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https://www.readbyqxmd.com/read/28645195/mutational-biases-influence-parallel-adaptation
#1
Arlin Stoltzfus, David M McCandlish
While mutational biases strongly influence neutral molecular evolution, the role of mutational biases in shaping the course of adaptation is less clear. Here we consider the frequency of transitions relative to transversions among adaptive substitutions. Because mutation rates for transitions are higher than those for transversions, if mutational biases influence the dynamics of adaptation, then transitions should be over-represented among documented adaptive substitutions. To test this hypothesis, we assembled 2 sets of data on putatively adaptive amino acid replacements that have occurred in parallel during evolution, either in nature or in the laboratory...
June 22, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28644134/the-conundrum-of-the-epstein-barr-virus-associated-gastric-carcinoma-in-the-americas
#2
REVIEW
Gonzalo Carrasco-Avino, Ismael Riquelme, Oslando Padilla, Miguel Villaseca, Francisco R Aguayo, Alejandro H Corvalan
Epstein-Barr virus-associated gastric carcinoma shows a higher prevalence in the Americas than Asia. We summarize all studies of Epstein Barr virus-associated gastric carcinoma in the Americas, focusing on host characteristics, environmental associations and phylogeographic diversity of Epstein-Barr virus strains. In the Americas, the prevalence of Epstein Barr virus-associated gastric carcinoma is 11.4%, more frequent in males and portray predominantly diffuse-type histology. EBERs, EBNAs, BARTs and LMP are the highest expressed genes; their variations in healthy individuals may explain the phylogeographic diversity of Epstein-Barr virus across the region...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28642484/mir-100-5p-inhibition-induces-apoptosis-in-dormant-prostate-cancer-cells-and-prevents-the-emergence-of-castration-resistant-prostate-cancer
#3
Noushin Nabavi, Nur Ridzwan Nur Saidy, Erik Venalainen, Anne Haegert, Abhijit Parolia, Hui Xue, Yuwei Wang, Rebecca Wu, Xin Dong, Colin Collins, Francesco Crea, Yuzhuo Wang
Carcinoma of the prostate is the most common cancer in men. Treatment of aggressive prostate cancer involves a regiment of radical prostectomy, radiation therapy, chemotherapy and hormonal therapy. Despite significant improvements in the last decade, the treatment of prostate cancer remains unsatisfactory, because a significant fraction of prostate cancers develop resistance to multiple treatments and become incurable. This prompts an urgent need to investigate the molecular mechanisms underlying the evolution of therapy-induced resistance of prostate cancer either in the form of castration-resistant prostate cancer (CRPC) or transdifferentiated neuroendocrine prostate cancer (NEPC)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642345/evolution-of-nonspectral-rhodopsin-function-at-high-altitudes
#4
Gianni M Castiglione, Frances E Hauser, Brian S Liao, Nathan K Lujan, Alexander Van Nynatten, James M Morrow, Ryan K Schott, Nihar Bhattacharyya, Sarah Z Dungan, Belinda S W Chang
High-altitude environments present a range of biochemical and physiological challenges for organisms through decreases in oxygen, pressure, and temperature relative to lowland habitats. Protein-level adaptations to hypoxic high-altitude conditions have been identified in multiple terrestrial endotherms; however, comparable adaptations in aquatic ectotherms, such as fishes, have not been as extensively characterized. In enzyme proteins, cold adaptation is attained through functional trade-offs between stability and activity, often mediated by substitutions outside the active site...
June 22, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28642229/evolutionary-dynamics-of-the-kinetochore-network-in-eukaryotes-as-revealed-by-comparative-genomics
#5
Jolien Je van Hooff, Eelco Tromer, Leny M van Wijk, Berend Snel, Geert Jpl Kops
During eukaryotic cell division, the sister chromatids of duplicated chromosomes are pulled apart by microtubules, which connect via kinetochores. The kinetochore is a multiprotein structure that links centromeres to microtubules, and that emits molecular signals in order to safeguard the equal distribution of duplicated chromosomes over daughter cells. Although microtubule-mediated chromosome segregation is evolutionary conserved, kinetochore compositions seem to have diverged. To systematically inventory kinetochore diversity and to reconstruct its evolution, we determined orthologs of 70 kinetochore proteins in 90 phylogenetically diverse eukaryotes...
June 22, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28642169/a-novel-method-to-quantify-base-substitution-mutations-at-the-10-6-per-bp-level-in-dna-samples
#6
Satoshi Yamashita, Naoko Iida, Hideyuki Takeshima, Naoko Hattori, Maeda Masahiro, Takayoshi Kishino, Reiko Nagano, Taichi Shimazu, Shoichiro Tsugane, Toshikazu Ushijima
Somatic base substitution mutations of frequencies at the 10(-6)/bp level are expected to be present in many biomedical samples, such as tissues exposed to carcinogenic factors and exhausted stem cells. However, measurement of such rare mutations has been very difficult in human DNA samples. Here, we invented the use of 100 copies of genomic DNA as a template for amplicon deep sequencing so that a real mutation in a single DNA molecule would be detected at a variant allele frequency of 1% while sequencing errors have less frequency...
June 19, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28642015/convergent-and-unidirectional-evolution-of-extremely-long-aedeagi-in-the-largest-feather-mite-genus-proctophyllodes-acari-proctophyllodidae-evidence-from-comparative-molecular-and-morphological-phylogenetics
#7
Pavel B Klimov, Sergey V Mironov, Barry M OConnor
Proctophyllodid feather mites (400+ species) are permanent (full-time) symbionts commonly occurring on passerine birds. Phenotypic evolution of these mites appears to be greatly influenced by characters related to reproduction (>87.5% of a total of 32 taxonomically important discrete characters) and male genitalic characters (21.9%). Because sexual selection could the major evolutionary driver in this system, we test the theoretical expectation that genitalic or sexually dimorphic characters should evolve more rapidly and divergently then other characters...
June 19, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28641416/water-anion-hydrogen-bonding-dynamics-ultrafast-ir-experiments-and-simulations
#8
Steven A Yamada, Ward H Thompson, Michael D Fayer
Many of water's remarkable properties arise from its tendency to form an intricate and robust hydrogen bond network. Understanding the dynamics that govern this network is fundamental to elucidating the behavior of pure water and water in biological and physical systems. In ultrafast nonlinear infrared experiments, the accessible time scales are limited by water's rapid vibrational relaxation (1.8 ps for dilute HOD in H2O), precluding interrogation of slow hydrogen bond evolution in non-bulk systems. Here, hydrogen bonding dynamics in bulk D2O were studied from the perspective of the much longer lived (36...
June 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28641396/geneticization-in-mim-omim%C3%A2-exploring-historic-and-epistemic-drivers-of-contemporary-understandings-of-genetic-disease
#9
Rachel A Ankeny
Prior to the genomic sequencing era, the bible for those working in clinical genetics was McKusick's Mendelian Inheritance in Man (MIM), which appeared in multiple editions between the 1960s and the late 1990s. This catalogue was organized according to general patterns of inheritance and focused on phenotypes. Beginning in the mid-1980s, it was replaced by Online Mendelian Inheritance in Man (OMIM®), a continuously updated catalogue documenting molecular relationships between genetic variation and phenotypic expression...
June 21, 2017: Journal of Medicine and Philosophy
https://www.readbyqxmd.com/read/28641092/nuclear-mechanotransduction-sensing-the-force-from-within
#10
REVIEW
Avathamsa Athirasala, Nivi Hirsch, Amnon Buxboim
The cell nucleus is a hallmark of eukaryotic evolution, where gene expression is regulated and the genome is replicated and repaired. Yet, in addition to complex molecular processes, the nucleus has also evolved to serve physical tasks that utilize its optical and mechanical properties. Nuclear mechanotransduction of externally applied forces and extracellular stiffness is facilitated by the physical connectivity of the extracellular environment, the cytoskeleton and the nucleoskeletal matrix of lamins and chromatin...
June 19, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28640697/current-clinical-challenges-in-childhood-ependymoma-a-focused-review
#11
Thomas E Merchant
Ependymoma is a locally aggressive tumor with metastatic potential that arises in diverse locations throughout the brain and spine in children. Tumor and treatment may result in significant morbidity. Cure remains elusive for many patients owing to diverse biology and resistance to conventional therapy. The implementation of systematic postoperative irradiation in clinical trials during the past 20 years has increased the proportion of patients achieving durable disease control with excellent results, as measured by objective functional outcome measures...
June 22, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28640696/insights-from-molecular-profiling-of-adult-glioma
#12
Phedias Diamandis, Kenneth D Aldape
The comprehensive molecular profiling of cancer has resulted in new insights into the biology and classification of numerous tumor types. In the case of primary brain tumors that commonly affect adults, an emerging set of disease-defining biomarker sets is reshaping existing diagnostic entities that had previously been defined on the basis of their microscopic appearance. Substantial progress has been made in this regard for common primary brain tumors in adults, especially diffuse gliomas, where large-scale profiling efforts have led to the incorporation of highly prevalent molecular alterations that promote a biologically based classification as an adjunct to the traditional histopathologic approach...
June 22, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28640577/laser-ablation-molecular-isotopic-spectrometry-for-molecules-formation-chemistry-in-fs-laser-ablated-plasmas
#13
Huaming Hou, Xianglei Mao, Vassilia Zorba, Richard E Russo
Recently, laser ablated molecular isotopic spectrometry (LAMIS) has expanded its capability to explore molecules formation mechanism in laser induced plasma in addition to isotope analysis. LAMIS is powerful tool for tracking the origination of atoms that involved in formation of investigated molecules by labeling atoms with its isotopic substitution. The evolutionary formation pathways of organic molecules, especially of C2 dimers and CN radicals, were frequently reported. However, very little is known about the formation pathways for metallic radicals and heterodimers in laser ablated plasma...
June 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28640150/evaluation-of-research-topic-evolution-in-psychiatry-using-co-word-analysis
#14
Ying Wu, Xing Jin, Yunzhen Xue
With the rapid increase in the incidence of mental disorders and mental issues, psychiatry has become one of the fastest growing clinical medical disciplines. Development priorities and research foci in this field have evolved over different periods.All the articles in 10 psychiatric journals with the highest impact factors were selected from the Science Citation Index (SCI) in Web of Science from 2001 to 2015. The information visualization software Sci was used to conduct co-word and clustering analyses on these articles...
June 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28637852/testing-the-molecular-clock-using-mechanistic-models-of-fossil-preservation-and-molecular-evolution
#15
Rachel C M Warnock, Ziheng Yang, Philip C J Donoghue
Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling...
June 28, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28637270/in-planta-recapitulation-of-isoprene-synthases-evolution-from-ocimene-synthases
#16
Mingai Li, Jia Xu, Alberto Algarra Alarcon, Silvia Carlin, Enrico Barbaro, Luca Cappellin, Violeta Velikova, Urska Vrhovsek, Francesco Loreto, Claudio Varotto
Isoprene is the most abundant biogenic volatile hydrocarbon compound naturally emitted by plants and plays a major role in atmospheric chemistry. It has been proposed that isoprene synthases (IspS) may readily evolve from other terpene synthases, but this hypothesis has not been experimentally investigated.We isolated and functionally validated in Arabidopsis the first isoprene synthase gene, AdoIspS, from a monocotyledonous species (Arundo donax L., Poaceae). Phylogenetic reconstruction indicates that AdoIspS and dicots isoprene synthases most likely originated by parallel evolution from TPS-b monoterpene synthases...
June 16, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28637269/announcing-the-genome-atlas-of-bamboo-and-rattan-gabr-project-promoting-research-in-evolution-and-in-economically-and-ecologically-beneficial-plants
#17
Hansheng Zhao, Shancen Zhao, Benhua Fei, Huan Liu, Huanming Yang, Honghai Dai, Dan Wang, Wei Jin, Feng Tang, Qiang Gao, Hang Xun, Yuwei Wang, Lianghua Qi, Xianghua Yue, Shuyan Lin, Lianfeng Gu, Lubin Li, Tiansheng Zhu, Qiang Wei, Zhen Su, Tarmeze Bin Wan Ariffin Wan, Daniel A Ofori, George Mbeva Muthike, Yigardu Mulatu Mengesha, Roberto Magno de Castro E Silva, Antonio Ludovico Beraldo, Zhimin Gao, Xin Liu, Zehui Jiang
Bamboo and rattan are widely grown for manufacturing, horticulture, and agroforestry. Bamboo and rattan production might help reduce poverty, boost economic growth, mitigate climate change, and protect the natural environment. Despite progress in research, sufficient molecular and genomic resources to study these species are lacking. We launched the Genome Atlas of Bamboo and Rattan (GABR) project, a comprehensive, coordinated international effort to accelerate understanding of BR genetics through genome analysis...
June 16, 2017: GigaScience
https://www.readbyqxmd.com/read/28637223/millions-of-years-behind-slow-adaptation-of-ruminants-to-grasslands
#18
Olja Toljagic, Kjetil L Voje, Michael Matschiner, Lee Hsiang Liow, Thomas F Hansen
The Late-Cretaceous appearance of grasses, followed by the Cenozoic advancement of grasslands as dominant biomes, has contributed to the evolution of a range of specialized herbivores adapted to new diets, as well as to increasingly open and arid habitats. Many mammals including ruminants, the most diversified ungulate suborder, evolved high-crowned (hypsodont) teeth as an adaptation to tooth-wearing diets and habitats. The impact of different causes of tooth wear is still a matter of debate, and the temporal pattern of hypsodonty evolution in relation to the evolution of grasslands remains unclear...
June 20, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28636881/mitochondrial-genome-of-helice-tientsinensis-brachyura-grapsoidea-varunidae-gene-rearrangements-and-higher-level-phylogeny-of-the-brachyura
#19
Zhao-Zhe Xin, Yu-Liu, Dai-Zhen Zhang, Zheng-Fei Wang, Hua-Bin Zhang, Bo-Ping Tang, Chun-Lin Zhou, Xin-Yue Chai, Qiu-Ning Liu
The mitochondrial genome (mt genome) provides important information for understanding molecular evolution and phylogeny. The further understand the molecular evolution and phylogeny of Helice tientsinensis, the complete mt genome was determined. It is 16,212bp long and includes 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and a control region. The genome composition of H. tientsinensis was highly A+T biased 69.0% and showed negative AT skew (-0.017) and GC skew (-0.289). One PCG, all rRNAs and 12 of the tRNAs appeared to be rearranged with respect to the pancrustacean ground pattern gene order...
June 18, 2017: Gene
https://www.readbyqxmd.com/read/28636600/hidden-morphological-diversity-among-early-tetrapods
#20
Jason D Pardo, Matt Szostakiwskyj, Per E Ahlberg, Jason S Anderson
Phylogenetic analysis of early tetrapod evolution has resulted in a consensus across diverse data sets in which the tetrapod stem group is a relatively homogenous collection of medium- to large-sized animals showing a progressive loss of 'fish' characters as they become increasingly terrestrial, whereas the crown group demonstrates marked morphological diversity and disparity. The oldest fossil attributed to the tetrapod crown group is the highly specialized aïstopod Lethiscus stocki, which shows a small size, extreme axial elongation, loss of limbs, spool-shaped vertebral centra, and a skull with reduced centres of ossification, in common with an otherwise disparate group of small animals known as lepospondyls...
June 21, 2017: Nature
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