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PubMed2004

Male-biased mutation rate and divergence in autosomal, z-linked and w-linked introns of chicken and Turkey.

To investigate mutation-rate variation between autosomes and sex chromosomes in the avian genome, we have analyzed divergence between chicken (Gallus gallus) and turkey (Meleagris galopavo) sequences from 33 autosomal, 28 Z-linked, and 14 W-linked introns with a total ungapped alignment length of approximately 43,000 bp. There are pronounced differences in the mean divergence among autosomes and sex chromosomes (autosomes [A] = 10.08%, Z chromosome = 10.99%, and W chromosome = 5.74%), and we use these data to estimate the male-to-female mutation-rate ratio (alpha(m)) from Z/A, Z/W, and A/W comparisons at 1.71, 2.37, and 2.52, respectively. Because the alpha(m) estimates of the three comparisons do not differ significantly, we find no statistical support for a specific reduction in the Z chromosome mutation rate (Z reduction estimated at 4.89%, P = 0.286). The idea of mutation-rate reduction in the sex chromosome hemizygous in one sex (i.e., X in mammals, Z in birds) has been suggested on the basis of theory on adaptive mutation-rate evolution. If it exists in birds, the effect would, thus, seem to be weak; a preliminary power analysis suggests that it is significantly less than 18%. Because divergence may vary within chromosomal classes as a result of variation in mutation and/or selection, we developed a novel double-bootstrapping method, bootstrapping both by introns and sites from concatenated alignments, to estimate confidence intervals for chromosomal class rates and for alpha(m). The narrowest interval for the alpha(m) estimate is 1.88 to 2.97 from the Z/W comparison. We also estimated alpha(m) using maximum likelihood on data from all three chromosome classes; this method yielded alpha(m) = 2.47 and approximate 95% confidence intervals of 2.27 to 2.68. Our data are broadly consistent with the idea that mutation-rate differences between chromosomal classes can be explained by the male mutation bias alone.

Animals↗
PubMed1997

Patterns and rates of indel evolution in processed pseudogenes from humans and murids.

Patterns and rates of indel (deletions and insertions) evolution were characterized in 156 independently derived processed pseudogenes from humans and murids (mice and rats). A total of 441 deletions and 161 insertions were unambiguously identified. On a subset of 109 pseudogenes, we verified and confirmed the assumption that indels occur almost exclusively in the pseudogene and, therefore, in comparisons between pseudogenes and their functional paralogs, it is possible to assign polarity to the indel event. By comparing the characteristics of terminal truncations with those of internal deletions, we find support for the hypothesis that truncations are generated through a different pathway than internal deletions. The number of deletions and insertions per pseudogene was found to increase monotonically with time. Deletions occur on average once every 40 nucleotide substitutions, whereas insertions are much rarer, occurring once every 100 substitutions, indicating that the mechanisms involved in deletion formation are most probably different from those responsible for the formation of insertions. The age of the pseudogene, however, explained only 20 and 13%, respectively, of the variation in the number of deletions and insertions per site, indicating that factors other than evolutionary time may play a significant role in the evolutionary dynamics of indel accumulation. Since the rate of substitution has been previously shown to be higher in murids than in humans, we deduce that deletions and insertions accumulate proportionally faster in murids than in humans. Deletions and insertions in murid and human genomes do not contribute significantly to genome size.

Animals↗
PubMed2006

The kinetics of Lagenidium giganteum growth in liquid and solid cultures.

AIMS: Production of the mosquito biolarvacide Lagenidium giganteum in solid culture has been proposed as an economic alternative to production in liquid culture because of observations of improved shelf life and efficacy upon storage. Understanding the differences between these production systems and estimating growth rate in solid culture are important for commercialization. In order to address these needs a logistic model was developed to describe the growth kinetics of L. giganteum produced in solid and liquid cultures. METHODS AND RESULTS: Kinetic parameters in the logistic model were estimated by nonlinear regression of CO2 evolution rate (CER) and biomass data from solid and liquid cultivation experiments. Lagenidium giganteum biomass was measured using DNA extracted directly from samples. The logistic model was fit to experimental biomass and CER data with low standard errors for parameter estimates. The model was validated in two independent experiments by examining prediction of biomass using on-line CER measurements. CONCLUSIONS: There were significant differences between maximum biomass density, maintenance coefficients, and specific growth rates for liquid and solid cultures. The maximum biomass density (mg dw ml-1) was 11 times greater for solid cultivation compared with liquid cultivation of L. giganteum; however, the maintenance coefficient (mg CO2 h-1 (mg dw)-1) was six times greater for liquid cultivation than in solid cultivation. The specific growth rate at 30 degrees C was approximately 30% greater in liquid cultivation compared with solid cultivation. Slower depletion of substrate and lower endogenous metabolism may explain the longer shelf life of L. giganteum produced in solid culture. SIGNIFICANCE AND IMPACT OF THE STUDY: A simple logistic model was developed which allows real-time estimation of L. giganteum biomass from on-line CER measurements. Parameter estimates for liquid and solid cultivation models also elucidated observations of longer shelf life for production in solid culture.

Biomass↗
PubMed1991

Bluetongue virus evolution: sequence analyses of the genomic S1 segments and major core protein VP7.

The S1 segments, encoding the group-specific antigen, VP7, from the five United States prototype BTV serotypes were cloned as full-length entities. The nucleotide and deduced amino acid sequences of segment S1 of BTV-2 were determined and compared with BTV-10, -11, -13, and -17, completing the sequencing of this cognate gene segment from all five US BTV serotypes. Each segment is 1156 bp long and contains an open reading frame encoding the 349-amino acid VP7 protein. Most (greater than 94%) of the amino acids of VP7 among the serotypes are conserved, including the location (position 255) of a single lysine residue. Secondary structure analyses of VP7 predict a putative eight-stranded beta-barrel between amino acid positions 150 and 250, a structure similar to that observed in ssRNA viruses. The S1 genes are flanked by conserved 5' and 3' noncoding regions. Stem-loop structures are predicted at the 3' end of each gene (nucleotide positions 1058-1097). The S1 segments of BTV-2, -10, -11, and -17 have greater than 93% of the nucleotides conserved, while less than 80% of their bases are identical with BTV-13. Analyses of nucleotide mismatches in each codon position of the VP7 open reading frame, transition frequencies, and evolutionary distances show that of the five, BTV-13 is the most distantly related and that BTV-10 and -17 are the most closely related serotypes. Evolutionary distance calculations of segment L2 from BTV-10, -11, and -17 concur with these observations. Comparison of this relationship with hybridization data of segment M3, which codes for VP5, suggests that BTV-17 has evolved by a combination of genetic drift and genomic reassortment. The data also indicate that the five US BTV serotypes are derived from two distinct gene pools. Evolution distances were used to estimate an evolution rate of 2.2 x 10(-3) nucleotide substitution/site/year for BTV segment S1. This rate is similar to the genes of retroviruses and implies an absence of RNA polymerase proofreading activity for dsRNA viruses.

Amino Acid Sequence↗
PubMed1996

Classical swine fever virus diversity and evolution.

By analysing the nucleotide sequence data generated from both the E2 (gp55) and the NS5B genes of classical swine fever virus (CSFV), in addition to previously published data from the 5'NCR, we were able to divide 115 CSFV isolates into two major groups, five subgroups and two disparate isolates. Further discrimination was possible by analysis of sequence data from the E2 region. The three sequencing based methods were compared to monoclonal antibody (MAb) typing and to limited restriction enzyme (RE) mapping. Although both MAb and RE methods confirmed the previous classification the resolution was inferior. We estimated an approximate evolution rate for CSFV from an analysis of the virus variation observed in a single geographical area over a 6 year period. Applying this proposed rate to each of our deduced CSFV subgroups enabled us to calculate the approximate dates of divergence for each subgroup.

Animals↗
PubMed2006

[Analysis of nucleotide diversity at the cytochrome b and cytochrome oxidase 1 genes at the population, species, and genus levels].

Algorithms of nucleotide diversity measures and other measures of genetic divergence at the molecular level are analyzed. Based on a database of p-distances, we have compared genetic divergence of populations (1) and taxa of different rank, such as sibling species (2), species within a genus (3), and species from different genera within a family (4). Based on the theory and algorithms of distance calculation from the primary DNA sequences, as well as the actual distances estimated from literature, it is recommended to use in analysis of experimental data a specific model selected from the eight available ones. The empirical data for more than 24,000 vertebrate and invertebrate species demonstrate that the data series are realistic and interpretable when p-distance or its various estimates are used. This testifies to the applicability of p-distance for most interspecies and intraspecies comparisons of genetic divergence up to the family level by two genes compared. Data on p-distances revealed various and increasing levels of genetic divergence of the sequences of genes Cyt-b and Co-1 in four groups compared. Mean unweighted scores of distances for the four groups were as follows: Cyt-b (1) 1.55 +/- 0.56, (2) 5.52 +/- 1.34, (3) 10.69 +/- 1.34, (4) 18.51 +/- 2.09 and Co-1 (1) 0.55 +/- 0.19, (2) 4.91 +/- 0.83, (3) 9.66 +/- 0.72, (4) 14.69 +/- 1.02. Differences in divergence between the genes themselves at the four levels were also found, although the total mean distances for the two genes did not show statistically significant differences. This conforms to the ample evidence showing different and nonuniform evolution rates of these and other genes and their various regions. The results of the analysis of the nucleotide and allozyme divergence within species and higher taxa of animals, first, are in a good agreement with these results, including data on protein gene markers, and, second, this evidence suggests that in animals, phyletic evolution is likely to prevail at the molecular level, while speciation mainly corresponds to the type D1 geographic model). The prevalence of the D1 speciation mode does not mean that the other modes are absent. There are at least seven various modes of speciation. Recognition of speciation modes is a task that seems to require construction of a quantitative genetic model (theory) of speciation. Although, in view of a vast diversity of the possible causes of reproductive isolating barriers (RIBs) and speciation initiation, as well as the "empirical nature" of the formalized approach, proposed in the present work, some newly arising questions may be left without an answer. Their solution probably lied in increasing the number of descriptors and members of equations, proposed in this study, on the basis of DNA markers and other genomic characteristics.

Animals↗
PubMed1998

The carboxyl-terminal tripeptide of the manganese-stabilizing protein is required for quantitative assembly into photosystem II and for high rates of oxygen evolution activity.

The extrinsic manganese stabilizing protein of photosystem II is required for Mn retention by the O2-evolving complex, accelerates the rate of O2 evolution, and protects photosytem II against photoinhibition. We report results from studies of the in vitro reconstitution of spinach photosytem II with recombinant manganese stabilizing protein with C-terminal deletions of two, three, and four amino acids. The deletions were the result of amber mutations introduced by site-directed mutagenesis. Removal of the C-terminal dipeptide (Glu-Gln) did not diminish the ability of the manganese stabilizing protein either to rebind to or to restore high rates of O2 evolution to photosystem II preparations depleted of the native protein. Deletion of the C-terminal tripeptide (Leu-Glu-Gln) resulted in weakened but specific binding of manganese stabilizing protein to photosystem II and minimal recovery of O2 evolution activity. Removal of the C-terminal tetrapeptide (Gln-Leu-Glu-Gln) eliminated the ability of the subunit to interact stably with all of its available binding sites on photosystem II, as evidenced by the fact that this mutant was totally inactive in restoring O2 evolution activity. Evidence is presented to indicate that these mutational effects on the binding and function of the manganese stabilizing protein may be due to major changes in tertiary structure. The truncation mutations lacking either the C-terminal tri- or tetrapeptide exhibit apparent size increases of 25 and 40%, respectively, when compared either to a mutant lacking the C-terminal dipeptide or to the wild-type protein.

Arabidopsis↗
PubMed2007

Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula.

Codon bias is generally thought to be determined by a balance between mutation, genetic drift, and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes. In this paper, I study associations between codon usage, gene expression, and molecular evolution at synonymous and nonsynonymous sites in the long-lived, woody perennial plant Populus tremula (Salicaceae). Using expression data for 558 genes derived from expressed sequence tags (EST) libraries from 19 different tissues and developmental stages, I study how gene expression levels within single tissues as well as across tissues affect codon usage and rates sequence evolution at synonymous and nonsynonymous sites. I show that gene expression have direct effects on both codon usage and the level of selective constraint of proteins in P. tremula, although in different ways. Codon usage genes is primarily determined by how highly expressed a genes is, whereas rates of sequence evolution are primarily determined by how widely expressed genes are. In addition to the effects of gene expression, protein length appear to be an important factor influencing virtually all aspects of molecular evolution in P. tremula.

Codon↗
PubMed2006

[Expression and function of AOX1 gene family during the greening of etiolated rice seedlings].

Under constant light, increases in V(t) (total respiration rate), V(alt) (capacity of alternative pathway), and V(alt)/V(t) ration values (Figs.1-3) in fully etiolated rice seedlings leaves were founded. Northern hybridization with special probes for rice AOX1a, AOX1b and AOX1c revealed that the AOX1c mRNA was mainly present under constant light (Fig.4). SHAM (salicylhydroxamic acid) decreased the relative oxygen evolution rate and chlorophyll content during the rapid greening of the etiolated rice seedlings (Figs.6, 7). We found that illumination caused bigger increase in V(alt) in fully etiolated rice seedlings than in any partially etiolated rice seedlings (Fig.8A), while the soluble sugar contents did not show any significant differences (Fig.8B). This revealed the connection between greening process and cyanide-resistant respiration in rice seedlings. We infer that one of the possible functions of the cyanide-resistant respiration is to maintain a high rate of respiratory electron transport for the essential biosynthesis processes at the early stage of chloroplast development. Cyanide-resistant respiration may provide a regulatory mechanism for the balance between the requirements of the energy and substances.

Blotting, Northern↗
PubMed1994

Partitioning of the Leaf CO2 Exchange into Components Using CO2 Exchange and Fluorescence Measurements.

Photorespiration was calculated from chlorophyll fluorescence and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) kinetics and compared with CO2 evolution rate in the light, measured by three gas-exchange methods in mature sunflower (Helianthus annuus L.) leaves. The gas-exchange methods were (a) postillumination CO2 burst at unchanged CO2 concentration, (b) postillumination CO2 burst with simultaneous transfer into CO2-free air, and (c) extrapolation of the CO2 uptake to zero CO2 concentration at Rubisco active sites. The steady-state CO2 compensation point was proportional to O2 concentration, revealing the Rubisco specificity coefficient (Ksp) of 86. Electron transport rate (ETR) was calculated from fluorescence, and photorespiration rate was calculated from ETR using CO2 and O2 concentrations, Ksp, and diffusion resistances. The values of the best-fit mesophyll diffusion resistance for CO2 ranged between 0.3 and 0.8 s cm-1. Comparison of the gas-exchange and fluorescence data showed that only ribulose-1,5-bisphosphate (RuBP) carboxylation and photorespiratory CO2 evolution were present at limiting CO2 concentrations. Carboxylation of a substrate other than RuBP, in addition to RuBP carboxylation, was detected at high CO2 concentrations. A simultaneous decarboxylation process not related to RuBP oxygenation was also detected at high CO2 concentrations in the light. We propose that these processes reflect carboxylation of phosphoenolpyruvate, formed from phosphoglyceric acid and the subsequent decarboxylation of malate.

Journal Article↗
PubMedDate not supplied

[The parameters of the molecular evolution of the 11S globulins of plants].

Nucleotide sequences of cloned cDNA coding for soybean storage protein glycinin and deduced amino acid sequences of basic polypeptides (subfamily II) of glycinin are compared with the amino acid sequences of 11S globulins from other plants. An average number of amino acid substitutions in various evolutionary branches is calculated. A proportional dependence is established between the average number of substitutions per site (the evolutionary distance) and the hypothetical term of divergence of corresponding taxa. The evolution rate of 11S globulins and a term of divergence of the two subfamilies of 11S globulin polypeptides in Fabaceae is estimated.

Amino Acid Sequence↗
PubMed1988

Effects of linkage on rates of molecular evolution.

When an advantageous mutation is fixed in a population by selection, a closely linked selectively neutral or mildly detrimental mutation may "hitchhike" to fixation along with it. It has been suggested that hitchhiking might increase the rate of molecular evolution. Computer simulations and a mathematical argument show that complete linkage to either advantageous or deleterious mutations does not affect the substitution of selectively neutral mutations. However, the simulations show that linkage to selected background mutations decreases the rate of fixation of advantageous mutations and increases the rate of fixation of detrimental mutations. This is true whether the linked background mutations are advantageous or detrimental, and it verifies and extends previous observations that linkage tends to reduce the effects of selection on evolution. These results can be interpreted in terms of the Hill-Robertson effect: a locus linked to another locus under selection experiences a reduction in effective population size. The interpretation of differences in evolutionary rates between different genomes or different regions of a genome may be confounded by the effects of strong linkage and selection. Recombination is expected to reduce the overall rate of molecular evolution while enhancing the rate of adaptive evolution.

Biological Evolution↗
PubMed2003

Stimulation of potato tuber respiration by cold stress is associated with an increased capacity of both plant uncoupling mitochondrial protein (PUMP) and alternative oxidase.

The CO2 evolution of intact potato tubers (Solanum tuberosum, L., var. "Bintje") was analyzed during a 10-day period of their warm (25 +/- 2 degrees C) or cold (5 +/- 1 degrees C) storage, to evaluate cold-stress effects on expression and activities of plant uncoupling mitochondrial protein (PUMP) and alternative oxidase (AOX). CO2 evolution rates were analyzed at 20 degrees C, to reflect their possible capacities. The 20 degrees C CO2 production declined from 13 to 8 mg kg(-1) h(-1) after 2 days of warm storage and then (after 3 to 7 days) decreased from 8 to 6.5 mg kg(-1) h(-1). In contrast, 20 degrees C CO2 evolution did not change after the first day of cold storage, increased up to 14.5 mg kg(-1) h(-1) after 2 days, and decreased to about 12 mg kg(-1) h(-1) after 3 to 7 days of cold storage. Cold storage increased PUMP expression as detected by Western blots and led to elevated capacities of both PUMP (44%) and CN-resistant AOX (10 times), but not the cytochrome pathway. Since we found that cold storage led to about the same mitochondrial respiration of 40 nmol O2 min(-1) mg(-1) attributable to each of the respective proteins, we conclude that both AOX and PUMP equally contribute to adaptation of potato tubers to cold.

Adaptation, Physiological↗
PubMed2006

Evolutionary mechanisms of persistence and diversification of a calicivirus within endemically infected natural host populations.

In order to understand the evolutionary mechanisms of persistence and diversification within the Caliciviridae, we have been exploiting endemic infection of feline calicivirus within five geographically distinct household groups of cats. By sequencing immunodominant and variable regions of the capsid gene, we identified the relative contribution of the different evolutionary processes employed by the virus to ensure its long-term survival in the host population. Such strategies included progressive evolution of a given variant of a strain through mutation accumulation within an individual, sequential reinfection with either a variant of the same strain or with a different strain, and mixed infection. Recombination between different strains in this study has been reported in detail elsewhere (K. P. Coyne et al., J. Gen. Virol. 87:921-926, 2006). Here, we provide evidence to suggest that true long-term persistent infection in individuals is relatively rare, with the majority of apparent viral carriers undergoing a combination of progressive evolution and cyclical reinfection. Progressive evolution at the individual level and variant reinfection at both the individual and population levels were associated with positive selection. Two measures of evolution rate were determined; for a virus progressively evolving within an individual (1.32 x 10(-2) to 2.64 x 10(-2) substitutions per nucleotide per year, i.e., no transmission) and for a strain circulating within a population (3.84 x 10(-2) to 4.56 x 10(-2) substitutions per nucleotide per year, i.e., including transmission). Reiteration of both progressive evolution and variant reinfection appeared to lead to a gradual increase in the diversity of a given strain of virus, both in the individual and in the population, until eventually new strains emerged.

Animals↗
PubMed2002

Evidence for a slowed rate of molecular evolution in the order acipenseriformes.

A test of the hypothesis that the members of the order Acipenseriformes (sturgeons and paddlefishes) possess a slowed rate of molecular evolution was carried out by conducting relative-rate comparisons with representatives of four groups of teleost fishes (Cypriniformes, Elopomorpha, Salmonidae, and Percomorpha) using 21 nuclear or mitochondrial protein loci and the nuclear and mitochondrial small subunit rRNA genes, obtained from the literature or our own research. In 70 out of 81 comparisons between individual taxa (86%), acipenseriform sequences showed slower rates of change than the homologous teleost loci examined. When teleost sequences are considered together, 21 of the 23 loci show slower rates of substitution in the acipenseriform lineage. Teleost proteins show 1.85 times as many unique amino acid differences as acipenseriform proteins, when both are compared with outlier sequences. These results support a hypothesis of slowed molecular evolutionary rate in the Acipenseriformes.

Animals↗
PubMed2006

The rate of adaptive evolution in enteric bacteria.

Here we estimate the rate of adaptive substitution in a set of 410 genes that are present in 6 Escherichia coli and 6 Salmonella enterica genomes. We estimate that more than 50% of amino acid substitutions in this set of genes have been fixed by positive selection between the E. coli and S. enterica lineages. We also show that the proportion of adaptive substitutions is uncorrelated with the rate of amino acid substitution or gene function but that it may be correlated with levels of synonymous codon usage bias.

Adaptation, Biological↗
PubMed1998

Genetic evolution of hepatitis G virus in chronically infected individual patients.

Comparative sequence analysis of different isolates of hepatitis G virus (HGV) has demonstrated significant intersubject genetic heterogeneity, but few data on intrasubject genetic evolution have been reported. To further investigate the genetic diversification of the HGV genome, 36 plasma samples from eleven patients chronically infected with HGV serially obtained 2-4 years apart were analysed. We determined the viral nucleotide sequence of the 5' non-coding (NC) and the NS3 regions by directly sequencing the RT-PCR amplified products obtained from the viral RNAs. Intrasubject sequence variation was found to be 1.3-2.4 x 10(-3) base substitutions per genome site per year within the 5' NC region and 1.3-9.4 x 10(-3) base substitutions per genome site per year within the NS3 region. Depending on the genomic region analysed (i.e. 5' NC or NS3 region), pairwise comparisons and phylogenetic reconstructions showed that intersubject genetic distances were 17.5- to 20.8-fold greater than intrasubject ones. Overall, the evolution rate of HGV in the regions analysed is not significantly different from that found in hepatitis C virus.

Chronic Disease↗
PubMed2006

Photophysical and photocatalytic properties of SrTiO3 doped with Cr cations on different sites.

Usually, SrTiO3 monodoped with Cr cations at the Ti4+ site hardly shows visible light photocatalytic activity. Revealing the origin of this issue is important for us to find an alternative approach to make SrTiO3 active under visible light irradiation. In this paper, two Cr-doped SrTiO3-(Sr0.95Cr0.05)TiO3 and Sr(Ti0.95Cr0.05)O3-were synthesized by a conventional solid-state reaction method, and their photophysical and photocatalytic properties were studied comparatively. It was found that both (Sr0.95Cr0.05)TiO3 and Sr(Ti0.95Cr0.05)O3 showed considerable absorption to visible light. However, their photocatalytic activities for H2 evolution from aqueous methanol solution under visible light irradiation were significantly different: the H2 evolution rate over (Sr0.95Cr0.05)TiO3 (approximately 21 micromol/h) was more than 100 times that over Sr(Ti0.95Cr0.05)O3 (approximately 0.2 micromol/h). X-ray photoelectron spectroscopy analysis results revealed that the Cr cations doped at the Sr2+ site were all trivalent state (Cr3+), while those doped at the Ti4+ site were mixed valent states (Cr3+ and Cr6+). The different photocatalytic activities of H2 evolution are supposed to closely relate to the different valent states of Cr doped at different sites (Sr2+ or Ti4+) in SrTiO3. Possible electronic structures of (Sr0.95Cr0.05)TiO3 and Sr(Ti0.95Cr0.05)O3 were proposed in relation to their photophysical and photocatalytic properties.

Catalysis↗