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https://www.readbyqxmd.com/read/29684710/genomic-characterization-of-endemic-salmonella-enterica-serovar-typhimurium-and-salmonella-enterica-serovar-i-4-5-12-i-isolated-in-malaysia
#1
Soo Tein Ngoi, Kien-Pong Yap, Kwai Lin Thong
Salmonella enterica serovar Typhimurium (S. Typhimurium) and the monophasic variant Salmonella I 4,[5],12:i:- are two clinically-important non-typhoidal Salmonella serovars worldwide. However, the genomic information of these two organisms, especially the monophasic variant, is still lacking in Malaysia. The objective of the study was to compare the genomic features of a monophasic variant and two endemic S. Typhimurium strains isolated from humans. All three strains were subjected to whole genome sequencing followed by comparative genomic and phylogenetic analyses...
April 20, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29684598/extreme-halophilic-archaea-derive-from-two-distinct-methanogen-class-ii-lineages
#2
Monique Aouad, Najwa Taib, Anne Oudart, Michel Lecocq, Manolo Gouy, Céline Brochier-Armanet
Phylogenetic analyses of conserved core genes have disentangled most of the ancient relationships in Archaea. However, some groups remain debated, like the DPANN, a deep-branching super-phylum composed of nanosized archaea with reduced genomes. Among these, the Nanohaloarchaea require high-salt concentrations for growth. Their discovery in 2012 was significant because they represent, together with Halobacteria (a Class belonging to Euryarchaeota), the only two described lineages of extreme halophilic archaea...
April 20, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29681080/identification-and-characterisation-of-a-previously-unknown-drought-tolerance-associated-microrna-in-barley
#3
Hui Zhou, Syed Sarfraz Hussain, Michael Hackenberg, Natalia Bazanova, Omid Eini, Jie Li, Perry Gustafson, Bujun Shi
Drought is the most serious abiotic stress, which causes crop losses on worldwide scale. The present study identified a previously unknown microRNA (designated as hvu-miRX) of 21 nucleotides (nt) in barley. Its precursor (designated pre-miRX) and primary transcript (designated pri-miRX) were also identified, with lengths of 73 nt and 559 nt, respectively. The identified upstream sequence of pri-miRX contains both the TATA box and the CAAT box, which are both required for transcription initiation. Transient promoter activation assays showed that the core promoter region of pri-miRX ranged 500 nt from the transcription start site...
April 22, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29680695/microbiological-quality-and-antimicrobial-resistance-characterization-of-salmonella-spp-in-fresh-milk-value-chains-in-ghana
#4
Angela Parry-Hanson Kunadu, Mark Holmes, Eric L Miller, Andrew J Grant
Consumer perception of poor hygiene of fresh milk products is a major barrier to promotion of milk consumption as an intervention to alleviate the burden of malnutrition in Ghana. Fresh milk is retailed raw, boiled, or processed into unfermented cheese and spontaneously fermented products in unlicensed outlets. In this study, we have determined microbiological quality of informally retailed fresh milk products and characterized the genomic diversity and antimicrobial resistance (AMR) patterns of non-typhoidal Salmonella (NTS) in implicated products...
April 14, 2018: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29679745/integrated-genomic-and-metabolomic-profiling-of-isc1-an-emerging-leishmania-donovani-population-in-the-indian-subcontinent
#5
Bart Cuypers, Maya Berg, Hideo Imamura, Franck Dumetz, Géraldine De Muylder, Malgorzata A Domagalska, Suman Rijal, Narayan Raj Bhattarai, Ilse Maes, Mandy Sanders, James A Cotton, Pieter Meysman, Kris Laukens, Jean-Claude Dujardin
Leishmania donovani is the responsible agent for visceral leishmaniasis (VL) in the Indian subcontinent (ISC). The disease is lethal without treatment and causes 0.2 to 0.4 million cases each year. Recently, reports of VL in Nepalese hilly districts have increased as well as VL cases caused by L. donovani from the ISC1 genetic group, a new and emerging genotype. In this study, we perform for the first time an integrated, untargeted genomics and metabolomics approach to characterize ISC1, in comparison with the Core Group (CG), main population that drove the last outbreak of VL in the ISC...
April 18, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29678910/serotype-diversity-and-antimicrobial-resistance-among-salmonella-enterica-isolated-from-patients-at-an-equine-referral-hospital
#6
I M Leon, S D Lawhon, K N Norman, D S Threadgill, N Ohta, J Vinasco, H M Scott
Although Salmonella enterica can produce life-threatening colitis in horses, certain serotypes are more commonly associated with clinical disease. Our aim was to evaluate the proportional morbidity attributed to different serotypes, as well as phenotypic and genotypic antimicrobial resistance (AMR) of Salmonella isolated from patients at an equine referral hospital in the southern United States. Two-hundred-fifty-five Salmonella isolates were obtained from clinical samples of patients admitted to the hospital between 2007 and 2015...
April 20, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29678658/essentiality-conservation-evolutionary-pressure-and-codon-bias-in-bacterial-genomes
#7
Maddalena Dilucca, Giulio Cimini, Andrea Giansanti
Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than on genes that are either nonessential or peculiar to a single or a few species. In order to further assess this expectation, we study here how essentiality of a gene is connected with its degree of conservation among several unrelated bacterial species, each one characterised by its own codon usage bias...
April 17, 2018: Gene
https://www.readbyqxmd.com/read/29678218/developing-inclusivity-and-exclusivity-panels-for-testing-diagnostic-and-detection-tools-targeting-burkholderia-pseudomallei-the-causative-agent-of-melioidosis
#8
Charles H D Williamson, David M Wagner, Paul Keim, Jason W Sahl
Background: Diagnostic tools designed to target Burkholderia pseudomallei , the causative agent of melioidosis that was classified as a Tier 1 Select Agent by the U.S. Centers for Disease Control and Prevention, have typically suffered from false-positive and false-negative results because of a lack of understanding of the genomic diversity of B. pseudomallei and its genetic near neighbors. Objective: In this review, we discuss a strategy for using comparative genomics to guide the design of inclusivity and exclusivity panels for the validation of assays as defined by the Standard Method Performance Requirement (SMPR®)...
April 20, 2018: Journal of AOAC International
https://www.readbyqxmd.com/read/29676996/involvement-of-spata31-copy-number-variable-genes-in-human-lifespan
#9
Cemalettin Bekpen, Chen Xie, Almut Nebel, Diethard Tautz
The SPATA31 ( alias FAM75A) gene family belongs to the core duplicon families that are thought to have contributed significantly to hominoid evolution. It is also among the gene families with the strongest signal of positive selection in hominoids. It has acquired new protein domains in the primate lineage and a previous study has suggested that the gene family has expanded its function into UV response and DNA repair. Here we show that over-expression of SPATA31A1 in fibroblast cells leads to premature senescence due to interference with aging-related transcription pathways...
April 19, 2018: Aging
https://www.readbyqxmd.com/read/29674682/author-correction-segregation-of-mitochondrial-dna-heteroplasmy-through-a-developmental-genetic-bottleneck-in-human-embryos
#10
Vasileios I Floros, Angela Pyle, Sabine Dietmann, Wei Wei, Walfred W C Tang, Naoko Irie, Brendan Payne, Antonio Capalbo, Laila Noli, Jonathan Coxhead, Gavin Hudson, Moira Crosier, Henrik Strahl, Yacoub Khalaf, Mitinori Saitou, Dusko Ilic, M Azim Surani, Patrick F Chinnery
In the version of this Letter originally published, an author error led to the affiliations for Brendan Payne, Jonathan Coxhead and Gavin Hudson being incorrect. The correct affiliations are: Brendan Payne: 3 Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK. 6 Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK; this is a new affiliation 6 and subsequent existing affiliations have been renumbered. Jonathan Coxhead: 11 Genomic Core Facility, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK; this is a new affiliation 11 and subsequent existing affiliations have been renumbered...
April 19, 2018: Nature Cell Biology
https://www.readbyqxmd.com/read/29673772/widespread-enhancer-activity-from-core-promoters
#11
REVIEW
Alejandra Medina-Rivera, David Santiago-Algarra, Denis Puthier, Salvatore Spicuglia
Gene expression in higher eukaryotes is precisely regulated in time and space through the interplay between promoters and gene-distal regulatory regions, known as enhancers. The original definition of enhancers implies the ability to activate gene expression remotely, while promoters entail the capability to locally induce gene expression. Despite the conventional distinction between them, promoters and enhancers share many genomic and epigenomic features. One intriguing finding in the gene regulation field comes from the observation that many core promoter regions display enhancer activity...
April 16, 2018: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/29672875/mapping-qtl-for-production-traits-in-segregating-pi%C3%A3-train-pig-populations-using-genome-wide-association-study-results-of-f2-crosses
#12
M Schmid, M Maushammer, S Preuß, J Bennewitz
In this study, genome-wide association study (GWAS) results of porcine F2 crosses were used to map QTL in outcross Piétrain populations. For this purpose, two F2 crosses (Piétrain × Meishan, n = 304; Piétrain × Wild Boar, n = 291) were genotyped with the PorcineSNP60v2 BeadChip and phenotyped for the dressing yield, carcass length, daily gain and drip loss traits. GWASs were conducted in the pooled F2 cross applying single marker mixed linear models. For the investigated traits, between two and five (in total 15) QTL core regions, spanning 250 segregating SNPs around a significant trait-associated peak SNP, were identified...
April 19, 2018: Animal Genetics
https://www.readbyqxmd.com/read/29672509/robustness-encoded-across-essential-and-accessory-replicons-of-the-ecologically-versatile-bacterium-sinorhizobium-meliloti
#13
George C diCenzo, Alex B Benedict, Marco Fondi, Graham C Walker, Turlough M Finan, Alessio Mengoni, Joel S Griffitts
Bacterial genome evolution is characterized by gains, losses, and rearrangements of functional genetic segments. The extent to which large-scale genomic alterations influence genotype-phenotype relationships has not been investigated in a high-throughput manner. In the symbiotic soil bacterium Sinorhizobium meliloti, the genome is composed of a chromosome and two large extrachromosomal replicons (pSymA and pSymB, which together constitute 45% of the genome). Massively parallel transposon insertion sequencing (Tn-seq) was employed to evaluate the contributions of chromosomal genes to growth fitness in both the presence and absence of these extrachromosomal replicons...
April 19, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29672343/polygenic-risk-score-for-schizophrenia-is-not-strongly-associated-with-the-expression-of-specific-genes-or-gene-sets
#14
David Curtis
BACKGROUND: The polygenic risk score (PRS) is derived from single nucleotide polymorphisms (SNPs) including those that are genome-wide significant and also including a large number of others more weakly associated with schizophrenia. Such variants are widely dispersed, though concentrated near genes expressed in the brain, and it has been proposed that these SNP associations result from impacts on cell regulatory networks that ultimately affect the expression or function of a modest number of 'core' genes...
April 18, 2018: Psychiatric Genetics
https://www.readbyqxmd.com/read/29671892/frequent-loss-of-claudin-4-expression-in-dedifferentiated-and-undifferentiated-endometrial-carcinomas
#15
Basile Tessier-Cloutier, Robert A Soslow, Colin J R Stewart, Martin Köbel, Cheng-Han Lee
INTRO: Dedifferentiated/undifferentiated endometrial carcinomas (DDEC/UEC) are aggressive endometrial cancers with frequent genomic inactivation of core components of switch/sucrose non-fermentable (SWI/SNF) complex proteins. Claudin-4, an epithelial intercellular tight junction protein was recently found to be expressed in SWI/SNF-deficient undifferentiated carcinomas but not SWI/SNF-deficient sarcomas. The aim of this study is to examine claudin-4 expression in UEC/DDEC and other high-grade uterine carcinomas...
April 19, 2018: Histopathology
https://www.readbyqxmd.com/read/29671722/the-complete-replicons-of-16-ensifer-meliloti-strains-offer-insights-into-intra-and-inter-replicon-gene-transfer-transposon-associated-loci-and-repeat-elements
#16
Matthew Nelson, Joseph Guhlin, Brendan Epstein, Peter Tiffin, Michael J Sadowsky
Ensifer meliloti (formerly Rhizobium meliloti and Sinorhizobium meliloti) is a model bacterium for understanding legume-rhizobial symbioses. The tripartite genome of E. meliloti consists of a chromosome, pSymA and pSymB, and in some instances strain-specific accessory plasmids. The majority of previous sequencing studies have relied on the use of assemblies generated from short read sequencing, which leads to gaps and assembly errors. Here we used PacBio-based, long-read assemblies and were able to assemble, de novo, complete circular replicons...
April 19, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29671267/reporter-gene-assays-using-viral-functional-genomics-libraries
#17
Genevieve Welch, Robert Damoiseaux, Loren Miraglia
While transfectable libraries are the workhorse for many screening cores, there is one obvious area where these reagents are not useful-hard to transfect cell lines and primary cells. One solution to this problem is the use of virus to introduce genomic reagents. This strategy is more commonplace now than ever before with libraries covering cDNAs, shDNAs, miRNAs, and guide RNAs readily available. Maintenance and use of these libraries are more challenging than the transient transfection approach due to the viral production step, and the infrastructure necessary to generate them...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29669889/molecular-preadaptation-to-antimony-resistance-in-leishmania-donovani-on-the-indian-subcontinent
#18
F Dumetz, B Cuypers, H Imamura, D Zander, E D'Haenens, I Maes, M A Domagalska, J Clos, J-C Dujardin, G De Muylder
Antimonials (Sb) were used for decades for chemotherapy of visceral leishmaniasis (VL). Now abandoned in the Indian subcontinent (ISC) because of Leishmania donovani resistance, this drug offers a unique model for understanding drug resistance dynamics. In a previous phylogenomic study, we found two distinct populations of L. donovani : the core group (CG) in the Gangetic plains and ISC1 in the Nepalese highlands. Sb resistance was only encountered within the CG, and a series of potential markers were identified...
April 25, 2018: MSphere
https://www.readbyqxmd.com/read/29669884/iron-acquisition-and-siderophore-release-by-carbapenem-resistant-sequence-type-258-klebsiella-pneumoniae
#19
Victoria I Holden, Meredith S Wright, Sébastien Houle, Abigail Collingwood, Charles M Dozois, Mark D Adams, Michael A Bachman
Klebsiella pneumoniae is rapidly acquiring resistance to all known antibiotics, including carbapenems. Multilocus sequence type ST258 (sequence type 258), carrying a gene encoding the K. pneumoniae carbapenemase ( bla KPC ) on a transmissible plasmid, is the most prevalent carbapenem-resistant Enterobacteriaceae (CRE) in the United States and has disseminated worldwide. Previously, whole-genome sequencing identified core genome single nucleotide variants that divide ST258 into two distinct clades, ST258a and ST258b...
April 25, 2018: MSphere
https://www.readbyqxmd.com/read/29669843/the-association-of-polymorphisms-in-nucleotide-excision-repair-genes-with-ovarian-cancer-susceptibility
#20
Zhiguang Zhao, Anqi Zhang, Yuan Zhao, Junmiao Xiang, Danyang Yu, Zongwen Liang, Chaoyi Xu, Qiong Zhang, Jianmin Li, Ping Duan
Nucleotide excision repair (NER), the core mechanism of DNA repair pathway, was commonly used to maintain genomic stability and prevent tumorigenesis. Previous investigations have demonstrated that single nucleotide polymorphisms (SNPs) of NER pathway genes were associated with various types of cancer. However, there was no research elucidating the genetic association of entire NER pathway with ovarian cancer susceptibility. Therefore, we conducted genotyping for 17 SNPs of six NER core genes (XPA, XPC, XPG, ERCC1, ERCC2 and ERCC4) in 89 ovarian cancer cases and 356 cancer-free controls...
April 18, 2018: Bioscience Reports
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