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https://www.readbyqxmd.com/read/28651411/-introduction-to-bayesian-variable-selection-methods-in-high-dimensional-omics-data-analysis
#1
X Q Dong, S H Xu, R Tao, T Wang
With the rapid development of genome sequencing technology and bioinformatics in recent years, it has become possible to measure thousands of omics data which might be associated with the progress of diseases, i.e."high-dimensional data" . This type of omics data have a common feature that the number of variable p is usually greater than the observation cases n, and often has high correlation between independent variables. Therefore, it is a great statistical challenge to identify really meaningful variables from omics data...
May 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28651407/-homology-analysis-and-historical-tracing-for-inter-continental-burkholderia-pseudomallei-strains-of-sequence-type-562
#2
X Zheng, L X Wang, H Wu, H Chen, X Zhu, J R He, L X Xia, W Li
Objective: To understand the homology of sequence type 562 (ST562) strains of Burkholderia pseudomallei which circulated in two separate continents (Asia and Australia) at different times. Methods:SpeⅠrestriction fragments and 4-locus multiple locus variable number tandem repeat analysis (MLVA-4) profiles were extracted from MSHR5858 (ST562 Australia strain) and 350105 (ST562 historical strain of Hainan) genomes respectively by in silico analysis and then compared with the PFGE and MLVA-4 results of five ST562 clinical isolates from Hainan to test their homology...
May 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28651382/assignment-of-sigma-factors-of-rna-polymerase-to-promoters-in-corynebacterium-glutamicum
#3
Hana Dostálová, Jiří Holátko, Tobias Busche, Lenka Rucká, Andrey Rapoport, Petr Halada, Jan Nešvera, Jörn Kalinowski, Miroslav Pátek
Corynebacterium glutamicum is an important industrial producer of various amino acids and other metabolites. The C. glutamicum genome encodes seven sigma subunits (factors) of RNA polymerase: the primary sigma factor SigA (σ(A)), the primary-like σ(B) and five alternative sigma factors (σ(C), σ(D), σ(E), σ(H) and σ(M)). We have developed in vitro and in vivo methods to assign particular sigma factors to individual promoters of different classes. In vitro transcription assays and measurements of promoter activity using the overexpression of a single sigma factor gene and the transcriptional fusion of the promoter to the gfpuv reporter gene enabled us to reliably define the sigma factor dependency of promoters...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28651334/tsgsis-a-high-dimensional-grouped-variable-selection-approach-for-detection-of-whole-genome-snp-snp-interactions
#4
Yao-Hwei Fang, Jie-Huei Wang, Chao A Hsiung
Motivation: Identification of single nucleotide polymorphism (SNP) interactions is an important and challenging topic in genome-wide association studies (GWAS). Many approaches have been applied to detecting whole-genome interactions. However, these approaches to interaction analysis tend to miss causal interaction effects when the individual marginal effects are uncorrelated to trait, while their interaction effects are highly associated with the trait. Results: A grouped variable selection technique, called two-stage grouped sure independence screening (TS-GSIS), is developed to study interactions that may not have marginal effects...
June 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28651329/high-speed-and-high-ratio-referential-genome-compression
#5
Yuansheng Liu, Hui Peng, Limsoon Wong, Jinyan Li
Motivation: The rapidly increasing number of genomes generated by high-throughput sequencing platforms and assembly algorithms is accompanied by problems in data storage, compression and communication. Traditional compression algorithms are unable to meet the demand of high compression ratio due to the intrinsic challenging features of DNA sequences such as small alphabet size, frequent repeats and palindromes. Reference-based lossless compression, by which only the differences between two similar genomes are stored, is a promising approach with high compression ratio...
June 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28651291/development-of-a-reference-standard-library-of-chloroplast-genome-sequences-genometrakrcp
#6
Ning Zhang, Padmini Ramachandran, Jun Wen, James A Duke, Helen Metzman, William McLaughlin, Andrea R Ottesen, Ruth E Timme, Sara M Handy
Precise, species-level identification of plants in foods and dietary supplements is difficult. While the use of DNA barcoding regions (short regions of DNA with diagnostic utility) has been effective for many inquiries, it is not always a robust approach for closely related species, especially in highly processed products. The use of fully sequenced chloroplast genomes, as an alternative to short diagnostic barcoding regions, has demonstrated utility for closely related species. The U. S. Food and Drug Administration (FDA) has also developed species-specific DNA-based assays targeting plant species of interest by utilizing chloroplast genome sequences...
June 26, 2017: Planta Medica
https://www.readbyqxmd.com/read/28651214/dna-methylation-and-the-preservation-of-cell-identity
#7
REVIEW
Ozren Bogdanović, Ryan Lister
DNA methylation is a major epigenetic modification of vertebrate genomes that is mostly associated with transcriptional repression. During embryogenesis, DNA methylation together with other epigenetic factors plays an essential role in selecting and maintaining cell identity. Recent technological advances are now allowing for the exploration of this mark at unprecedented resolution. This has resulted in a wealth of studies describing the developmental roles of DNA methylation in various vertebrate model systems...
June 23, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28651191/probing-safety-of-nanoparticles-by-outlining-sea-urchin-sensing-and-signaling-cascades
#8
Andi Alijagic, Annalisa Pinsino
Among currently identified issues presenting risks and benefits to human and ocean health, engineered nanoparticles (ENP) represent a priority. Predictions of their economic and social impact appear extraordinary, but their release in the environment at an uncontrollable rate is in striking contrast with the extremely limited number of studies on environmental impact, especially on the marine environment. The sea urchin has a remarkable sensing environmental system whose function and diversity came into focus during the recent years, after sea urchin genome sequencing...
June 23, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28651097/population-and-performance-analyses-of-four-major-populations-with-illumina-s-fgx-forensic-genomics-system
#9
Jennifer D Churchill, Nicole M M Novroski, Jonathan L King, Lay Hong Seah, Bruce Budowle
The MiSeq FGx Forensic Genomics System (Illumina) enables amplification and massively parallel sequencing of 59 STRs, 94 identity informative SNPs, 54 ancestry informative SNPs, and 24 phenotypic informative SNPs. Allele frequency and population statistics data were generated for the 172 SNP loci included in this panel on four major population groups (Chinese, African Americans, US Caucasians, and Southwest Hispanics). Single-locus and combined random match probability values were generated for the identity informative SNPs...
June 17, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28651079/a-survey-of-oenophages-during-wine-making-reveals-a-novel-group-with-unusual-genomic-characteristics
#10
Cécile Philippe, Fety Jaomanjaka, Olivier Claisse, Rémi Laforgue, Julie Maupeu, Melina Petrel, Claire Le Marrec
Oenophages have so far been mostly isolated from red wines under malolactic fermentation (MLF), and correspond to temperate or ex-temperate phages of Oenococcus oeni. Their genomes are clustered into 4 integrase gene sequence groups, which are also related to the chromosomal integration site. Our aims were to survey the occurrence of oenophages in a broader and more diverse collection of samples than those previously explored. Active phages were isolated from 33 out of 166 samples, which mostly originated from must and MLF...
June 17, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28651078/leuconostoc-mesenteroides-and-leuconostoc-pseudomesenteroides-bacteriophages-genomics-and-cross-species-host-ranges
#11
Silvina A Pujato, Daniela M Guglielmotti, Manuel Martínez-García, Andrea Quiberoni, Francisco J M Mojica
Unveiling virus-host interactions are relevant for understanding the biology and evolution of microbes globally, but in particular, it has also a paramount impact on the manufacture of fermented dairy products. In this study, we aim at characterizing phages infecting the commonly used heterofermentative Leuconostoc spp. on the basis of host range patterns and genome analysis. Host range of six Leuconostoc phages was investigated using three methods (efficiency of plaquing, spot and turbidity tests) against Ln...
June 12, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28651022/can-natural-variation-in-grain-p-concentrations-be-exploited-in-rice-breeding-to-lower-fertilizer-requirements
#12
Fanmiao Wang, James Douglas Morrison King, Terry Rose, Tobias Kretzschmar, Matthias Wissuwa
Agricultural usage of phosphorus (P) is largely driven by the amount of P removed from fields in harvested plant matter as offtake needs to be balanced by P fertilizer application. Reducing P concentration in grains is a way to decrease P offtake and reduce P fertilizer requirements or soil P mining where insufficient P is applied. Our objective was to assesses the genotypic variation for grain P concentration present within the rice gene pool and resolve to what extent it is affected by environment (P supply) or associated with genetic factors...
2017: PloS One
https://www.readbyqxmd.com/read/28651019/in-silico-genomic-insights-into-aspects-of-food-safety-and-defense-mechanisms-of-a-potentially-probiotic-lactobacillus-pentosus-mp-10-isolated-from-brines-of-naturally-fermented-alore%C3%A3-a-green-table-olives
#13
Hikmate Abriouel, Beatriz Pérez Montoro, María Del Carmen Casado Muñoz, Charles W Knapp, Antonio Gálvez, Nabil Benomar
Lactobacillus pentosus MP-10, isolated from brines of naturally fermented Aloreña green table olives, exhibited high probiotic potential. The genome sequence of L. pentosus MP-10 is currently considered the largest genome among lactobacilli, highlighting the microorganism's ecological flexibility and adaptability. Here, we analyzed the complete genome sequence for the presence of acquired antibiotic resistance and virulence determinants to understand their defense mechanisms and explore its putative safety in food...
2017: PloS One
https://www.readbyqxmd.com/read/28651018/meta-analysis-of-mirna-expression-profiles-for-prostate-cancer-recurrence-following-radical-prostatectomy
#14
Elnaz Pashaei, Elham Pashaei, Maryam Ahmady, Mustafa Ozen, Nizamettin Aydin
BACKGROUND: Prostate cancer (PCa) is a leading reason of death in men and the most diagnosed malignancies in the western countries at the present time. After radical prostatectomy (RP), nearly 30% of men develop clinical recurrence with high serum prostate-specific antigen levels. An important challenge in PCa research is to identify effective predictors of tumor recurrence. The molecular alterations in microRNAs are associated with PCa initiation and progression. Several miRNA microarray studies have been conducted in recurrence PCa, but the results vary among different studies...
2017: PloS One
https://www.readbyqxmd.com/read/28651004/a-human-endogenous-retrovirus-derived-gene-that-can-contribute-to-oncogenesis-by-activating-the-erk-pathway-and-inducing-migration-and-invasion
#15
Cécile Lemaître, Jhen Tsang, Caroline Bireau, Thierry Heidmann, Marie Dewannieux
Endogenous retroviruses are cellular genes of retroviral origin captured by their host during the course of evolution and represent around 8% of the human genome. Although most are defective and transcriptionally silenced, some are still able to generate retroviral-like particles and proteins. Among these, the HERV-K(HML2) family is remarkable since its members have amplified relatively recently and many of them still have full length coding genes. Furthermore, they are induced in cancers, especially in melanoma, breast cancer and germ cell tumours, where viral particles, as well as the envelope protein (Env), can be detected...
June 26, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28651001/pptfdb-a-pigeonpea-transcription-factor-database-for-exploring-functional-genomics-in-legumes
#16
Akshay Singh, Ajay Kumar Sharma, Nagendra Kumar Singh, Tilak Raj Sharma
Pigeonpea (Cajanus cajan L.), a diploid legume crop, is a member of the tribe Phaseoleae. This tribe is descended from the millettioid (tropical) clade of the subfamily Papilionoideae, which includes many important legume crop species such as soybean (Glycine max), mung bean (Vigna radiata), cowpea (Vigna ungiculata), and common bean (Phaseolus vulgaris). It plays major role in food and nutritional security, being rich source of proteins, minerals and vitamins. We have developed a comprehensive Pigeonpea Transcription Factors Database (PpTFDB) that encompasses information about 1829 putative transcription factors (TFs) and their 55 TF families...
2017: PloS One
https://www.readbyqxmd.com/read/28651000/assessing-the-impact-of-benzo-a-pyrene-on-marine-mussels-application-of-a-novel-targeted-low-density-microarray-complementing-classical-biomarker-responses
#17
Mohamed Banni, Susanna Sforzini, Volker M Arlt, Audrey Barranger, Lorna J Dallas, Caterina Oliveri, Yann Aminot, Beniamina Pacchioni, Caterina Millino, Gerolamo Lanfranchi, James W Readman, Michael N Moore, Aldo Viarengo, Awadhesh N Jha
Despite the increasing use of mussels in environmental monitoring and ecotoxicological studies, their genomes and gene functions have not been thoroughly explored. Several cDNA microarrays were recently proposed for Mytilus spp., but putatively identified partial transcripts have rendered the generation of robust transcriptional responses difficult in terms of pathway identification. We developed a new low density oligonucleotide microarray with 465 probes covering the same number of genes. Target genes were selected to cover most of the well-known biological processes in the stress response documented over the last decade in bivalve species at the cellular and tissue levels...
2017: PloS One
https://www.readbyqxmd.com/read/28650998/functional-annotation-of-alzheimer-s-disease-associated-loci-revealed-by-gwass
#18
Zengpeng Han, Han Huang, Yue Gao, Qingyang Huang
Genome-wide association studies (GWASs) discovered a number of SNPs and genes associated with Alzheimer's disease (AD). However, how these SNPs and genes influence the liability to AD is not fully understood. We deployed computational approaches to explore the function and action mechanisms of AD -related SNPs and genes identified by GWASs, including the effects of 195 GWAS lead SNPs and 338 proxy SNPs on miRNAs binding and protein phosphorylation, their RegulomeDB and 3DSNP scores, and gene ontology, pathway enrichment and protein-protein interaction network of 126 AD-associated genes...
2017: PloS One
https://www.readbyqxmd.com/read/28650996/whole-transcriptomic-and-proteomic-analyses-of-an-isogenic-m-tuberculosis-clinical-strain-with-a-naturally-occurring-15-kb-genomic-deletion
#19
Carla Duncan, Frances B Jamieson, JoLynn Troudt, Linda Izzo, Helle Bielefeldt-Ohmann, Angelo Izzo, Carolina Mehaffy
Tuberculosis remains one of the most difficult to control infectious diseases in the world. Many different factors contribute to the complexity of this disease. These include the ability of the host to control the infection which may directly relate to nutritional status, presence of co-morbidities and genetic predisposition. Pathogen factors, in particular the ability of different Mycobacterium tuberculosis strains to respond to the harsh environment of the host granuloma, which includes low oxygen and nutrient availability and the presence of damaging radical oxygen and nitrogen species, also play an important role in the success of different strains to cause disease...
2017: PloS One
https://www.readbyqxmd.com/read/28650958/dynamics-and-impact-of-homologous-recombination-on-the-evolution-of-legionella-pneumophila
#20
Sophia David, Leonor Sánchez-Busó, Simon R Harris, Pekka Marttinen, Christophe Rusniok, Carmen Buchrieser, Timothy G Harrison, Julian Parkhill
Legionella pneumophila is an environmental bacterium and the causative agent of Legionnaires' disease. Previous genomic studies have shown that recombination accounts for a high proportion (>96%) of diversity within several major disease-associated sequence types (STs) of L. pneumophila. This suggests that recombination represents a potentially important force shaping adaptation and virulence. Despite this, little is known about the biological effects of recombination in L. pneumophila, particularly with regards to homologous recombination (whereby genes are replaced with alternative allelic variants)...
June 26, 2017: PLoS Genetics
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