosthetics). Thus, there developed a fruitful interdisciplinary cooperation between statistics, medicine, and physical anthropology.

Anthropology, Physical↗
PubMed2005

Historical demography, selection, and coalescence of mitochondrial and nuclear (genes in Prochilodus species of northern South America.

Fishes of the genus Prochilodus are ecologically and commercially important, ubiquitous constituents of large river biota in South America. Recent ecologic and demographic studies indicate that these fishes exist in large, stable populations with adult census numbers exceeding one million individuals. Abundance data present a stark contrast to very low levels of genetic diversity (theta) and small effective population sizes (Ne) observed in a mitochondrial (mt) DNA dataset obtained for two species, Prochilodus mariae, and its putative sister taxon, Prochilodus rubrotaeniatus. Both species occupy major river drainages (Orinoco, Essequibo, and Negro) of northeastern South America. Disparity between expectations based on current abundance and life history information and observed genetic data in these lineages could result from historical demographic bottlenecks, or alternatively, natural selection (i.e., a mtDNA selective sweep). To ascertain underlying processes that affect mtDNA diversity in these species we compared theta and Ne estimates obtained from two, unlinked nuclear loci (calmodulin intron-4 and elongation factor-1alpha intron-6) using an approach based on coalescent theory. Genetic diversity and Ne estimated from mtDNA and nuclear sequences were uniformly low in P. rubrotaeniatus from the Rio Negro, suggesting that this population has encountered a historical bottleneck. For all P. mariae populations, theta and Ne based on nuclear sequences were comparable to expectations based on current adult census numbers and were significantly greater than mtDNA estimates, suggesting that a selective mtDNA sweep has occurred in this species. Comparative genetic analysis indicates that a suite of evolutionary processes involving historical demography and natural selection have influenced patterns of genetic variation and speciation in this important Neotropical fish group.

Animals↗
PubMed1989

[Evolution of Alu repeats. Imitation model].

At present, nucleotide sequences of 100 different Alu repeats are known, i.e. 0.01% of the total number of Alu repeats in the genome. It is clear that one can not refer the evolutionary characteristics of Alu repeats obtained from the analysis of the available limited sample to all Alu repeats comprised in the genome, without additional statistical estimations. For supplementary investigation of such average evolutionary characteristics as the extent of intraspecific divergence, the rate of Alu repeats transposition (insertion, excision), we used the method of imitation simulation of the process of Alu repeats transposition in the genome. As a result of simulation, phylogenetic relations were obtained among all Alu repeats. It was shown that the evolutionary characteristics evaluated for different samples of repeats were similar. It was proved that the extent of divergence of Alu repeats in the model is twice as small as that evaluated, according to the real data (0.15, instead of 0.3). Possible reasons for such discrepancy have been discussed.

Genome, Human↗
PubMed1998

Molecular characterization of the creatine kinases and some historical perspectives.

Over the last 15 years, molecular characterization of the creatine kinase (CK) gene family has paralleled the molecular revolution of understanding gene structure, function, and regulation. In this review, we present a summary of advances in molecular analysis of the CK gene family with a few vignettes of historical interest. We describe how the muscle CK gene provided an essential model system to examine myogenic regulatory mechanisms, leading to the discovery of the binding site for the MyoD family of basic helix-loop-helix transcription factors essential in skeletal myogenesis and the characterization of the MEF2 family of factors with an A/T rich consensus binding site essential in skeletal myogenesis and cardiogenesis. Cloning and characterization of the four mRNAs and nuclear genes encoding the cytosolic CKs, muscle and brain CKs, and the mitochondrial (Mt) CKs, sarcomeric MtCK and ubiquitous MtCK, has allowed intriguing study of tissue-specific and cell-specific expression of the different CKs and analysis of structural, functional, regulatory, and evolutionary relationships among both the four CK proteins and genes. Current and future studies focus on understanding both cellular energetics facilitated by the CK enzymes, especially energy channelling from the site of production, the mitochondrial matrix and inner membrane, to various cytosolic foci of utilization, and regulation of MtCK gene expression at the cell and tissue-specific level as models of regulation of energy producing genes.

Amino Acid Sequence↗
PubMed2000

The alpha-mannosidases: phylogeny and adaptive diversification.

alpha-Mannosidase enzymes comprise a class of gylcoside hydrolases involved in the maturation and degradaton of glycoprotein-linked oligosaccharides. Various alpha-mannosidase enzymatic activities are encoded by an ancient and ubiquitous gene superfamily. A comparative sequence analysis was employed here to characterize the evolutionary relationships and dynamics of the alpha-mannosidase superfamily. A series of lineage-specific BLAST searches recovered the first ever recognized archaean and eubacterial alpha-mannosidase sequences, in addition to numerous eukaryotic sequences. Motif-based alignment and subsequent phylogenetic analysis of the entire superfamily revealed the presence of three well-supported monophyletic clades that represent discrete alpha-mannosidase families. The comparative method was used to evaluate the phylogenetic distribution of alpha-mannosidase functional variants within families. Results of this analysis demonstrate a pattern of functional diversification of alpha-mannosidase paralogs followed by conservation of function among orthologs. Nucleotide polymorphism among the most closely related pair of duplicated genes was analyzed to evaluate the role of natural selection in the functional diversification of alpha-mannosidase paralogs. Ratios of nonsynonymous and synonymous variation show an increase in the rate of nonsynonymous change after duplication and a relative excess of fixed nonsynonymous changes between the two groups of paralogs. These data point to a possible role for positive Darwinian selection in the evolution of alpha-mannosidase functional diversification following gene duplication.

Amino Acid Sequence↗