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https://www.readbyqxmd.com/read/28108177/discriminating-between-adaptive-and-carcinogenic-liver-hypertrophy-in-rat-studies-using-logistic-ridge-regression-analysis-of-toxicogenomic-data-the-mode-of-action-and-predictive-models
#1
Shujie Liu, Taisuke Kawamoto, Osamu Morita, Kouichi Yoshinari, Hiroshi Honda
Chemical exposure often results in liver hypertrophy in animal tests, characterized by increased liver weight, hepatocellular hypertrophy, and/or cell proliferation. While most of these changes are considered adaptive responses, there is concern that they may be associated with carcinogenesis. In this study, we have employed a toxicogenomic approach using a logistic ridge regression model to identify genes responsible for liver hypertrophy and hypertrophic hepatocarcinogenesis and to develop a predictive model for assessing hypertrophy-inducing compounds...
January 17, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/28107884/the-association-between-irritable-bowel-syndrome-and-the-coexistence-of-depression-and-insomnia
#2
Seung Ku Lee, Dae Wui Yoon, Sunghee Lee, Jinkwan Kim, Kyung-Mee Choi, Chol Shin
OBJECTIVE: The individual occurrence of depression or insomnia is a risk factor for irritable bowel syndrome (IBS), but few researchers have evaluated the association between comorbid depression and insomnia and IBS. The aim of the present study is to explore the relationship between IBS and the coexistence of depression and insomnia in a Korean population-based cohort study. METHODS: A total of 3429 individuals who were enrolled in the Korean Genome and Epidemiology Study were analysed...
February 2017: Journal of Psychosomatic Research
https://www.readbyqxmd.com/read/28107419/a-new-israeli-tobamovirus-isolate-infects-tomato-plants-harboring-tm-22-resistance-genes
#3
Neta Luria, Elisheva Smith, Victoria Reingold, Ilana Bekelman, Moshe Lapidot, Ilan Levin, Nadav Elad, Yehudit Tam, Noa Sela, Ahmad Abu-Ras, Nadav Ezra, Ami Haberman, Liron Yitzhak, Oded Lachman, Aviv Dombrovsky
An outbreak of a new disease infecting tomatoes occurred in October-November 2014 at the Ohad village in Southern Israel. Symptomatic plants showed a mosaic pattern on leaves accompanied occasionally by narrowing of leaves and yellow spotted fruit. The disease spread mechanically and rapidly reminiscent of tobamovirus infection. Epidemiological studies showed the spread of the disease in various growing areas, in the South and towards the Southeast and Northern parts of the country within a year. Transmission electron microscope (TEM) analysis showed a single rod-like form characteristic to the Tobamovirus genus...
2017: PloS One
https://www.readbyqxmd.com/read/28106529/a-joint-cross-border-investigation-of-a-cluster-of-multidrug-resistant-tuberculosis-in-austria-romania-and-germany-in-2014-using-classic-genotyping-and-whole-genome-sequencing-methods-lessons-learnt
#4
Lena Fiebig, Thomas A Kohl, Odette Popovici, Margarita Mühlenfeld, Alexander Indra, Daniela Homorodean, Domnica Chiotan, Elvira Richter, Sabine Rüsch-Gerdes, Beatrix Schmidgruber, Patrick Beckert, Barbara Hauer, Stefan Niemann, Franz Allerberger, Walter Haas
Molecular surveillance of multidrug-resistant tuberculosis (MDR-TB) using 24-loci MIRU-VNTR in the European Union suggests the occurrence of international transmission. In early 2014, Austria detected a molecular MDR-TB cluster of five isolates. Links to Romania and Germany prompted the three countries to investigate possible cross-border MDR-TB transmission jointly. We searched genotyping databases, genotyped additional isolates from Romania, used whole genome sequencing (WGS) to infer putative transmission links, and investigated pairwise epidemiological links and patient mobility...
January 12, 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/28105966/a-novel-approach-for-pathway-analysis-of-gwas-data-highlights-role-of-bmp-signaling-and-muscle-cell-differentiation-in-colorectal-cancer-susceptibility
#5
Aniket Mishra, Stuart MacGregor
Genome-wide association studies (GWAS) have revolutionized the field of gene mapping. As the GWAS field matures, it is becoming clear that for many complex traits, a proportion of the missing heritability is attributable to common variants of individually small effect. Detecting these small effects individually can be difficult, and statistical power would be increased if relevant variants could be grouped together for testing. Here, we propose a VEGAS2Pathway approach that aggregates association strength of individual markers into pre-specified biological pathways...
February 2017: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/28104616/sequential-colonization-of-periodontal-pathogens-in-induction-of-periodontal-disease-and-atherosclerosis-in-ldlrnull-mice
#6
Sasanka S Chukkapalli, Meena Easwaran, Mercedes F Rivera-Kweh, Irina M Velsko, Sriram Ambadapadi, Jiayin Dai, Hannu Larjava, Alexandra R Lucas, Lakshmyya Kesavalu
Periodontal disease (PD) and atherosclerotic vascular disease (ASVD) are both chronic inflammatory diseases with a polymicrobial etiology and have been epidemiologically associated. The purpose is to examine whether periodontal bacteria that infect the periodontium, can also infect vascular tissues and enhance pre-existing early aortic atherosclerotic lesions in LDLR(null) mice. Mice were orally infected with intermediate bacterial colonizer Fusobacterium nucleatum for the first 12 weeks followed by late bacterial colonizers (Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia) for the remaining 12 weeks mimicking the human oral microbiota ecological colonization...
January 18, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28104386/haemagglutinin-and-neuraminidase-sequencing-when-compared-to-whole-genome-sequencing-proved-sufficient-to-delineate-two-distinct-clusters-of-influenza-a-h1n1-pdm09-in-a-suspected-cross-site-renal-unit-influenza-outbreak
#7
Rebecca Houghton, Joanna Ellis, Monica Galiano, Tristan W Clark, Sarah Wyllie
OBJECTIVES: We describe haemagglutinin (HA) and neuraminidase (NA) sequencing in an apparent cross-site influenza A(H1N1) outbreak in renal transplant and haemodialysis patients, confirmed with whole genome sequencing (WGS). METHODS: Isolates were sequenced from influenza positive individuals. Phylogenetic trees were constructed using HA and NA sequencing and subsequently WGS. Sequence data was analysed to determine genetic relatedness of viruses obtained from inpatient and outpatient cohorts and compared with epidemiological outbreak information...
January 16, 2017: Journal of Infection
https://www.readbyqxmd.com/read/28103318/static-and-evolving-norovirus-genotypes-implications-for-epidemiology-and-immunity
#8
Gabriel I Parra, R Burke Squires, Consolee K Karangwa, Jordan A Johnson, Cara Lepore, Stanislav V Sosnovtsev, Kim Y Green
Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a large-scale genomics approach to analyze human norovirus sequences. Comparison of over 2000 nearly full-length ORF2 sequences representing most of the known GI and GII genotypes infecting humans showed a limited number (≤5) of distinct intra-genotypic variants within each genotype, with the exception of GII...
January 19, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28103310/epidemiological-and-molecular-characterization-of-a-mexican-population-isolate-with-high-prevalence-of-limb-girdle-muscular-dystrophy-type-2a-due-to-a-novel-calpain-3-mutation
#9
Carlos A Pantoja-Melendez, Antonio Miranda-Duarte, Bladimir Roque-Ramirez, Juan C Zenteno
Limb-Girdle Muscular Dystrophy type 2 (LGMD2) is a group of autosomally recessive inherited disorders defined by weakness and wasting of the shoulder and pelvic girdle muscles. In the past, several population isolates with high incidence of LGMD2 arising from founder mutation effects have been identified. The aim of this work is to describe the results of clinical, epidemiologic, and molecular studies performed in a Mexican village segregating numerous cases of LGMD2. A population census was conducted in the village to identify all LGMD affected patients...
2017: PloS One
https://www.readbyqxmd.com/read/28103259/characterization-and-genetic-variation-of-vibrio-cholerae-isolated-from-clinical-and-environmental-sources-in-thailand
#10
Achiraya Siriphap, Pimlapas Leekitcharoenphon, Rolf S Kaas, Chonchanok Theethakaew, Frank M Aarestrup, Orasa Sutheinkul, Rene S Hendriksen
Cholera is still an important public health problem in several countries, including Thailand. In this study, a collection of clinical and environmental V. cholerae serogroup O1, O139, and non-O1/non-O139 strains originating from Thailand (1983 to 2013) was characterized to determine phenotypic and genotypic traits and to investigate the genetic relatedness. Using a combination of conventional methods and whole genome sequencing (WGS), 78 V. cholerae strains were identified. WGS was used to determine the serogroup, biotype, virulence, mobile genetic elements, and antimicrobial resistance genes using online bioinformatics tools...
2017: PloS One
https://www.readbyqxmd.com/read/28102434/low-muscle-mass-and-risk-of-type-2-diabetes-in-middle-aged-and-older-adults-findings-from-the-koges
#11
Jang Won Son, Seong Su Lee, Sung Rae Kim, Soon Jib Yoo, Bong Yun Cha, Ho Young Son, Nam H Cho
AIMS/HYPOTHESIS: Asians have a propensity to develop type 2 diabetes with a lower BMI than Western populations. This discrepancy may be due to differences in body fat and muscle mass for a given BMI. However, unlike adiposity, it is unclear whether muscle mass affects the risk of type 2 diabetes in Asian populations. METHODS: We conducted a 2-yearly prospective assessment of 6895 participants who were free of diabetes at the baseline examination as part of the Korean Genome Epidemiology Study...
January 19, 2017: Diabetologia
https://www.readbyqxmd.com/read/28100788/genomic-infectious-disease-epidemiology-in-partially-sampled-and-ongoing-outbreaks
#12
Xavier Didelot, Christophe Fraser, Jennifer Gardy, Caroline Colijn
Genomic data is increasingly being used to understand infectious disease epidemiology. Isolates from a given outbreak are sequenced, and the patterns of shared variation are used to infer which isolates within the outbreak are most closely related to each other. Unfortunately, the phylogenetic trees typically used to represent this variation are not directly informative about who infected whom - a phylogenetic tree is not a transmission tree. However, a transmission tree can be inferred from a phylogeny while accounting for within-host genetic diversity by colouring the branches of a phylogeny according to which host those branches were in...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28100596/genomic-epidemiology-of-penicillin-non-susceptible-pneumococci-with-non-vaccine-serotypes-causing-invasive-disease-in-the-usa
#13
Cheryl P Andam, Patrick K Mitchell, Alanna Callendrello, Qiuzhi Chang, Jukka Corander, Chrispin Chaguza, Lesley McGee, Bernard W Beall, William P Hanage
Conjugate vaccination against seven pneumococcal serotypes (PCV7) reduced disease prevalence due to antibiotic resistant strains throughout the 2000s; however, disease caused by resistant non-vaccine type (NVT) strains increased. Some of these emerging strains were derived from vaccine types (VT) that had changed their capsule by recombination. The introduction of vaccine targeting 13 serotypes (PCV13) in 2010 has led to concern that this scenario will repeat itself. We generated high quality draft genomes from 265 isolates of NVT pneumococci not susceptible to penicillin (PNSP) in 2009 and compared them with 581 isolates from 2012-2013, collected by the Active Bacterial Core surveillance (ABCs) of the Centers for Disease Control and Prevention (CDC)...
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28100285/characterization-of-the-complete-mitochondrial-genome-of-setaria-digitata-nematoda-setariidae-from-china
#14
G-H Liu, J-Y Li, X-Q Zhu
Setaria digitata is a filarial parasite that causes fatal cerebrospinal nematodiasis in goats, horses and sheep, resulting in substantial economic losses to livestock farmers. In the present study, the complete mitochondrial (mt) genome of S. digitata from China was determined, characterized and compared with that of S. digitata from Sri Lanka. The identity of the mt genomes was 98.3% between S. digitata from China and Sri Lanka, and the complete mt genome sequence of S. digitata from China was slightly shorter (25 bp) than that from Sri Lanka...
January 19, 2017: Journal of Helminthology
https://www.readbyqxmd.com/read/28099825/transmission-of-extensively-drug-resistant-tuberculosis-in-south-africa
#15
N Sarita Shah, Sara C Auld, James C M Brust, Barun Mathema, Nazir Ismail, Pravi Moodley, Koleka Mlisana, Salim Allana, Angela Campbell, Thuli Mthiyane, Natashia Morris, Primrose Mpangase, Hermina van der Meulen, Shaheed V Omar, Tyler S Brown, Apurva Narechania, Elena Shaskina, Thandi Kapwata, Barry Kreiswirth, Neel R Gandhi
Background Drug-resistant tuberculosis threatens recent gains in the treatment of tuberculosis and human immunodeficiency virus (HIV) infection worldwide. A widespread epidemic of extensively drug-resistant (XDR) tuberculosis is occurring in South Africa, where cases have increased substantially since 2002. The factors driving this rapid increase have not been fully elucidated, but such knowledge is needed to guide public health interventions. Methods We conducted a prospective study involving 404 participants in KwaZulu-Natal Province, South Africa, with a diagnosis of XDR tuberculosis between 2011 and 2014...
19, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28099518/evaluation-of-methods-for-the-concentration-and-extraction-of-viruses-from-sewage-in-the-context-of-metagenomic-sequencing
#16
Mathis Hjort Hjelmsø, Maria Hellmér, Xavier Fernandez-Cassi, Natàlia Timoneda, Oksana Lukjancenko, Michael Seidel, Dennis Elsässer, Frank M Aarestrup, Charlotta Löfström, Sílvia Bofill-Mas, Josep F Abril, Rosina Girones, Anna Charlotte Schultz
Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentration to allow for sensitive virus detection. Additionally, viruses harbor a large diversity of both surface and genome structures, which makes universal viral genomic extraction difficult...
2017: PloS One
https://www.readbyqxmd.com/read/28098174/novel-g9-rotavirus-strains-co-circulate-in-children-and-pigs-taiwan
#17
Fang-Tzy Wu, Krisztián Bányai, Baoming Jiang, Luke Tzu-Chi Liu, Szilvia Marton, Yhu-Chering Huang, Li-Min Huang, Ming-Hui Liao, Chao A Hsiung
Molecular epidemiologic studies collecting information of the spatiotemporal distribution of rotavirus VP7 (G) and VP4 (P) genotypes have shown evidence for the increasing global importance of genotype G9 rotaviruses in humans and pigs. Sequence comparison of the VP7 gene of G9 strains identified different lineages to prevail in the respective host species although some of these lineages appear to be shared among heterologous hosts providing evidence of interspecies transmission events. The majority of these events indicates the pig-to-human spillover, although a reverse route of transmission cannot be excluded either...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28098150/a-survey-of-sub-saharan-gene-flow-into-the-mediterranean-at-risk-loci-for-coronary-artery-disease
#18
Miguel M Álvarez-Álvarez, Daniela Zanetti, Robert Carreras-Torres, Pedro Moral, Georgios Athanasiadis
This study tries to find detectable signals of gene flow of Sub-Saharan origin into the Mediterranean in four genomic regions previously associated with coronary artery disease. A total of 366 single-nucleotide polymorphisms were genotyped in 772 individuals from 10 Mediterranean countries. Population structure analyses were performed, in which a noticeable Sub-Saharan component was found in the studied samples. The overall percentage of this Sub-Saharan component presents differences between the two Mediterranean coasts...
January 18, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28098053/dairy-consumption-is-associated-with-a-lower-incidence-of-the-metabolic-syndrome-in-middle-aged-and-older-korean-adults-the-korean-genome-and-epidemiology-study-koges
#19
Dasom Kim, Jihye Kim
This cohort study examined the association between total and individual dairy products and the risk of developing the metabolic syndrome (MetS) and its components in Korean adults from the Korean Genome and Epidemiology Study. We prospectively analysed 5510 participants aged 40-69 years without the MetS at baseline during a 10-year follow-up period. Dairy consumption was assessed with a semi-quantitative FFQ at baseline and after 4 years. The MetS was defined according to the criteria by the National Cholesterol Education Program Adult Treatment Panel III...
January 18, 2017: British Journal of Nutrition
https://www.readbyqxmd.com/read/28097530/virus-induced-hepatocellular-carcinoma-with-special-emphasis-on-hbv
#20
REVIEW
Ming Wang, Dong Xi, Qin Ning
Hepatocellular carcinoma (HCC) is a common malignant tumor with high lethality, and the hepatitis B virus (HBV) is a chief cause. HBV can accelerate HCC via multiple mechanisms. First, HBV induces immune reactions that lead to repeated hepatic inflammation, fibrosis and a deficient immune microenvironment. Subsequently, HBV can modify host genes near the insertion point through DNA integration to cause host cell genome instability and to generate carcinogenic fusion proteins. Additionally, HBV expresses diverse active proteins, especially HBx and HBs, which have a range of transactivation functions such as regulation of apoptosis, interference with intracellular signaling pathways, and alteration of epigenetics...
January 17, 2017: Hepatology International
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