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At least 271 records · Page 15Linked to original sources
PubMed2005

Increased rates of molecular evolution in an equatorial plant clade: an effect of environment or phylogenetic nonindependence?

A recent study of environmental effects on rates of molecular evolution in the plant subgenus Mearnsia shows that species occurring in more equatorial latitudes have higher rates of substitution in rDNA sequences as compared to their more southerly congeners (Wright et al. 2003). However, we believe that the statistical approach employed by Wright et al. (2003) insufficiently accounts for the phylogenetic nonindependence of the species examined, given that all six equatorial species of Mearnsia form a clade. To distinguish between the effect of latitude and that of phylogenetic nonindependence, we have employed a variety of comparative approaches that use independent contrasts to test for an effect of environment across this entire subgenus. We find very little evidence for an effect of latitude on rate of molecular evolution using these approaches and believe that the shared evolutionary history of the clade is a plausible explanation of the apparent rate difference between equatorial and subequatorial Mearnsia species.

DNA, Plant↗
PubMed1991

The relative rate of DNA evolution in primates.

In 73 relative-rate tests involving the sequences of 17 genes between humans and six nonhuman primate taxa, there is only one significant (P less than 0.01) difference in evolutionary rate--i.e., that between human and Old World-monkey psi eta-globin genes. No evolutionary rate difference between humans and Old World monkeys is evident from analysis of 18 other genes with a total length of 6 kb. This and the comparison, between humans and other primate taxa, of new extended psi eta-globin sequences suggest that earlier observations of evolutionary-rate differences between humans and other primates were based on differences that are peculiar to psi eta-globin and that are not representative of the whole genome, which appears to be evolving at a stochastically uniform rate. This is supported by whole-genome single-copy DNA and mitochondrial DNA comparisons, neither of which shows any evidence of evolutionary-rate variation among primate taxa. Uniformity in the evolutionary rate of the DNA of primate and other mammalian taxa is inconsistent with current mammalian fossil-record interpretation. Either there has been a general slowing down in rate across lineages or the fossil record has been misinterpreted.

Animals↗
PubMed1996

Synchronization affector of autonomous short-period-sustained oscillation of Saccharomyces cerevisiae.

When the yeast Saccharomyces cerevisiae was grown under aerobic continuous culture, an autonomous short-period-sustained oscillation appeared. This oscillation was observed in concentrations of various extracellular and intracellular parameters, such as ethanol, acetate, glycogen, dissolved oxygen and intracellular pH. In this work the synchronization affecter of this oscillation was investigated. Ethanol was found not to be the synchronizer of the oscillation because a pulse of ethanol did not affect the phase or period of the oscillation. The oscillation was dependent on the aeration rate, i.e., the oscillation occurred only between 150 and 600 ml min-1. However, the oxygen concentration did not influence synchronization as an upward shift in the oxygen concentration of the gas flow did not affect the sustainability of the oscillation. On the other hand, synchronization was stopped by an enhanced gas flow rate, keeping dissolved oxygen tension at the oscillatory condition, suggesting that synchronization was caused by a volatile compound in the culture. A stepwise increase in carbon dioxide concentration of the gas flow rate ceased synchronization, yet the oscillation seem to continue in each individual cell. Oscillatory behaviour of intracellular pH and carbon dioxide evolution rate showed a phase difference of 90 degrees. Based on these facts it is postulated that carbon dioxide, through the influence of its dissociation on intracellular pH, could be the synchronization affector of the autonomous short-period-sustained oscillation of S. cerevisiae.

Carbon Dioxide↗
PubMed2001

External doses in the environment from the Tokai-mura criticality accident.

On 30 September 1999, a criticality accident occurred at a uranium processing plant operated by JCO in Tokai-mura, Japan and the criticality remained for about 20 h. Almost all doses to the neighbouring residents were brought by neutrons and gamma rays emitted from the facility rather than fission products released to the environment. External doses in the environment were evaluated using radiation monitoring data and radiation transport calculation. A pattern of the dose rate evolution was modelled based on the records of gamma ray monitors in the JCO facilities. Relations between the ambient dose equivalent rates of neutrons/gamma rays and the distance from the facility were determined from the monitoring data obtained around the accident site. Conversion from the ambient dose equivalent to the effective dose equivalent was made assuming the energy spectra calculated by the radiation transport code, ANISN. It was estimated that the people who stayed outside the 350 m zone would receive doses of less than 1 mSv.

Gamma Rays↗
PubMed1997

Phylogeny and rates of molecular evolution of planktonic foraminifera: SSU rDNA sequences compared to the fossil record.

Planktonic foraminifera are marine protists, whose calcareous shells form oceanic sediments and are widely used for stratigraphic and paleoenvironmental analyses. The fossil record of planktonic foraminifera is compared here to their molecular phylogeny inferred from ribosomal DNA sequences. Eighteen partial SSU rDNA sequences from species representing all modern planktonic families (Globigerinidae, Hastigerinidae, Globorotaliidae, Candeinidae) were obtained and compared to seven sequences representing the major groups of benthic foraminifera. The phylogenetic analyses indicate a polyphyletic origin for the planktonic foraminifera. The Candeinidae, the Globorotaliidae, and the clade Globigerinidae + Hastigerinidae seem to have originated independently, at different epochs in the evolution of foraminifera. Inference of their relationships, however, is limited by substitution rates of heterogeneity. Rates of SSU rDNA evolution vary from 4.0 x 10(-9) substitutions/site/year in the Globigerinidae to less than 1.0 x 10(-9) substitutions/site/year in the Globorotaliidae. These variations may be related to different levels of adaptation to the planktonic mode of life. A clock-like evolution is observed among the Globigerinidae, for which molecular and paleontological data are congruent. Phylogeny of the Globorotaliidae is clearly biased by rapid rates of substitution in two species (G. truncatulinoides and G. menardii). Our study reveals differences in absolute rates of evolution at all taxonomic levels in planktonic foraminifera and demonstrates their effect on phylogenetic reconstructions.

Animals↗
PubMed2005

The evolution of mutation rate in finite asexual populations.

In this article, we model analytically the evolution of mutation rate in asexual organisms. Three selective forces are present. First, everything else being equal, individuals with higher mutation rate have a larger fitness, thanks to the energy and time saved by not replicating DNA accurately. Second, as a flip side, the genome of these individuals is replicated with errors that may negatively affect fitness. Third, and conversely, replication errors have a potential benefit if beneficial mutations are to be generated. Our model describes the fate of modifiers of mutation rate under the three forces and allows us to predict the long-term evolutionary trajectory of mutation rate. We obtain three major results. First, in asexuals, the needs for both adaptation and genome preservation are not evolutionary forces that can stabilize mutation rate at an intermediate optimum. When adaptation has a significant role, it primarily destabilizes mutation rate and yields the emergence of strong-effect mutators. Second, in contrast to what is usually believed, the appearance of modifiers with large mutation rate is more likely when the fitness cost of each deleterious mutation is weak, because the cost of replication errors is then paid after a delay. Third, in small populations, and even if adaptations are needed, mutation rate is always blocked at the minimum attainable level, because the rate of adaptation is too slow to play a significant role. Only populations whose size is above a critical mass see their mutation rate affected by the need for adaptation.

Adaptation, Physiological↗
PubMed1985

Flexibility of scoliosis. What does it mean? Is this terminology appropriate?

This work is a critical analysis of the term "flexibility of scoliosis." The authors demonstrate that this measure includes two very different and noncorrelated phenomena: the collapse and the reducibility of the structural curve. In 228 paralytic curves, these two phenomena were quantified and correlated with different parameters of scoliosis: sex, stage of maturation, curve pattern, number of vertebrae in the curve, spinal and abdominal test values, and the scoliotic evolution rate. Reducibility can be predicted since it is an elasticity process. Collapse is more complex, but it is a prognostic factor for evolution and effectiveness of treatment. The preliminary results of a similar study of idiopathic scoliosis are the same.

Adolescent↗
PubMed1995

Mitochondrial DNA sequence evolution in sharks: rates, patterns, and phylogenetic inferences.

Abundant representation of sharks in the fossil record makes this group a superb system in which to investigate rates and patterns of molecular evolution and to explore the strengths and weaknesses of phylogenetic inferences from molecular data. In this report, the molecular evolution of the cytochrome b gene in sharks is described and the information related to results from phylogenetic analysis of the data evaluated in the light of a phylogeny derived independently of the molecular data. Across divergent lineages of sharks there is evidence for significant substitution rate variation, departure from compositional equilibrium, and substantial homoplasy; nevertheless, the signal of evolutionary history is evident in patterns of shared transversions and amino acid replacements.

Animals↗
PubMed1976

Increase effected by calcium ion in the rate of oxygen evolution from preparations of Phormidium luridum.

The presence of Ca2+ causes a twentyfold or greater increase in the rate of oxygen evolution by cell-free preparations of Phormidium luridum. The requirement for Ca2+ is specific; other divalent cations are much less effective or are inhibitory. The rate of the Hill reaction is maximal at 30 mM CaCl2 in both detergent-free and Brij 35 preparations. The 3-(3,4-dichlorophenyl)-1,1-dimethylurea-insensitive component of oxygen-evolving activity in each preparation also shows the requirement for added Ca2+. This indicates that Ca2+ is acting close to the oxygen-evolving reaction center of Photosystem II. Defatted bovine serum albumin increases the rate of oxygen evolution in the detergent-free preparation, but does not compete with Ca2+, discounting fatty acid mediation of the effects of Ca2+. Neither excess Hill acceptor nor uncouplers of photophosphorylation diminish the stimulatory effects of Ca2+.

Calcium↗
PubMedDate not supplied

[Molecular bases of evolution].

The general notions of the theory of evolution are listed. The unity of the "engineering principles" of the living nature is emphasized. The generalists and specialists species are discussed. The estimation of their evolution rates must be different if it is expressed by the number of species or by the morphological changes. The principles of "protein engineering" of the organisms and the role of metals in protein evolution are discussed. It is suggested that in the presence of ions of transition metals and zinc the Fox's proteinoids can possess more specific forms of enzymatic activity. In the evolution of language the horizontal transfer plays a much more important role than in the biological evolution. However in this case also the initial basis of the language remains. The random drift is considered and it is shown that in concordance with the neutralist theory there are no grounds to replace the calculation of the rates of mutational changes per time unity by the calculation per generation. The molecular drive is the main source of the evolutionary novelties. The drive is connected with drift. The synonymic mutations and the mutations in non-functional DNA are evolutionary important. The future mathematical theory of evolution must be based on the theory of Markov's chains with the stochastic matrix changing along the chain and containing the set of the non-diagonal members equal to zero. The results obtained in the theory of ontogeny are presented. The evolution of species is the evolution of ontogenies, the formation of the molecular theory of evolution can be possible only on the basis of the molecular theory of ontogeny. The internal causes of extinction of species reduce the accumulation of neutral and pseudo-neutral mutations.

Animals↗
PubMed1979

[Sulfate transport across the limiting double membrane or envelope, of spinach chloroplasts].

Evidence is presented for low rates of carrier-mediated uptake of sulphate, thiosulphate and sulphite into the stroma of the C3 plant Spinacia oleracea. Uptake of sulphate in the dark was followed using two techniques (1) uptake of sulphate [35S] as determined by silicon oil centrifugal filtration and (2) uptake as indicated by inhibition of CO2-dependent O2 evolution rates after addition of sulphate. Sulphate, thiosulphate and sulphite were transported across the envelope leading to an accumulation in the chloroplasts. Sulphate for each molecule of sulphate entering the chloroplast, one molecule of phosphate leaves the stroma, and vice-versa. The uptake of sulphate by isolated intact chloroplasts exchanging for internal free phosphate induced a lower rate of photophosphorylation, which in turn inhibited CO2-dependent O2 evolution. The presence, on the inner membrane of the chloroplasts envelope, of a specific sulphate carrier, distinct from the phosphate translocator, is discussed.

Adenosine Diphosphate↗
PubMed2006

No accelerated rate of protein evolution in male-biased Drosophila pseudoobscura genes.

Sexually dimorphic traits are often subject to diversifying selection. Genes with a male-biased gene expression also are probably affected by sexual selection and have a high rate of protein evolution. We used SAGE to measure sex-biased gene expression in Drosophila pseudoobscura. Consistent with previous results from D. melanogaster, a larger number of genes were male biased (402 genes) than female biased (138 genes). About 34% of the genes changed the sex-related expression pattern between D. melanogaster and D. pseudoobscura. Combining gene expression with protein divergence between both species, we observed a striking difference in the rate of evolution for genes with a male-biased gene expression in one species only. Contrary to expectations, D. pseudoobscura genes in this category showed no accelerated rate of protein evolution, while D. melanogaster genes did. If sexual selection is driving molecular evolution of male-biased genes, our data imply a radically different selection regime in D. pseudoobscura.

Amino Acid Substitution↗
PubMed2005

Post-anthesis development of inferior and superior spikelets in rice in relation to abscisic acid and ethylene.

The purpose of this study was to test the hypothesis that the interaction between abscisic acid (ABA) and ethylene may be involved in mediating the post-anthesis development of spikelets in rice (Oryza sativa L.). Two rice genotypes were field-grown, and the changes of ABA, ethylene, and 1-aminocylopropane-1-carboxylic acid (ACC) levels in spikelets during grain filling and their relationships with endosperm-division and grain-filling rates were investigated. The results showed that earlier-flowering superior spikelets exerted dominance over later-flowering inferior spikelets in endosperm cell-division and grain-filling rates. The two genotypes behaved the same. Later-flowering spikelets had higher levels of ethylene and ACC than earlier-flowering spikelets. The ethylene evolution rate was significantly and negatively correlated with the cell division and grain filling rates. By contrast to ethylene, later-flowering spikelets contained a lower ABA content/concentration and showed a low content ratio of ABA to ACC than earlier-flowering ones. The cell-division and grain-filling rates were significantly and positively correlated with both ABA contents and the ratio of ABA to ACC. Application of cobalt ion (inhibitor of ethylene synthesis) or ABA at an early grain-filling stage significantly increased endosperm cell division rate and cell number, grain-filling rate, and grain weight of inferior spikelets. Application of ethephon (an ethylene-releasing agent) or fluridone (an inhibitor of carotenoid synthesis) had the opposite effect. The results suggest that antagonistic interactions between ABA and ethylene mediate endosperm cell-division and grain-filling in rice. A higher ratio of ABA to ethylene in rice spikelets is required to maintain a faster grain-filling rate.

Abscisic Acid↗
PubMed2006

[Progress in the study of gene duplication].

Gene duplication is one of the most important factors that influence the evolution of genome size, the origination of novel gene, the genetic robustness against null mutations, the speciation, etc. Duplication can be created by unequal crossing over, retroposition, or whole genome (or chromosomal) duplication. In this review, we summarized the studies of the molecular mechanisms of gene duplication, the preservation of duplicated gene, the selections acting on duplicated gene, the alternative ways of divergence and the evolution rate.

Animals↗
PubMed2002

[Mortality rate trends for breast cancer in Rosario, Argentina. Association with socioeconomic factors].

This report is based on data from death certificates of all women whose cause of death was breast cancer, residents in Rosario City, during two 5-year-periods: 1977-81 and 1988-92, in order to know these rates evolution. Deaths, which were allocated to the last residence of the decedents, were aggregated into the 22 census areas of the city. Age-standardized mortality rates (SMR) by area were correlated with socioeconomic variables. The SMR for the whole city was not different in the two studied periods: 38%000 and 36%000, respectively. However, while small changes were found in the high socioeconomic areas, important increments were found in the poorest ones, mainly in postmenopausal women. Consequently, geographic correlations also changed between the two studied periods. While in the first period negative correlations were found with variables considered as socioenvironmental pointers, such as fertility and infant mortality rates, these associations were positive in the last one.

Aged↗
PubMed2006

Transition event statistics in genetics and disordered kinetics. Theoretical approaches for extracting rate distributions from experimental data.

We study the analogies between the theory of rate processes in disordered systems and the overdispersed molecular clocks in evolutionary biology. A biological "molecular clock" expresses the statistics of the number of amino acid or nucleotide substitutions during evolution. Random variations of the evolution rates lead to statistical (overdispersed) molecular clocks which are described by random point processes with random substitution rates. We find that the models for overdispersed molecular clocks are equivalent to those of the random-rate or random channel models used in disordered kinetics. The number of transport (reaction) events in disordered kinetics plays the same role as the number of substitution events in molecular biology. We study the connections between the (observed) statistics of the transition events and the statistics of random rate coefficients and random channels; a unified approach is developed which is valid both in molecular biology and in disordered kinetics. We develop methods for extracting statistical information about the variations of rate coefficients from experimental or observed data regarding the fluctuations of the numbers of substitution, reaction, or transport events. For systems with static disorder, the observed statistics of the number of reaction events, expressed in terms of probabilities at a given time or by the cumulants of the number of transition events at a given time, contains the information necessary for evaluating the cumulants or the probability density of the rate coefficients or the density of states for random channel kinetics. For dynamic disorder this is not possible; further information about multitime probability distributions of the reaction events is needed.

Amino Acid Substitution↗
PubMed1988

Light inhibition of mitochondrial respiration in a mutant of Chlamydomonas reinhardtii devoid of ribulose-1,5-bisphosphate carboxylase/oxygenase activity.

The effect of light on mitochondrial respiration has been investigated in Chlamydomonas reinhardtii rcl-u-1-10-6C, a mutant devoid of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activity. No CO2 uptake was observed in the light, confirming that there was no Rubisco activity, but the CO2 evolution rate was diminished by 65 to 80%. This inhibition was ascribable to a decrease in the tricarboxylic acid cycle (Krebs cycle) activity. At the same time, O2 evolution associated with stimulation of the O2 uptake appears. Darkness or addition of DCMU fully reversed the effect of light, indicating that the inhibitory process is linked to photosystem activities. Levels of pyridine nucleotides (NAD(H) and NADP(H)) and adenine nucleotides (ATP and ADP), the most probable mediators of the interaction between photosynthesis and respiration, were measured in dark and in light. During a dark to light transition the level of NADPH increased significantly whereas the NAD(H) pool remained almost fully oxidized. The level of ADP was always extremely low. These results suggest that the inhibition of Krebs cycle activity is due to a competition for cytosolic ADP between chloroplastic photophosphorylations and oxidative phosphorylations.

Chlamydomonas↗
PubMed1996

A remarkable nonlinear invariant for evolution with heterogeneous rates.

A model for DNA or protein sequence evolution is proposed where each position belongs to one of two distinct classes. The two classes evolve at different rates. For a phylogeny on four species, we find a cubic function of 4-tuple occurrence frequencies that is nontrivially invariant no matter what the proportion of positions in each rate class. This result refutes the major criticism of nonlinear polynomial invariants.

DNA↗