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https://www.readbyqxmd.com/read/27911438/evolutionary-convergence-in-experimental-pseudomonas-populations
#1
Peter A Lind, Andrew D Farr, Paul B Rainey
Model microbial systems provide opportunity to understand the genetic bases of ecological traits, their evolution, regulation and fitness contributions. Experimental populations of Pseudomonas fluorescens rapidly diverge in spatially structured microcosms producing a range of surface-colonising forms. Despite divergent molecular routes, wrinkly spreader (WS) niche specialist types overproduce a cellulosic polymer allowing mat formation at the air-liquid interface and access to oxygen. Given the range of ways by which cells can form mats, such phenotypic parallelism is unexpected...
December 2, 2016: ISME Journal
https://www.readbyqxmd.com/read/27910110/runs-of-homozygosity-current-knowledge-and-applications-in-livestock
#2
REVIEW
E Peripolli, D P Munari, M V G B Silva, A L F Lima, R Irgang, F Baldi
This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome...
December 1, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27910074/evolutional-characterization-of-photochemically-induced-stroke-in-rats-a-multimodality-imaging-and-molecular-biological-study
#3
Nai-Wei Liu, Chien-Chih Ke, Yonghua Zhao, Yi-An Chen, Kim-Chuan Chan, David Tat-Wei Tan, Jhih-Shian Lee, You-Yin Chen, Tun-Wei Hsu, Ya-Ju Hsieh, Chi-Wei Chang, Bang-Hung Yang, Wen-Sheng Huang, Ren-Shyan Liu
Photochemically induced cerebral ischemia is an easy-manipulated, reproducible, relatively noninvasive, and lesion controllable model for translational study of ischemic stroke. In order to longitudinally investigate the characterization of the model, magnetic resonance imaging, (18)F-2-deoxy-glucose positron emission tomography, fluorescence, and bioluminescence imaging system were performed in correlation with triphenyl tetrazolium chloride (TTC), hematoxylin-eosin staining, and immunohistochemistry examinations of glial fibrillary acidic protein, CD68, NeuN, von willebrand factor, and α-smooth muscle actin in the infarct zone...
December 1, 2016: Translational Stroke Research
https://www.readbyqxmd.com/read/27910009/cancer-cytogenetics-an-introduction
#4
Thomas S K Wan
The Philadelphia chromosome was the first chromosomal abnormality discovered in cancer using the cytogenetics technique in 1960, and was consistently associated with chronic myeloid leukemia. Over the past five decades, innovative technical advances in the field of cancer cytogenetics have greatly enhanced the detection ability of chromosomal alterations, and have facilitated the research and diagnostic potential of chromosomal studies in neoplasms. These developments notwithstanding, chromosome analysis of a single cell is still the easiest way to delineate and understand the relationship between clonal evolution and disease progression of cancer cells...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27908264/hypoxia-and-inflammation-in-prostate-cancer-progression-cross-talk-with-androgen-and-estrogen-receptors-and-cancer-stem-cells
#5
Matteo A Russo, Linda Ravenna, Laura Pellegrini, Elisa Petrangeli, Luisa Salvatori, Thea Magrone, Massimo Fini, Marco Tafani
Tumors are complex tissues in which transformed cells communicate with the surrounding microenvironment and evolve traits promoting their own survival and malignancy. Hypoxia and inflammation are constant characteristics of prostate tumor microenvironment influencing both cancer stem cells and differentiated tumor cells. HIFs and NF-kB are the key regulators of the transcriptional response to hypoxic and inflammatory stresses, respectively, and a crosstalk between HIFs and NF-kB pathways has been widely documented...
November 30, 2016: Endocrine, Metabolic & Immune Disorders Drug Targets
https://www.readbyqxmd.com/read/27908140/sequence-control-of-phase-separation-and-dewetting-in-ps-pvme-blend-thin-films-by-changing-molecular-weight-of-ps
#6
Tian Xia, Yaping Qin, Yajiang Huang, Ting Huang, Jianhui Xu, Youbing Li
The morphology evolution mechanism of polystyrene (PS)/poly (vinyl methyl ether) (PVME) blend thin films with different PS molecular weights (Mw) was studied. It was found that the morphology evolution was closely related to the molecular weight asymmetry between PS and PVME. In the film where Mw(PS) ≈ Mw(PVME), dewetting happened at the interface between the bottom layer and substrate after SD phase separation. While in the film where Mw(PS) > Mw(PVME), dewetting happened at the interface between the middle PS/PVME blend layer and bottom PVME layer near the substrate prior to phase separation...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27907154/pheromone-recognition-and-selectivity-by-comr-proteins-among-streptococcus-species
#7
Erin Shanker, Donald A Morrison, Antoine Talagas, Sylvie Nessler, Michael J Federle, Gerd Prehna
Natural transformation, or competence, is an ability inherent to bacteria for the uptake of extracellular DNA. This process is central to bacterial evolution and allows for the rapid acquirement of new traits, such as antibiotic resistance in pathogenic microorganisms. For the Gram-positive bacteria genus Streptococcus, genes required for competence are under the regulation of quorum sensing (QS) mediated by peptide pheromones. One such system, ComRS, consists of a peptide (ComS) that is processed (XIP), secreted, and later imported into the cytoplasm, where it binds and activates the transcription factor ComR...
December 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27906993/ancient-mitochondrial-capture-as-factor-promoting-mitonuclear-discordance-in-freshwater-fishes-a-case-study-in-the-genus-squalius-actinopterygii-cyprinidae-in-greece
#8
Silvia Perea, Jasna Vukić, Radek Šanda, Ignacio Doadrio
Hybridization and incomplete lineage sorting are common confounding factors in phylogeny and speciation resulting in mitonuclear disparity. Mitochondrial introgression, a particular case of hybridization, may, in extreme cases, lead to replacement of the mitochondrial genome of one species with that of another (mitochondrial capture). We investigated mitochondrial introgression involving two species of the cyprinid genus Squalius in the western Peloponnese region of Greece using molecular and morphological data...
2016: PloS One
https://www.readbyqxmd.com/read/27906966/archival-isolates-confirm-a-single-topotype-of-west-nile-virus-in-australia
#9
Bixing Huang, Natalie A Prow, Andrew F van den Hurk, Richard J N Allcock, Peter R Moore, Stephen L Doggett, David Warrilow
West Nile virus is globally wide-spread and causes significant disease in humans and animals. The evolution of West Nile virus Kunjin subtype in Australia (WNVKUN) was investigated using archival samples collected over a period of 50 years. Based on the pattern of fixed amino acid substitutions and time-stamped molecular clock analyses, a single long-term lineage (or topotype) was inferred. This implies that a bottleneck exists such that regional strains eventually die out and are replaced with strains from a single source...
December 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27906527/behavioral-epigenetics
#10
David S Moore
Why do we grow up to have the traits we do? Most 20th century scientists answered this question by referring only to our genes and our environments. But recent discoveries in the emerging field of behavioral epigenetics have revealed factors at the interface between genes and environments that also play crucial roles in development. These factors affect how genes work; scientists now know that what matters as much as which genes you have (and what environments you encounter) is how your genes are affected by their contexts...
December 1, 2016: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27906129/the-evolutionary-origin-of-bilaterian-smooth-and-striated-myocytes
#11
Thibaut Brunet, Antje Hl Fischer, Patrick Rh Steinmetz, Antonella Lauri, Paola Bertucci, Detlev Arendt
The dichotomy between smooth and striated myocytes is fundamental for bilaterian musculature, but its evolutionary origin is unsolved. In particular, interrelationships of visceral smooth muscles remain unclear. Absent in fly and nematode, they have not yet been characterized molecularly outside vertebrates. Here, we characterize expression profile, ultrastructure, contractility and innervation of the musculature in the marine annelid Platynereis dumerilii and identify smooth muscles around the midgut, hindgut and heart that resemble their vertebrate counterparts in molecular fingerprint, contraction speed, and nervous control...
December 1, 2016: ELife
https://www.readbyqxmd.com/read/27906002/hiv-1-genetic-diversity-and-its-distribution-characteristics-among-newly-diagnosed-hiv-1-individuals-in-hebei-province-china
#12
Xinli Lu, Cuiying Zhao, Wei Wang, Chenxi Nie, Yuqi Zhang, Hongru Zhao, Suliang Chen, Ze Cui
BACKGROUND: Since the first HIV-1 case in 1989, Hebei province has presented a clearly rising trend of HIV-1 prevalence, and HIV-1 genetic diversity has become the vital barrier to HIV prevention and control in this area. To obtain detailed information of HIV-1 spread in different populations and in different areas of Hebei, a cross-sectional HIV-1 molecular epidemiological investigation was performed across the province. METHODS: Blood samples of 154 newly diagnosed HIV-1 individuals were collected from ten prefectures in Hebei using stratified sampling...
January 19, 2016: AIDS Research and Therapy
https://www.readbyqxmd.com/read/27905871/phyinformr-phylogenetic-experimental-design-and-phylogenomic-data-exploration-in-r
#13
Alex Dornburg, J Nick Fisk, Jules Tamagnan, Jeffrey P Townsend
BACKGROUND: Analyses of phylogenetic informativeness represent an important step in screening potential or existing datasets for their proclivity toward convergent or parallel evolution of molecular sites. However, while new theory has been developed from which to predict the utility of sequence data, adoption of these advances have been stymied by a lack of software enabling application of advances in theory, especially for large next-generation sequence data sets. Moreover, there are no theoretical barriers to application of the phylogenetic informativeness or the calculation of quartet internode resolution probabilities in a Bayesian setting that more robustly accounts for uncertainty, yet there is no software with which a computationally intensive Bayesian approach to experimental design could be implemented...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27905833/non-conventional-expression-systems-for-the-production-of-vaccine-proteins-and-immunotherapeutic-molecules
#14
Isabelle Legastelois, Sophie Buffin, Isabelle Peubez, Charlotte Mignon, Régis Sodoyer, Bettina Werle
The increasing demand for recombinant vaccine antigens or immunotherapeutic molecules calls into question the universality of current protein expression systems. Vaccine production can require relatively low amounts of expressed materials, but represents an extremely diverse category consisting of different target antigens with marked structural differences. In contrast, monoclonal antibodies, by definition share key molecular characteristics and require a production system capable of very large outputs, which drives the quest for highly efficient and cost-effective systems...
December 1, 2016: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/27905607/a-heat-capacity-model-of-t-3-2-dependence-for-quantum-dots
#15
Amirul Edham Roslee, Saifful Kamaluddin Muzakir, Jamil Ismail, Mashitah M Yusoff, Rajan Jose
This article addresses the heat capacity of quantum dots (QDs) using density functional theory (DFT). By analyzing the evolution of phonon density of states and heat capacity as CdSe clusters grow from a molecular cluster into larger quantum confined solids, we have shown that their heat capacity does not fit very well with the Debye T(3) model. We observed that the number of phonon modes, which is discrete, increases as the particles grow, and the dispersion relation shows a quadratic behavior in contrast to the bulk solids whose dispersion relation is linear and equal to the sound velocity...
December 1, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27904954/the-mathematics-of-xenology-di-cographs-symbolic-ultrametrics-2-structures-and-tree-representable-systems-of-binary-relations
#16
Marc Hellmuth, Peter F Stadler, Nicolas Wieseke
The concepts of orthology, paralogy, and xenology play a key role in molecular evolution. Orthology and paralogy distinguish whether a pair of genes originated by speciation or duplication. The corresponding binary relations on a set of genes form complementary cographs. Allowing more than two types of ancestral event types leads to symmetric symbolic ultrametrics. Horizontal gene transfer, which leads to xenologous gene pairs, however, is inherent asymmetric since one offspring copy "jumps" into another genome, while the other continues to be inherited vertically...
November 30, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27903259/differential-variation-patterns-between-hubs-and-bottlenecks-in-human-protein-protein-interaction-networks
#17
Erli Pang, Yu Hao, Ying Sun, Kui Lin
BACKGROUND: The identification, description and understanding of protein-protein networks are important in cell biology and medicine, especially for the study of system biology where the focus concerns the interaction of biomolecules. Hubs and bottlenecks refer to the important proteins of a protein interaction network. Until now, very little attention has been paid to differentiate these two protein groups. RESULTS: By integrating human protein-protein interaction networks and human genome-wide variations across populations, we described the differences between hubs and bottlenecks in this study...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27902924/simple-mechanisms-of-early-life-simulation-model-on-the-origin-of-semi-cells
#18
Adrian Klein, Martin Bock, Wolfgang Alt
The development of first cellular structures played an important role in the early evolution of life. Early evolution of life probably took place on a molecular level in a reactive environment. The iron-sulfur theory postulates the formation of cell-like structures on catalytic surfaces. Experiments show that H2S together with FeS and other metallic centers drive auto-catalytic surface reactions, in which organic molecules such as pyruvic and amino acids occur. It is questionable which mechanisms are needed to form cell-like structures under these conditions...
November 27, 2016: Bio Systems
https://www.readbyqxmd.com/read/27902382/the-genetic-diversity-and-phenotypic-associations-of-feline-caliciviruses-from-cats-in-switzerland
#19
Andrea M Spiri, Julien Thézé, Marina L Meli, Valentino Cattori, Alice Berger, Adolf Steinrigl, Oliver G Pybus, Regina Hofmann-Lehmann, Barbara Willi
Feline calicivirus (FCV) is a common viral pathogen in domestic cats worldwide. The variable regions of the capsid (VP1) gene of FCV have one of the highest recorded rates of molecular evolution. Understanding the genetic diversity and phylogeny of FCV is a prerequisite to exploring the epidemiology and pathogenesis of this virus and to the development of efficacious vaccine strategies. In this study, we undertook a nationwide molecular characterization of FCV using for the first time nearly complete capsid (VP1) gene sequences...
October 7, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27902372/molecular-characterization-of-emerging-g9p-4-rotavirus-strains-possessing-a-rare-e6-nsp4-or-t1-nsp3-genotype-on-a-genogroup-2-backbone-using-a-refined-classification-framework
#20
Gauri N Pradhan, Atul M Walimbe, Shobha D Chitambar
Rotavirus infections associated with unusual strains are an emerging concern in rotavirus vaccination program. Recently, an increase in circulation of unusual G9P[4] strain was reported from different regions of India, placing it at the third position after G1P[8] and G2P[4], the most common rotavirus strains. The aim of the present study was to analyze complete genomic constellation of three G9P[4] strains (RV09, RV10 and RV11), determine their genetic relatedness with other genogroup-2 strains and understand the evolution of a rare E6 and other NSP4 genotypes...
November 2, 2016: Journal of General Virology
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