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PubMed1982

A mathematical model of biological evolution.

In order to understand generally how the biological evolution rate depends on relevant parameters such as mutation rate, intensity of selection pressure and its persistence time, the following mathematical model is proposed: dNn(t)/dt = (mn(t) - mu)Nn(t) + muNn-1(t) (n = 0,1,2,3,...), where Nn(t) and mn(t) are respectively the number and Malthusian parameter of replicons with step number n in a population at time t and mean is the mutation rate, assumed to be a positive constant. The step number of each replicon is defined as either equal to or larger by one than that of its parent, the latter case occurring when and only when mutation has taken place. The average evolution rate defined by v infinity identical to lim t leads to infinity sigma infinity n = o nNn(t)/t sigma infinity n = o Nn(t) is rigorously obtained for the case (i) mn(t) = mn is independent of t (constant fitness model), where mn is essentially periodic with respect to n, and for the case (ii) mn(t) = s(-1) n+[t/tau] (periodic fitness model), together with the long time average -m infinity of the average Malthusian parameter -m identical to sigma infinity n = o mn(t)Nn(t)/sigma infinity n = o Nn(t). The biological meaning of the results is discussed, comparing them with the features of actual molecular evolution and with some results of computer simulation of the model for finite populations.

Animals↗
PubMed1997

Analysis of the reaction coordinate of photosynthetic water oxidation by kinetic measurements of 355 nm absorption changes at different temperatures in photosystem II preparations suspended in either H2O or D2O.

Flash-induced absorption changes at 355 nm were measured at different temperatures within the range of 2 degrees C </= theta </= 25 degrees C in dark-adapted PS II core complexes from spinach [O2 evolution rate: 1500 +/- 100 micromol of O2 (mg of Chl)-1 h-1] that were dissolved either in H2O- or in D2O-containing buffer. Comparative measurements were performed at 20 degrees C in H2O- or D2O-containing suspensions of PS II membrane fragments [O2 evolution rate: 600 +/- 40 micromol of O2 (mg of Chl)-1 h-1]. The results obtained reveal the following: (a) The activation energies of the individual redox steps in the water oxidizing complex (WOC) are dependent on the redox state Si with EA(S1-->S2) = 14 kJ/mol, EA(S2-->S3) = 35 kJ/mol, and EA(S3-->-->S0 + O2) = 21 kJ/mol for theta > 11 degrees C, 67 kJ/mol for theta < 11 degrees C in PS II core complexes dissolved in H2O; (b) replacement of exchangeable protons by deuterons causes only minor changes (</=15%) of the activation energies; and (c) the rate constants of these reactions in PS II core complexes are characterized by H/D isotope ratios, ki(H)/ki(D), of 1.6, 2.3, and 1.5 for the transitions S1 --> S2, S2 --> S3, and S3 -->--> S0 + O2, respectively. The corresponding values of PS II membrane fragments are 1.3, 1.3, and 1. 4. Based on these results and corresponding EA data reported in the literature for PS II membrane fragments from spinach [Renger, G., & Hanssum, B. (1992) FEBS Lett. 299, 28-32] and PS II particles from the thermophilic cyanobacterium Synechococcus vulcanus Copeland [Koike, H., Hanssum, B., Inoue, Y., & Renger, G. (1987) Biochim. Biophys. Acta 893, 524-533], the reaction coordinate of the redox sequence in the WOC is inferred to be almost invariant to the evolutionary development from cyanobacteria to higher plants. Furthermore, the rather high activation energy of the S2 --> S3 transition provides evidence for a significant structural change coupled with this reaction. Implications for the mechanism of photosynthetic water oxidation are discussed.

Deuterium Oxide↗
PubMed1985

Constant rate of evolution in the antigenicity of glucose 6-phosphate dehydrogenase revealed by the enzyme inhibition method.

Rabbit and chicken antisera against pure and impure rat glucose 6-phosphate dehydrogenase (G6PD) samples were prepared, and their inhibition potencies (RIP) were measured against G6PDs from 26 vertebrate and invertebrate species. The results demonstrated that the -logRIP values of antisera against G6PDs from various test species neatly correlate with paleontologically estimated divergence times between rat and the test species. This suggests that the antigenicity of G6PD has evolved at a constant rate. The correlation coefficients were evidently greater with chicken antisera than with rabbit antisera, but did not markedly differ between chicken antisera elicited to pure and impure rat G6PD samples. Based on the data obtained with chicken antisera, it is estimated that lineages which separated 250-300 million years ago differ in their G6PDs by one unit of the -logRIP.

Animals↗
PubMed2005

Evolving dark energy with w not = -1.

Theories of evolving quintessence are constructed that generically lead to deviations from the w = -1 prediction of nonevolving dark energy. The small mass scale that governs evolution, m(phi) approximately = 10(-33) eV, is radiatively stable, and the "Why now?" problem is solved. These results rest on seesaw cosmology: Fundamental physics and cosmology can be broadly understood from only two mass scales, the weak scale nu and the Planck scale M. Requiring a scale of dark energy rho(DE)(1/4) governed by nu2/M and a radiatively stable evolution rate m(phi) given by nu4/M3 leads to a distinctive form for the equation of state w(z). Dark energy resides in the potential of a hidden axion field that is generated by a new QCD-like force that gets strong at the scale lambda approximately = nu2/M approximately = rho(DE)(1/4). The evolution rate is given by a second seesaw that leads to the axion mass m(phi) approximately = lambda2/f, with f approximately = M.

Journal Article↗
PubMed2005

Molecular characterization and hydrogen production of a new species of anaerobe.

For the fermentative hydrogen production process with carbohydrates, isolation and identification of hydrogen-producing bacteria (HPB) with high yield and high evolution rate are very important. Improved Hungater rolling tube technique and plate method of culture bottle (PMCB) were used to enumerate and isolate the HPB. The HPB-Li and Ren (HPB-LR) medium was designed to inoculate and isolate HPB under temperature of 37 degrees C and pH of 4.0-6.7. In this study, an isolate of HPB with high yield and high evolution rate was isolated, named Rennanqilyf3 (R3), which is a gram-positive, straight rod, non-spore forming, encapsulated, strict anaerobe, with long peritrichous flagella and three to four metachromatic granules. It performs ethanol-type fermentation, and glucose is its optimum carbon source for hydrogen production. The 16S rDNA sequencing of the R3 isolate indicated that it might be a new species. The hydrogen production capacity of the R3 isolate varied with the glucose concentration and pH. The optimum glucose concentration was 12.0 g/L (with H2 yield of 58.6 mmolH2/L-culture) and the optimum initial pH was 5.5 (with H2 yield of 34.2 mmolH2/L-culture). The maximum rate of cell proliferation were 0.46 and 0.63 g/L when glucose concentration was 15.0 g/L and pH was 5.5, respectively. The maximum yields of ethanol and acetic acid were achieved when the glucose concentration was 12.0 g/L and the pH was 5.5.

Bacteria, Anaerobic↗
PubMed2006

Comparative rates of evolution in endosymbiotic nuclear genomes.

BACKGROUND: The nucleomorphs associated with secondary plastids of cryptomonads and chlorarachniophytes are the sole examples of organelles with eukaryotic nuclear genomes. Although not as widespread as their prokaryotic equivalents in mitochondria and plastids, nucleomorph genomes share similarities in terms of reduction and compaction. They also differ in several aspects, not least in that they encode proteins that target to the plastid, and so function in a different compartment from that in which they are encoded. RESULTS: Here, we test whether the phylogenetically distinct nucleomorph genomes of the cryptomonad, Guillardia theta, and the chlorarachniophyte, Bigelowiella natans, have experienced similar evolutionary pressures during their transformation to reduced organelles. We compared the evolutionary rates of genes from nuclear, nucleomorph, and plastid genomes, all of which encode proteins that function in the same cellular compartment, the plastid, and are thus subject to similar selection pressures. Furthermore, we investigated the divergence of nucleomorphs within cryptomonads by comparing G. theta and Rhodomonas salina. CONCLUSION: Chlorarachniophyte nucleomorph genes have accumulated errors at a faster rate than other genomes within the same cell, regardless of the compartment where the gene product functions. In contrast, most nucleomorph genes in cryptomonads have evolved faster than genes in other genomes on average, but genes for plastid-targeted proteins are not overly divergent, and it appears that cryptomonad nucleomorphs are not presently evolving rapidly and have therefore stabilized. Overall, these analyses suggest that the forces at work in the two lineages are different, despite the similarities between the structures of their genomes.

Bacterial Proteins↗
PubMed2003

Rate of evolution of the specific surface area of surface snow layers.

The snowpack can impact atmospheric chemistry by exchanging adsorbed or dissolved gases with the atmosphere. Modeling this impact requires the knowledge of the specific surface area (SSA) of snow and its variations with time. We have therefore measured the evolution of the SSA of eight recent surface snow layers in the Arctic and the French Alps, using CH4 adsorption at liquid nitrogen temperature (77 K). The SSA of fresh snow layers was found to decrease with time, from initial values in the range 613-1540 cm2/g to values as low as 257 cm2/g after 6 days. This is explained by snow metamorphism, which causes modifications in crystal shapes, here essentially crystal rounding and the disappearance of microstructures. A parametrization of the rate of SSA decrease is proposed. We fit the SSA decrease to an exponential law and find that the time constant alpha(exp) (day(-1)) depends on temperature according to alpha(exp) = 76.6 exp (-1708/7), with Tin kelvin. Our parametrization predicts that the SSA of a snow layer evolving at -40 degrees C will decrease by a factor of 2 after 14 days, while a similar decrease at -1 degrees C will only require 5 days. Wind was found to increase the rate of SSA decrease, but insufficient data did not allow a parametrization of this effect.

Adsorption↗
PubMed1982

Effects of plutonium on soil microorganisms.

As a first phase in an investigation of the role of the soil microflora in Pu complex formation and solubilization in soil, the effects of Pu concentration, form, and specific activity on microbial types, colony-forming units, and CO(2) evolution rate were determined in soils amended with C and N sources to optimize microbial activity. The effects of Pu differed with organism type and incubation time. After 30 days of incubation, aerobic sporeforming and anaerobic bacteria were significantly affected by soil Pu levels as low as 1 mug/g when Pu was added as the hydrolyzable Pu(NO(3))(4) (solubility, <0.1% in soil). Other classes of organisms, except the fungi, were significantly affected at soil Pu levels of 10 mug/g. Fungi were affected only at soil Pu levels of 180 mug/g. Soil CO(2) evolution rate and total accumulated CO(2) were affected by Pu only at the 180 mug/g level. Because of the possible role of resistant organisms in complex formation, the mechanisms of effects of Pu on the soil fungi were further evaluated. The effect of Pu on soil fungal colony-forming units was a function of Pu solubility in soil and Pu specific activity. When Pu was added in a soluble, complexed form [Pu(2)(diethylenetriaminepentaacetate)(3)], effects occurred at Pu levels of 1 mug/g and persisted for at least 95 days. Toxicity was due primarily to radiation effects rather than to chemical effects, suggesting that, at least in the case of the fungi, formation of Pu complexes would result primarily from ligands associated with normal (in contrast to chemically-induced) biochemical pathways.

Journal Article↗
PubMed1998

Ribonuclease k6: chromosomal mapping and divergent rates of evolution within the RNase A gene superfamily.

We have localized the gene encoding human RNase k6 to within approximately 120 kb on the long (q) arm of chromosome 14 by HAPPY mapping. With this information, the relative positions of the six human RNase A ribonucleases that have been mapped to this locus can be inferred. To further our understanding of the individual lineages comprising the RNase A superfamily, we have isolated and characterized 10 novel genes orthologous to that encoding human RNase k6 from Great Ape, Old World, and New World monkey genomes. Each gene encodes a complete ORF with no less than 86% amino acid sequence identity to human RNase k6 with the eight cysteines and catalytic histidines (H15 and H123) and lysine (K38) typically observed among members of the RNase A superfamily. Interesting trends include an unusually low number of synonymous substitutions (Ks) observed among the New World monkey RNase k6 genes. When considering nonsilent mutations, RNase k6 is a relatively stable lineage, with a nonsynonymous substitution rate of 0.40 x 10(-9) nonsynonymous substitutions/nonsynonymous site/year (ns/ns/yr). These results stand in contrast to those determined for the primate orthologs of the two closely related ribonucleases, the eosinophil-derived neurotoxin (EDN) and eosinophil cationic protein (ECP), which have incorporated nonsilent mutations at very rapid rates (1.9 x 10(-9) and 2.0 x 10(-9) ns/ns/yr, respectively). The uneventful trends observed for RNase k6 serve to spotlight the unique nature of EDN and ECP and the unusual evolutionary constraints to which these two ribonuclease genes must be responding. [The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF037081-AF037090.]

Amino Acid Sequence↗
PubMed1999

Changes of Respiration Rate, Ethylene Evolution, and Abscisic Acid Content in Developing Inflorescence and Young Fruit of Olive (Olea europaea L. cv. Konservolia).

Simultaneous measurements of respiration, ethylene production, and abscisic acid (ABA) concentrations, as well as the growth parameters length, fresh weight (FW), and dry weight (DW) of olive (Olea europaea L. cv. Konservolia) inflorescence were carried out at short intervals (3-7 days) during the period from bud burst until the 3rd week after full bloom (AFB), when young fruit reached 8 mm in length. The axis of inflorescence elongated remarkably during the 3rd week after bud burst (ABB), massive bract shedding occurred during the 4th week ABB, full bloom (FB) was observed 7 weeks ABB, and massive floral organ abscission 1 week AFB. The results showed a continuous increase in inflorescence FW and DW from bud burst until 4 days before FB. Respiration rate, ethylene production, and levels of ABA were relatively high during the first 3 weeks ABB. After this period, respiration and ethylene followed a similar pattern of changes, inversely to that of ABA concentration. An accumulation of inflorescence ABA 6 and 4 days before FB was associated with the minimum values of respiration and ethylene production on the same dates. The sharp decrease in the ABA concentration during FB and 3 days later was followed by a high rise in ethylene and an increase in respiration rate, which both rose further 1 week AFB. The results suggest a possible correlation of ABA with the early stage of floral abscission, whereas ethylene production seems to be correlated with the terminal separatory activity in olive inflorescence abscission processes.Key Words. Abscisic acid-Abscission-Ethylene-Inflorescence-Olive-Respirationhttp://link.springer-ny.com/link/service/journals/00344/bibs/18n1p1.html

Journal Article↗
PubMed2001

Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins.

BACKGROUND: Detection of changes in a protein's evolutionary rate may reveal cases of change in that protein's function. We developed and implemented a simple relative rates test in an attempt to assess the rate constancy of protein evolution and to detect cases of functional diversification between orthologous proteins. The test was performed on clusters of orthologous protein sequences from complete bacterial genomes (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae), complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and partially sequenced mammalian genomes (human, mouse and rat). RESULTS: Amino-acid sequence evolution rates are significantly correlated on different branches of phylogenetic trees representing the great majority of analyzed orthologous protein sets from all three domains of life. However, approximately 1% of the proteins from each group of species deviates from this pattern and instead shows variation that is consistent with an acceleration of the rate of amino-acid substitution, which may be due to functional diversification. Most of the putative functionally diversified proteins from all three species groups are predicted to function at the periphery of the cells and mediate their interaction with the environment. CONCLUSIONS: Relative rates of protein evolution are remarkably constant for the three species groups analyzed here. Deviations from this rate constancy are probably due to changes in selective constraints associated with diversification between orthologs. Functional diversification between orthologs is thought to be a relatively rare event. However, the resolution afforded by the test designed specifically for genomic-scale datasets allowed us to identify numerous cases of possible functional diversification between orthologous proteins.

Animals↗
PubMed1999

Systematic biology of gymnotiform and mormyriform electric fishes: phylogenetic relationships, molecular clocks and rates of evolution in the mitochondrial rRNA genes

The phylogenetic relationships of both African and South American electric fish orders are reviewed at their intra-ordinal level taking into consideration recent studies in which cladistic principles have been employed. Several concordant topologies emerge from the different data sets, but some unsettled issues still remain. From the studies available, a consensus topology has been suggested for the Mormyriformes and for the Gymnotiformes. Subsequently, the evolutionary relationships of these two electric fish clades are considered within each respective superorder, i.e. in relation to the other osteoglossomorph and ostariophysan orders. The inter-ordinal phylogenies are used as a framework to test the molecular clock hypothesis with two gene fragments of the mitochondrial genome. Gymnotiformes, Siluriformes and Characiformes are accumulating mutations at the same pace in relation to their respective outgroups, but for all the other combinations of sister clades tested the molecular clock can be statistically rejected. Fossil records are then surveyed and used to calibrate absolute rates of genetic differentiation for each main lineage (orders) of both osteoglossomorphs and ostariophysans. The most conserved regions (stems) of the 12S and 16S gene fragments used are evolving at an average rate of 0.123 % 10(6 )years-1 for the osteoglossomorphs and 0.137 % 10(6 )years-1 for the ostariophysans, with no significant difference between these two values. The rate of mutation in the loops, the faster-evolving segments, estimated for closely related electric fish taxa is 0.82 % 10(6 )years-1 for four Brienomyrus species and 1.01 % 10(6 )years-1 for the four eigenmanniid genera. When the entire molecule (loops + stems) is considered, the rate of mutation in both mormyriforms and gymnotiforms converges to a rounded value of 0.23 % 10(6 )years-1.

Journal Article↗
PubMedDate not supplied

The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes.

The duplication of genes and even complete genomes may be a prerequisite for major evolutionary transitions and the origin of evolutionary novelties. However, the evolutionary mechanisms of gene evolution and the origin of novel gene functions after gene duplication have been a subject of many debates. Recently, we compiled 26 groups of orthologous genes, which included one gene from human, mouse, and chicken, one or two genes from the tetraploid Xenopus and two genes from zebrafish. Comparative analysis and mapping data showed that these pairs of zebrafish genes were probably produced during a fish-specific genome duplication that occurred between 300 and 450 Mya, before the teleost radiation (Taylor et al. 2001). As discussed here, many of these retained duplicated genes code for DNA binding proteins. Different models have been developed to explain the retention of duplicated genes and in particular the subfunctionalization model of Force et al. (1999) could explain why so many developmental control genes have been retained. Other models are harder to reconcile with this particular set of duplicated genes. Most genes seem to have been subjected to strong purifying selection, keeping properties such as charge and polarity the same in both duplicates, although some evidence was found for positive Darwinian selection, in particular for Hox genes. However, since only the cumulative pattern of nucleotide substitutions can be studied, clear indications of positive Darwinian selection or neutrality may be hard to find for such anciently duplicated genes. Nevertheless, an increase in evolutionary rate in about half of the duplicated genes seems to suggest that either positive Darwinian selection has occurred or that functional constraints have been relaxed at one point in time during functional divergence.

Amino Acid Sequence↗
PubMed1993

Region-specific rates of molecular evolution: a fourfold reduction in the rate of accumulation of "silent" mutations in transcribed versus nontranscribed regions of homologous DNA fragments derived from two closely related mouse species.

We have sequenced homologous DNA fragments of 2.7 and 2.8 kbp derived from the closely related mouse species Mus musculus domesticus (M. domesticus) and Mus musculus musculus (M. musculus), respectively. These two species diverged approximately 1 million years ago. Each DNA fragment contains 1.35 kbp of the 3' end of the constitutively expressed 2.2-kbp aprt (adenine phosphoribosyltransferase) gene and a similarly sized nontranscribed region downstream of the aprt gene. The aprt gene region contains protein coding sequences (0.35 kbp), intronic sequences (0.75 kbp), and a 3' nontranslated sequence (0.25 kbp). Both the M. domesticus and M. musculus downstream regions share three partial copies of the B1 repetitive element with the M. musculus downstream region containing an additional complete copy of this element. A comparison of the 2.7- and 2.8-kbp DNA fragments revealed a total of 63 molecular alterations (i.e., mutations) that were approximately fourfold more abundant in the nontranscribed downstream region than in the transcribed aprt gene. Of the 11 mutations observed in the transcribed region, 7 were found in introns, 3 in the 3' untranslated sequence, and 1 was a synonymous change in an exon. A comparison of the human and M. domesticus aprt genes has previously revealed no homology in either the intronic or 3' nontranslated regions with the exception of a 26-bp sequence in intron 3 and sequences at the exon/intron boundaries necessary for correct mRNA splicing (Broderick et al., Proc. Natl. Acad. Sci. USA, 84:3349, 1987). Therefore, there does not appear to be selective pressure for sequences within these regions. We conclude that there is a lower rate of accumulation of "silent" mutations in the transcribed mouse aprt gene than in a contiguous nontranscribed downstream region. A possible molecular mechanism involving preferential DNA repair for the transcribed region is discussed.

Adenine Phosphoribosyltransferase↗
PubMed2003

Evaluation of spectrofluorometry as a tool for estimation in fed-batch fermentations.

Native culture fluorescence was investigated as an additional source of information for predicting biomass and glucose concentrations in a fed-batch fermentation of Alcaligenes eutrophus. Partial least squares (PLS) regression and a feed forward neural network (FFNN) coupled with principle component analysis (PCA) were each used to model the kinetics of the fermentation. Data from three fermentations was combined to form a training set for model calibration and data from a fourth fermentation was used as the testing set. The fluorescent soft-sensors were compared with a previously developed feed forward neural network soft-sensor model which used oxygen uptake rate (OUR), carbon dioxide evolution rate (CER), aeration rate, feed rate, and fermentor volume to estimate biomass and glucose concentrations. The best model performance for predicting both biomass and glucose concentrations was achieved using the native fluorescence-based models. Real data predictions of the biomass concentration in the testing set were obtained using both the PLS and FFNN PCA modeling utilizing fluorescence measurements plus the rate of change of the fluorescence measurements. Accurate predictions of the glucose concentration in the testing set were obtained using the FFNN PCA modeling technique utilizing the rate of change of the fluorescence measurements. Substrate exhaustion was indicated qualitatively by a first-order PLS model utilizing the rate of change of fluorescence measurements. These results indicate that native culture fluorescence shows promise for providing additional valuable information to enhance predictive modeling which cannot be extracted from other easily acquired measurements.

Algorithms↗
PubMed1994

Response rates--an evolution.

The documented frequency of response of cancers to common chemotherapy agents and combinations appears to have decreased over the decades. Multiple reasons exist for this decline including: changes in eligibility and evaluability criteria; changes in the type of patients entered onto trial; and, altered criteria for response and methods for response assessment. The disinclination to publish negative results also permits a bias in a favor of overestimating a drug's efficacy. Circumspection now is advised in assessing data from older trials.

Antineoplastic Agents↗