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Journal of Molecular Evolution

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https://read.qxmd.com/read/30770947/a-new-editorial-beginning-at-journal-of-molecular-evolution
#1
EDITORIAL
David A Liberles
No abstract text is available yet for this article.
February 15, 2019: Journal of Molecular Evolution
https://read.qxmd.com/read/30659315/in-vitro-selection-of-a-dna-aptamer-by-cell-selex-as-a-molecular-probe-for-cervical-cancer-recognition-and-imaging
#2
Jine Wang, Tian Gao, Yu Luo, Zhili Wang, Yajie Zhang, Ye Zhang, Yuanyuan Zhang, Renjun Pei
Aptamers have become the most promising recognition reagents in terms of early diagnosis and effective treatment of cancers. In this study, using cervical cancer as a model, we have identified a DNA aptamer specifically binding to cervical cancer cells with high affinity using the cell-SELEX (systematic evolution of ligands by exponential enrichment) method, in which a negative selection was carried out using normal epithelial cells as control. The binding abilities of 6 selected truncated aptamers were determined by laser confocal fluorescence microscopy and flow cytometry, while most of them only recognize the target cells and do not bind the control cells, and the aptamer C-9S with 51-mer shows the best binding affinity to Ca Ski cells (target cells) with a dissociation constant value of 19...
January 19, 2019: Journal of Molecular Evolution
https://read.qxmd.com/read/30631891/an-extension-of-the-kimura-two-parameter-model-to-the-natural-evolutionary-process
#3
Takuma Nishimaki, Keiko Sato
Accurate estimates of genetic difference are required for research in evolutionary biology. Here we extend the Kimura two-parameter (K2P) model by considering gaps (insertions and/or deletions) and introduce a new measure for estimating genetic difference between two nucleotide sequences in terms of nucleotide changes that have occurred during the evolutionary process. Using the nuclear ribosomal DNA internal transcribed spacer 2 region from the genus Physalis, we demonstrate that species identification and phylogenetic studies strongly depend on evolutionary models...
January 10, 2019: Journal of Molecular Evolution
https://read.qxmd.com/read/30607448/gene-encoding-a-novel-enzyme-of-ldh2-mdh2-family-is-lost-in-plant-and-animal-genomes-during-transition-to-land
#4
L V Puzakova, M V Puzakov, A A Soldatov
L-Lactate/malate dehydrogenases (LDH/MDH) and type 2 L-lactate/malate dehydrogenases (LDH2/MDH2) belong to NADH/NADPH-dependent oxidoreductases (anaerobic dehydrogenases). They form a large protein superfamily with multiple enzyme homologs found in all branches of life: from bacteria and archaea to eukaryotes, and play an essential role in metabolism. Here, we describe the gene encoding a new enzyme of LDH2/MDH2 oxidoreductase family. This gene is found in genomes of all studied groups/classes of bacteria and fungi...
January 4, 2019: Journal of Molecular Evolution
https://read.qxmd.com/read/30604018/understanding-the-evolution-of-mitochondrial-genomes-in-phaeophyceae-inferred-from-mitogenomes-of-ishige-okamurae-ishigeales-and-dictyopteris-divaricata-dictyotales
#5
Feng Liu, Yongyu Zhang, Yuping Bi, Weizhou Chen, Fiona Wanjiku Moejes
To gain further insight into the evolution of mitochondrial genomes (mtDNAs) in Phaeophyceae, the first recorded characterization of an Ishigeophycidae mtDNA from Ishige okamurae (Yendo), and only the second recorded characterization of a Dictyotophycidae mtDNA from Dictyopteris divaricata (Okamura) Okamura are presented in this study. The 35,485 bp I. okamurae mtDNA contained 36 protein-coding genes (PCGs), 22 tRNAs, three rRNAs, and four open reading frames (orfs), and the 32,021 bp D. divaricata mtDNA harbored 35 PCGs, 25 tRNAs, three rRNAs, and three orfs...
January 2, 2019: Journal of Molecular Evolution
https://read.qxmd.com/read/30604017/alarmones-as-vestiges-of-a-bygone-rna-world
#6
Ricardo Hernández-Morales, Arturo Becerra, Antonio Lazcano
All known alarmones are ribonucleotides or ribonucleotide derivatives that are synthesized when cells are under stress conditions, triggering a stringent response that affects major processes such as replication, gene expression, and metabolism. The ample phylogenetic distribution of alarmones (e.g., cAMP, Ap(n)A, cGMP, AICAR, and ZTP) suggests that they are very ancient molecules that may have already been present in cellular systems prior to the evolutionary divergence of the Archaea, Bacteria, and Eukarya domains...
January 2, 2019: Journal of Molecular Evolution
https://read.qxmd.com/read/30604016/genetic-code-error-minimization-as-a-non-adaptive-but-beneficial-trait
#7
LETTER
Steven E Massey
In a recent Letter, Di Giulio questions the use of the term 'neutral' when describing the process by which error minimization may have arisen as a side-product of genetic code expansion, resulting from the addition of similar amino acids to similar codons (Di Giulio, in J Mol Evol 86(9):593-597, 2018). However, I point out that in this scenario error minimization is non-adaptive, and so 'neutral' is an appropriate term to describe its imperviousness to direct selection. Error minimization is a form of mutational robustness, and so commonly viewed as beneficial...
January 2, 2019: Journal of Molecular Evolution
https://read.qxmd.com/read/30604015/amino-acids-in-life-a-prebiotic-division-of-labor
#8
LETTER
Jason Allen Davidson
There are more than 20 amino acids used in Biology, and their utilization is enigmatic. Here, I propose that there was a prebiotic division of labor between two subsets of amino acids. The first set is the alpha-L set, which includes all the genetically encoded amino acids. These convey heritable information. The second set is all the remaining types, which includes the D-enantiomers incorporated in non-ribosomally encoded peptides and those used in signaling. These convey proximally mediated information about the environment...
January 2, 2019: Journal of Molecular Evolution
https://read.qxmd.com/read/30564861/biophysical-spandrels-form-a-hot-spot-for-kosmotropic-mutations-in-bacteriophage-thermal-adaptation
#9
A Carl Whittington, Darin R Rokyta
Temperature plays a dominating role in protein structure and function, and life has evolved myriad strategies to adapt proteins to environmental thermal stress. Cellular systems can utilize kosmotropic osmolytes, the products of complex biochemical pathways, to act as chemical chaperones. These extrinsic molecules, e.g., trehalose, alter local water structure to modulate the strength of the hydrophobic effect and increase protein stability. In contrast, simpler genetic systems must rely on intrinsic mutation to affect protein stability...
December 18, 2018: Journal of Molecular Evolution
https://read.qxmd.com/read/30456442/genes-encoding-mammalian-oviductal-proteins-involved-in-fertilization-are-subjected-to-gene-death-and-positive-selection
#10
Carla Moros-Nicolás, Sophie Fouchécourt, Ghylène Goudet, Philippe Monget
Oviductal proteins play an important role in mammalian fertilization, as proteins from seminal fluid. However, in contrast with the latter, their phylogenetic evolution has been poorly studied. Our objective was to study in 16 mammals the evolution of 16 genes that encode oviductal proteins involved in at least one of the following steps: (1) sperm-oviduct interaction, (2) acrosome reaction, and/or (3) sperm-zona pellucida interaction. Most genes were present in all studied mammals. However, some genes were lost along the evolution of mammals and found as pseudogenes: annexin A5 (ANXA5) and deleted in malignant brain tumor 1 (DMBT1) in tarsier; oviductin (OVGP1) in megabat; and probably progestagen-associated endometrial protein (PAEP) in tarsier, mouse, rat, rabbit, dolphin, and megabat; prostaglandin D2 synthase (PTGDS) in microbat; and plasminogen (PLG) in megabat...
December 2018: Journal of Molecular Evolution
https://read.qxmd.com/read/30456440/folding-assembly-and-persistence-the-essential-nature-and-origins-of-biopolymers
#11
Calvin M Runnels, Kathryn A Lanier, Justin Krish Williams, Jessica C Bowman, Anton S Petrov, Nicholas V Hud, Loren Dean Williams
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 observe that all three biopolymer types are pre-organized, conditionally self-complementary, chemically unstable in aqueous media yet persistent because of kinetic trapping, with chiral monomers and directional chains...
December 2018: Journal of Molecular Evolution
https://read.qxmd.com/read/30426144/delineation-of-the-genera-haemoproteus-and-plasmodium-using-rna-seq-and-multi-gene-phylogenetics
#12
Jasper Toscani Field, Josh Weinberg, Staffan Bensch, Nubia E Matta, Gediminas Valkiūnas, Ravinder N M Sehgal
Members of the order Haemosporida are protist parasites that infect mammals, reptiles and birds. This group includes the causal agents of malaria, Plasmodium parasites, the genera Leucocytozoon and Fallisia, as well as the species rich genus Haemoproteus with its two subgenera Haemoproteus and Parahaemoproteus. Some species of Haemoproteus cause severe disease in avian hosts, and these parasites display high levels of diversity worldwide. This diversity emphasizes the need for accurate evolutionary information...
December 2018: Journal of Molecular Evolution
https://read.qxmd.com/read/30392157/the-diabetes-susceptibility-gene-slc30a8-that-encodes-the-zinc-transporter-znt8-is-a-pseudogene-in-guinea-pigs-potentially-contributing-to-low-guinea-pig-islet-zinc-content
#13
LETTER
Kristen E Syring, Karin J Bosma, James K Oeser, Masakazu Shiota, Richard M O'Brien
In most mammals pancreatic islet beta cells have very high zinc levels that promote the crystallization and storage of insulin. Guinea pigs are unusual amongst mammals in that their islets have very low zinc content. The selectionist theory of insulin evolution proposes that low environmental zinc led to the selection of a mutation in Guinea pig insulin that negated the requirement for zinc binding. In mice deletion of the Slc30a8 gene, that encodes the zinc transporter ZnT8, markedly reduces islet zinc content...
December 2018: Journal of Molecular Evolution
https://read.qxmd.com/read/30382299/why-prokaryotes-genomes-lack-genes-with-introns-processed-by-spliceosomes
#14
EDITORIAL
Guillermo Lamolle, Héctor Musto
No abstract text is available yet for this article.
December 2018: Journal of Molecular Evolution
https://read.qxmd.com/read/30370448/positive-selection-in-the-evolution-of-mammalian-crisps
#15
Alberto Vicens, Claudia L Treviño
Cysteine-RIch Secretory Proteins (CRISPs) constitute a versatile family, with functions in reptilian venom and mammalian reproduction. Mammals generally express three CRISPs, four in mice, and all are highly expressed in male reproductive tissues, either testis or accessory organs. Because reproductive proteins often evolve adaptively in response to post-copulatory sexual selection, we hypothesized that mammalian CRISPs, with important roles in male reproduction, could have undergone positive selection promoting their divergence...
December 2018: Journal of Molecular Evolution
https://read.qxmd.com/read/30361751/a-non-neutral-origin-for-error-minimization-in-the-origin-of-the-genetic-code
#16
LETTER
Massimo Di Giulio
Massey (J Mol Evol 67:510-516, 2008; J Theor Biol 408:237-242, 2016; Nat Comput. https://doi.org/10.1007/s11047-017-9669-3, 2018) claims that the error minimization of the genetic code is derived by means of a neutral process and was not due to the action of natural selection. Here, I argue that this neutralist hypothesis of the origin of error minimization is not based directly on any neutral process but it could be only indirectly. On the contrary, it has been natural selection that has acted during the origin of the genetic code determining the property that similar amino acids are coded by similar codons within the genetic code table...
December 2018: Journal of Molecular Evolution
https://read.qxmd.com/read/30327830/evolutionary-genetics-of-hypoxia-and-cold-tolerance-in-mammals
#17
Kangli Zhu, Deyan Ge, Zhixin Wen, Lin Xia, Qisen Yang
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, subterranean burrows and marine environments by different mammals provide opportunities to conduct such analyses. Here, we focused on six genes in the hypoxia inducible factor (HIF) pathway and two non-shivering thermogenesis (NST)-related genes [PPAR co-activator 1 (PGC-1) and uncoupling protein 1 (UCP1)] in representative species of pikas and other mammals to understand whether these loci were targeted by natural selection during independent invasions to conditions characterized by hypoxia and temperature fluctuations by high-altitude, subterranean and marine mammals...
December 2018: Journal of Molecular Evolution
https://read.qxmd.com/read/30456441/genomic-signatures-among-acanthamoeba-polyphaga-entoorganisms-unveil-evidence-of-coevolution
#18
Víctor Serrano-Solís, Paulo Eduardo Toscano Soares, Sávio T de Farías
The definition of a genomic signature (GS) is "the total net response to selective pressure". Recent isolation and sequencing of naturally occurring organisms, hereby named entoorganisms, within Acanthamoeba polyphaga, raised the hypothesis of a common genomic signature despite their diverse and unrelated evolutionary origin. Widely accepted and implemented tests for GS detection are oligonucleotide relative frequencies (OnRF) and relative codon usage (RCU) surveys. A common pattern and strong correlations were unveiled from OnRFs among A...
November 20, 2018: Journal of Molecular Evolution
https://read.qxmd.com/read/30306205/circular-permutation-obscures-universality-of-a-ribosomal-protein
#19
Nicholas A Kovacs, Petar I Penev, Amitej Venapally, Anton S Petrov, Loren Dean Williams
Functions, origins, and evolution of the translation system are best understood in the context of unambiguous and phylogenetically based taxonomy and nomenclature. Here, we map ribosomal proteins onto the tree of life and provide a nomenclature for ribosomal proteins that is consistent with phylogenetic relationships. We have increased the accuracy of homology relationships among ribosomal proteins, providing a more informative picture of their lineages. We demonstrate that bL33 (bacteria) and eL42 (archaea/eukarya) are homologs with common ancestry and acute similarities in sequence and structure...
October 2018: Journal of Molecular Evolution
https://read.qxmd.com/read/30302501/ancestral-and-compensatory-mutations-that-promote-antiviral-resistance-in-influenza-n1-neuraminidase-revealed-by-a-phylonumerics-approach
#20
Elma H Akand, Kevin M Downard
Implementation of a new phylonumerics approach to construct a mass tree representing over 6000 H1N1 human influenza strains has enabled ancestral and compensatory descendant mutations to be identified in N1 neuraminidase that promote antiviral resistance and restore viral fitness. Adjacent to the H275Y resistance mutation site, mutations S299A and S247N, respectively, lead the evolution of oseltamivir-resistant strains and restore viral fitness to those strains thereafter. Importantly the mass tree phylonumerics approach can identify such mutations globally, without any positional bias, so that functionally linked or compensatory mutations remote in the sequence or structure of the protein can be identified and interrogated...
October 2018: Journal of Molecular Evolution
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