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Genome wide selection

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https://www.readbyqxmd.com/read/28918554/genome-wide-identification-classification-evolutionary-analysis-and-gene-expression-patterns-of-the-protein-kinase-gene-family-in-wheat-and-aegilops-tauschii
#1
Jun Yan, Peisen Su, Zhaoran Wei, Eviatar Nevo, Lingrang Kong
In this study we systematically identified and classified PKs in Triticum aestivum, Triticum urartu and Aegilops tauschii. Domain distribution and exon-intron structure analyses of PKs were performed, and we found conserved exon-intron structures within the exon phases in the kinase domain. Collinearity events were determined, and we identified various T. aestivum PKs from polyploidizations and tandem duplication events. Global expression pattern analysis of T. aestivum PKs revealed that some PKs might participate in the signaling pathways of stress response and developmental processes...
September 16, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28918012/gene-editing-with-helper-dependent-adenovirus-can-efficiently-introduce-multiple-changes-simultaneously-over-a-large-genomic-region
#2
Donna J Palmer, Nathan C Grove, Dustin L Turner, Philip Ng
Helper-dependent adenoviral vectors (HDAds) possess long homology arms that mediate high-efficiency gene editing. These long homology arms may permit simultaneous introduction of multiple modifications into a large genomic region or may permit a single HDAd to correct many different individual mutations spread widely across a gene. We investigated this important potential using an HDAd bearing 13 genetic markers in the region of homology to the target CFTR locus in human iPSCs and found that all markers can be simultaneously introduced into the target locus, with the two farthest markers being 22...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28916739/a-moso-bamboo-wrky-gene-pewrky83-confers-salinity-tolerance-in-transgenic-arabidopsis-plants
#3
Min Wu, Huanlong Liu, Guomin Han, Ronghao Cai, Feng Pan, Yan Xiang
The WRKY family are transcription factors, involved in plant development, and response to biotic and abiotic stresses. Moso bamboo is an important bamboo that has high ecological, economic and cultural value and is widely distributed in the south of China. In this study, we performed a genome-wide identification of WRKY members in moso bamboo and identified 89 members. By comparative analysis in six grass genomes, we found the WRKY gene family may have experienced or be experiencing purifying selection. Based on relative expression levels among WRKY IIc members under three abiotic stresses, PeWRKY83 functioned as a transcription factor and was selected for detailed analysis...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916647/the-effect-of-common-inversion-polymorphisms-in-2l-t-and-in-3r-mo-on-patterns-of-transcriptional-variation-in-drosophila-melanogaster
#4
Erik Lavington, Andrew D Kern
Chromosomal inversions are an ubiquitous feature of genetic variation. Theoretical models describe several mechanisms by which inversions can drive adaptation and be maintained as polymorphisms. While inversions have been shown previously to be under selection, or contain genetic variation under selection, the specific phenotypic consequences of inversions leading to their maintenance remain unclear. Here we use genomic sequence and expression data from the Drosophila Genetic Reference Panel to explore the effects of two cosmopolitan inversions, In(2L)t and In(3R)Mo, on patterns of transcriptional variation...
September 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28915899/association-between-polymorphisms-of-tas2r16-and-susceptibility-to-colorectal-cancer
#5
Jonathan Barontini, Marco Antinucci, Sergio Tofanelli, Maurizio Cammalleri, Massimo Dal Monte, Federica Gemignani, Pavel Vodicka, Roberto Marangoni, Ludmila Vodickova, Juozas Kupcinskas, Veronika Vymetalkova, Asta Forsti, Federico Canzian, Angelika Stein, Victor Moreno, Nicola Mastrodonato, Francesca Tavano, Anna Panza, Roberto Barale, Stefano Landi, Daniele Campa
BACKGROUND: Genetics plays an important role in the susceptibility to sporadic colorectal cancer (CRC). In the last 10 years genome-wide association studies (GWAS) have identified over 40 independent low penetrance polymorphic variants. However, these loci only explain around 1‑4% of CRC heritability, highlighting the dire need of identifying novel risk loci. In this study, we focused our attention on the genetic variability of the TAS2R16 gene, encoding for one of the bitter taste receptors that selectively binds to salicin, a natural antipyretic that resembles aspirin...
September 15, 2017: BMC Gastroenterology
https://www.readbyqxmd.com/read/28912584/niche-harmony-search-algorithm-for-detecting-complex-disease-associated-high-order-snp-combinations
#6
Shouheng Tuo, Junying Zhang, Xiguo Yuan, Zongzhen He, Yajun Liu, Zhaowen Liu
Genome-wide association study is especially challenging in detecting high-order disease-causing models due to model diversity, possible low or even no marginal effect of the model, and extraordinary search and computations. In this paper, we propose a niche harmony search algorithm where joint entropy is utilized as a heuristic factor to guide the search for low or no marginal effect model, and two computationally lightweight scores are selected to evaluate and adapt to diverse of disease models. In order to obtain all possible suspected pathogenic models, niche technique merges with HS, which serves as a taboo region to avoid HS trapping into local search...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28911041/culture-independent-molecular-methods-for-detection-of-antifungal-resistance-mechanisms-and-fungal-identification
#7
David S Perlin, Nathan P Wiederhold
Resistance to azoles and echinocandins has emerged as a significant factor affecting the clinical management of patients with invasive fungal infections. Immunosuppressed patients at high risk for invasive fungal infections often have prolonged or repeated exposure to antifungals resulting in either the well-documented selection of naturally occurring, less susceptible fungal species, or the in situ development of specific resistance mechanisms. Nucleic acid-based molecular diagnostics are particularly well suited for the rapid detection of low-abundance fungal pathogens and identification of the infecting pathogen to the genus and species levels, as well as assessment of resistance mechanisms...
August 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28910965/actinobacteria-phylogenomics-selective-isolation-from-an-iron-oligotrophic-environment-and-siderophore-functional-characterization-unveil-new-desferrioxamine-traits
#8
Pablo Cruz-Morales, Hilda E Ramos-Aboites, Cuauhtémoc Licona-Cassani, Nelly Selem-Mójica, Paulina M Mejía-Ponce, Valeria Souza-Saldívar, Francisco Barona-Gómez
Desferrioxamines are hydroxamate siderophores widely conserved in both aquatic and soil-dwelling Actinobacteria. While the genetic and enzymatic bases of siderophore biosynthesis and their transport in model families of this phylum are well understood, evolutionary studies are lacking. Here, we perform a comprehensive desferrioxamine-centric (des genes) phylogenomic analysis, which includes the genomes of six novel strains isolated from an iron and phosphorous depleted oasis in the Chihuahuan desert of Mexico...
September 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28910747/transcriptome-analysis-of-rana-chensinensis-liver-under-trichlorfon-stress
#9
Yu Ma, Bo Li, Yang Ke, Yongan Zhang, Yuhui Zhang
Trichlorfon is a selective organophosphate insecticide that is widely applied in aquaculture and agriculture for control of various parasites. However, repeated and excess applications of trichlorfon often lead to water pollution and threaten non-targeted species. Our previous studies showed that trichlorfon could cause oxidative stress, lipid peroxidation and hepatic lesions in the liver of Rana chensinensis, but the related molecular mechanisms remain unclear. To explore the interference of trichlorfon in gene transcription, the differentially expressed genes in the liver of R...
September 11, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28910568/network-of-phosphatases-and-hdac-complexes-at-repressed-chromatin
#10
I J de Castro, H A Amin, V Vinciotti, P Vagnarelli
Tight regulation of gene expression is achieved by a variety of protein complexes that selectively bind chromatin, modify it and change its transcription competency. Histone acetylases (HATs) and deacetylases (HDACs) play an important role in this process. They can generate transcriptionally active or inactive chromatin through the addition (HATs) or removal (HDACs) of acetyl groups on histones, respectively. Repo-Man is a Protein Phosphatase 1 targeting subunit that accumulates on chromosomes during mitotic exit and mediates the removal of mitotic histone H3 phosphorylations...
September 14, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28904774/phenotypic-differentiation-of-the-solidago-virgaurea-complex-along-an-elevational-gradient-insights-from-a-common-garden-experiment-and-population-genetics
#11
Masaaki Hirano, Shota Sakaguchi, Koichi Takahashi
Plant species distributed along wide elevational or latitudinal gradients show phenotypic variation due to their heterogeneous habitats. This study investigated whether phenotypic variation in populations of the Solidago virgaurea complex along an elevational gradient is caused by genetic differentiation. A common garden experiment was based on seeds collected from nine populations of the S. virgaurea complex growing at elevations from 1,597 m to 2,779 m a.s.l. on Mt. Norikura in central Japan. Population genetic analyses with microsatellite markers were used to infer the genetic structure and levels of gene flow between populations...
September 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28903535/modeling-the-multiple-facets-of-speciation-with-gene-flow-toward-inferring-the-divergence-history-of-lake-whitefish-species-pairs-coregonus-clupeaformis
#12
Clément Rougeux, Louis Bernatchez, Pierre-Alexandre Gagnaire
Parallel divergence across replicated species pairs occurring in similar environmental contrasts may arise through distinct evolutionary scenarios. Deciphering whether such parallelism actually reflects repeated parallel divergence driven by divergent selection or a single divergence event with subsequent gene flow needs to be ascertained. Reconstructing historical gene flow is therefore of fundamental interest to understand how demography and selection jointly shaped genomic divergence during speciation. Here, we use an extended modeling framework to explore the multiple facets of speciation-with-gene-flow with demo-genetic divergence models that capture both temporal and genomic variation in effective population size and migration rate...
August 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28903315/risk-assessment-models-for-genetic-risk-predictors-of-lung-cancer-using-two-stage-replication-for-asian-and-european-populations
#13
Yang Cheng, Tao Jiang, Meng Zhu, Zhihua Li, Jiahui Zhang, Yuzhuo Wang, Liguo Geng, Jia Liu, Wei Shen, Cheng Wang, Zhibin Hu, Guangfu Jin, Hongxia Ma, Hongbing Shen, Juncheng Dai
In the past ten years, great successes have been accumulated by taking advantage of both candidate-gene studies and genome-wide association studies. However, limited studies were available to systematically evaluate the genetic effects for lung cancer risk with large-scale and different ethnic populations. We systematically reviewed relevant literatures and filtered out 241 important genetic variants identified in 124 articles. A two-stage case-control study within specific subgroups was performed to assess the effects [Training set: 2,331 cases vs...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28901686/shifting-the-focus-toward-rare-variants-in-schizophrenia-to-close-the-gap-from-genotype-to-phenotype
#14
REVIEW
M Leonor Bustamante, Luisa Herrera, Pablo A Gaspar, Rodrigo Nieto, Alejandro Maturana, María José Villar, Valeria Salinas, Hernán Silva
Schizophrenia (SZ) is a disorder with a high heritability and a complex architecture. Several dozen genetic variants have been identified as risk factors through genome-wide association studies including large population-based samples. However, the bulk of the risk cannot be accounted for by the genes associated to date. Rare mutations have been historically seen as relevant only for some infrequent, Mendelian forms of psychosis. Recent findings, however, show that the subset of patients that present a mutation with major effect is larger than expected...
October 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28901565/review-article-next-generation-transformative-advances-in-the-pathogenesis-and-management-of-autoimmune-hepatitis
#15
REVIEW
A J Czaja
BACKGROUND: Advances in autoimmune hepatitis that transform current concepts of pathogenesis and management can be anticipated as products of ongoing investigations driven by unmet clinical needs and an evolving biotechnology. AIM: To describe the advances that are likely to become transformative in autoimmune hepatitis, based on the direction of current investigations. METHODS: Pertinent abstracts were identified in PubMed by multiple search terms...
September 13, 2017: Alimentary Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28900502/a-bap1-mutation-specific-microrna-signature-predicts-clinical-outcomes-in-clear-cell-renal-cell-carcinoma-patients-with-wild-type-bap1
#16
Yu-Zheng Ge, Lu-Wei Xu, Chang-Cheng Zhou, Tian-Ze Lu, Wen-Tao Yao, Ran Wu, You-Cai Zhao, Xiao Xu, Zhi-Kai Hu, Min Wang, Xiao-Bing Yang, Liu-Hua Zhou, Bing Zhong, Zheng Xu, Wen-Cheng Li, Jia-Geng Zhu, Rui-Peng Jia
Background: Clear cell renal cell carcinoma (ccRCC) is the most prevalent histologic subtype of kidney cancers in adults, which could be divided into two distinct subgroups according to the BRCA1 associated protein-1 (BAP1) mutation status. In the current study, we comprehensively analyzed the genome-wide microRNA (miRNA) expression profiles in ccRCC, with the aim to identify the differentially expressed miRNAs between BAP1 mutant and wild-type tumors, and generate a BAP1 mutation-specific miRNA signature for ccRCC patients with wild-type BAP1...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28900432/assessing-and-exploiting-functional-diversity-in-germplasm-pools-to-enhance-abiotic-stress-adaptation-and-yield-in-cereals-and-food-legumes
#17
REVIEW
Sangam L Dwivedi, Armin Scheben, David Edwards, Charles Spillane, Rodomiro Ortiz
There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28900136/differential-effects-of-soluble-and-aggregating-polyq-proteins-on-cytotoxicity-and-type-1-myosin-dependent-endocytosis-in-yeast
#18
Lisa L Berglund, Xinxin Hao, Beidong Liu, Julie Grantham, Thomas Nyström
Huntington's disease develops when the polyglutamine (polyQ) repeat in the Huntingtin (Htt) protein is expanded to over 35 glutamines rendering it aggregation-prone. Here, using Htt exon-1 as a polyQ model protein in a genome-wide screen in yeast, we show that the normal and soluble Htt exon-1 is toxic in cells with defects in type-1 myosin-dependent endocytosis. The toxicity of Htt is linked to physical interactions with type-1 myosins, which occur via the Htt proline-rich region, leading to a reduction in actin patch polarization and clathrin-dependent endocytosis...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28900023/gene-expression-in-leishmania-is-regulated-predominantly-by-gene-dosage
#19
Stefano A Iantorno, Caroline Durrant, Asis Khan, Mandy J Sanders, Stephen M Beverley, Wesley C Warren, Matthew Berriman, David L Sacks, James A Cotton, Michael E Grigg
Leishmania tropica, a unicellular eukaryotic parasite present in North and East Africa, the Middle East, and the Indian subcontinent, has been linked to large outbreaks of cutaneous leishmaniasis in displaced populations in Iraq, Jordan, and Syria. Here, we report the genome sequence of this pathogen and 7,863 identified protein-coding genes, and we show that the majority of clinical isolates possess high levels of allelic diversity, genetic admixture, heterozygosity, and extensive aneuploidy. By utilizing paired genome-wide high-throughput DNA sequencing (DNA-seq) with RNA-seq, we found that gene dosage, at the level of individual genes or chromosomal "somy" (a general term covering disomy, trisomy, tetrasomy, etc...
September 12, 2017: MBio
https://www.readbyqxmd.com/read/28899973/top2a-and-ezh2-provide-early-detection-of-an-aggressive-prostate-cancer-subgroup
#20
David P Labbé, Christopher J Sweeney, Myles Brown, Phillip Galbo, Spencer Rosario, Kristine M Wadosky, Sheng-Yu Ku, Martin Sjöström, Mohammed Alshalalfa, Nicholas Erho, Elai Davicioni, R Jeffrey Karnes, Edward M Schaeffer, Robert B Jenkins, Robert B Den, Ashley E Ross, Michaela Bowden, Ying Huang, Kathryn P Gray, Felix Y Feng, Daniel E Spratt, David W Goodrich, Kevin H Eng, Leigh Ellis
PURPOSE: Current clinical parameters do not stratify indolent from aggressive prostate cancer (PCa). Aggressive PCa, defined by the progression from localized disease to metastasis, is responsible for the majority of PCa-associated mortality. Recent gene expression profiling has proven successful in predicting the outcome of PCa patients, however they have yet to provide targeted therapy approaches that could inhibit a patient's progression to metastatic disease. EXPERIMENTAL DESIGN: We have interrogated a total of seven primary PCa cohorts (N = 1,900), two metastatic castration resistant PCa datasets (N = 293) and one prospective cohort (N = 1,385) to assess the impact of TOP2A and EZH2 expression on PCa cellular program and patient outcomes...
September 12, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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