Human long noncoding RNAs are substantially less folded than messenger RNAs.

abstract：:Despite its poorly adapted codon usage, HIV-1 replicates and is expressed extremely well in human host cells. HIV-1 has recently been shown to package non-lysyl transfer RNAs (tRNAs) in addition to the tRNA(Lys) needed for priming reverse transcription and integration of the HIV-1 genome. By comparing the codon usage ...

journal_title：Molecular biology and evolution

authors： van Weringh A,Ragonnet-Cronin M,Pranckeviciene E,Pavon-Eternod M,Kleiman L,Xia X

更新日期：2011-06-01 00:00:00

abstract：:The mitochondrial (mt) DNA control region (CR) of dogs and wolves contains an array of imperfect 10 bp tandem repeats. This region was studied for 14 domestic dogs representing the four major phylogenetic groups of nonrepetitive CR and for 5 wolves. Three repeat types were found among these individuals, distributed so...

journal_title：Molecular biology and evolution

authors： Savolainen P,Arvestad L,Lundeberg J

更新日期：2000-04-01 00:00:00

abstract：:Parentally biased expression of transcripts (genomic imprinting) in adult tissues, including the brain, can influence and possibly drive the evolution of behavioral traits. We have previously found that paternally determined cues are involved in population-specific mate choice decisions between two populations of the ...

journal_title：Molecular biology and evolution

authors： Lorenc A,Linnenbrink M,Montero I,Schilhabel MB,Tautz D

更新日期：2014-12-01 00:00:00

abstract：:We report the genomic organization and deduced protein sequence of a cephalochordate member of the Otx homeobox gene family (AmphiOtx) and show its probable single-copy state in the genome. We also present molecular phylogenetic analysis indicating that there was single ancestral Otx gene in the first chordates which ...

journal_title：Molecular biology and evolution

authors： Williams NA,Holland PW

更新日期：1998-05-01 00:00:00

abstract：:Clines in chromosomal inversion polymorphisms-presumably driven by climatic gradients-are common but there is surprisingly little evidence for selection acting on them. Here we address this long-standing issue in Drosophila melanogaster by using diagnostic single nucleotide polymorphism (SNP) markers to estimate inver...

journal_title：Molecular biology and evolution

authors： Kapun M,Fabian DK,Goudet J,Flatt T

更新日期：2016-05-01 00:00:00

abstract：:Mitochondrial transcription factor B (mtTFB), an essential component in regulating the expression of mitochondrial DNA-encoded genes in both yeast and humans, is a dimethyladenosine methyltransferase (DMT) that has acquired a secondary role in mitochondrial transcription. So far, mtTFB has only been well studied in Op...

journal_title：Molecular biology and evolution

authors： Shutt TE,Gray MW

更新日期：2006-06-01 00:00:00

abstract：:Non-long terminal repeat retroelements continue to impact the human genome through cis-activity of long interspersed element-1 (LINE-1 or L1) and trans-mobilization of Alu. Current activity is dominated by modern subfamilies of these elements, leaving behind an evolutionary graveyard of extinct Alu and L1 subfamilies....

journal_title：Molecular biology and evolution

authors： Wagstaff BJ,Kroutter EN,Derbes RS,Belancio VP,Roy-Engel AM

更新日期：2013-01-01 00:00:00

abstract：:A 32-kb region including the Adh structural gene was analyzed with six restriction endonucleases in 20 lines of Drosophila pseudoobscura, one line of D. persimilis, and one line of D. miranda. Nineteen lines of D. pseudoobscura from a single population were estimated to be polymorphic at one in every 15 nucleotides (p...

journal_title：Molecular biology and evolution

authors： Schaeffer SW,Aquadro CF,Anderson WW

更新日期：1987-05-01 00:00:00

abstract：:The origin and maintenance of sex remains one of the most debated topics in evolutionary biology. Investigations of the molecular genetic consequences of asexuality, such as direct estimation of mutation and recombination rates in asexual lineages, are critical for explaining the prevalence of sex in nature. In this s...

journal_title：Molecular biology and evolution

authors： Xu S,Omilian AR,Cristescu ME

更新日期：2011-01-01 00:00:00

abstract：:Genetic variation in contemporary South Asian populations follows a northwest to southeast decreasing cline of shared West Eurasian ancestry. A growing body of ancient DNA evidence is being used to build increasingly more realistic models of demographic changes in the last few thousand years. Through high-quality mode...

journal_title：Molecular biology and evolution

authors： Yelmen B,Mondal M,Marnetto D,Pathak AK,Montinaro F,Gallego Romero I,Kivisild T,Metspalu M,Pagani L

更新日期：2019-08-01 00:00:00

abstract：:The AID/APOBEC family (comprising AID, APOBEC1, APOBEC2, and APOBEC3 subgroups) contains members that can deaminate cytidine in RNA and/or DNA and exhibit diverse physiological functions (AID and APOBEC3 deaminating DNA to trigger pathways in adaptive and innate immunity; APOBEC1 mediating apolipoprotein B RNA editing...

journal_title：Molecular biology and evolution

authors： Conticello SG,Thomas CJ,Petersen-Mahrt SK,Neuberger MS

更新日期：2005-02-01 00:00:00

abstract：:There are three common alleles (A, B, and O) at the human ABO blood group locus. We compared nucleotide sequences of these alleles, and relatively large numbers of nucleotide differences were found among them. These differences correspond to the divergence time of at least a few million years, which is unusually large...

journal_title：Molecular biology and evolution

authors： Saitou N,Yamamoto F

更新日期：1997-04-01 00:00:00

abstract：:Serum response factor (SRF) and myocyte enhancer factor 2 (MEF2) represent two types of members of the MCM1, AGAMOUS, DEFICIENS, and SRF (MADS)-box transcription factor family present in animals and fungi. Each type has distinct biological functions, which are reflected by the distinct specificities of the proteins bo...

journal_title：Molecular biology and evolution

authors： Wu W,Huang X,Cheng J,Li Z,de Folter S,Huang Z,Jiang X,Pang H,Tao S

更新日期：2011-01-01 00:00:00

abstract：:Although any genotype-phenotype relationships are a result of evolution, little is known about how natural selection and neutral drift, two distinct driving forces of evolution, operate to shape the relationships. By analyzing ∼500 yeast quantitative traits, we reveal a basic "supervisor-worker" gene architecture unde...

journal_title：Molecular biology and evolution

authors： Chen H,Wu CI,He X

更新日期：2018-03-01 00:00:00

abstract：:A long-standing enigma concerns the geographic and ecological origins of the intensively studied vinegar fly, Drosophila melanogaster. This globally distributed human commensal is thought to originate from sub-Saharan Africa, yet until recently, it had never been reported from undisturbed wilderness environments that ...

journal_title：Molecular biology and evolution

authors： Sprengelmeyer QD,Mansourian S,Lange JD,Matute DR,Cooper BS,Jirle EV,Stensmyr MC,Pool JE

更新日期：2020-03-01 00:00:00

abstract：:Human c-Myb proto-oncogene is highly expressed in hematopoietic progenitors as well as leukemia and certain solid tumor. However, the regulatory mechanisms of its expression and biological functions remain largely unclear. Recently, c-Myb has been shown to be targeted by microRNA-150 (miR-150) which thereby controls B...

journal_title：Molecular biology and evolution

authors： Lin YC,Kuo MW,Yu J,Kuo HH,Lin RJ,Lo WL,Yu AL

更新日期：2008-10-01 00:00:00

abstract：:Evolution at silent sites is often used to estimate the pace of selectively neutral processes or to infer differences in divergence times of genes. However, silent sites are subject to selection in favor of preferred codons, and the strength of such selection varies dramatically across genes. Here, we use the relation...

journal_title：Molecular biology and evolution

authors： Hirsh AE,Fraser HB,Wall DP

更新日期：2005-01-01 00:00:00

abstract：:It is known that the effective population size (Ne) and the mutation rate (u) vary across the genome. Here, we show that ignoring this heterogeneity may lead to biased estimates of past demography. To solve the problem, we develop new methods for jointly inferring past changes in population size and detecting variatio...

journal_title：Molecular biology and evolution

authors： Zeng K,Jackson BC,Barton HJ

更新日期：2019-02-01 00:00:00

abstract：:It has recently been observed by Ho et al. (Ho SYW, Phillips MJ, Cooper A, Drummond AJ. 2005. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol. 22(7):1561-1568) that apparent rates of molecular evolution increase when measured over short timespans. I i...

journal_title：Molecular biology and evolution

authors： Woodhams M

更新日期：2006-12-01 00:00:00

abstract：:Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective population size over time. Among the most successful is a G...

journal_title：Molecular biology and evolution

authors： Gill MS,Lemey P,Faria NR,Rambaut A,Shapiro B,Suchard MA

更新日期：2013-03-01 00:00:00

abstract：:The evolution of amniotes has involved major molecular innovations in the epidermis. In particular, distinct structural proteins that undergo covalent cross-linking during cornification of keratinocytes facilitate the formation of mechanically resilient superficial cell layers and help to limit water loss to the envir...

journal_title：Molecular biology and evolution

authors： Strasser B,Mlitz V,Hermann M,Rice RH,Eigenheer RA,Alibardi L,Tschachler E,Eckhart L

更新日期：2014-12-01 00:00:00

abstract：:Cytochrome c oxidase (COX) consists of 13 subunits, 3 encoded in the mitochondrial genome and 10 in the nucleus. Little is known of the role of the nuclear-encoded subunits, some of which exhibit tissue-specific isoforms. Subunit VIa is unique in having tissue-specific isoforms in all mammalian species examined. We ex...

journal_title：Molecular biology and evolution

authors： Schmidt TR,Jaradat SA,Goodman M,Lomax MI,Grossman LI

更新日期：1997-06-01 00:00:00

abstract：:Statistical criteria have long been the standard for selecting the best model for phylogenetic reconstruction and downstream statistical inference. Although model selection is regarded as a fundamental step in phylogenetics, existing methods for this task consume computational resources for long processing time, they ...

journal_title：Molecular biology and evolution

authors： Abadi S,Avram O,Rosset S,Pupko T,Mayrose I

更新日期：2020-11-01 00:00:00

abstract：:During the course of a random sequencing project of the genome of the dimorphic yeast Yarrowia lipolytica, we have identified sequences that were repeated in the genome and that matched the reverse transcriptase (RT) sequence of non-long terminal repeat (non-LTR) retrotransposons. Extension of sequencing on each side ...

journal_title：Molecular biology and evolution

authors： Casaregola S,Neuvéglise C,Bon E,Gaillardin C

更新日期：2002-05-01 00:00:00

abstract：:Most phylogenetic models assume that the evolutionary process is stationary and reversible. In addition to being biologically improbable, these assumptions also impair inference by generating models under which the likelihood does not depend on the position of the root. Consequently, the root of the tree cannot be inf...

journal_title：Molecular biology and evolution

authors： Cherlin S,Heaps SE,Nye TMW,Boys RJ,Williams TA,Embley TM

更新日期：2018-04-01 00:00:00

abstract：:The genetic basis of organisms' adaptation to different environments is a central issue of molecular evolution. The budding yeast Saccharomyces cerevisiae and its relatives predominantly ferment glucose into ethanol even in the presence of oxygen. This was suggested to be an adaptation to glucose-rich habitats, but th...

journal_title：Molecular biology and evolution

authors： Lin Z,Li WH

更新日期：2011-01-01 00:00:00

abstract：:The noncoding-DNA content of organelle and nuclear genomes can vary immensely. Both adaptive and nonadaptive explanations for this variation have been proposed. This study addresses a nonadaptive explanation called the mutational-hazard hypothesis and applies it to the mitochondrial, plastid, and nuclear genomes of th...

journal_title：Molecular biology and evolution

authors： Smith DR,Lee RW

更新日期：2010-10-01 00:00:00

abstract：:Duplication, resulting in gene redundancy, is well known to be a driving force of evolutionary change. Gene families are therefore useful targets for approaching genome evolution. To address the gene death process, we examined the fate of the 10-member-large S288C DUP240 family in 15 Saccharomyces cerevisiae strains. ...

journal_title：Molecular biology and evolution

authors： Wirth B,Louis VL,Potier S,Souciet JL,Despons L

更新日期：2005-09-01 00:00:00

abstract：:Alpha-defensins are a family of mammalian antimicrobial peptides that exhibit variable activity against a panel of microbes, including bacteria, fungi, and enveloped viruses. We have employed a maximum-likelihood approach to detect evidence of positive selection (adaptive evolution) in the evolution of these important...

journal_title：Molecular biology and evolution

authors： Lynn DJ,Lloyd AT,Fares MA,O'Farrelly C

更新日期：2004-05-01 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