Hydrogen peroxide-induced gene expression across kingdoms: a comparative analysis.

abstract：:Phylogenetic reconstruction of the evolutionary history of closely related organisms may be difficult because of the presence of unsorted lineages and of a relatively high proportion of heterozygous sites that are usually not handled well by phylogenetic programs. Genomic data may provide enough fixed polymorphisms to...

journal_title：Molecular biology and evolution

authors： Lischer HE,Excoffier L,Heckel G

更新日期：2014-04-01 00:00:00

abstract：:To gain insight into the evolution of the methionine biosynthesis pathway, in vivo complementation tests were performed. The substrate specificity of three enzymes that intrinsically use different homoserine-esterified substrates and have different sulfur assimilation pathways was examined: two cystathionine gamma-syn...

journal_title：Molecular biology and evolution

authors： Hacham Y,Gophna U,Amir R

更新日期：2003-09-01 00:00:00

abstract：:Alcohol dehydrogenase genes were amplified by PCR, cloned, and sequenced from 11 putative nonhybrid species of the angiosperm genus Paeonia. Sequences of five exons and six intron regions of the Adh gene were used to reconstruct the phylogeny of these species. Two paralogous genes, Adh1A, and Adh2, were found; an addi...

journal_title：Molecular biology and evolution

authors： Sang T,Donoghue MJ,Zhang D

更新日期：1997-10-01 00:00:00

abstract：:The diatom Phaeodactylum tricornutum harbors a plastid that is surrounded by four membranes and evolved by way of secondary endosymbiosis. Like land plants, most of its plastid proteins are encoded as preproteins on the nuclear genome of the host cell and are resultantly redirected into the organelle. Because two more...

journal_title：Molecular biology and evolution

authors： Hempel F,Bullmann L,Lau J,Zauner S,Maier UG

更新日期：2009-08-01 00:00:00

abstract：:Functional redundancy in genomes arises from genes with overlapping functions, allowing phenotypes to persist after gene knockouts. Evolutionary redundancy or evolvability of a genome is one step removed, in that functional redundancy is absent but the genome has the potential to evolve to restore a lost phenotype. Ex...

journal_title：Molecular biology and evolution

authors： Heineman RH,Bull JJ,Molineux IJ

更新日期：2009-06-01 00:00:00

abstract：:Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster...

journal_title：Molecular biology and evolution

authors： Cardona T,Murray JW,Rutherford AW

更新日期：2015-05-01 00:00:00

abstract：:A phylogenetic tree of a gene family of nicotinic acetylcholine receptor subunits was constructed using 84 nucleotide sequences of receptor subunits from 18 different species in order to elucidate the evolutionary origin of receptor subunits. The tree constructed showed that the common ancestor of all subunits may hav...

journal_title：Molecular biology and evolution

authors： Tsunoyama K,Gojobori T

更新日期：1998-05-01 00:00:00

abstract：:In chickens, there is a single functional gene (VH1) coding for the heavy chain variable region of immunoglobulins, and immunoglobulin diversity is generated by gene conversion of the VH1 gene by many variable region pseudogenes (psi VH's) that exist on the 5' side of the VH1 gene. To understand the evolution of this ...

journal_title：Molecular biology and evolution

authors： Ota T,Nei M

更新日期：1995-01-01 00:00:00

abstract：:Long noncoding RNAs (lncRNAs) do not code for proteins but function as RNAs. Because the functions of an RNA rely on either its sequence or secondary structure, lncRNAs should be folded at least as strongly as messenger RNAs (mRNAs), which serve as messengers for translation and are generally thought to lack secondary...

journal_title：Molecular biology and evolution

authors： Yang JR,Zhang J

更新日期：2015-04-01 00:00:00

abstract：:Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patter...

journal_title：Molecular biology and evolution

authors： Melin AD,Wells K,Moritz GL,Kistler L,Orkin JD,Timm RM,Bernard H,Lakim MB,Perry GH,Kawamura S,Dominy NJ

更新日期：2016-04-01 00:00:00

abstract：:Significance levels obtained from a chi 2 contingency test are suspect when sample sizes are small. Traditionally this has meant that data must be combined. However, such an approach may obscure heterogeneity and hence potentially reduce the power of the statistical test. In this paper, we present a Monte Carlo soluti...

journal_title：Molecular biology and evolution

authors： Roff DA,Bentzen P

更新日期：1989-09-01 00:00:00

abstract：:Various hypotheses for the peopling of the Japanese archipelago have been proposed, which can be classified into three models: transformation, replacement, and hybridization. In recent years, one of the hybridization models ("dual-structure model") has been widely accepted. According to this model, Neolithic hunter-ga...

journal_title：Molecular biology and evolution

authors： Nakagome S,Sato T,Ishida H,Hanihara T,Yamaguchi T,Kimura R,Mano S,Oota H,Asian DNA Repository Consortium.

更新日期：2015-06-01 00:00:00

abstract：:The chemokine receptor CCR5 can serve as a coreceptor for M-tropic HIV-1 infection and both M-tropic and T-tropic SIV infection. We sequenced the entire CCR5 gene from 10 nonhuman primates: Pongo pygmaeus, Hylobates leucogenys, Trachypithecus francoisi, Trachypithecus phayrei, Pygathrix nemaeus, Rhinopithecus roxellan...

journal_title：Molecular biology and evolution

authors： Zhang YW,Ryder OA,Zhang YP

更新日期：1999-09-01 00:00:00

abstract：:Knotted-like (KNOX) proteins constitute a group of homeodomain proteins involved in pattern formation in developing tissues of angiosperms and other green plants. We conducted phylogenetic analyses of nucleotide and amino acid sequences of all known KNOX proteins in order to examine their evolution. Our analyses revea...

journal_title：Molecular biology and evolution

authors： Bharathan G,Janssen BJ,Kellogg EA,Sinha N

更新日期：1999-04-01 00:00:00

abstract：:Much like other indigenous domesticated animals, Tibetan chickens living at high altitudes (2,200-4,100 m) show specific physiological adaptations to the extreme environmental conditions of the Tibetan Plateau, but the genetic bases of these adaptations are not well characterized. Here, we assembled a de novo genome o...

journal_title：Molecular biology and evolution

authors： Wang MS,Li Y,Peng MS,Zhong L,Wang ZJ,Li QY,Tu XL,Dong Y,Zhu CL,Wang L,Yang MM,Wu SF,Miao YW,Liu JP,Irwin DM,Wang W,Wu DD,Zhang YP

更新日期：2015-07-01 00:00:00

abstract：:Whether higher-order chromatin organization is related to genome stability over evolutionary time remains elusive. We find that regions of conserved gene order across the genus Drosophila are larger if they harbor genes bound by B-type lamin (Lam) and Suppressor of Under-Replication (SUUR), two proteins located at the...

journal_title：Molecular biology and evolution

authors： Ranz JM,Díaz-Castillo C,Petersen R

更新日期：2012-01-01 00:00:00

abstract：:Genome and transcript sequences are composed of long strings of nucleotide monomers (A, C, G, and T/U) that require different quantities of nitrogen atoms for biosynthesis. Here, it is shown that the strength of selection acting on transcript nitrogen content is influenced by the amount of nitrogen plants require to c...

journal_title：Molecular biology and evolution

authors： Kelly S

更新日期：2018-07-01 00:00:00

abstract：:Hybridization between different species plays an important role in plant genome evolution, as well as is a widely used approach for crop improvement. McClintock has predicted that plant wide hybridization constitutes a "genomic shock" whereby cryptic transposable elements may be activated. However, direct experimental...

journal_title：Molecular biology and evolution

authors： Shan X,Liu Z,Dong Z,Wang Y,Chen Y,Lin X,Long L,Han F,Dong Y,Liu B

更新日期：2005-04-01 00:00:00

abstract：:In this article, we address the issue of estimating the phylogenetic tree based on sequence data across a set of genes. Recognizing that the individual gene trees may not all share the same evolutionary history due to lateral gene transfer or differences in rates of evolution for instance, we develop a robust algorith...

journal_title：Molecular biology and evolution

authors： Xu X,Dunn KA,Field C

更新日期：2015-08-01 00:00:00

abstract：:Despite the general assumption that site-specific mutation rates are independent of the local sequence context, a growing body of evidence suggests otherwise. To further examine context-dependent patterns of mutation, we amassed 5,645 spontaneous mutations in wild- type (WT) and mismatch-repair deficient (MMR(-)) muta...

journal_title：Molecular biology and evolution

authors： Sung W,Ackerman MS,Gout JF,Miller SF,Williams E,Foster PL,Lynch M

更新日期：2015-07-01 00:00:00

abstract：:With the desire to model population genetic processes under increasingly realistic scenarios, forward genetic simulations have become a critical part of the toolbox of modern evolutionary biology. The SLiM forward genetic simulation framework is one of the most powerful and widely used tools in this area. However, its...

journal_title：Molecular biology and evolution

authors： Haller BC,Messer PW

更新日期：2019-03-01 00:00:00

abstract：:During the adaptation of an organism to a parasitic lifestyle, various gene functions may be rendered superfluous due to the fact that the host may supply these needs. As a consequence, obligate symbiotic bacterial pathogens tend to undergo reductive genomic evolution through gene death (nonfunctionalization or pseudo...

journal_title：Molecular biology and evolution

authors： Dagan T,Blekhman R,Graur D

更新日期：2006-02-01 00:00:00

abstract：:Coevolutionary conflict among imprinted genes that influence traits such as offspring growth may arise when maternal and paternal genomes have different evolutionary optima. This conflict is expected in outcrossing taxa with multiple paternity, but not self-fertilizing taxa. MEDEA (MEA) is an imprinted plant gene that...

journal_title：Molecular biology and evolution

authors： Miyake T,Takebayashi N,Wolf DE

更新日期：2009-04-01 00:00:00

abstract：:Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to crea...

journal_title：Molecular biology and evolution

authors： Priyam A,Woodcroft BJ,Rai V,Moghul I,Munagala A,Ter F,Chowdhary H,Pieniak I,Maynard LJ,Gibbins MA,Moon H,Davis-Richardson A,Uludag M,Watson-Haigh NS,Challis R,Nakamura H,Favreau E,Gómez EA,Pluskal T,Leonard G,Rump

更新日期：2019-12-01 00:00:00

abstract：:Convergent and parallel amino acid substitutions in protein evolution, collectively referred to as molecular convergence here, have small probabilities under neutral evolution. For this reason, molecular convergence is commonly viewed as evidence for similar adaptations of different species. The surge in the number of...

journal_title：Molecular biology and evolution

authors： Zou Z,Zhang J

更新日期：2015-08-01 00:00:00

abstract：:The most deviant isochore pattern within mammals was found in rat and mouse; most other mammals possess a different kind of isochore organization called the "general pattern." However, isochore patterns remain largely unknown in rodents other than mouse and rat. To investigate the taxonomic distribution of isochore pa...

journal_title：Molecular biology and evolution

authors： Robinson M,Gautier C,Mouchiroud D

更新日期：1997-08-01 00:00:00

abstract：:Two recent studies have presented conflicting views on variation present within the 294 base third domain of the 12S rRNA gene in the genus Drosophila, and in D. pseudoobscura in particular. One study suggested that this gene is highly invariant across the genus, while another recovered 22 distinct haplotypes from 22 ...

journal_title：Molecular biology and evolution

authors： Noor MA,Larkin JC

更新日期：2000-06-01 00:00:00

abstract：:Endogenous retroviruses are ubiquitous in the vertebrate genomes. On occasion, hosts recruited retroviral genes to mediate their own biological functions, a process formally known as co-option or exaptation. Much remains unknown about the extent of retroviral gene co-option in vertebrates, although more than ten retro...

journal_title：Molecular biology and evolution

authors： Wang J,Han GZ

更新日期：2020-11-01 00:00:00

abstract：:Crabs of the infra-order Brachyura are one of the most diverse groups of crustaceans with approximately 7,000 described species in 98 families, occurring in marine, freshwater, and terrestrial habitats. The relationships among the brachyuran families are poorly understood due to the high morphological complexity of th...

journal_title：Molecular biology and evolution

authors： Tsang LM,Schubart CD,Ahyong ST,Lai JC,Au EY,Chan TY,Ng PK,Chu KH

更新日期：2014-05-01 00:00:00

abstract：:The activation peptide of mammalian trypsinogens contains a highly conserved tetra-aspartate sequence (D19-D20-D21-D22) preceding the K23-I24 scissile peptide bond, which is hydrolyzed as the first step in the activation process. Here, we examined the evolution and function of trypsinogen activation peptides through i...

journal_title：Molecular biology and evolution

authors： Chen JM,Kukor Z,Le Maréchal C,Tóth M,Tsakiris L,Raguénès O,Férec C,Sahin-Tóth M

更新日期：2003-11-01 00:00:00