abstract：:The early evolution of life is a period with many important events with a lot of big and open questions. One of them is the evolution of metabolic pathways, which means the origin and assembly of enzymes that act together. The retrograde hypothesis was the first attempt to explain the origin and evolutionary history o...

journal_title：Journal of molecular evolution

authors： Becerra A

更新日期：2021-01-28 00:00:00

abstract：:A fundamental paradox motivates the study of plant mitochondrial genomics: the mutation rate is very low (lower than in the nucleus) but the rearrangement rate is high. A landmark paper published in Journal of Molecular Evolution in 1988 established these facts and revealed the paradox. Jeffrey Palmer and Laura Herbon...

journal_title：Journal of molecular evolution

authors： Christensen AC

更新日期：2021-01-24 00:00:00

abstract：:Molluscan shells are composed of calcium carbonates, with small amounts of extracellular matrices secreted from mantle epithelial cells. Many types of shell matrix proteins (SMPs) have been identified from molluscan shells or mantle cells. The pen shell Atrina pectinata (Pinnidae) has two different shell microstructur...

journal_title：Journal of molecular evolution

authors： Shimizu K,Kintsu H,Awaji M,Matumoto T,Suzuki M

更新日期：2020-12-01 00:00:00

abstract：:Proteins are commonly used as molecular targets against pathogens such as viruses and bacteria. However, pathogens can evolve rapidly permitting their populations to increase in protein diversity over time and thus escape to the activity of a molecular therapy. Subsequently, in order to design more durable and robust ...

journal_title：Journal of molecular evolution

authors： Arenas M

更新日期：2020-08-01 00:00:00

abstract：:Amino acid substitution models represent substitution rates among amino acids during the evolution. The models play an important role in analyzing protein sequences, especially inferring phylogenies. The rapid evolution of flaviviruses is expanding the threat in public health. A number of models have been estimated fo...

journal_title：Journal of molecular evolution

authors： Le TK,Vinh LS

更新日期：2020-07-01 00:00:00

abstract：:Orphan genes, lacking detectable homologs in outgroup species, typically represent 10-30% of eukaryotic genomes. Efforts to find the source of these young genes indicate that de novo emergence from non-coding DNA may in part explain their prevalence. Here, we investigate the roots of orphan gene emergence in the Droso...

journal_title：Journal of molecular evolution

authors： Heames B,Schmitz J,Bornberg-Bauer E

更新日期：2020-05-01 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：:Skin pigmentation is a complex, conspicuous, highly variable human trait that exhibits a remarkable correlation with latitude. The evolutionary history and genetic basis of skin color variation has been the subject of intense research in the last years. This article reviews the major hypotheses explaining skin color d...

journal_title：Journal of molecular evolution

authors： Rocha J

更新日期：2020-01-01 00:00:00

abstract：:In mammals, chicken-type (c-type) lysozymes are part of the innate immune system, killing bacteria by degrading peptidoglycan in their cell walls. Many of the studies on the evolution of c-type lysozymes have focused on its new digestive function, including the duplicated stomach lysozymes in ruminants. Similarly, in ...

journal_title：Journal of molecular evolution

authors： He C,Wei Y,Zhu Y,Xia Y,Irwin DM,Liu Y

更新日期：2019-12-01 00:00:00

abstract：:We recently sequenced the genome of the first subterrestrial metazoan, the nematode Halicephalobus mephisto. A central finding was a dramatic expansion of genes encoding avrRpt2 induced gene (AIG1), and 70 kDa heat shock (Hsp70) domains. While the role of Hsp70 in thermotolerance is well established, the contribution ...

journal_title：Journal of molecular evolution

authors： Guerin MN,Weinstein DJ,Bracht JR

更新日期：2019-12-01 00:00:00

abstract：:In this study, a new strategy for the selection of aptamers against small-molecule target was established using gold nanoparticles (AuNPs) as the separation matrix and Zinc(II)-Protoporphyrin IX (ZnPPIX) as the target molecule without the immobilization step due to the absorption of ssDNA on AuNPs. The progress of the...

journal_title：Journal of molecular evolution

authors： Li W,Luo Y,Gao T,Yang L,Wang J,Pei R

更新日期：2019-09-01 00:00:00

abstract：:In this article, we investigated the structural and dynamical evolutionary behaviour of a set of ten thioredoxin proteins as formed by three extant forms and seven resurrected ones in laboratory. Starting from the crystallographic structures, we performed all-atom molecular dynamics simulations and compare the traject...

journal_title：Journal of molecular evolution

authors： Del Galdo S,Alba J,Amadei A,D'Abramo M

更新日期：2019-07-01 00:00:00

abstract：:Unravelling gene structure requires the identification and understanding of the constraints that are often associated with the evolutionary history and functional domains of genes. We speculated in this manuscript with the possibility of the existence in orthologs of an emergent highly conserved gene structure that mi...

journal_title：Journal of molecular evolution

authors： Fuertes MA,Rodrigo JR,Alonso C

更新日期：2019-04-01 00:00:00

abstract：:Life as we know it requires three basic types of polymers: polypeptide, polynucleotide, and polysaccharide. Here we evaluate both universal and idiosyncratic characteristics of these biopolymers. We incorporate this information into a model that explains much about their origins, selection, and early evolution. We obs...

journal_title：Journal of molecular evolution

authors： Runnels CM,Lanier KA,Williams JK,Bowman JC,Petrov AS,Hud NV,Williams LD

更新日期：2018-12-01 00:00:00

abstract：:Low oxygen and fluctuant ambient temperature pose serious challenges to mammalian survival. Physiological adaptations in mammals to hypoxia and low temperatures have been intensively investigated, yet their underlying molecular mechanisms need further exploration. Independent invasions of high-altitude plateaus, subte...

journal_title：Journal of molecular evolution

authors： Zhu K,Ge D,Wen Z,Xia L,Yang Q

更新日期：2018-12-01 00:00:00

abstract：:In vitro run-off transcription by T7 RNA polymerase generates heterogeneous 3'-ends because the enzyme tends to add untemplated adenylates. To generate homogeneous 3'-termini, HDV ribozymes have been used widely. Their sequences are added to the 3'-terminus such that co-transcriptional self-cleavage generates homogene...

journal_title：Journal of molecular evolution

authors： Akoopie A,Müller UF

更新日期：2018-08-01 00:00:00

abstract：:Gene duplication creates a second copy of a gene either in tandem to the ancestral locus or dispersed to another chromosomal location. When the ancestral copy of a dispersed duplicate is lost from the genome, it creates the appearance that the gene was "relocated" from the ancestral locus to the derived location. Gene...

journal_title：Journal of molecular evolution

authors： Hart MLI,Vu BL,Bolden Q,Chen KT,Oakes CL,Zoronjic L,Meisel RP

更新日期：2018-07-01 00:00:00

abstract：:It is generally considered that if an RNA World ever existed that it would be driven by an RNA capable of RNA replication. Whether such a catalytic RNA could emerge in an RNA World or not, there would need to be prior routes to increasing complexity in order to produce it. It is hypothesized here that increasing seque...

journal_title：Journal of molecular evolution

authors： Tirumalai MR,Tran Q,Paci M,Chavan D,Marathe A,Fox GE

更新日期：2018-06-01 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：:Group selection is a matter of acute controversy among evolutionary biologists. The most well-publicized debate in this regard is that between Edward O. Wilson and Richard Dawkins. As is widely known, Edward O. Wilson is very excited about the idea of social selection and eusociality; by contrast Richard Dawkins favor...

journal_title：Journal of molecular evolution

authors： Voskarides K

更新日期：2018-04-01 00:00:00

abstract：:Horizontal gene transfer (HGT) has a major impact on the evolution of prokaryotic genomes, as it allows genes evolved in different contexts to be combined in a single genome, greatly enhancing the ways evolving organisms can explore the gene content space and adapt to the environment. A systematic analysis of HGT in a...

journal_title：Journal of molecular evolution

authors： Paquola ACM,Asif H,Pereira CAB,Feltes BC,Bonatto D,Lima WC,Menck CFM

更新日期：2018-04-01 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：:Hypoxia at deep-sea hydrothermal vents represents one of the most basic challenges for metazoans, which then requires specific adaptations to acquire oxygen to meet their metabolic needs. Hydrothermal vent scale-worms (Polychaeta; Polynoidae) express large amounts of extracellular single- and multi-domain hemoglobins,...

journal_title：Journal of molecular evolution

authors： Projecto-Garcia J,Le Port AS,Govindji T,Jollivet D,Schaeffer SW,Hourdez S

更新日期：2017-12-01 00:00:00

abstract：:It has been suggested that inorganic membranes were forerunners of organic membranes at the origin of life. Such membranes, interposed between alkaline fluid in submarine vents and the more acidic Hadean ocean, were thought to house inorganic molecular machines. H+ flowed down the pH gradient (ΔpH) from ocean to vent ...

journal_title：Journal of molecular evolution

authors： Jackson JB

更新日期：2017-08-01 00:00:00

abstract：:As illustrated by the mitochondrion and the eukaryotic cell, little in biology makes sense except in light of mutualism. Mutualisms are persistent, intimate, and reciprocal exchanges; an organism proficient in obtaining certain benefits confers those on a partner, which reciprocates by conferring different benefits. M...

journal_title：Journal of molecular evolution

authors： Lanier KA,Petrov AS,Williams LD

更新日期：2017-08-01 00:00:00

abstract：:The C-terminal domain of methionyl-tRNA synthetase (MetRS-C) from Nanoarchaeum equitans is homologous to a tRNA-binding protein consisting of 111 amino acids (Trbp111) from Aquifex aeolicus. The crystal structure of MetRS-C showed that it existed as a homodimer, and that each monomer possessed an oligonucleotide/oligo...

journal_title：Journal of molecular evolution

authors： Suzuki H,Kaneko A,Yamamoto T,Nambo M,Hirasawa I,Umehara T,Yoshida H,Park SY,Tamura K

更新日期：2017-06-01 00:00:00

abstract：:The dominant paradigm in origin of life research is that of an RNA world. However, despite experimental progress towards the spontaneous formation of RNA, the RNA world hypothesis still has its problems. Here, we introduce a novel computational model of chemical reaction networks based on RNA secondary structure and a...

journal_title：Journal of molecular evolution

authors： Hordijk W

更新日期：2017-04-01 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：:Domains are folded structures and evolutionary building blocks of protein molecules. Their three-dimensional atomic conformations, which define biological functions, can be coarse-grained into levels of a hierarchy. Here we build global dynamical models for the evolution of domains at fold and fold superfamily (FSF) l...

journal_title：Journal of molecular evolution

authors： Tal G,Boca SM,Mittenthal J,Caetano-Anollés G

更新日期：2016-05-01 00:00:00

abstract：:Several studies in Drosophila have shown a paucity of male-biased genes (i.e., genes that express higher in males than in females) on the X chromosome. Dosage compensation (DC) is a regulatory mechanism of gene expression triggered in males that hypertranscribes the X-linked genes to the level of transcription in fema...

journal_title：Journal of molecular evolution

authors： Gallach M,Betrán E

更新日期：2016-05-01 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：:Processes exhibiting diversity and selection would have been necessary to promote chemical evolution on early Earth. In this work, a model process was developed using non-kinetic selection to synthesize and isolate small molecule imidazolium catalysts. These catalysts were purified by affinity chromatography and recyc...

journal_title：Journal of molecular evolution

authors： Clairmont RM,Bommarius AS,Weber AL

更新日期：2015-08-01 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：:Cyclooxygenase (COX) enzymatically converts arachidonic acid into prostaglandin G/H in animals and has importance during pregnancy, digestion, and other physiological functions in mammals. COX genes have mainly been described from vertebrates, where gene duplications are common, but few studies have examined COX in in...

journal_title：Journal of molecular evolution

authors： Havird JC,Kocot KM,Brannock PM,Cannon JT,Waits DS,Weese DA,Santos SR,Halanych KM

更新日期：2015-04-01 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：:RNA has a myriad of biological roles in contemporary life. We use the RNA paradigm for genotype-phenotype mappings to study the evolution of multiple coding in dependence to mutation rates. We study three different one-to-many genotype-phenotype mappings which have the potential to encode the information for multiple ...

journal_title：Journal of molecular evolution

authors： de Boer FK,Hogeweg P

更新日期：2014-12-01 00:00:00

abstract：:Lepidoptera (comprised of butterflies and moths) is one of the largest groups of insects, including more than 160,000 described species. Chemoreception plays important roles in the adaptation of these species to a wide range of niches, e.g., plant hosts, egg-laying sites, and mates. This study investigated the molecul...

journal_title：Journal of molecular evolution

authors： Engsontia P,Sangket U,Chotigeat W,Satasook C

更新日期：2014-08-01 00:00:00

abstract：:We propose a genealogy-sampling algorithm, Sequential Markov Ancestral Recombination Tree (SMARTree), that provides an approach to estimation from SNP haplotype data of the patterns of coancestry across a genome segment among a set of homologous chromosomes. To enable analysis across longer segments of genome, the seq...

journal_title：Journal of molecular evolution

authors： Zheng C,Kuhner MK,Thompson EA

更新日期：2014-05-01 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：:The internal transcribed spacer region (ITS) of the nuclear rDNA cistron represents the barcoding locus for Fungi. Intragenomic variation of this multicopy gene can interfere with accurate phylogenetic reconstruction of biological entities. We investigated the amount and nature of this variation for the lichenized fun...

journal_title：Journal of molecular evolution

authors： Lücking R,Lawrey JD,Gillevet PM,Sikaroodi M,Dal-Forno M,Berger SA

更新日期：2014-02-01 00:00:00