Shaping of Drosophila alcohol dehydrogenase through evolution: relationship with enzyme functionality.

abstract：:The nearly neutral theory attributes most nucleotide substitution and polymorphism to genetic drift acting on weakly selected mutants, and assumes that the selection coefficients for these mutants are drawn from a continuous distribution. This means that parameter estimation can require numerical integration, and this...

journal_title：Journal of molecular evolution

authors： Welch JJ,Eyre-Walker A,Waxman D

更新日期：2008-10-01 00:00:00

abstract：:There have been two distinct phases of evolution of the genetic code: an ancient phase--prior to the divergence of the three domains of life, during which the standard genetic code was established--and a modern phase, in which many alternative codes have arisen in specific groups of genomes that differ only slightly f...

journal_title：Journal of molecular evolution

authors： Sengupta S,Higgs PG

更新日期：2015-06-01 00:00:00

abstract：:The circadian clock regulates a multitude of plant developmental and metabolic processes. In crop species, it contributes significantly to plant performance and productivity and to the adaptation and geographical range over which crops can be grown. To understand the clock in barley and how it relates to the component...

journal_title：Journal of molecular evolution

authors： Calixto CP,Waugh R,Brown JW

更新日期：2015-02-01 00:00:00

abstract：:Prediction of the thermodynamic behaviors of biomolecules at high temperature and pressure is fundamental to understanding the role of hydrothermal systems in the origin and evolution of life on the primitive Earth. However, available thermodynamic dataset for amino acids, essential components for life, cannot represe...

journal_title：Journal of molecular evolution

authors： Kitadai N

更新日期：2014-04-01 00:00:00

abstract：:Males of three inbred lines of Drosophila melanogaster were heat-shocked 90 min at 37 degrees C. The progenies from treated and untreated males mated with untreated females of the same line were checked for their chromosomal insertion patterns of various mobile elements by either in situ hybridization or Southern blot...

journal_title：Journal of molecular evolution

authors： Arnault C,Biémont C

更新日期：1989-05-01 00:00:00

abstract：:The study of genetic evolution within the context of adaptive radiations offers insights to genes and selection pressures that result in rapid morphological change. Cichlid fishes are very species-rich and variable in coloration, behavior, and morphology, and so provide a classical model system for studying the geneti...

journal_title：Journal of molecular evolution

authors： Fan S,Elmer KR,Meyer A

更新日期：2011-08-01 00:00:00

abstract：:In studies of molecular evolution, the assumption that protein evolution is reversible has often been made, but rarely tested. Here we use a large set of orthologous murid protein coding sequences to perform a simple test of reversibility, and find no evidence to reject the assumption of reversibility in protein evolu...

journal_title：Journal of molecular evolution

authors： Smith NG,Eyre-Walker A

更新日期：2001-05-01 00:00:00

abstract：:Collagen is an important structural protein and the most abundant protein in mammals. In several research fields, structural analysis of collagens is performed. Fibrillar collagens almost entirely consist of continuous repeats of GXY, where G is glycine, X is often proline or alanine and Y is often hydroxyproline or a...

journal_title：Journal of molecular evolution

authors： Kleinnijenhuis AJ,van Holthoon FL

更新日期：2018-06-01 00:00:00

abstract：:Alu elements are not distributed homogeneously throughout the human genome: old elements are preferentially found in the GC-rich parts of the genome, while young Alus are more often found in the GC-poor parts of the genome. The process giving rise to this differential distribution remains poorly understood. Here we in...

journal_title：Journal of molecular evolution

authors： Belle EM,Webster MT,Eyre-Walker A

更新日期：2005-03-01 00:00:00

abstract：:Several algae that were previously classified in the phylum Xanthophyta (yellow-green algae) were assigned in 1971 to a new phylum, Eustigmatophyta. It was anticipated that the number of algae reclassified to Eustigmatophyta would increase. However, due to the fact that the morphological characteristics that segregate...

journal_title：Journal of molecular evolution

authors： Ehara M,Hayashi-Ishimaru Y,Inagaki Y,Ohama T

更新日期：1997-08-01 00:00:00

abstract：:Tests for positive selection have mostly been developed to look for diversifying selection where change away from the current amino acid is often favorable. However, in many cases we are interested in directional selection where there is a shift toward specific amino acids, resulting in increased fitness in the specie...

journal_title：Journal of molecular evolution

authors： Thiltgen G,Dos Reis M,Goldstein RA

更新日期：2017-01-01 00:00:00

abstract：:The 70-kDa heat-shock protein (HSP70) constitutes the most conserved protein present in all organisms that is known to date. Based on global alignment of HSP70 sequences from organisms representing all three domains, numerous sequence signatures that are specific for prokaryotic and eukaryotic homologs have been ident...

journal_title：Journal of molecular evolution

authors： Gupta RS,Golding GB

更新日期：1993-12-01 00:00:00

abstract：:A model of nucleotide substitution that allows the transition/transversion rate bias to vary across sites was constructed. We examined the fit of this model using likelihood-ratio tests by analyzing 13 protein coding genes and 1 pseudogene. Likelihood-ratio testing indicated that a model that allows variation in the t...

journal_title：Journal of molecular evolution

authors： Huelsenbeck JP,Nielsen R

更新日期：1999-01-01 00:00:00

abstract：:To get deeper insight into the evolution of phosphoenolpyruvate carboxylase we have identified PEPC fragments (about 1,100 bp) of another 12 plants species not yet investigated in this context. The selected plants include one Chlorophyta, two Bryophyta, four Pteridophyta, and five Spermatophyta species. The obtained p...

journal_title：Journal of molecular evolution

authors： Gehrig HH,Heute V,Kluge M

更新日期：1998-01-01 00:00:00

abstract：:Synechococcus and Prochlorococcus have made great contributions to earth's photosynthetic biomass. ATP-binding cassette (ABC) protein systems have been characterized to play important roles in various physiological functions, including carbon fixation, phosphate assimilation, and vitamin B(12) metabolism. In this stud...

journal_title：Journal of molecular evolution

authors： Bu L,Xiao J,Lu L,Xu G,Li J,Zhao F,Li X,Wu J

更新日期：2009-10-01 00:00:00

abstract：:Many proteins exhibit sequence periodicity, often correlated with a visible structural periodicity. The statistical significance of such periodicity can be assessed by means of a chi-squared-based test, with significance thresholds being calculated from shuffled sequences. Comparison of the complete proteomes of 45 sp...

journal_title：Journal of molecular evolution

authors： Gatherer D,McEwan NR

更新日期：2005-04-01 00:00:00

abstract：:The codons in four mammalian messenger RNAs (rabbit beta hemoglobin, rat pre-proinsulin, rat pre-growth hormone and human chorionic somatomammotropin) show a predominance of C and G in third nucleotide positions. The C:U ratio is about 2 to 1, and the G:A ratio is about 4 to 1. The possibility is discussed that this d...

journal_title：Journal of molecular evolution

authors： Jukes TH

更新日期：1978-06-20 00:00:00

abstract：:A major goal of evolutionary biology is to understand how beneficial mutations translate into increased fitness. Here, we study beneficial mutations that arise in experimental populations of yeast evolved in glucose-rich media. We find that fitness increases are caused by enhanced maximum growth rate (R) that come at ...

journal_title：Journal of molecular evolution

authors： Sezmis AL,Malerba ME,Marshall DJ,McDonald MJ

更新日期：2018-02-01 00:00:00

abstract：:Selection pressures on proteins are usually measured by comparing homologous nucleotide sequences (Zuckerkandl and Pauling 1965). Recently we introduced a novel method, termed volatility, to estimate selection pressures on proteins on the basis of their synonymous codon usage (Plotkin and Dushoff 2003; Plotkin et al. ...

journal_title：Journal of molecular evolution

authors： Plotkin JB,Dushoff J,Desai MM,Fraser HB

更新日期：2006-11-01 00:00:00

abstract：:Transfer RNA (tRNA) is the central intellectual property in the evolution of life on Earth. tRNA evolved from repeats and inverted repeats of known sequence. The anticodon and the T stem-loop-stems are homologs with significant conserved sequence identity. A number of models have been advanced to explain tRNA evolutio...

journal_title：Journal of molecular evolution

authors： Burton ZF

更新日期：2020-04-01 00:00:00

abstract：:The best reconstructions of the history of life will use both molecular time estimates and fossil data. Errors in molecular rate estimation typically are unaccounted for and no attempts have been made to quantify this uncertainty comprehensively. Here, focus is primarily on fossil calibration error because this error ...

journal_title：Journal of molecular evolution

authors： van Tuinen M,Hadly EA

更新日期：2004-08-01 00:00:00

abstract：:We outline a method for estimating quantitatively the influence of point mutations and selection on the frequencies of codons and amino acids. We show how the mutation rate, i.e., the rate of amino acid replacement due to point mutation, can be affected by the codon usage as well as by the rates of the involved base e...

journal_title：Journal of molecular evolution

authors： Frömmel C,Holzhütter HG

更新日期：1984-01-01 00:00:00

abstract：:Lake Malawi is home to more than 450 species of endemic cichlids, which provide a spectacular example of adaptive radiation. To clarify the phylogenetic relationships among these fish, we examined the presence and absence of SINEs (short interspersed repetitive elements) at orthologous loci. We identified six loci at ...

journal_title：Journal of molecular evolution

authors： Takahashi K,Nishida M,Yuma M,Okada N

更新日期：2001-10-01 00:00:00

abstract：:Studies during the last 20 years have shown that the chromosomes of many organisms, especially those of higher vertebrates, consist of a series of segments having different properties. These can be recognized as, for example, G- and R-bands. Recent studies have indicated that genes tend to lie in the R-bands rather th...

journal_title：Journal of molecular evolution

authors： Sumner AT,de la Torre J,Stuppia L

更新日期：1993-08-01 00:00:00

abstract：:The RpoS sigma factor in proteobacteria regulates genes in stationary phase and in response to stress. Although of conserved function, the RpoS regulon may have different gene composition across species due to high genomic diversity and to known environmental conditions that select for RpoS mutants. In this study, the...

journal_title：Journal of molecular evolution

authors： Chiang SM,Schellhorn HE

更新日期：2010-06-01 00:00:00

abstract：:Human endogenous retroviruses (HERVs) are the remnants of ancient germ cell infection by exogenous retroviruses and occupy up to 8% of the human genome. It has been suggested that HERV sequences have contributed to primate evolution by regulating the expression of cellular genes and mediating chromosome rearrangements...

journal_title：Journal of molecular evolution

authors： Macfarlane C,Simmonds P

更新日期：2004-11-01 00:00:00

abstract：:Factors involved in the selection of the 20 protein L-alpha-amino acids during chemical evolution and the early stages of Darwinian evolution are discussed. The selection is considered on the basis of the availability in the primitive ocean, function in proteins, the stability of the amino acid and its peptides, stabi...

journal_title：Journal of molecular evolution

authors： Weber AL,Miller SL

更新日期：1981-01-01 00:00:00

abstract：:We have investigated the evolvability of an insoluble random polypeptide, RP3-34, to a soluble form through iterative mutation and selection with the aid of the green fluorescent protein (GFP) folding reporter. To assess the solubility of the polypeptides in the selected clones of each generation, the polypeptide gene...

journal_title：Journal of molecular evolution

authors： Ito Y,Kawama T,Urabe I,Yomo T

更新日期：2004-02-01 00:00:00

abstract：:Calmodulin is a calcium-binding EF-hand protein that is an activator of many enzymes as well as ion pumps and channels. Due to its multiple targets and its central role in the cell, understanding the evolutionary history of calmodulin genes should provide insights into the origin of genetic complexity in eukaryotes. W...

journal_title：Journal of molecular evolution

authors： Karabinos A,Bhattacharya D

更新日期：2000-08-01 00:00:00

abstract：:We describe the structure of a gene expressed in the salivary gland cells of the dipteran Chironomus tentans and show that it encodes 1 of the approximately 15 secretory proteins exported by the gland cells. This sp115,140 gene consists of approximately 65 copies of a 42-bp sequence in a central uninterrupted core blo...

journal_title：Journal of molecular evolution

authors： Galli J,Lendahl U,Paulsson G,Ericsson C,Bergman T,Carlquist M,Wieslander L

更新日期：1990-07-01 00:00:00