keyword
MENU ▼
Read by QxMD icon Read
search

Genome wide selection

keyword
https://www.readbyqxmd.com/read/29150926/viral-short-orfs-and-their-possible-functions
#1
REVIEW
Yaara Finkel, Noam Stern-Ginossar, Michal Schwartz
Definition of functional genomic elements is one of the greater challenges of the genomic era. Traditionally, putative short Open Reading Frames (sORFs) coding for less than 100 amino acids were disregarded due to computational and experimental limitations, however it has become clear over the past several years that translation of sORFs is pervasive and serves diverse functions. The development of ribosome profiling, allowing identification of translated sequences genome-wide, revealed wide-spread, previously unidentified translation events...
November 18, 2017: Proteomics
https://www.readbyqxmd.com/read/29150689/distinct-genetic-architectures-for-phenotype-means-and-plasticities-in-zea-mays
#2
Aaron Kusmec, Srikant Srinivasan, Dan Nettleton, Patrick S Schnable
Phenotypic plasticity describes the phenotypic variation of a trait when a genotype is exposed to different environments. Understanding the genetic control of phenotypic plasticity in crops such as maize is of paramount importance for maintaining and increasing yields in a world experiencing climate change. Here, we report the results of genome-wide association analyses of multiple phenotypes and two measures of phenotypic plasticity in a maize nested association mapping (US-NAM) population grown in multiple environments and genotyped with ~2...
September 2017: Nature Plants
https://www.readbyqxmd.com/read/29150509/the-tape-measure-protein-is-involved-in-the-heat-stability-of-lactococcus-lactis-phages
#3
Hany Geagea, Simon J Labrie, Muriel Subirade, Sylvain Moineau
Virulent lactococcal phages are still a major risk for milk fermentation processes as they may lead to slowdowns and low quality fermented dairy products, particularly cheeses. Some of the phage control strategies used by the industry rely on heat treatments. Recently, a few Lactococcus lactis phages were found to be highly thermo-resistant. To identify the genetic determinant(s) responsible for the thermal resistance of lactococcal phages, we used the virulent phage CB14 (sk1virus/936 group) to select for phage mutants with increased heat stability...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29149730/divergence-of-insulin-superfamily-ligands-receptors-and-igf-binding-proteins-in-marine-versus-freshwater-stickleback-evidence-of-selection-in-known-and-novel-genes
#4
Tim Pellissier, Hend Al Nafea, Sara V Good
Three-spine stickleback (Gasterosteus aculeatus) is a teleost model for understanding genetic, physiological and morphological changes accompanying freshwater (FW) adaptation. There is growing evidence that the insulin superfamily plays important roles in traits involved in marine and FW adaptation. We performed a candidate gene analysis to look for evidence of selection on 33 insulin superfamily ligand-receptor genes and insulin-like growth factor binding proteins (Igfbp's) in stickleback. Using genotype data from 11 marine and 10 FW populations, we calculated the number of SNPs per site in regulatory and intronic regions, the number of synonymous and nonsynonymous mutations in coding regions, Wright's fixation index (Fst), and performed t-tests to identify SNPs with divergent genotype frequencies between marine/FW versus Atlantic/Pacific populations...
November 10, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29142828/metabolic-engineering-of-ustilago-trichophora-tz1-for-improved-malic-acid-production
#5
Thiemo Zambanini, Hamed Hosseinpour Tehrani, Elena Geiser, Christiane K Sonntag, Joerg M Buescher, Guido Meurer, Nick Wierckx, Lars M Blank
Ustilago trichophora RK089 has been found recently as a good natural malic acid producer from glycerol. This strain has previously undergone adaptive laboratory evolution for enhanced substrate uptake rate resulting in the strain U. trichophora TZ1. Medium optimization and investigation of process parameters enabled titers and rates that are able to compete with those of organisms overexpressing major parts of the underlying metabolic pathways. Metabolic engineering can likely further increase the efficiency of malate production by this organism, provided that basic genetic tools and methods can be established for this rarely used and relatively obscure species...
June 2017: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29142288/identification-of-small-rnas-abundant-in-burkholderia-cenocepacia-biofilms-reveal-putative-regulators-with-a-potential-role-in-carbon-and-iron-metabolism
#6
Andrea Sass, Sanne Kiekens, Tom Coenye
Small RNAs play a regulatory role in many central metabolic processes of bacteria, as well as in developmental processes such as biofilm formation. Small RNAs of Burkholderia cenocepacia, an opportunistic pathogenic beta-proteobacterium, are to date not well characterised. To address that, we performed genome-wide transcriptome structure analysis of biofilm grown B. cenocepacia J2315. 41 unannotated short transcripts were identified in intergenic regions of the B. cenocepacia genome. 15 of these short transcripts, highly abundant in biofilms, widely conserved in Burkholderia sp...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29141909/local-fitness-landscapes-predict-yeast-evolutionary-dynamics-in-directionally-changing-environments
#7
Florien A Gorter, Mark G M Aarts, Bas J Zwaan, J Arjan G M de Visser
The fitness landscape is a concept that is widely used for understanding and predicting evolutionary adaptation. The topography of the fitness landscape depends critically on the environment, with potentially far-reaching consequences for evolution under changing conditions. However, few studies have assessed directly how empirical fitness landscapes change across conditions, or validated the predicted consequences of such change. We previously evolved replicate yeast populations in the presence of either gradually increasing or constant high concentrations of the heavy metals cadmium (Cd), nickel (Ni), and zinc (Zn), and analysed their phenotypic and genomic changes...
November 15, 2017: Genetics
https://www.readbyqxmd.com/read/29141655/long-term-balancing-selection-contributes-to-adaptation-in-arabidopsis-and-its-relatives
#8
Qiong Wu, Ting-Shen Han, Xi Chen, Jia-Fu Chen, Yu-Pan Zou, Zi-Wen Li, Yong-Chao Xu, Ya-Long Guo
BACKGROUND: In contrast to positive selection, which reduces genetic variation by fixing beneficial alleles, balancing selection maintains genetic variation within a population or species and plays crucial roles in adaptation in diverse organisms. However, which genes, genome-wide, are under balancing selection and the extent to which these genes are involved in adaptation are largely unknown. RESULTS: We performed a genome-wide scan for genes under balancing selection across two plant species, Arabidopsis thaliana and its relative Capsella rubella, which diverged about 8 million generations ago...
November 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/29141633/genome-modification-of-cxcr4-by-staphylococcus-aureus-cas9-renders-cells-resistance-to-hiv-1-infection
#9
Qiankun Wang, Shuliang Chen, Qiaoqiao Xiao, Zhepeng Liu, Shuai Liu, Panpan Hou, Li Zhou, Wei Hou, Wenzhe Ho, Chunmei Li, Li Wu, Deyin Guo
BACKGROUND: The CRISPR/Cas9 system has been widely used for genome editing in mammalian cells. CXCR4 is a co-receptor for human immunodeficiency virus type 1 (HIV-1) entry, and loss of CXCR4 function can protect cells from CXCR4 (X4)-tropic HIV-1 infection, making CXCR4 an important target for HIV-1 gene therapy. However, the large size of the CRISPR/SpCas9 system presents an obstacle to its efficient delivery into primary CD4(+) T cells. Recently, a small Staphylococcus aureus Cas9 (SaCas9) has been developed as a genome editing tool can address this question...
November 15, 2017: Retrovirology
https://www.readbyqxmd.com/read/29137622/genome-wide-scan-for-runs-of-homozygosity-identifies-potential-candidate-genes-associated-with-local-adaptation-in-valle-del-belice-sheep
#10
Salvatore Mastrangelo, Marco Tolone, Maria T Sardina, Gianluca Sottile, Anna M Sutera, Rosalia Di Gerlando, Baldassare Portolano
BACKGROUND: Because very large numbers of single nucleotide polymorphisms (SNPs) are now available throughout the genome, they are particularly suitable for the detection of genomic regions where a reduction in heterozygosity has occurred and they offer new opportunities to improve the accuracy of inbreeding ([Formula: see text]) estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from the parents are identical...
November 14, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29137430/genome-wide-analysis-and-functional-prediction-of-long-non-coding-rnas-in-mouse-uterus-during-the-implantation-window
#11
Qi Wang, Nan Wang, Rui Cai, Fan Zhao, Yongjie Xiong, Xiao Li, Aihua Wang, Pengfei Lin, Yaping Jin
Establishment of the receptive uterus is a crucial step for embryo implantation. In this study, the expression profiles and characterization of long non-coding RNAs (lncRNAs) in pregnant mouse uteri on day 4, day 5 at implantation sites and inter-implantation sites were conducted using RNA-seq. A total of 7,764 putative lncRNA transcripts were identified, including 6,179 known lncRNA transcripts and 1,585 novel lncRNA transcripts. Bioinformatics analysis of the cis and trans lncRNA targets showed that the differentially expressed lncRNAs were mainly involved in tissue remodelling, immune response and metabolism-related processes, indicating that lncRNAs could be involved in the regulation of embryo implantation...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137313/rna-seq-reveals-distinctive-rna-profiles-of-small-extracellular-vesicles-from-different-human-liver-cancer-cell-lines
#12
Martina Berardocco, Annalisa Radeghieri, Sara Busatto, Marialucia Gallorini, Chiara Raggi, Clarissa Gissi, Igea D'Agnano, Paolo Bergese, Armando Felsani, Anna C Berardi
Liver cancer (LC) is one of the most common cancers and represents the third highest cause of cancer-related deaths worldwide. Extracellular vesicle (EVs) cargoes, which are selectively enriched in RNA, offer great promise for the diagnosis, prognosis and treatment of LC. Our study analyzed the RNA cargoes of EVs derived from 4 liver-cancer cell lines: HuH7, Hep3B, HepG2 (hepato-cellular carcinoma) and HuH6 (hepatoblastoma), generating two different sets of sequencing libraries for each. One library was size-selected for small RNAs and the other targeted the whole transcriptome...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29135286/vitamin-b12-supplementation-influences-methylation-of-genes-associated-with-type-2-diabetes-and-its-intermediate-traits
#13
Dilip K Yadav, Smeeta Shrestha, Karen A Lillycrop, Charu V Joglekar, Hong Pan, Joanna D Holbrook, Caroline Hd Fall, Chittaranjan S Yajnik, Giriraj R Chandak
AIM: To investigate the effect of B12 and/or folic acid supplementation on genome-wide DNA methylation. METHODS: We performed Infinium HumanMethylation450 BeadChip (Zymo Research, CA, USA) assay in children supplemented with B12 and/or folic acid (n = 12 in each group) and investigated the functional mechanism of selected differentially methylated loci. RESULTS: We noted significant methylation changes postsupplementation in B12 (589 differentially methylated CpGs and 2892 regions) and B12 + folic acid (169 differentially methylated CpGs and 3241 regions) groups...
November 14, 2017: Epigenomics
https://www.readbyqxmd.com/read/29133146/association-of-genetic-polymorphisms-with-erythrocyte-traits-verification-of-snps-reported-in-a-previous-gwas-in-a-japanese-population
#14
Toshio Seiki, Mariko Naito, Asahi Hishida, Sahoko Takagi, Takashi Matsunaga, Tae Sasakabe, Yuta Hattori, Sayo Kawai, Rieko Okada, Guang Yin, Nobuyuki Hamajima, Kenji Wakai
Erythrocyte count and volume are the commonly used hematological indices for anemia that change in various diseases. To date, however, only one study ever exists that addressed erythrocyte trait-associated single nucleotide polymorphisms (SNPs) in a Japanese population. Because that study was performed in patients with various diseases, we confirmed the reported associations in a general population. Participants in the current study were from the Shizuoka component of the Japan Multi-Institutional Collaborative Cohort Study, which included 4971 men and women aged 35 to 69years who were recruited between 2006 and 2007...
November 10, 2017: Gene
https://www.readbyqxmd.com/read/29132403/the-interplay-of-demography-and-selection-during-maize-domestication-and-expansion
#15
Li Wang, Timothy M Beissinger, Anne Lorant, Claudia Ross-Ibarra, Jeffrey Ross-Ibarra, Matthew B Hufford
BACKGROUND: The history of maize has been characterized by major demographic events, including population size changes associated with domestication and range expansion, and gene flow with wild relatives. The interplay between demographic history and selection has shaped diversity across maize populations and genomes. RESULTS: We investigate these processes using high-depth resequencing data from 31 maize landraces spanning the pre-Columbian distribution of maize, and four wild teosinte individuals (Zea mays ssp...
November 13, 2017: Genome Biology
https://www.readbyqxmd.com/read/29132318/bugmat-and-findneighbour-command-line-and-server-applications-for-investigating-bacterial-relatedness
#16
Oriol Mazariegos-Canellas, Trien Do, Tim Peto, David W Eyre, Anthony Underwood, Derrick Crook, David H Wyllie
BACKGROUND: Large scale bacterial sequencing has made the determination of genetic relationships within large sequence collections of bacterial genomes derived from the same microbial species an increasingly common task. Solutions to the problem have application to public health (for example, in the detection of possible disease transmission), and as part of divide-and-conquer strategies selecting groups of similar isolates for computationally intensive methods of phylogenetic inference using (for example) maximal likelihood methods...
November 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29132308/effect-of-two-non-synonymous-ecto-5-nucleotidase-variants-on-the-genetic-architecture-of-inosine-5-monophosphate-imp-and-its-degradation-products-in-japanese-black-beef
#17
Yoshinobu Uemoto, Tsuyoshi Ohtake, Nanae Sasago, Masayuki Takeda, Tsuyoshi Abe, Hironori Sakuma, Takatoshi Kojima, Shinji Sasaki
BACKGROUND: Umami is a Japanese term for the fifth basic taste and is an important sensory property of beef palatability. Inosine 5'-monophosphate (IMP) contributes to umami taste in beef. Thus, the overall change in concentration of IMP and its degradation products can potentially affect the beef palatability. In this study, we investigated the genetic architecture of IMP and its degradation products in Japanese Black beef. First, we performed genome-wide association study (GWAS), candidate gene analysis, and functional analysis to detect the causal variants that affect IMP, inosine, and hypoxanthine...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29132293/genomic-regions-associated-with-host-response-to-porcine-reproductive-and-respiratory-syndrome-vaccination-and-co-infection-in-nursery-pigs
#18
Jenelle R Dunkelberger, Nick V L Serão, Ziqing Weng, Emily H Waide, Megan C Niederwerder, Maureen A Kerrigan, Joan K Lunney, Raymond R R Rowland, Jack C M Dekkers
BACKGROUND: The WUR1000125 (WUR) single nucleotide polymorphism (SNP) can be used as a genetic marker for host response to porcine reproductive and respiratory syndrome (PRRS), PRRS vaccination, and co-infection with porcine circovirus type 2b (PCV2b). Objectives of this study were to identify genomic regions other than WUR associated with host response to PRRS vaccination and PRRSV/PCV2b co-infection and regions with a different effect on host response to co-infection, depending on previous vaccination for PRRS...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29131388/saccharomyces-interspecies-hybrids-as-model-organisms-for-studying-yeast-adaptation-to-stressful-environments
#19
Ksenija Lopandic
The strong development of molecular biology techniques and next-generation sequencing technologies in the last two decades has significantly improved our understanding of the evolutionary history of Saccharomyces yeasts. It has been shown that many strains isolated from man-made environments are not pure genetic lines, but contain genetic materials from different species that substantially increase their genome complexity. A number of strains have been described as interspecies hybrids, implying different yeast species that under specific circumstances exchange and recombine their genomes...
November 13, 2017: Yeast
https://www.readbyqxmd.com/read/29131015/therapeutic-response-to-paroxetine-in-major-depressive-disorder-predicted-by-dna-methylation
#20
Naohiro Takeuchi, Shinpei Nonen, Masaki Kato, Masataka Wakeno, Yoshiteru Takekita, Toshihiko Kinoshita, Fumihiko Kugawa
BACKGROUND: Antidepressants have variable therapeutic effects, depending on genetic and environmental factors. Approximately 30% of major depressive disorder (MDD) patients do not respond significantly to antidepressants such as paroxetine, a selective serotonin reuptake inhibitor (SSRI). However, the biological mechanisms behind this phenomenon are mostly unknown. Here, we examined the role of patients' epigenetic background in SSRI efficacy. METHODS: Genome-wide DNA methylation analysis of the peripheral blood of Japanese MDD patients was performed by using the Infinium HumanMethylation450 BeadChip...
November 4, 2017: Neuropsychobiology
keyword
keyword
21601
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"