Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Evolutionary analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 199 records · Page 11Linked to original sources
PubMed1980

Mouse globin system: a functional and evolutionary analysis.

Structural and functional analysis of the mouse alpha-globin and beta-globin genes reveals that the globin genes are encoded in discontinous bits of coding information and that each gene locus is much more complex than was originally supposed. Each seems to consist of an array of several authentic genes as well as several apparently inactive pseudogenes. Comparison of the sequences of some of these genes to one another indicates that chromosomal DNA is a dynamic structure. Flanking and intervening sequences change in two ways: quickly, by duplication and extensive insertions and deletions, and slowly, by point mutation. Active coding sequences are usually limited to the slower mode of evolution. In addition to identifying fast and slow modes of evolution, it has also been possible to test the function of several signals that surround these genes and to identify those that appear to play a role in gene expression.

Animals↗
PubMed1999

Molecular and evolutionary analysis of Borrelia burgdorferi 297 circular plasmid-encoded lipoproteins with OspE- and OspF-like leader peptides.

We previously described two OspE and three OspF homologs in Borrelia burgdorferi 297 (D. R. Akins, S. F. Porcella, T. G. Popova, D. Shevchenko, S. I. Baker, M. Li, M. V. Norgard, and J. D. Radolf, Mol. Microbiol. 18:507-520, 1995; D. R. Akins, K. W. Bourell, M. J. Caimano, M. V. Norgard, and J. D. Radolf, J. Clin. Investig. 101:2240-2250, 1998). In this study, we characterized four additional lipoproteins with OspE/F-like leader peptides (Elps) and demonstrated that all are encoded on plasmids homologous to cp32 and cp18 from the B31 and N40 strains, respectively. Statistical analysis of sequence similarities using the binary comparison algorithm revealed that the nine lipoproteins from strain 297, as well as the OspE, OspF, and Erp proteins from the N40 and B31 strains, fall into three distinct families. Based upon the observation that these lipoproteins all contain highly conserved leader peptides, we now propose that the ancestors of each of the three families arose from gene fusion events which joined a common N terminus to unrelated proteins. Additionally, further sequence analysis of the strain 297 circular plasmids revealed that rearrangements appear to have played an important role in generating sequence diversity among the members of these three families and that recombinational events in the downstream flanking regions appear to have occurred independently of those within the lipoprotein-encoding genes. The association of hypervariable regions with genes which are differentially expressed and/or subject to immunological pressures suggests that the Lyme disease spirochete has exploited recombinatorial processes to foster its parasitic strategy and enhance its immunoevasiveness.

Amino Acid Sequence↗
PubMed1995

Remarkable N2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences.

To demonstrate the extent of phylogenetic diversity of diazotrophic bacteria associated with rice roots, we characterized phylogenetically 23 nifH gene sequences obtained by PCR amplification of mixed organism DNA extracted directly from rice roots without culturing the organisms. The analyses document the presence of eight novel NifH types, which appear to be a variety of significant components of the diazotrophic community, dominated mainly by proteobacteria.

Amino Acid Sequence↗
PubMed1997

Investigation of the dynamics of the spread of human immunodeficiency virus to brain and other tissues by evolutionary analysis of sequences from the p17gag and env genes.

The time of spread of human immunodeficiency virus type 1 (HIV-1) from lymphoid to nonlymphoid tissues in the course of infection was investigated by sequence comparisons of variants infecting a range of lymphoid and nonlymphoid tissues from three individuals with AIDS in the pl7gag gene and regions flanking the V1/V2 hypervariable regions. Phylogenetic analysis in both regions revealed several lineages in each individual that contained sequences from both lymphoid and nonlymphoid tissues such as the brain. This observation contrasts strongly with the previously described organ-specific sequences in the V3 region in this study population and other investigations. Although individual pairwise comparisons of relatively short sequences such as p17gag are subject to considerable stochastic error, we found that the diversity of gag sequences in variants from lymphoid tissue was consistently lower than that found among variants amplified from the brain. By estimating mean synonymous pairwise distances in the p17gag region, we were able to make an approximate calculation of the ages of populations in different tissues. Those from lymphoid tissue ranged from 2.65 to 5.6 years in the three study subjects, compared with 4.1 to 6.2 years for variants in the brain. Indeed, variants infecting the brain were no more closely related to each other than they were to variants infecting other tissues in the body. In two of the three individuals, these times of divergence indicate that infection of the brain may have occurred as an early event in the progression to disease, preceding the onset of AIDS by several years. This study is the first in which it was possible to estimate times of diversification in different tissues in vivo and is of importance in understanding the dynamics of the spread of HIV-1 into nonlymphoid tissues and its possible adaptation for replication in different cell types.

Acquired Immunodeficiency Syndrome↗
PubMed2003

Structural and evolutionary analysis of an orangutan foamy virus.

The full-length proviral genome of a foamy virus infecting a Bornean orangutan was amplified, and its sequence was analyzed. Although the genome showed a clear resemblance to other published foamy virus genomes from apes and monkeys, phylogenetic analysis revealed that simian foamy virus SFVora was evolutionarily equidistant from foamy viruses from other hominoids and from those from Old World monkeys. This finding suggests an independent evolution within its host over a long period of time.

Animals↗
PubMed1995

Genetic diversity of N2-fixing bacteria associated with rice roots by molecular evolutionary analysis of a nifD library.

The rhizosphere of wetland rice has significant N2-fixing activity. It has been suggested that N2 fixation in the rice root zone is associated with the activity of various N2-fixing heterotrophic bacteria that inhabit the rice rhizosphere. Because of the generic diversity, many different isolation media and conditions are required to count and isolate these bacteria. In an attempt to overcome any bias from culture-dependent methods we amplified nifD segments from crude rice root DNA by the polymerase chain reaction. The nifD fragments were then cloned into a pT7 Blue T-vector to construct a nifD library. Sixteen cloned nifD genes chosen at random from the library were sequenced. A comparison with published sequences indicated the presence of seven novel groups of NifD proteins, which implies the existence of at least seven components in the diazotrophic community of rice roots, dominated mainly by proteobacteria. We also observed genetic variability within the clusters, which suggests the coexistence of many closely related bacterial lineages. However, we did not find Azospirillum-like nifD clones, although many reports indicated the widespread presence of Azospirillum spp. Therefore, it remains to be clarified whether Azospirillum species are the widespread N2-fixing bacteria in rice roots.

Amino Acid Sequence↗
PubMed2005

Comparative and evolutionary analysis of genes encoding small GTPases and their activating proteins in eukaryotic genomes.

Both small GTPase and its activating protein (GAP) superfamilies exist in various eukaryotes. The small GTPases regulate a wide variety of cellular processes by cycling between active GTP- and inactive GAP-bound conformations. The GAPs promote GTPase inactivation by stimulating the GTP hydrolysis. In this study, we identified 111 small GTPases and 85 GAPs in rice, 65 GAPs in Arabidopsis, 90 small GTPases in Drosophila melanogaster, and 35 GAPs in Saccharomyces cerevisiaeby genome-wide analysis. We then analyzed and compared a total of 498 small GTPases and 422 GAPs from these four eukaryotic and human genomes. Both animals and yeast genomes contained five families of small GTPases and their GAPs. However, plants had only four of these five families because of a lack of the Ras and RasGAP genes. Small GTPases were conserved with common motifs, but GAPs exhibited higher and much more rapid divergence. On the basis of phylogenetic analysis of all small GTPases and GAPs in five eukaryotic organisms, we estimated that their ancestors had small sizes of small GTPases and GAPs and their large-scale expansions occurred after the divergence from their ancestors. Further investigation showed that genome duplications represented the major mechanism for such expansions. Nonsynonymous substitutions per site (Ka) and synonymous substitutions per site (Ks) analyses showed that most of the divergence due to a positive selection occurred in common ancestors, suggesting a major functional divergence in an ancient era.

Amino Acid Motifs↗
PubMed2002

Structural, functional, and evolutionary analysis of moeZ, a gene encoding an enzyme required for the synthesis of the Pseudomonas metabolite, pyridine-2,6-bis(thiocarboxylic acid).

BACKGROUND: Pyridine-2,6-bis(thiocarboxylic acid) (pdtc) is a small secreted metabolite that has a high affinity for transition metals, increases iron uptake efficiency by 20% in Pseudomonas stutzeri, has the ability to reduce both soluble and mineral forms of iron, and has antimicrobial activity towards several species of bacteria. Six GenBank sequences code for proteins similar in structure to MoeZ, a P. stutzeri protein necessary for the synthesis of pdtc. RESULTS: Analysis of sequences similar to P. stutzeri MoeZ revealed that it is a member of a superfamily consisting of related but structurally distinct proteins that are members of pathways involved in the transfer of sulfur-containing moieties to metabolites. Members of this family of enzymes are referred to here as MoeB, MoeBR, MoeZ, and MoeZdR. MoeB, the molybdopterin synthase activating enzyme in the molybdopterin cofactor biosynthesis pathway, is the most characterized protein from this family. Remarkably, lengths of greater than 73% nucleic acid homology ranging from 35 to 486 bp exist between Pseudomonas stutzeri moeZ and genomic sequences found in some Mycobacterium, Mesorhizobium, Pseudomonas, Streptomyces, and cyanobacteria species. CONCLUSIONS: The phylogenetic relationship among moeZ sequences suggests that P. stutzeri may have acquired moeZ through lateral gene transfer from a donor more closely related to mycobacteria and cyanobacteria than to proteobacteria. The importance of this relationship lies in the fact that pdtc, the product of the P. stutzeri pathway that includes moeZ, has an impressive set of capabilities, some of which could make it a potent pathogenicity factor.

Amino Acid Sequence↗
PubMed2001

Molecular evolutionary analysis of a histone gene repeating unit from Drosophila simulans.

A repeating unit of the histone gene cluster from Drosophila simulans containing the H1, H2A, H2B and H4 genes (the H3 gene region has already been analyzed) was cloned and analyzed. A nucleotide sequence of about 4.6 kbp was determined to study the nucleotide divergence and molecular evolution of the histone gene cluster. Comparison of the structure and nucleotide sequence with those of Drosophila melanogaster showed that the four histone genes were located at identical positions and in the same directions. The proportion of different nucleotide sites was 6.3% in total. The amino acid sequence of H1 was divergent, with a 5.1% difference. However, no amino acid change has been observed for the other three histone proteins. Analysis of the GC contents and the base substitution patterns in the two lineages, D. melanogaster and D. simulans, with a common ancestor showed the following. 1) A strong negative correlation was found between the GC content and the nucleotide divergence in the whole repeating unit. 2) The mode of molecular evolution previously found for the H3 gene was also observed for the whole repeating unit of histone genes; the nucleotide substitutions were stationary in the 3' and spacer regions, and there was a directional change of the codon usage to the AT-rich codons. 3) No distinct difference in the mode or pattern of molecular evolution was detected for the histone gene repeating unit in the D. melanogaster and D. simulans lineages. These results suggest that selectional pressure for the coding regions of histones, which eliminate A and T, is less effective in the D. melanogaster and D. simulans lineages than in the other GC-rich species.

Amino Acid Sequence↗
PubMed2004

Reproductive measures, fitness, and migrating Mennonites: an evolutionary analysis.

Given the same reproductive span, more children with shorter interbirth intervals and less parental attention per child should not do as well. There should be intermediate optima in family sizes, but only two studies have demonstrated optima. The goal here is to determine whether the relationship between fitness and fertility is linear and whether this relationship masks underlying variation in reproductive behaviors in a Mennonite congregation that lived in two disease settings, Prussia/Russia vs. Kansas. The relationships between children born and fitness were determined by calculating linear and quadratic regressions for total, Prussia/Russia vs. Kansas, and families with deaths vs. families with no deaths for total, Prussia/Russia, and Kansas. Variation was examined in terms of measures of reproductive success and reproductive span. Comparisons were made by t tests with Bonferroni correction. Regressions demonstrate equally well that the more children women bear, the higher the reproductive success, whether in the harsher disease ecology of rural Prussia/Russia or in less challenging rural Kansas and whether the women experience deaths or not. Prussian/Russian mothers bore significantly more children (6.5+/-0.3) than Kansan mothers (5.6+/-0.2) over longer reproductive spans but did not significantly increase the number of surviving children (4.9+/-0.2 vs. 4.7+/-0.2, respectively). Families experiencing deaths vs. no deaths exhibit significantly longer reproductive spans, reflecting a significantly earlier start at childbearing and a later finish, and produce significantly more children (5.4+/-0.2 vs. 4.2+/-0.2). Cox regressions were run, and the most significant covariates to negatively affect survivorship to 15 years were death in the family and length of the previous interbirth intervals. There was variation in families, but perhaps most had adequate nutrition, which may explain the lack of optima in fitness.

Adolescent↗
PubMed1988

Control of responding by sounds of different quality: an evolutionary analysis.

Two experiments investigated the acquisition of discriminations between two acoustic stimuli of different quality (noise bursts vs. a 2-kHz pulsed signal) when features of the everyday environment were incorporated into the experiments. In Experiment 1, rats were trained, using food, to press a lever. Throughout all sessions, 5-s trials of noise bursts (the random stimulus) were presented, after variable intertrial intervals, through a remote speaker mounted outside the experimental enclosure. The noise burst occurred randomly with respect to reinforcement of lever pressing and had no programmed relationship to the animal's behavior. When lever pressing was established, the 2-kHz signal was presented through a speaker adjacent to the response lever according to a different set of variable intertrial intervals. A response in the presence of the 2-kHz signal terminated the trial and was reinforced. The 2-kHz signal acquired control of responding within the first few trials, whereas the random stimulus exerted no control of responding. In Experiment 2, rats were trained to press the lever in the presence of the 2-kHz signal presented through the adjacent speaker on a variable intertrial interval. After 14 sessions, 5-s trials of noise bursts (random stimulus) were presented through the remote speaker on the second variable intertrial interval. The random stimulus initially elicited exploratory behavior, which then rapidly declined. Subsequently, the random stimulus exerted no or weak control of responding. The introduction of the random stimulus had no effect on responding in the presence of the adjacent stimulus. In Experiments 3 and 4 the random stimulus was presented through the adjacent speaker, and the stimulus correlated with reinforcement was presented through the remote speaker. In both experiments, there was persistent control of responding by the random stimulus and slow development of control by the stimulus correlated with reinforcement. In Experiment 5, both stimuli were presented through the adjacent speaker. There was persistent control of responding by the random stimulus.

Animals↗
PubMed2005

[In silico and systematic molecular evolutionary analysis of human SIAH1b inactivation].

"Seven in absentia homolog" (SIAH) is E3 ubiquitin ligase gene. It is reported that mice have three SIAH homolog genes, Siah1a, Siah1b and Siah2, while men have SIAH1 and SIAH2 genes. It has recently been reported that, among these genes, mouse Siah1b gene is a direct target of p53. However, the nature of human "SIAH1b" gene remains unknown. In this study, we identified it on chromosome X by using a computed searching methods (in silico cloning). Using cDNA from human tissues, we attempted to amplify this region by PCR, but failed to amplify it. By analyzing the structure of human "SIAH1b" gene, we found that Alu was inserted immediately before its coding region, and that this gene had a number of base substitutions in its coding region, compared to its homolog genes in mouse or man. From these findings, we suggest that human "SIAH1b" gene had been inactivated by insertion of Alu, and estimate that the inactivation occurred about 30-58 million years ago from the substitution rates of base during evolution.

Animals↗
PubMed2005

[Cloning and Evolutionary Analysis of Homologous Sequences of CYP86MF Gene in Cruciferae.].

In order to direct the construction of plant germplasms by elucidating the relatives among plants at the level of gene, CYP86MF gene analogues from 11 species of 6 genera in Cuciferae were respectively obtained by PCR strategy using gene specific primers designed from conserved regions of CYP86MF gene reported. Sequence comparisonindicated that the similarities among the genes at nucleotide level were over 80%, and the similarities at amino acid level remained above 70%. The differences between the genes at nucleotide and amino acid level between species were 1.0% ~ 5.7% and 2.6% ~ 7.3% respectively, while those between genera 5.6% ~ 22.5% and 7.3% ~ 31.2%, respectively. Phylogenetic analysis showed that Brassica was closely related to Raphanus, followed by Rorippa Scop, Arabidopsis Heynh, Capsella Medic orderly, most distantly related to Orychophrogmus. It was concluded that CYP86MF gene was not applicable to specie and subspecie taxon but genus taxon because the differences of sequences in nucleotides and amino acids were lower between species than genera.

Amino Acid Sequence↗