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https://www.readbyqxmd.com/read/27924811/insights-into-the-evolution-of-pathogenicity-of-escherichia-coli-from-genomic-analysis-of-intestinal-e-coli-of-marmota-himalayana-in-qinghai-tibet-plateau-of-china
#1
Shan Lu, Dong Jin, Shusheng Wu, Jing Yang, Ruiting Lan, Xiangning Bai, Sha Liu, Qiong Meng, Xuejiao Yuan, Juan Zhou, Ji Pu, Qiang Chen, Hang Dai, Yuanyuan Hu, Yanwen Xiong, Changyun Ye, Jianguo Xu
Escherichia coli is both of a widespread harmless gut commensal and a versatile pathogen of humans. Domestic animals are a well-known reservoir for pathogenic E. coli. However, studies of E. coli populations from wild animals that have been separated from human activities had been very limited. Here we obtained 580 isolates from intestinal contents of 116 wild Marmot Marmota himalayana from Qinghai-Tibet plateau, China, with five isolates per animal. We selected 125 (hereinafter referred to as strains) from the 580 isolates for genome sequencing, based on unique pulse field gel electrophoresis patterns and at least one isolate per animal...
December 7, 2016: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/27923400/allele-specific-expression-in-the-human-heart-and-its-application-to-postoperative-atrial-fibrillation-and-myocardial-ischemia
#2
Martin I Sigurdsson, Louis Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary Aranki, Gregory S Couper, Stanton K Shernan, Jon G Seidman, Simon C Body, Jochen D Muehlschlegel
BACKGROUND: Allele-specific expression (ASE) is differential expression of each of the two chromosomal alleles of an autosomal gene. We assessed ASE patterns in the human left atrium (LA, n = 62) and paired samples from the left ventricle (LV, n = 76) before and after ischemia, and tested the utility of differential ASE to identify genes associated with postoperative atrial fibrillation (poAF) and myocardial ischemia. METHODS: Following genotyping from whole blood and whole-genome sequencing of LA and LV samples, we called ASE using sequences overlapping heterozygous SNPs using rigorous quality control to minimize false ASE calling...
December 6, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27920765/novel-pathways-for-ameliorating-the-fitness-cost-of-gentamicin-resistant-small-colony-variants
#3
Martin Vestergaard, Wilhelm Paulander, Bingfeng Leng, Jesper B Nielsen, Henrik T Westh, Hanne Ingmer
Small colony variants (SCVs) of the human pathogen Staphylococcus aureus are associated with persistent infections. Phenotypically, SCVs are characterized by slow growth and they can arise upon interruption of the electron transport chain that consequently reduce membrane potential and thereby limit uptake of aminoglycosides (e.g., gentamicin). In this study, we have examined the pathways by which the fitness cost of SCVs can be ameliorated. Five gentamicin resistant SCVs derived from S. aureus JE2 were independently selected on agar plates supplemented with gentamicin...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920554/next-generation-sequence-detects-arap3-as-a-novel-oncogene-in-papillary-thyroid-carcinoma
#4
Qing-Xuan Wang, En-Dong Chen, Ye-Feng Cai, Yi-Li Zhou, Zhou-Ci Zheng, Ying-Hao Wang, Yi-Xiang Jin, Wen-Xu Jin, Xiao-Hua Zhang, Ou-Chen Wang
PURPOSE: Thyroid cancer is the most frequent malignancies of the endocrine system, and it has became the fastest growing type of cancer worldwide. Much still remains unknown about the molecular mechanisms of thyroid cancer. Studies have found that some certain relationship between ARAP3 and human cancer. However, the role of ARAP3 in thyroid cancer has not been well explained. This study aimed to investigate the role of ARAP3 gene in papillary thyroid carcinoma. METHODS: Whole exon sequence and whole genome sequence of primary papillary thyroid carcinoma (PTC) samples and matched adjacent normal thyroid tissue samples were performed and then bioinformatics analysis was carried out...
2016: OncoTargets and Therapy
https://www.readbyqxmd.com/read/27918528/origin-of-modern-syphilis-and-emergence-of-a-pandemic-treponema-pallidum-cluster
#5
Natasha Arora, Verena J Schuenemann, Günter Jäger, Alexander Peltzer, Alexander Seitz, Alexander Herbig, Michal Strouhal, Linda Grillová, Leonor Sánchez-Busó, Denise Kühnert, Kirsten I Bos, Leyla Rivero Davis, Lenka Mikalová, Sylvia Bruisten, Peter Komericki, Patrick French, Paul R Grant, María A Pando, Lucía Gallo Vaulet, Marcelo Rodríguez Fermepin, Antonio Martinez, Arturo Centurion Lara, Lorenzo Giacani, Steven J Norris, David Šmajs, Philipp P Bosshard, Fernando González-Candelas, Kay Nieselt, Johannes Krause, Homayoun C Bagheri
The abrupt onslaught of the syphilis pandemic that started in the late fifteenth century established this devastating infectious disease as one of the most feared in human history(1). Surprisingly, despite the availability of effective antibiotic treatment since the mid-twentieth century, this bacterial infection, which is caused by Treponema pallidum subsp. pallidum (TPA), has been re-emerging globally in the last few decades with an estimated 10.6 million cases in 2008 (ref. 2). Although resistance to penicillin has not yet been identified, an increasing number of strains fail to respond to the second-line antibiotic azithromycin(3)...
December 5, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27916276/a-surveillance-mechanism-ensures-repair-of-dna-lesions-during-zygotic-reprogramming
#6
Sabrina Ladstätter, Kikuë Tachibana-Konwalski
Sexual reproduction culminates in a totipotent zygote with the potential to produce a whole organism. Sperm chromatin reorganization and epigenetic reprogramming that alter DNA and histone modifications generate a totipotent embryo. Active DNA demethylation of the paternal genome has been proposed to involve base excision and DNA repair-based mechanisms. The nature and consequence of DNA lesions generated during reprogramming are not known. Using mouse genetics and chemical biology, we discovered that Tet3-dependent zygotic reprogramming generates paternal DNA lesions that are monitored by a surveillance mechanism...
November 21, 2016: Cell
https://www.readbyqxmd.com/read/27915479/trends-in-next-generation-sequencing-and-a-new-era-for-whole-genome-sequencing
#7
REVIEW
Sang Tae Park, Jayoung Kim
This article is a mini-review that provides a general overview for next-generation sequencing (NGS) and introduces one of the most popular NGS applications, whole genome sequencing (WGS), developed from the expansion of human genomics. NGS technology has brought massively high throughput sequencing data to bear on research questions, enabling a new era of genomic research. Development of bioinformatic software for NGS has provided more opportunities for researchers to use various applications in genomic fields...
November 2016: International Neurourology Journal
https://www.readbyqxmd.com/read/27915180/self-primed-isothermal-amplification-for-genomic-dna-detection-of-human-papillomavirus
#8
Wei Lu, Qingpan Yuan, Zhiliu Yang, Bo Yao
Rolling circle amplification (RCA) is an isothermal amplification technique with high efficiency and perfect accuracy for nucleic acids detection. However, RCA technique suffers the limitation to detect short DNA or RNA molecules. For long nucleic acid molecules, enzymatic restriction as well as heat denaturation process is usually required, which makes the amplification not effective and strictly isothermal. In this article, a simple and efficient one-pot self-primed isothermal amplification (SIA) was developed for detection of genomic DNA directly based on the combination of nicking endonuclease assisted strand displacement amplification (SDA) and exponential RCA...
October 10, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27915106/insights-gained-from-ancient-biomolecules-into-past-and-present-tuberculosis-a-personal-perspective
#9
REVIEW
Helen D Donoghue
Ancient and historical tuberculosis (TB) can be recognized by its typical paleopathology in human remains. Using paleomicrobiology, it is possible to detect many more individuals infected with TB but with no visible lesions. Due to advances in molecular analysis over the past two decades, it is clear that TB was widespread in humans from the Neolithic period until the present day. Past human populations were associated with different lineages of the Mycobacterium tuberculosis (MTB) complex, thereby elucidating early human migrations...
November 30, 2016: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/27913844/global-dna-methylation-profiling-of-manganese-exposed-human-neuroblastoma-sh-sy5y-cells-reveals-epigenetic-alterations-in-parkinson-s-disease-associated-genes
#10
Prashant Tarale, Saravanadevi Sivanesan, Atul P Daiwile, Reinhard Stöger, Amit Bafana, Pravin K Naoghare, Devendra Parmar, Tapan Chakrabarti, Krishnamurthi Kannan
Manganese (Mn) is an essential trace element required for optimal functioning of cellular biochemical pathways in the central nervous system. Elevated exposure to Mn through environmental and occupational exposure can cause neurotoxic effects resulting in manganism, a condition with clinical symptoms identical to idiopathic Parkinson's disease. Epigenetics is now recognized as a biological mechanism involved in the etiology of various diseases. Here, we investigated the role of DNA methylation alterations induced by chronic Mn (100 µM) exposure in human neuroblastoma (SH-SY5Y) cells in relevance to Parkinson's disease...
December 2, 2016: Archives of Toxicology
https://www.readbyqxmd.com/read/27912729/genomic-insights-from-whole-genome-sequencing-of-four-clonal-outbreak-campylobacter-jejuni-assessed-within-the-global-c-jejuni-population
#11
Clifford G Clark, Chrystal Berry, Matthew Walker, Aaron Petkau, Dillon O R Barker, Cai Guan, Aleisha Reimer, Eduardo N Taboada
BACKGROUND: Whole genome sequencing (WGS) is useful for determining clusters of human cases, investigating outbreaks, and defining the population genetics of bacteria. It also provides information about other aspects of bacterial biology, including classical typing results, virulence, and adaptive strategies of the organism. Cell culture invasion and protein expression patterns of four related multilocus sequence type 21 (ST21) C. jejuni isolates from a significant Canadian water-borne outbreak were previously associated with the presence of a CJIE1 prophage...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27912242/deciphering-the-origin-of-dogs-from-fossils-to-genomes
#12
Adam H Freedman, Robert K Wayne
Understanding the timing and geographic context of dog origins is a crucial component for understanding human history, as well as the evolutionary context in which the morphological and behavioral divergence of dogs from wolves occurred. A substantial challenge to understanding domestication is that dogs have experienced a complicated demographic history. An initial severe bottleneck was associated with domestication followed by postdivergence gene flow between dogs and wolves, as well as population expansions, contractions, and replacements...
November 28, 2016: Annual Review of Animal Biosciences
https://www.readbyqxmd.com/read/27909820/genomic-analysis-reveals-the-presence-of-a-class-d-beta-lactamase-with-broad-substrate-specificity-in-animal-bite-associated-capnocytophaga-species
#13
S Zangenah, A F Andersson, V Özenci, P Bergman
Capnocytophga canimorsus and Capnocytophga cynodegmi can be transmitted from cats and dogs to humans, and can cause a wide range of infections including wound infections, sepsis, or endocarditis. We and others recently discovered two new Capnocytophaga species, C. canis and C. stomatis, mainly associated with wound infections. The first-line treatment of animal bite related infections is penicillin, and in case of allergy, doxycycline and trimethoprim/sulfamethoxazole. However, there is a lack of antibiotic susceptibility patterns for animal bite associated Capnocytophaga species...
December 1, 2016: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/27908998/whole-genome-sequencing-applied-to-the-molecular-epidemiology-of-shiga-toxin-producing-escherichia-coli-o157-h7-in-argentina
#14
Claudia Carolina Carbonari, Nahuel Fittipaldi, Sarah Teatero, Taryn B T Athey, Luis Pianciola, Marcelo Masana, Roberto G Melano, Marta Rivas, Isabel Chinen
Shiga toxin-producing Escherichia coli strains are worldwide associated with sporadic human infections and outbreaks. In this work, we report the availability of high-quality draft whole-genome sequences for 19 O157:H7 strains isolated in Argentina.
December 1, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27908673/darwin-comes-to-clinic
#15
Arthur L Beaudet
What might be the benefits of whole-genome rather than whole-exome sequencing (WES) for identifying the genetic causes of human disabilities? A recent paper by Doan et al. focuses attention on mutations in human accelerated regions (HARs), a subset of genomic regulatory elements showing accelerated evolution between chimpanzees and humans.
November 28, 2016: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/27908293/autosomal-genetic-control-of-human-gene-expression-does-not-differ-across-the-sexes
#16
Irfahan Kassam, Luke Lloyd-Jones, Alexander Holloway, Kerrin S Small, Biao Zeng, Andrew Bakshi, Andres Metspalu, Greg Gibson, Tim D Spector, Tonu Esko, Grant W Montgomery, Joseph E Powell, Jian Yang, Peter M Visscher, Allan F McRae
BACKGROUND: Despite their nearly identical genomes, males and females differ in risk, incidence, prevalence, severity and age-at-onset of many diseases. Sexual dimorphism is also seen in human autosomal gene expression, and has largely been explored by examining the contribution of genotype-by-sex interactions to variation in gene expression. RESULTS: In this study, we use data from a mixture of pedigree and unrelated individuals with verified European ancestry to investigate the sex-specific genetic architecture of gene expression measured in whole blood across n=1048 males and n=1005 females by treating gene expression intensities in the sexes as two distinct traits and estimating the genetic correlation (r G) between them...
December 1, 2016: Genome Biology
https://www.readbyqxmd.com/read/27908234/sustained-early-disruption-of-mitochondrial-function-contributes-to-arsenic-induced-prostate-tumorigenesis
#17
B Singh, M Kulawiec, K M Owens, A Singh, K K Singh
Arsenic is a well-known human carcinogen that affects millions of people worldwide, but the underlying mechanisms of carcinogenesis are unclear. Several epidemiological studies have suggested increased prostate cancer incidence and mortality due to exposure to arsenic. Due to lack of an animal model of arsenic-induced carcinogenesis, we used a prostate epithelial cell culture model to identify a role for mitochondria in arsenic-induced prostate cancer. Mitochondrial morphology and membrane potential was impacted within a few hours of arsenic exposure of non-neoplastic prostate epithelial cells...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27907920/aneuploidy-detection-and-mtdna-quantification-in-bovine-embryos-with-different-cleavage-onset-using-a-next-generation-sequencing-based-protocol
#18
Miroslav Hornak, David Kubicek, Petr Broz, Pavlina Hulinska, Katerina Hanzalova, Darren Griffin, Marie Machatkova, Jiri Rubes
Bovine embryos are now routinely used in agricultural systems as a means of disseminating superior genetics worldwide, ultimately with the aim of feeding an ever-growing population. Further investigations, common for human IVF embryos, thus have priority to improve cattle IVF, as has screening for aneuploidy (abnormal chromosome number). Although the incidence and consequences of aneuploidy are well documented in human preimplantation embryos, they are less well known for the embryos of other animals. To address this, we assessed aneuploidy levels in thirty-one 2-cell bovine embryos derived from early- and late-cleaving zygotes...
December 2, 2016: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/27907889/denovo-db-a-compendium-of-human-de-novo-variants
#19
Tychele N Turner, Qian Yi, Niklas Krumm, John Huddleston, Kendra Hoekzema, Holly A F Stessman, Anna-Lisa Doebley, Raphael A Bernier, Deborah A Nickerson, Evan E Eichler
Whole-exome and whole-genome sequencing have facilitated the large-scale discovery of de novo variants in human disease. To date, most de novo discovery through next-generation sequencing focused on congenital heart disease and neurodevelopmental disorders (NDDs). Currently, de novo variants are one of the most significant risk factors for NDDs with a substantial overlap of genes involved in more than one NDD. To facilitate better usage of published data, provide standardization of annotation, and improve accessibility, we created denovo-db (http://denovo-db...
October 5, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27906186/preimplantation-factor-is-an-anti-apoptotic-effector-in-human-trophoblasts-involving-p53-signaling-pathway
#20
Hadia Moindjie, Esther Dos Santos, Rita-Josiane Gouesse, Nelly Swierkowski-Blanchard, Valérie Serazin, Eytan R Barnea, François Vialard, Marie-Noëlle Dieudonné
From the earliest stages of gestation, embryonic-maternal interaction has a key role in a successful pregnancy. Various factors present during gestation may significantly influence this type of juxta/paracrine interaction. PreImplantation Factor (PIF) is a recently identified factor with activity at the fetomaternal interface. PIF is secreted by viable embryos and directly controls placental development by increasing the invasive capacity of human extravillous trophoblasts (EVTs). To further specify PIF's role in the human placenta, we analyzed the genome-wide expression profile of the EVT in the presence of a synthetic PIF analog (sPIF)...
December 1, 2016: Cell Death & Disease
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