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At least 1,621 records · Page 90Linked to original sources
PubMed2004

Phylogeny of the Picornaviridae and differential evolutionary divergence of picornavirus proteins.

A rooted phylogenetic analysis of the viral family Picornaviridae identified several major clusters within this viral family. The genus Parechovirus, including Ljungan virus, was found to be basal to the family. Within the family, there were two major subgroups: (1) a cluster including viruses assigned to the genera Enterovirus and Rhinovirus; and (2) a cluster including Teschovirus, Cardiovirus, Erbovirus, Aphthovirus, and probably Kobuvirus. Within the former cluster, the genera Enterovirus and Rhinovirus were found not to be monophyletic. Principal components analysis was used to identify different patterns with regard to the relative sequence divergence of the 11 polyproteins encoded by the picornavirus genome. In comparisons of closely related pairs of viruses, the nonstructural proteins were generally more conserved than the capsid proteins 1B, 1C, and 1D. This pattern is most likely explained by the predominance of host antibody-driven selection on the differentiation of closely related viral genomes. However, the same pattern was not seen in more distantly related pairs of viruses, which showed a number of distinct patterns with regard to the relative conservation of the 11 proteins.

Biological Evolution↗
PubMed2003

Dimerization in aminergic G-protein-coupled receptors: application of a hidden-site class model of evolution.

G-Protein-coupled receptors (GPCRs) are an important superfamily of transmembrane proteins involved in cellular communication. Recently, it has been shown that dimerization is a widely occurring phenomenon in the GPCR superfamily, with likely important physiological roles. Here we use a novel hidden-site class model of evolution as a sequence analysis tool to predict possible dimerization interfaces in GPCRs. This model aims to simulate the evolution of proteins at the amino acid level, allowing the analysis of their sequences in an explicitly evolutionary context. Applying this model to aminergic GPCR sequences, we first validate the general reasoning behind the model. We then use the model to perform a family specific analysis of GPCRs. Accounting for the family structure of these proteins, this approach detects different evolutionarily conserved and accessible patches on transmembrane (TM) helices 4-6 in different families. On the basis of these findings, we propose an experimentally testable dimerization mechanism, involving interactions among different combinations of these helices in different families of aminergic GPCRs.

Amino Acid Substitution↗
PubMed2005

Quantitative analysis of the corticocortical projections to the middle temporal area in the marmoset monkey: evolutionary and functional implications.

The connections of the middle temporal area (MT) were investigated in the marmoset, one of the smallest primates. Reflecting the predictions of studies that modeled cortical allometric growth and development, we found that in adult marmosets MT is connected to a more extensive network of cortical areas than in larger primates, including consistent connections with retrosplenial, cingulate, and parahippocampal areas and more widespread connections with temporal, frontal, and parietal areas. Quantitative analyses reveal that MT receives the majority of its afferents from other motion-sensitive areas in the temporal lobe and from the occipitoparietal transition areas, each of these regions containing approximately 30% of the projecting cells. Projections from the primary visual area (V1) and the second visual area (V2) account for approximately 20% of projecting neurons, whereas "ventral stream" and higher-order association areas form quantitatively minor projections. A relationship exists between the percentage of supragranular layer neurons forming the projections from different areas and their putative hierarchical rank. However, this relationship is clearer for projections from ventral stream areas than it is for projections from dorsal stream or frontal areas. These results provide the first quantitative data on the connections of MT and extend current understanding of the relationship between cortical anatomy and function in evolution.

Animals↗
PubMed2005

Ice age cloning--comparison of the Quaternary evolutionary histories of sexual and clonal forms of spiny loaches (Cobitis; Teleostei) using the analysis of mitochondrial DNA variation.

Recent advances in population history reconstruction offered a powerful tool for comparisons of the abilities of sexual and clonal forms to respond to Quaternary climatic oscillations, ultimately leading to inferences about the advantages and disadvantages of a given mode of reproduction. We reconstructed the Quaternary historical biogeography of the sexual parental species and clonal hybrid lineages within the Europe-wide hybrid complex of Cobitis spiny loaches. Cobitis elongatoides and Cobitis taenia recolonizing Europe from separated refuges met in central Europe and the Pontic region giving rise to hybrid lineages during the Holocene. Cobitis elongatoides due to its long-term reproductive contact with the remaining parental species of the complex--C. tanaitica and C. spec.--gave rise to two clonal hybrid lineages probably during the last interglacial or even earlier, which survived the Würmian glaciation with C. elongatoides. These lineages followed C. elongatoides postglacial expansion and probably decreased its dispersal rate. Our data indicate the frequent origins of asexuality irrespective of the parental populations involved and the comparable dispersal potential of diploid and triploid lineages.

Animals↗
PubMed1988

The sheep metallothionein gene family. Structure, sequence and evolutionary relationship of five linked genes.

Southern blot analysis of the sheep genome revealed a metallothionein gene family with at least nine members. Two overlapping cosmid clones spanning approximately 67 kb and containing five metallothionein genes have been isolated. DNA sequence analysis reveals that one of these is a metallothionein II variant, three are metallothionein I variants and one is a truncated metallothionein pseudogene containing only the first exon. The predicted amino acid sequence was compared with previously reported amino acid composition data of sheep metallothioneins [Whanger, P. D., Oh, S.-H. & Deagen, J. T. (1981) J. Nutr. 111, 1207-1215], and this suggests that we have isolated the genes encoding the major protein isoforms found in the sheep liver. The promoter regions of these genes contain many conserved elements, among them metal-regulatory elements and putative glucocorticoid-responsive elements. However, there are a number of differences between these genes in the arrangement of these elements. Sequence comparisons indicate that the multiple metallothionein I genes and the pseudogene appear to have resulted from sequential duplication events, and a larger cluster of metallothionein I genes may have been disrupted leading to the formation of the pseudogene.

Amino Acid Sequence↗
PubMed2005

Highly divergent genes for methanopterin-linked C1 transfer reactions in Lake Washington, assessed via metagenomic analysis and mRNA detection.

The origins and the evolutionary history of tetrahydromethanopterin-linked C1 transfer reactions that are part of two environmentally important biotransformations, methylotrophy and methanogenesis, are still not well understood. In previous studies, we have expanded the known phylogenetic diversity of these reactions by identifying genes highly diverging from the ones associated with cultivated Proteobacteria, Planctomycetes, or Archaea (M. G. Kalyuzhnaya, M. E. Lidstrom, and L. Chistoserdova, Microb. Ecol. 48:463-472, 2004; M. G. Kalyuzhnaya, O. Nercessian, M. E. Lidstrom, and L. Chistoserdova, Environ. Microbiol. 7:1269-1274, 2005). Here we used a metagenomic approach to demonstrate that these divergent genes are present with high abundance in the microbial community inhabiting Lake Washington sediment. We also gained preliminary insights into the genomic composition of the organisms possessing these genes by sequencing genomic fragments from three uncultured microbes possessing the genes of interest. Phylogenetic analyses suggested that, although distantly related to each other, these organisms deeply diverge from known Bacteria and Archaea, with more relation to the former, suggesting their affiliation with a new bacterial phylum. We also demonstrate, via specific mRNA detection, that these divergent genes are expressed in the environment, pointing toward their potential role in local carbon cycling.

Archaea↗
PubMed2006

Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus-group plasmids, including Bacillus anthracis pXO1.

The plasmids of the members of the Bacillus cereus sensu lato group of organisms are essential in defining the phenotypic traits associated with pathogenesis and ecology. For example, Bacillus anthracis contains two plasmids, pXO1 and pXO2, encoding toxin production and encapsulation, respectively, that define this species pathogenic potential, whereas the presence of a Bt toxin-encoding plasmid defines Bacillus thuringiensis isolates. In this study the plasmids from B. cereus isolates that produce emetic toxin or are linked to periodontal disease were sequenced and analyzed. Two periodontal isolates examined contained almost identical approximately 272-kb plasmids, named pPER272. The emetic toxin-producing isolate contained one approximately 270-kb plasmid, named pCER270, encoding the cereulide biosynthesis gene cluster. Comparative sequence analyses of these B. cereus plasmids revealed a high degree of sequence similarity to the B. anthracis pXO1 plasmid, especially in a putative replication region. These plasmids form a newly defined group of pXO1-like plasmids. However, these novel plasmids do not contain the pXO1 pathogenicity island, which in each instance is replaced by plasmid specific DNA. Plasmids pCER270 and pPER272 share regions that are not found in any other pXO1-like plasmids. Evolutionary studies suggest that these plasmids are more closely related to each other than to other identified B. cereus plasmids. Screening of a population of B. cereus group isolates revealed that pXO1-like plasmids are more often found in association with clinical isolates. This study demonstrates that the pXO1-like plasmids may define pathogenic B. cereus isolates in the same way that pXO1 and pXO2 define the B. anthracis species.

Amino Acid Sequence↗
PubMed1992

Structural properties and evolutionary relationships of PspA, a surface protein of Streptococcus pneumoniae, as revealed by sequence analysis.

Analysis of the sequence for the gene encoding PspA (pneumococcal surface protein A) of Streptococcus pneumoniae revealed the presence of four distinct domains in the mature protein. The structure of the N-terminal half of PspA was highly consistent with that of an alpha-helical coiled-coil protein. The alpha-helical domain was followed by a proline-rich domain (with two regions in which 18 of 43 and 5 of 11 of the residues are prolines) and a repeat domain consisting of 10 highly conserved 20-amino-acid repeats. A fourth domain consisting of a hydrophobic region too short to serve as a membrane anchor and a poorly charged region followed the repeats and preceded the translation stop codon. The C-terminal region of PspA did not possess features conserved among numerous other surface proteins, suggesting that PspA is attached to the cell by a mechanism unique among known surface proteins of gram-positive bacteria. The repeat domain of PspA was found to have significant homology with C-terminal repeat regions of proteins from Streptococcus mutans, Streptococcus downei, Clostridium difficile, and S. pneumoniae. Comparisons of these regions with respect to functions and homologies suggested that, through evolution, the repeat regions may have lost or gained a mechanism for attachment to the bacterial cell.

Amino Acid Sequence↗
PubMed2001

Locomotor function of the dorsal fin in teleost fishes: experimental analysis of wake forces in sunfish.

A key evolutionary transformation of the locomotor system of ray-finned fishes is the morphological elaboration of the dorsal fin. Within Teleostei, the dorsal fin primitively is a single midline structure supported by soft, flexible fin rays. In its derived condition, the fin is made up of two anatomically distinct portions: an anterior section supported by spines, and a posterior section that is soft-rayed. We have a very limited understanding of the functional significance of this evolutionary variation in dorsal fin design. To initiate empirical hydrodynamic study of dorsal fin function in teleost fishes, we analyzed the wake created by the soft dorsal fin of bluegill sunfish (Lepomis macrochirus) during both steady swimming and unsteady turning maneuvers. Digital particle image velocimetry was used to visualize wake structures and to calculate in vivo locomotor forces. Study of the vortices generated simultaneously by the soft dorsal and caudal fins during locomotion allowed experimental characterization of median-fin wake interactions. During high-speed swimming (i.e. above the gait transition from pectoral- to median-fin locomotion), the soft dorsal fin undergoes regular oscillatory motion which, in comparison with analogous movement by the tail, is phase-advanced (by 30% of the cycle period) and of lower sweep amplitude (by 1.0 cm). Undulations of the soft dorsal fin during steady swimming at 1.1 bodylength s(-1) generate a reverse von Kármán vortex street wake that contributes 12% of total thrust. During low-speed turns, the soft dorsal fin produces discrete pairs of counterrotating vortices with a central region of high-velocity jet flow. This vortex wake, generated in the latter stage of the turn and posterior to the center of mass of the body, counteracts torque generated earlier in the turn by the anteriorly positioned pectoral fins and thereby corrects the heading of the fish as it begins to translate forward away from the turning stimulus. One-third of the laterally directed fluid force measured during turning is developed by the soft dorsal fin. For steady swimming, we present empirical evidence that vortex structures generated by the soft dorsal fin upstream can constructively interact with those produced by the caudal fin downstream. Reinforcement of circulation around the tail through interception of the dorsal fin's vortices is proposed as a mechanism for augmenting wake energy and enhancing thrust. Swimming in fishes involves the partitioning of locomotor force among several independent fin systems. Coordinated use of the pectoral fins, caudal fin and soft dorsal fin to increase wake momentum, as documented for L. macrochirus, highlights the ability of teleost fishes to employ multiple propulsors simultaneously for controlling complex swimming behaviors.

Animal Structures↗
PubMed1993

[The basic types and forms of the fine structure of mitochondrial cristae: the degree of their evolutionary stability (capacity for morphological transformations)].

The organellological analysis being made of the fine structure of mitochondria in different species of the kingdom Protista, and in different cells of representatives of the kingdoms Plantae and Animalia (Metazoa). On the base of this analysis the following classification of types and forms of the fine structure of mitochondrial cristae is proposed. The Ist type, with lamellar (flat) cristae includes four morphological forms: ribbon, sheet, bundle-like and rounded ones (discoidal and plate-like). The 2nd type, with vesicular cristae, includes bubble, ampule, and sac-like ones. The 3rd type with tubular cristae. Among the representatives of each kingdom (Protista, Plantae and Metazoa) all the three types of mitochondrial cristae have been observed. The majority of cells of higher plants and higher animals have lamellar mitochondrial cristae, but sometimes (in some tissues) there are cells with tubular or vesicular mitochondrial cristae. On the base of the above classification some other conclusions have been made. Among the eukaryotes the vesicular cristae are spread as widely as tubular and lamellar ones. Only in a few macrotaxa (superphyla and phyla) of Protista all the investigated organisms have mitochondria of similar cristal organization. For example, Ciliophora have only tubular, and Cryptophyta only lamellar mitochondrial cristae. In the majority of protistan macrotaxa a certain mitochondrial type of cristae may dominate, but there is the number of species with some different mitochondrial patterns (Euglenophyta, Chlorophyta, Chrysophyta, Mycetozoa, etc.). In some macrotaxa (Chrysophyta, Mycetozoa, etc.) such mitochondrial patterns as mentioned above, are characteristic of the lower organisms. Finally, in some macrotaxa of Protista mitochondrial cristae of two or three types may appear in different species, sometimes even within the same genus; for example--Sporozoa, Myxospora and Ascetospora. In the course of ontogenesis of the vertebrates and insects, cell mitochondria in some of their tissues can change their morphological type from lamellar to tubular or vesicular. Similar transformations of mitochondrial cristae were observed in the life cycles of some trypanosomes (Kinetoplastida) and in the flagellate Polytoma (Chlorophyta) due to modifications in the culture conditions. It is undoubtedly that the principle of morphological concervatism in the organization of mitochondrial cristae may be used for purposes of systematics and phylogeny, however only after a thorough comparative organellological analysis of the fine structure in numerous species of the examined taxon.

Animals↗
PubMed2004

Bordetella species are distinguished by patterns of substantial gene loss and host adaptation.

Pathogens of the bacterial genus Bordetella cause respiratory disease in humans and animals. Although virulence and host specificity vary across the genus, the genetic determinants of this diversity remain unidentified. To identify genes that may underlie key phenotypic differences between these species and clarify their evolutionary relationships, we performed a comparative analysis of genome content in 42 Bordetella strains by hybridization of genomic DNA to a microarray representing the genomes of three Bordetella species and by subtractive hybridization. Here we show that B. pertussis and B. parapertussis are predominantly differentiated from B. bronchiseptica by large, species-specific regions of difference, many of which encode or direct synthesis of surface structures, including lipopolysaccharide O antigen, which may be important determinants of host specificity. The species also exhibit sequence diversity at a number of surface protein-encoding loci, including the fimbrial major subunit gene, fim2. Gene loss, rather than gene acquisition, accompanied by the proliferation of transposons, has played a fundamental role in the evolution of the pathogenic bordetellae and may represent a conserved evolutionary mechanism among other groups of microbial pathogens.

Animals↗
PubMed2003

Identification and characterization of C1orf36, a transcript highly expressed in photoreceptor cells, and mutation analysis in retinitis pigmentosa.

By means of computational methods, we identified an uncharacterized human transcript, Chromosome 1 open reading frame 36 (C1orf36), that is expressed in the retina and that maps to 1q32.3. The cDNA contains an open reading frame of 585bp that encodes a 195-aminoacid protein with a predicted mass of 22.7kDa. An alternatively spliced transcript in a retinoblastoma cell line, encoding for a truncated peptide, was also identified. PCR experiments performed using human cDNA from several sources indicate that C1orf36 has a preferential expression in the retina. Accordingly, in situ hybridization experiments, performed using as probe a murine C1orf36 cDNA fragment, detected a hybridization signal on mouse retinal adult sections. The C1orf36 protein shares homology with putative proteins in Mus musculus and Fugu rubripes, suggesting evolutionary conservation of its function. Additional sequence analysis of the C1orf36 gene product predicts its subcellular mitochondrial localization and the presence of both evolutionary conserved phosphorylation sites and regions adopting a coiled-coil conformation. We also defined the genomic structure of the gene. This enabled us to perform a mutational analysis of the C1orf36 coding region of about 300 patients affected by retinitis pigmentosa. No pathological mutations were detected in this analysis.

Amino Acid Sequence↗
PubMed2005

Molecular phylogeny and divergence times of deuterostome animals.

The phylogenetic relationships among deuterostome animals have been debated for many years, and a diversity of hypotheses have been proposed based on both morphological and molecular data. Here we have assembled sequences of 217 nuclear-encoded proteins to address specific questions concerning their relationships and times of origin. We recovered significant support for urochordates as the closest relative of vertebrates with an analysis of 59 proteins (17,400 amino acids) and suggest that the basal position of urochordates found in previous molecular studies may have been the result of long-branch attraction biases. Our results also support Ambulacraria, the pairing of hemichordates with echinoderms (nine proteins; 2,382 amino acids), and Cyclostomata, the pairing of lampreys with hagfish (25 proteins; 6,895 amino acids). In addition, 325 shared proteins (102,110 amino acids) were obtained from the complete genomes of six vertebrates and a urochordate for phylogenetic analysis and divergence time estimation. An evolutionary timescale was estimated using a local (Bayesian) molecular clock method. We found that most major lineages of deuterostomes arose prior to the Cambrian Explosion of fossils (approximately 520 MYA) and that several lineages had originated before periods of global glaciation in the Precambrian.

Animals↗
PubMed2002

Genetic, geographic, and linguistic variation among South American Indians: possible sex influence.

To better understand the relationship between genetic variability, geographical distance, and linguistic affiliation in South Amerinds, and to elucidate whether the migration rate is the same for both sexes, spatial autocorrelation, Mantel's test, and F(ST) analyses were performed in four sets of populations and alleles (group 1: 48 populations, 12 alleles; group 2: 16 (all belonging to the Tupi linguistic group) and 12; group 3: 21 and 17; and group 4: 28 and 4 haplotypes). Groups 1-3 included blood group and protein (i.e., serum protein, red cell enzymes, and immunoglobulin systems), while group 4 was concerned with mitochondrial DNA (mtDNA) only. The latter set was also subjected to a molecular analysis of variance (AMOVA) evaluation. The frequencies of statistically significant correlograms were lower than those obtained in other populations when the blood groups and protein systems were considered, but 3 of the 4 mtDNA haplogroups gave suggestions of population structure. The variability in this organelle is also significantly correlated with language when geography is held constant. Migration per generation is generally low, but higher estimates were obtained for females. The AMOVA results suggest that populations whose members speak the same language are genetically homogeneous and may be viewed as the ultimate evolutionary unit at this level of analysis.

Biological Evolution↗
PubMed2002

Genetic analysis of Group A rotaviruses: evidence for interspecies transmission of rotavirus genes.

Rotaviruses are the major cause of severe gastroenteritis in young children and animals. The rotavirus genome is composed of eleven segments of double-stranded RNA and can undergo genetic reassortment during mixed infections, leading to progeny viruses with novel or atypical phenotypes. There are numerous descriptions of rotavirus strains isolated from human and animals that share genetic and antigenic features of viruses from heterologous species. In many cases, genetic analysis by hybridization has clearly demonstrated the genetic relatedness of gene segments to those from viruses isolated from different species. Together with the observation that some virus strains appear to have been transmitted to a different species as a whole genome constellation, these data suggest that interspecies transmission occurs naturally, albeit at low frequencies. Although interspecies transmission has not been documented directly, there is an increasing number of reports of atypical rotaviruses that are apparently derived from transmission between: humans, cats and dogs; humans and cattle; humans and pigs; pigs and cattle; and pigs and horses. Interspecies evolutionary relationships are supported by phylogenetic analysis of rotavirus genes from different species. The emergence of novel strains derived from interspecies transmission has implications for the design and implementation of successful human rotavirus vaccine strategies.

Animals↗
PubMed1999

ITS2 sequences of Dictyocaulus species from cattle, roe deer and moose in Sweden: molecular evidence for a new species.

Total DNA was isolated from adult lungworms of the genus Dictyocaulus, collected from cattle, moose (Alces alces) and roe deer (Capreolus capreolus) in Sweden. The second ribosomal internal transcribed spacer was amplified with PCR, and DNA sequences were determined from nine individual worms that all came from different hosts in order to avoid analysis of siblings. The sequence data obtained were aligned and compared with similar data derived from German lungworm isolates from cattle and fallow deer (Cervus dama). These analyses clearly showed that specimens of the cattle lungworm, Dictyocaulus viviparus, were almost identical irrespective of their geographical origin. However, when the second internal transcribed spacer sequence of D. viviparus was compared with that of lungworms from moose and roe deer, major differences were noticed. Although lungworms collected from these cervids had identical second internal transcribed spacer sequences, they proved to be genetically different from Dictyocaulus eckerti of German fallow deer, displaying a 66.5% similarity. In an evolutionary tree, inferred by maximum likelihood analysis, the Dictyocaulus species from cattle and wild cervids clustered as compared with Dictyocaulus filaria from sheep. The study has thus demonstrated that A. alces and C. capreolus in Sweden are parasitised with a Dictyocaulus species that is different from D. viviparus and D. eckerti, indicating that we are dealing with a new species in moose and roe deer.

Animals↗
PubMed2004

A repeat DNA sequence from the Y chromosome in species of the genus Microtus.

In most mammals, the Y chromosome is composed of a large amount of constitutive heterochromatin. In some Microtus species, this feature is also extended to the X chromosome, resulting in enlarged (giant) sex chromosomes. Several repeated DNA sequences have been described in the gonosomal heterochromatin of these species, indicating that it has heterogeneous and species-specific composition and distribution. We have cloned an AT-rich, 851-bp long, repeated DNA sequence specific for M. cabrerae Y chromosome heterochromatin. The analysis of other species of the genus Microtus indicated that this sequence is also located on the Y chromosome (male-specific) in three species (M. agrestis, M. oeconomus and M. nivalis), present on both Y and X chromosomes and on some autosomes in M. arvalis and absent in the genome of M. guentheri. Our data also suggest that the mechanism of heterochromatin amplification operating on the sex chromosomes could have been different in each species since the repeated sequences of the gonosomal heterochromatic blocks in M. cabrerae and M. agrestis are different. The absence of this sequence in the mouse genome indicates that its evolutionary origin could be recent. Future analysis of the species distribution, localization and sequence of this repeat DNA family in arvicolid rodent species could help to establish the unsolved phylogenetic relationships in this rodent group.

Animals↗