Selection conflicts, gene expression, and codon usage trends in yeast.

abstract：:The human S100 gene family encodes the EF-hand superfamily of calcium-binding proteins, with at least 14 family members clustered relatively closely together on chromosome 1q21. We have analyzed the most recently available genomic sequence of the human S100 gene cluster for evidence of tandem gene duplications during ...

journal_title：Journal of molecular evolution

authors： Kulski JK,Lim CP,Dunn DS,Bellgard M

更新日期：2003-04-01 00:00:00

abstract：:cDNA encoding the adhesive protein of the mussel Mytilus coruscus (Mcfp1) was isolated. The coding region encoded 848 amino acids (a.a.) comprising the 20-a.a. signal peptide, the 21-a.a. nonrepetitive linker, and the 805-a.a. repetitive domain. Although the first 204 nucleotides and the 3'-untranslated region of Mcfp...

journal_title：Journal of molecular evolution

authors： Inoue K,Takeuchi Y,Takeyama S,Yamaha E,Yamazaki F,Odo S,Harayama S

更新日期：1996-10-01 00:00:00

abstract：:It is known that globin genes contain three exons with the middle exon coding for a four-helical supersecondary structure responsible for heme binding. Since this portion of the globin peptide chain can be structurally superimposed onto the cytochrome c and cytochrome b5 chains (Argos and Rossmann 1979), it can be inf...

journal_title：Journal of molecular evolution

authors： Argos P,Rossmann MG

更新日期：1980-12-01 00:00:00

abstract：:The neutral theory of molecular evolution states that most mutations are deleterious or neutral. It results that the evolutionary rate of a given position in an alignment is a function of the level of constraint acting on this position. Inferring evolutionary rates from a set of aligned sequences is hence a powerful m...

journal_title：Journal of molecular evolution

authors： Dutheil J

更新日期：2008-09-01 00:00:00

abstract：:An emergent problem in the study of pathogen evolution is our ability to determine the extent to which their rapidly evolving genomes recombine. Such information is necessary and essential for locating pathogenicity loci using association studies, and it also directs future screening, therapeutic and vaccination strat...

journal_title：Journal of molecular evolution

authors： Greenspan G,Geiger D,Gotch F,Bower M,Patterson S,Nelson M,Gazzard B,Stebbing J

更新日期：2004-03-01 00:00:00

abstract：:The DNA sequences of three members of the Alu family of repeated sequences located 5' to the chimpanzee alpha 2 gene have been determined. The base sequences of the three corresponding human Alu family repeats have been previously determined, permitting the comparison of identical Alu family members in human and chimp...

journal_title：Journal of molecular evolution

authors： Sawada I,Willard C,Shen CK,Chapman B,Wilson AC,Schmid CW

更新日期：1985-01-01 00:00:00

abstract：:There is an 8/13 sequence match between actin and flagellin in their N-terminal regions. ...

journal_title：Journal of molecular evolution

authors： Harris RJ,Elder D

更新日期：2002-02-01 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：:Insertions and deletions of entire codons have recently been discovered as a mechanism by which B cells, in addition to conventional base substitution, evolve the antibodies produced by their immunoglobulin genes. These events frequently seem to involve repetitive sequence motifs in the antibody-encoding genes, and it...

journal_title：Journal of molecular evolution

authors： Lantto J,Ohlin M

更新日期：2002-03-01 00:00:00

abstract：:The specificity of interaction of amino acids with triplets in the acceptor helix stem of tRNA was investigated by means of a statistical analysis of 1400 tRNA sequences. The imprint of a prototypic genetic code at position 3-5 of the acceptor helix was detected, but only for those major amino acids, glycine, alanine,...

journal_title：Journal of molecular evolution

authors： Möller W,Janssen GM

更新日期：1992-06-01 00:00:00

abstract：:Cytochrome proteins perform a broad spectrum of biological functions ranging from oxidative metabolism to electron transport and are thus essential to all organisms. The b-type cytochrome proteins bind heme noncovalently, are expressed in many different forms and are localized to various cellular compartments. We repo...

journal_title：Journal of molecular evolution

authors： Kula ME,Allay ER,Rozek CE

更新日期：1995-10-01 00:00:00

abstract：:We have used three reference sequences representative of bacterial drug resistance pumps and sugar transport proteins to collect the 91 most closely related sequences from a composite, nonredundant protein sequence database. Having eliminated certain very close relatives, the remainder were subjected to analysis and a...

journal_title：Journal of molecular evolution

authors： Parish JH,Bentley J

更新日期：1996-02-01 00:00:00

abstract：:In this paper we present a new method for detecting block duplications in a genome. It is more stringent than previous ones in that it requires a more rigorous definition of paralogous genes and that it requires the paralogous proteins on the two blocks to be contiguous. In addition, it provides three criterion choice...

journal_title：Journal of molecular evolution

authors： Cavalcanti AR,Ferreira R,Gu Z,Li WH

更新日期：2003-01-01 00:00:00

abstract：:Actin is a highly conserved protein although many isoforms exist. In vertebrates and insects the different actin isoforms can be grouped by their amino acid sequence and tissue-specific gene expression into muscle and nonmuscle actins, suggesting that the different actins may have a functional significance. We ask her...

journal_title：Journal of molecular evolution

authors： Mounier N,Sparrow JC

更新日期：1997-01-01 00:00:00

abstract：:A systematic way of inferring evolutionary relatedness of microbial organisms from the oligopeptide content, i.e., frequency of amino acid K-strings in their complete proteomes, is proposed. The new method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of align...

journal_title：Journal of molecular evolution

authors： Qi J,Wang B,Hao BI

更新日期：2004-01-01 00:00:00

abstract：:The observed and expected frequencies of occurrence of microsatellites in the yeast Saccharomyces cerevisiae were investigated. In all cases, the observed frequencies exceeded the expected ones. In contrast to predictions by Messier et al. (1996), there is no critical number of repeats beyond which the observed freque...

journal_title：Journal of molecular evolution

authors： Pupko T,Graur D

更新日期：1999-03-01 00:00:00

abstract：:One of the pupal cuticle protein (PCP) genes has been found within an intron of a Drosophila housekeeping gene (the Gart locus) that encodes three enzymes involved in the purine pathway. This intronic gene has been described as a gene within a gene, and the gene is now called a "nested" gene. Because the intronic PCP ...

journal_title：Journal of molecular evolution

authors： Moriyama EN,Gojobori T

更新日期：1989-05-01 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：:MicroRNAs (miRNAs) are small noncoding RNA molecules which are processed into ~20-24 nt molecules that can regulate the gene expression post-transcriptionally. MiRNA gene clusters have been identified in a range of species, where in miRNAs are often processed from polycistronic transcripts. In this study, a computatio...

journal_title：Journal of molecular evolution

authors： de Souza Gomes M,Donoghue MT,Muniyappa M,Pereira RV,Guerra-Sá R,Spillane C

更新日期：2013-06-01 00:00:00

abstract：:Explicit evaluation of the accuracy and power of maximum likelihood and Bayesian methods for detecting site-specific positive Darwinian selection presents a challenge because selective consequences of single amino acid changes are generally unknown. We exploited extensive molecular and functional characterization of a...

journal_title：Journal of molecular evolution

authors： Cavatorta JR,Savage AE,Yeam I,Gray SM,Jahn MM

更新日期：2008-11-01 00:00:00

abstract：:Characterization of sequences homologous to the Drosophila melanogaster gypsy transposable element was carried out in Drosophila subobscura (gypsyDS). They were found to be widely distributed among natural populations of this species. From Southern blot and in situ analyses, these sequences appear to be mobile in this...

journal_title：Journal of molecular evolution

authors： Alberola TM,de Frutos R

更新日期：1993-02-01 00:00:00

abstract：:Analysis of mitochondrial DNAs (mtDNAs) from parthenogenetic lizards of the Heteronotia binoei complex with restriction enzymes revealed an approximately 5-kb addition present in all 77 individuals. Cleavage site mapping suggested the presence of a direct tandem duplication spanning the 16S and 12S rRNA genes, the con...

journal_title：Journal of molecular evolution

authors： Zevering CE,Moritz C,Heideman A,Sturm RA

更新日期：1991-11-01 00:00:00

abstract：:tRNA with a terminal UCCA-3' forms a structure in which the 3'-sequence folds back. The adenine of glycyl-AMP can base-pair with the uridine of the UCCA-3' region, which places the glycine residue in close proximity to the 3'-terminal adenosine of tRNA, possibly enabling the transfer of glycine from glycyl-AMP to tRNA...

journal_title：Journal of molecular evolution

authors： Tamura K

更新日期：2015-10-01 00:00:00

abstract：:We analyzed precursor messenger RNAs (pre-mRNAs) of 12 eukaryotic species. In each species, three groups of highly expressed genes, ribosomal proteins, heat shock proteins, and amino-acyl tRNA synthetases, were compared with a control group (randomly selected genes). The purine-pyrimidine (R-Y) composition of pre-mRNA...

journal_title：Journal of molecular evolution

authors： Paz A,Mester D,Nevo E,Korol A

更新日期：2007-02-01 00:00:00

abstract：:Previously we suggested that four proteins including aldolase and triose phosphate isomerase (TPI) evolved with approximately constant rates over long periods covering the whole animal phyla. The constant rates of aldolase and TPI evolution were reexamined based on three different models for estimating evolutionary di...

journal_title：Journal of molecular evolution

authors： Nikoh N,Iwabe N,Kuma K,Ohno M,Sugiyama T,Watanabe Y,Yasui K,Shi-cui Z,Hori K,Shimura Y,Miyata T

更新日期：1997-07-01 00:00:00

abstract：:Oligonucleotide cataloguing has been used to characterize a number of 5S RNA species from various Procaryotes. Such catalogs can be used to establish certain and detailed phylogenetic relationships among organisms. Confining attention at present to four Families of Procaryotes, theEnterobacteriaceae, theBacillaceae, t...

journal_title：Journal of molecular evolution

authors： Sogin SJ,Sogin ML,Woese CR

更新日期：1972-06-01 00:00:00

abstract：:Fimbrial adhesins allow bacteria to interact with and attach to their environment. The bacteria possibly benefit from these interactions, but all external structures including adhesins also allow bacteria to be identified by other organisms. Thus adhesion molecules might be under multiple forms of selection including ...

journal_title：Journal of molecular evolution

authors： Peek AS,Souza V,Eguiarte LE,Gaut BS

更新日期：2001-02-01 00:00:00

abstract：:The mitochondrial genetic variability in European rabbit (Oryctolagus cuniculus) populations present in Europe and North Africa from 11,000 years ago to the present day has been analyzed using ancient DNA techniques. DNA was extracted from 90 rabbit bones found in 22 archaeological sites dated between the Mesolithic a...

journal_title：Journal of molecular evolution

authors： Hardy C,Callou C,Vigne JD,Casane D,Dennebouy N,Mounolou JC,Monnerot M

更新日期：1995-03-01 00:00:00

abstract：:Ubiquitin is remarkable for its ubiquitous distribution and its extreme protein sequence conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences of several ubiquitin repeats from each of humans, chicken, Xenopus, Drosophila, barley, and yeast have re...

journal_title：Journal of molecular evolution

authors： Sharp PM,Li WH

更新日期：1987-01-01 00:00:00

abstract：:The local stability of unbranched biosynthetic pathways is examined by mathematical analysis and computer simulation using a novel nonlinear formalism that appears to accurately describe biochemical systems. Four factors affecting the stability are examined: strength of feedback inhibition, equalization of the values...

journal_title：Journal of molecular evolution

authors： Savageau MA

更新日期：1975-08-05 00:00:00