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At least 433 records · Page 24Linked to original sources
PubMed2003

[Molecular evolution of satellite DNA CLsat in lizards of the Darevskia species (Sauria: Lacertidae): correlation with species diversity].

The structure and evolution of a satellite DNA family was examined in lizards from the genus Darevskia (family Lacertidae). Comparison of tandem units of repeated DNA (satDNA), CLsat, in all species from the genus Darevskia has shown that their variability is largely based on single-nucleotide substitutions, which constitute about 50 diagnostic positions underlying classification of the family into three subfamilies. Maximum differences between the subfamilies reached 25%. At this level of tandem unit divergence between the subfamilies, no cross-hybridization between them was observed (at 65 degrees C). The individual variability of one subfamily within the species was on average 5% while the variability between species consensuses within a subfamily was 10%. The presence of highly conserved regions in all monomers and some features of their organization show that satellites of all Darevskia species belong to one satDNA family. The organization of unit sequences of satellites CLsat and Agi also detected by us in another lizard genus, Lacerts s. str. was compared. Similarity that was found between these satellites suggests their relatedness and common origin. A possible pathway of evolution of these two satDNA families is proposed. The distribution and content of CLsat repeat subfamilies in all species of the genus was examined by Southern blotting hybridization. Seven species had mainly CLsatI (83 to 96%); three species, approximately equal amounts of CLsatI and CLsatIII (the admixture of CLsatII was 2-3%); and five species, a combination of all three subfamilies in highly varying proportions. Based on these results as well as on zoogeographic views on phylogeny and taxonomy of the Darevskia species, hypotheses on the evolution of molecular-genetic relationships within this genus are advanced.

Animals↗
PubMed2004

[Molecular evolution and geographic origins of type 1 human lymphotrophic virus in Colombia detected by RFLP polymorphism].

The human T-lymphotropic virus type I (HTLV-I) infection is a public health problem in many endemic areas of Colombia. The subtyping of HTLV-I was based on the analysis of restriction fragment length polymorphisms (RFLP) in 3'LTR proviral DNA. From 31 HTLV-I isolates collected throughout Colombia, a RFLP analysis in a 737 bp 3'LTR fragment was performed. Fifty-eight percent (18/31) were identified as the Cosmopolitan subtype a, 19.4% (6/31) in the West African subtype b, 12.9% (4/31) in the Cosmopolitan subtype b and 9.6% (3/31) in the West African subtype c. The phylogenetic analysis of 3'LTR nucleotide sequences indicated that all the isolates in the current study were in the subgroup B or Japanese, in contrast with the highly divergent isolates from native Amerindians grouped in subgroup a or Transcontinental. The supported hypothesis was that of a post-Columbus introduction of virus represented in the African-American communities of the Colombian South Pacific. Some viral isolates from Colombian native Amerindians exhibited a nucleotide variation compatible with a Paleolithic introduction of the virus. The genetic diversity of HTLV-I in Colombia is complex and probably represents several independent introductions of lymphotropic virus.

Base Sequence↗
PubMed2004

[Nucleotide polymorphism in the drought induced transcription factor CBF4 region of Arabidopsis thaliana and its molecular evolution analyses].

Intraspecific nucleotide polymorphism in the drought induced transcription factor CBF4 region of Arabidopsis thaliana was analyzed with 17 core accessions growing in different ecoclimate. High density of single nucleotide polymorphism (SNP) and insertion/deletion (Indel) were found, on average 1 SNP per 35.8 bp and 1 Indel per 143 bp. Nucleotide polymorphism in non-coding region was three times higher than that in coding region. In coding region of CBF4, SNP frequency is one SNP per 96.4 bp, one nonsynonymous mutation was detected from 25 av, 203 av and 244 av accessions, which is the 205th site amino acid variation: gly <--> val caused by the 1034th site (corresponding to 19,696 site nucleotide of GenBank No. AB015478 as 1) nucleotide variation: G <--> T. Statistical result of nucleotide diversity showed that linkage disequilibrium (LD) existed in large-scale region of CBF4 and recombination event was also detected in 5' non-coding region. Identical to the results of other genes of Arabidopsis, different regions of the gene were seemingly under different selective pressures. Balancing selection resulted in high nucleotide diversity in 3' non-coding region, and the neutral mutation hypothesis can explain the DNA polymorphism in coding region, whereas, nature positive selection in the population affected nucleotide variation in 5' non-coding region of gene.

Arabidopsis↗
PubMed2005

Molecular evolution of enolase.

Enolase (EC 4.2.1.11) is an enzyme of the glycolytic pathway catalyzing the dehydratation reaction of 2-phosphoglycerate. In vertebrates the enzyme exists in three isoforms: alpha, beta and gamma. The amino-acid and nucleotide sequences deposited in the GenBank and SwissProt databases were subjected to analysis using the following bioinformatic programs: ClustalX, GeneDoc, MEGA2 and S.I.F.T. (sort intolerant from tolerant). Phylogenetic trees of enolases created with the use of the MEGA2 program show evolutionary relationships and functional diversity of the three isoforms of enolase in vertebrates. On the basis of calculations and the phylogenetic trees it can be concluded that vertebrate enolase has evolved according to the "birth and death" model of evolution. An analysis of amino acid sequences of enolases: non-neuronal (NNE), neuron specific (NSE) and muscle specific (MSE) using the S.I.F.T. program indicated non-uniform number of possible substitutions. Tolerated substitutions occur most frequently in alpha-enolase, while the lowest number of substitutions has accumulated in gamma-enolase, which may suggest that it is the most recently evolved isoenzyme of enolase in vertebrates.

Animals↗
PubMed2005

Analysis of the molecular evolution of Listeria monocytogenes isolated from Japanese meats and environment.

Food contaminated by Listeria monocytogenes is a problem on a worldwide level because it is a serious food-borne pathogen. Although 3 evolutionary divisions have been reported for L. monocytogenes, the evolution of Japanese isolates has not yet been clarified. Thus, in order to determine the lineage of these Japanese isolates, we classified and conducted phylogenetic analysis of 407 bp (position 1116-1522) of the iap gene derived from 88 isolates from Japanese listeriosis patients, foods and environment. The isolates were classified into 18 types commonly accompanied by serotypes, and the types were divided into 3 lineages. Our results suggest that these Japanese isolates belong to the 3 lineages of L. monocytogenes isolated in other countries.

Animals↗
PubMed2006

Molecular evolution of serine/arginine splicing factors family (SR) by positive selection.

The serine-rich (SR) protein family is involved in the pre-mRNA splicing process and the DNA sequences of the corresponding genes are highly conserved in the metazoan organisms. The mammalian SR proteins consist of one or two characteristic RNA binding domains (RBD), containing the signature sequences RDAEDA and SWQDLKD and a RS (arginine/serine-rich) domain. We used the amino acid and nucleotide sequences deposited in GenBank and Swiss-Prot databases to perform a phylogenetic analysis using bioinformatics tools. The results of the phylogenetic trees suggest that this family has evolved by several gene duplication events as a result of a positive selection mechanism.

Amino Acid Sequence↗
PubMed1995

Molecular evolution of the multigene family of intracellular lipid-binding proteins.

The intracellular lipid-binding proteins are a group of homologous proteins which bind and facilitate the transport of fatty acids, bile acids and retinoids. The evolutionary relationship of 51 family members from vertebrates and invertebrates was analyzed. The inferred phylogeny implies the occurrence of at least 14 gene duplications and contains five regions where the branching order is statistically non-significant--this uncertainty explaining most inconsistencies between previous phylogenetic analyses. The phylogeny also suggests that the intestinal fatty acid-binding protein and the liver fatty acid-binding protein/ileal lipid-binding protein subfamilies diverged from the other subfamilies before the vertebrate-invertebrate split. Finally, results presented herein indicate that the putative fatty acid-binding domain of NMDA receptor 1 is unlikely to be a member of this family.

Amino Acid Sequence↗
PubMed1995

[Studies on the molecular evolution of glucose transporter gene family].

Glucose transporter gene family which was involved in the glucose metabolism in the body has been considered as a candidate gene in the development of diabetes mellitus. We compared the nucleotide and amino acid sequences of the family in different species; deduced the hydrophilicity and hydrophobicity distribution of the amino acid; calculated the genetic distance and constructed the phylogenetic trees by UPGMA and N-J method. The results showed that the members of glucose transporter gene family are homologous; all the members of this family have a similar topology; It is suggested that the family may derived from a remote common ancester in which the gene duplication events of different origins took place; this evolutionary process is advantageous to the stability of the structure. The different branch length in the phylogenetic trees constructed by the N-J method indicated difference of evolutionary rates in the process of evolution. Also, the difference between the trees at protein and nucleotide level may result from the hidden substitution in the genome.

Animals↗
PubMed1998

[Human immunodeficiency virus and AIDS in terms of reverse transcriptase and molecular evolution].

Human immunodeficiency virus type 1 (HIV-1) evolves rapidly in the host. The computer analysis of the HIV-1 genome has shown that the mutation manner is dependent on oligonucleotide sequences (in particular, six bases long); thus HIV-1 adaptively evolves. The six-base-long interaction between template-primer oligonucleotide and the reverse transcriptase (RT) has been revealed by the crystal structure of RT, in vitro termination assay of plymerization, and hydroxyl radical footprint analysis. It has been thought that AIDS is caused by the large numbers of HIV-1 quasispecies yielded by the adaptive and rapid evolution in the host. However, the slow evolution and the high levels of viral RNA in the progressive HIV-1 infected individuals (progressives) were recently reported; in contrast, the adaptive and rapid evolution and the low viral-RNA levels were reported in the non-progressives. This suggests that the physiological environment, e.g. pH and dNTP balance, in which RT works in the progressives is different from that in the non-progressives.

Acquired Immunodeficiency Syndrome↗