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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/27911022/membrane-defects-and-genetic-redundancy-are-we-at-a-turning-point-for-dyt1-dystonia
#2
REVIEW
Ana Cascalho, Julie Jacquemyn, Rose E Goodchild
Heterozygosity for a 3-base pair deletion (ΔGAG) in TOR1A/torsinA is one of the most common causes of hereditary dystonia. In this review, we highlight current understanding of how this mutation causes disease from research spanning structural biochemistry, cell science, neurobiology, and several model organisms. We now know that homozygosity for ΔGAG has the same effects as Tor1a(KO) , implicating a partial loss of function mechanism in the ΔGAG/+ disease state. In addition, torsinA loss specifically affects neurons in mice, even though the gene is broadly expressed, apparently because of differential expression of homologous torsinB...
December 2, 2016: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/27910894/calcium-ions-function-as-a-booster-of-chromosome-condensation
#3
Rinyaporn Phengchat, Hideaki Takata, Kenichi Morii, Noriko Inada, Hideji Murakoshi, Susumu Uchiyama, Kiichi Fukui
Chromosome condensation is essential for the faithful transmission of genetic information to daughter cells during cell division. The depletion of chromosome scaffold proteins does not prevent chromosome condensation despite structural defects. This suggests that other factors contribute to condensation. Here we investigated the contribution of divalent cations, particularly Ca(2+), to chromosome condensation in vitro and in vivo. Ca(2+) depletion caused defects in proper mitotic progression, particularly in chromosome condensation after the breakdown of the nuclear envelope...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910249/the-hla-a-b-and-drb1-polymorphism-in-a-large-dataset-of-south-brazil-bone-marrow-donors-from-rio-grande-do-sul
#4
J A Boquett, J M Nunes, S Buhler, M Z de Oliveira, L F Jobim, M Jobim, N J R Fagundes, L Schüler-Faccini, A Sanchez-Mazas
Human leukocyte antigen (HLA) genes are very informative in population genetics studies and their variability has been widely used to reconstruct the history of geographic and/or demographic expansions of human populations. The characterization of HLA diversity at the population level is also fundamental in clinical studies, particularly for bone marrow transplantation programs. In this study, we investigated the HLA molecular variation in Rio Grande do Sul, South Brazil, in order to identify possible regional differences across this state...
December 2, 2016: HLA
https://www.readbyqxmd.com/read/27910110/runs-of-homozygosity-current-knowledge-and-applications-in-livestock
#5
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/27910049/gene-transfer-in-cardiomyocytes-derived-from-es-and-ips-cells
#6
Francesca Stillitano, Ioannis Karakikes, Roger J Hajjar
The advent of human induced pluripotent stem cell (hiPSC) technology has produced patient-specific hiPSC derived cardiomyocytes (hiPSC-CMs) that can be used as a platform to study cardiac diseases and to explore new therapies.The ability to genetically manipulate hiPSC-CMs not only is essential for identifying the structural and/or functional role of a protein but can also provide valuable information regarding therapeutic applications. In this chapter, we describe protocols for culture, maintenance, and cardiac differentiation of hiPSCs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27909891/canola-oil-rich-in-oleic-acid-improves-diastolic-heart-function-in-diet-induced-obese-rats
#7
Sijo Joseph Thandapilly, Pema Raj, Xavier Lieben Louis, Danielle Perera, Prasanga Yamanagedara, Peter Zahradka, Carla G Taylor, Thomas Netticadan
Obesity is a leading cause of cardiovascular disease. It directly affects heart structure and function and contributes to heart failure. Diet is a major factor involved in the development of obesity along with genetic factors. We examined the effects of monounsaturated and polyunsaturated fatty acid-rich oils on cardiac structure and function in the diet-induced rodent model of obesity (DIO). Obese prone (OP) rats were fed a high-fat diet (HF; 55% of kcal) for 12 weeks; Sprague-Dawley rats fed commercial chow served as control...
December 1, 2016: Journal of Physiological Sciences: JPS
https://www.readbyqxmd.com/read/27909816/ecological-and-physical-barriers-shape-genetic-structure-of-the-alpine-porcini-boletus-reticuloceps
#8
Bang Feng, Jian Wei Liu, Jianping Xu, Kuan Zhao, Zai Wei Ge, Zhu L Yang
The Alpine porcini, Boletus reticuloceps, is an ectomycorrhizal mushroom distributed in subalpine areas of Southwest China, central China, and Taiwan Island. This distribution pattern makes it an ideal organism to infer how ectomycorrhizal fungi have reacted to historical tectonic and climatic changes, and to illustrate the mechanism for the disjunction of organisms between Southwest China and Taiwan. In this study, we explored the phylogeographic pattern of B. reticuloceps by microsatellite genotyping, DNA sequencing, ecological factor analysis, and species distribution modeling...
December 1, 2016: Mycorrhiza
https://www.readbyqxmd.com/read/27909515/myocardial-biopsy-in-idiopathic%C3%A2-atrial-fibrillation-and-other-arrhythmias-nosological-diagnosis-clinical-and-morphological-parallels-and-treatment
#9
O V Blagova, A V Nedostup, E A Kogan, V A Sulimov, S A Abugov, A G Kupriyanova, V A Zaydenov, A E Donnikov, E V Zaklyazminskaya, E A Okisheva
BACKGROUND: The nosological nature of "idiopathic" arrhythmias and the effect of etiotropic and pathogenetic treatment are often unknown. METHODS AND RESULTS: 19 patients (42.6±11.3 years, 9 women) with atrial fibrillation (n = 16), supraventricular (n = 10) and ventricular (n = 4) premature beats, supraventricular (n = 2) and ventricular tachycardia (n = 1), left bundle branch block (n= 2), AV block (n = 2) without structural heart changes. Viruses were identified (polymerase chain reaction, PCR) along with measurement of anti-heart antibodies (AHA) and endomyocardial biopsy (EMB)...
June 2016: Journal of Atrial Fibrillation
https://www.readbyqxmd.com/read/27909431/the-microbiota-of-recreational-freshwaters-and-the-implications-for-environmental-and-public-health
#10
Chang Soo Lee, Minseok Kim, Cheonghoon Lee, Zhongtang Yu, Jiyoung Lee
The microbial communities in recreational freshwaters play important roles in both environmental and public health perspectives. In this study, the bacterial community structure and its associations with freshwater environments were investigated by analyzing the summertime microbiomes of three beach waters in Ohio (East Fork, Delaware, and Madison lakes) together with environmental and microbial water quality parameters. From the swimming season of 2009, 21 water samples were collected from the three freshwater beaches...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27909301/genetic-architecture-and-evolution-of-the-s-locus-supergene-in-primula-vulgaris
#11
Jinhong Li, Jonathan M Cocker, Jonathan Wright, Margaret A Webster, Mark McMullan, Sarah Dyer, David Swarbreck, Mario Caccamo, Cock van Oosterhout, Philip M Gilmartin
Darwin's studies on heterostyly in Primula described two floral morphs, pin and thrum, with reciprocal anther and stigma heights that promote insect-mediated cross-pollination. This key innovation evolved independently in several angiosperm families. Subsequent studies on heterostyly in Primula contributed to the foundation of modern genetic theory and the neo-Darwinian synthesis. The established genetic model for Primula heterostyly involves a diallelic S locus comprising several genes, with rare recombination events that result in self-fertile homostyle flowers with anthers and stigma at the same height...
December 2, 2016: Nature Plants
https://www.readbyqxmd.com/read/27908705/a-novel-method-for-in-silico-identification-of-regulatory-snps-in-human-genome
#12
Rong Li, Dexing Zhong, Ruiling Liu, Hongqiang Lv, Xinman Zhang, Jun Liu, Jiuqiang Han
Regulatory single nucleotide polymorphisms (rSNPs), kind of functional noncoding genetic variants, can affect gene expression in a regulatory way, and they are thought to be associated with increased susceptibilities to complex diseases. Here a novel computational approach to identify potential rSNPs is presented. Different from most other rSNPs finding methods which based on hypothesis that SNPs causing large allele-specific changes in transcription factor binding affinities are more likely to play regulatory functions, we use a set of documented experimentally verified rSNPs and nonfunctional background SNPs to train classifiers, so the discriminating features are found...
November 28, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27908231/the-mitochondrial-genome-the-nucleoid
#13
REVIEW
A A Kolesnikov
Mitochondrial DNA (mtDNA) in cells is organized in nucleoids containing DNA and various proteins. This review discusses questions of organization and structural dynamics of nucleoids as well as their protein components. The structures of mt-nucleoid from different organisms are compared. The currently accepted model of nucleoid organization is described and questions needing answers for better understanding of the fine mechanisms of the mitochondrial genetic apparatus functioning are discussed.
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27907895/mutlbsgenedb-mutated-ligand-binding-site-gene-database
#14
Pora Kim, Junfei Zhao, Pinyi Lu, Zhongming Zhao
Mutations at the ligand binding sites (LBSs) can influence protein structure stability, binding affinity with small molecules, and drug resistance in cancer patients. Our recent analysis revealed that ligand binding residues had a significantly higher mutation rate than other parts of the protein. Here, we built mutLBSgeneDB (mutated Ligand Binding Site gene DataBase) available at http://zhaobioinfo.org/mutLBSgeneDB We collected and curated over 2300 genes (mutLBSgenes) having ∼12 000 somatic mutations at ∼10 000 LBSs across 16 cancer types and selected 744 drug targetable genes (targetable_mutLBSgenes) by incorporating kinases, transcription factors, pharmacological genes, and cancer driver genes...
October 7, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27907193/phylogenetic-lineages-and-postglacial-dispersal-dynamics-characterize-the-genetic-structure-of-the-tick-ixodes-ricinus-in-northwest-europe
#15
Knut H Røed, Kjersti S Kvie, Gunnar Hasle, Lucy Gilbert, Hans Petter Leinaas
Dispersal and gene flow are important mechanisms affecting the dynamics of vectors and their pathogens. Here, patterns of genetic diversity were analyzed in many North European populations of the tick, Ixodes ricinus. Population sites were selected within and between areas separated by geographical barriers in order to evaluate the importance of tick transportation by birds in producing genetic connectivity across open sea and mountain ranges. The phylogenetic analyses of the mitochondrial control region and the cytochrome b gene revealed two distinct clades with supported sub-clades, with three genetic lineages: GB and WNo associated with Great Britain and western Norway respectively, and Eu with a wider distribution across continental Europe in agreement with much lower efficiency of tick dispersal by birds than by large mammals...
2016: PloS One
https://www.readbyqxmd.com/read/27907100/patterns-of-fish-connectivity-between-a-marine-protected-area-and-surrounding-fished-areas
#16
Rita Sahyoun, Paolo Guidetti, Antonio Di Franco, Serge Planes
Patterns of connectivity and self-recruitment are recognized as key factors shaping the dynamics of marine populations. Connectivity is also essential for maintaining and restoring natural ecological processes with genetic diversity contributing to the adaptation and persistence of any species in the face of global disturbances. Estimates of connectivity are crucial to inform the design of both marine protected areas (MPAs) and MPA networks. Among several approaches, genetic structure is frequently used as a proxy for patterns of connectivity...
2016: PloS One
https://www.readbyqxmd.com/read/27907032/genetic-structure-in-the-northern-range-margins-of-common-ash-fraxinus-excelsior-l
#17
Mari Mette Tollefsrud, Tor Myking, Jørn Henrik Sønstebø, Vaidotas Lygis, Ari Mikko Hietala, Myriam Heuertz
During post glacial colonization, loss of genetic diversity due to leading edge effects may be attenuated in forest trees because of their prolonged juvenile phase, allowing many migrants to reach the colonizing front before populations become reproductive. The northern range margins of temperate tree taxa in Europe are particularly suitable to study the genetic processes that follow colonization because they have been little affected by northern refugia. Here we examined how post glacial range dynamics have shaped the genetic structure of common ash (Fraxinus excelsior L...
2016: PloS One
https://www.readbyqxmd.com/read/27906075/nuclear-bodies-reorganize-during-myogenesis-in-vitro-and-are-differentially-disrupted-by-expression-of-fshd-associated-dux4
#18
Sachiko Homma, Mary Lou Beermann, Bryant Yu, Frederick M Boyce, Jeffrey Boone Miller
BACKGROUND: Nuclear bodies, such as nucleoli, PML bodies, and SC35 speckles, are dynamic sub-nuclear structures that regulate multiple genetic and epigenetic processes. Additional regulation is provided by RNA/DNA handling proteins, notably TDP-43 and FUS, which have been linked to ALS pathology. Previous work showed that mouse cell line myotubes have fewer but larger nucleoli than myoblasts, and we had found that nuclear aggregation of TDP-43 in human myotubes was induced by expression of DUX4-FL, a transcription factor that is aberrantly expressed and causes pathology in facioscapulohumeral dystrophy (FSHD)...
December 1, 2016: Skeletal Muscle
https://www.readbyqxmd.com/read/27905614/methanobactins-from-genome-to-function
#19
Laura M K Dassama, Grace E Kenney, Amy C Rosenzweig
Methanobactins (Mbns) are ribosomally produced, post-translationally modified peptide (RiPP) natural products that bind copper with high affinity using nitrogen-containing heterocycles and thioamide groups. In some methanotrophic bacteria, Mbns are secreted under conditions of copper starvation and then re-internalized as a copper source for the enzyme particulate methane monooxygenase (pMMO). Genome mining studies have led to the identification and classification of operons encoding the Mbn precursor peptide (MbnA) as well as a number of putative transport, regulatory, and biosynthetic proteins...
December 1, 2016: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/27905547/in-silico-mapping-of-protein-unfolding-mutations-for-inherited-disease
#20
Caitlyn L McCafferty, Yuri V Sergeev
The effect of disease-causing missense mutations on protein folding is difficult to evaluate. To understand this relationship, we developed the unfolding mutation screen (UMS) for in silico evaluation of the severity of genetic perturbations at the atomic level of protein structure. The program takes into account the protein-unfolding curve and generates propensities using calculated free energy changes for every possible missense mutation at once. These results are presented in a series of unfolding heat maps and a colored protein 3D structure to show the residues critical to the protein folding and are available for quick reference...
December 1, 2016: Scientific Reports
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