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https://www.readbyqxmd.com/read/28926727/early-pregnancy-intrauterine-fetal-exposure-to-maternal-smoking-and-impact-on-fetal-telomere-length
#1
Hooman Mirzakhani, Immaculata De Vivo, J Steven Leeder, Roger Gaedigk, Carrie A Vyhlidal, Scott T Weiss, Kelan Tantisira
BACKGROUND: Reduced telomere length, or its accelerated attrition, has been implicated in aging, mortality, and several human diseases, including respiratory diseases. Age dependent manifestation of telomere-mediated disease during life span indicates the role of developmental stage in these diseases and highlights the importance of fetal developmental process in utero and at earlier life stages. Environmental determinants during developmental and later stages of life could affect telomere length...
September 14, 2017: European Journal of Obstetrics, Gynecology, and Reproductive Biology
https://www.readbyqxmd.com/read/28925528/relatedness-of-wildlife-and-livestock-avian-isolates-of-the-nosocomial-pathogen-acinetobacter-baumannii-to-lineages-spread-in-hospitals-worldwide
#2
Gottfried Wilharm, Evelyn Skiebe, Paul G Higgins, Marie T Poppel, Ulrike Blaschke, Sarah Leser, Christine Heider, Magdalena Heindorf, Paul Brauner, Udo Jäckel, Karin Böhland, Christiane Cuny, Andżelina Łopińska, Piotr Kaminski, Mariusz Kasprzak, Marcin Bochenski, Olaf Ciebiera, Marcin Tobółka, Katarzyna M Żołnierowicz, Joachim Siekiera, Harald Seifert, Stéphanie Gagné, Suzana P Salcedo, Michael Kaatz, Franziska Layer, Jennifer K Bender, Stephan Fuchs, Torsten Semmler, Yvonne Pfeifer, Leszek Jerzak
The natural habitats and potential reservoirs of the nosocomial pathogen Acinetobacter baumannii are poorly defined. Here, we put forth and tested the hypothesis of avian reservoirs of A. baumannii. We screened tracheal and rectal swab samples from livestock (chicken, geese) and wild birds (white stork nestlings) and isolated A. baumannii from 3% of sampled chicken (n=220), 8% of geese (n=40) and 25% of white stork nestlings (n=661). Virulence of selected avian A. baumannii isolates was comparable to that of clinical isolates in the Galleria mellonella infection model...
September 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28924718/comprehensive-annotation-and-evolutionary-insights-into-the-canine-canis-lupus-familiaris-antigen-receptor-loci
#3
Jolyon Martin, Hannes Ponstingl, Marie-Paule Lefranc, Joy Archer, David Sargan, Allan Bradley
Dogs are an excellent model for human disease. For example, the treatment of canine lymphoma has been predictive of the human response to that treatment. However, an incomplete picture of canine (Canis lupus familiaris) immunoglobulin (IG) and T cell receptor (TR)-or antigen receptor (AR)-gene loci has restricted their utility. This work advances the annotation of the canine AR loci and looks into breed-specific features of the loci. Bioinformatic analysis of unbiased RNA sequence data was used to complete the annotation of the canine AR genes...
September 19, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28924032/staphylococcus-aureus-strain-newman-d2c-contains-mutations-in-major-regulatory-pathways-that-cripple-its-pathogenesis
#4
William E Sause, Richard Copin, Aidan O'malley, Rita Chan, Brian J Morrow, Peter T Buckley, Jeffrey Fernandez, A Simon Lynch, Bo Shopsin, Victor J Torres
Staphylococcus aureus is a major human pathogen that imposes a great burden on the healthcare system. In the development of anti-staphylococcal modalities intended to reduce the burden of staphylococcal disease, it is imperative to select appropriate models of S. aureus strains when assessing the efficacy of novel agents. Here, using whole genome sequencing, we reveal that the commonly used strain Newman D2C from the American Type Culture Collection (ATCC) contains mutations that render the strain essentially avirulent...
September 18, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28923495/crispr-cas9-engineering-of-adult-mouse-liver-demonstrates-that-the-dnajb1-prkaca-gene-fusion-is-sufficient-to-induce-tumors-resembling-fibrolamellar-hepatocellular-carcinoma
#5
Lars H Engelholm, Anjum Riaz, Denise Serra, Frederik Dagnæs-Hansen, Jens V Johansen, Eric Santoni-Rugiu, Steen H Hansen, Francesco Niola, Morten Frödin
BACKGROUND & AIMS: Fibrolamellar hepatocellular carcinoma (FL-HCC) is a primary liver cancer that predominantly affects young adults with no underlying liver disease. A somatic, 400 Kb deletion on chromosome 19 that fuses part of the DnaJ heat shock protein family (Hsp40) member B1 gene (DNAJB1) to the protein kinase cAMP-activated catalytic subunit alpha gene (PRKACA) has been repeatedly identified in patients with FL-HCC. However, the DNAJB1-PRKACA gene fusion has not been shown to induce liver tumorigenesis...
September 15, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28923009/apophysomyces-variabilis-draft-genome-sequence-and-comparison-of-predictive-virulence-determinants-with-other-medically-important-mucorales
#6
Hariprasath Prakash, Shivaprakash Mandya Rudramurthy, Prasad S Gandham, Anup Kumar Ghosh, Milner M Kumar, Chandan Badapanda, Arunaloke Chakrabarti
BACKGROUND: Apophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India. Among Apophysomyces species, A. elegans, A. trapeziformis and A. variabilis are commonly incriminated in human infections. The genome sequences of A. elegans and A. trapeziformis are available in public database, but not A. variabilis. We, therefore, performed the whole genome sequence of A. variabilis to explore its genomic structure and possible genes determining the virulence of the organism...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28922838/comparative-genomics-of-a-drug-resistant-pseudomonas-aeruginosa-panel-and-the-challenges-of-antimicrobial-resistance-prediction-from-genomes
#7
J Jeukens, I Kukavica-Ibrulj, J G Emond-Rheault, L Freschi, R C Levesque
Antimicrobial resistance (AMR) is now recognized as a global threat to human health. The accessibility of microbial whole-genome sequencing offers an invaluable opportunity for resistance surveillance via the resistome, i.e. the genes and mutations underlying AMR. Unfortunately, AMR prediction from genomic data remains extremely challenging, especially for species with a large pan-genome. One such organism, for which multidrug-resistant (MDR) isolates are frequently encountered in the clinic, is Pseudomonas aeruginosa...
October 2, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28920571/recurrent-seasonal-outbreak-of-an-emerging-serotype-of-shiga-toxin-producing-escherichia-coli-stec-o55-h7-stx2a-in-the-south-west-of-england-july-2014-to-september-2015
#8
Noëleen McFarland, Nick Bundle, Claire Jenkins, Gauri Godbole, Amy Mikhail, Tim Dallman, Catherine O'Connor, Noel McCarthy, Emer O'Connell, Juli Treacy, Girija Dabke, James Mapstone, Yvette Landy, Janet Moore, Rachel Partridge, Frieda Jorgensen, Caroline Willis, Piers Mook, Chas Rawlings, Richard Acornley, Charlotte Featherstone, Sharleen Gayle, Joanne Edge, Eleanor McNamara, Jeremy Hawker, Sooria Balasegaram
The first documented British outbreak of Shiga toxin-producing Escherichia coli (STEC) O55:H7 began in the county of Dorset, England, in July 2014. Since then, there have been a total of 31 cases of which 13 presented with haemolytic uraemic syndrome (HUS). The outbreak strain had Shiga toxin (Stx) subtype 2a associated with an elevated risk of HUS. This strain had not previously been isolated from humans or animals in England. The only epidemiological link was living in or having close links to two areas in Dorset...
September 7, 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/28920101/potential-therapeutic-targets-in-nrf2-dependent-protection-against-neonatal-respiratory-distress-disease-predicted-by-cdna-microarray-analysis-and-bioinformatics-tools
#9
Hye-Youn Cho, Xuting Wang, Jianying Li, Douglas A Bell, Steven R Kleeberger
Hyperoxia exposure of newborn rodents has served as a model for bronchopulmonary dysplasia (BPD) phenotypes found in a sub-population of human premature infants. We previously demonstrated that Nrf2 modulates molecular events during saccular-to-alveolar lung maturation and also has a protective role in the pathogenesis of hyperoxia-induced acute lung injury, mortality, arrest of saccular-to-alveolar transition, and lung injury, using Nrf2-deficient and wild-type neonate mice. In this review, we describe how whole-genome transcriptome analyses can identify the means through which Nrf2 transcriptionally modulates organ injury and morphology, cellular growth/proliferation, vasculature development, and immune response during BPD-like pathogenesis...
December 2016: Current Opinion in Toxicology
https://www.readbyqxmd.com/read/28912133/use-of-crispr-modified-human-stem-cell-organoids-to-study-the-origin-of-mutational-signatures-in-cancer
#10
Jarno Drost, Ruben van Boxtel, Francis Blokzijl, Tomohiro Mizutani, Nobuo Sasaki, Valentina Sasselli, Joep de Ligt, Sam Behjati, Judith E Grolleman, Tom van Wezel, Serena Nik-Zainal, Roland P Kuiper, Edwin Cuppen, Hans Clevers
Mutational processes underlie cancer initiation and progression. Signatures of these processes in cancer genomes may explain cancer etiology, and hold diagnostic and prognostic value. Here, we develop a strategy that can be used to explore the origin of cancer-associated mutational signatures. We used CRISPR/Cas9 technology to delete key DNA repair genes in human colon organoids, followed by delayed sub-cloning and whole-genome sequencing. We found that mutation accumulation in organoids deficient in the mismatch repair gene MLH1 is driven by replication errors and accurately models the mutation profiles observed in mismatch repair-deficient colorectal cancers...
September 14, 2017: Science
https://www.readbyqxmd.com/read/28911203/mutations-of-conserved-non-coding-elements-of-pitx2-in-patients-with-ocular-dysgenesis-and-developmental-glaucoma
#11
Meredith E Protas, Eric Weh, Tim Footz, Jay Kasberger, Scott C Baraban, Alex V Levin, L Jay Katz, Robert Ritch, Michael A Walter, Elena V Semina, Douglas B Gould
Mutations in FOXC1 and PITX2 constitute the most common causes of ocular anterior segment dysgenesis (ASD), and confer a high risk for secondary glaucoma. The genetic causes underlying ASD in approximately half of patients remain unknown, despite many of them being screened by whole exome sequencing. Here, we performed whole genome sequencing on DNA from two affected individuals from a family with dominantly inherited ASD and glaucoma to identify a 748-kb deletion in a gene desert that contains conserved putative PITX2 regulatory elements...
September 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28910637/intrahost-selection-pressures-drive-rapid-dengue-virus-microevolution-in-acute-human-infections
#12
Poornima Parameswaran, Chunling Wang, Surbhi Bharat Trivedi, Meghana Eswarappa, Magelda Montoya, Angel Balmaseda, Eva Harris
Dengue, caused by four dengue virus serotypes (DENV-1 to DENV-4), is a highly prevalent mosquito-borne viral disease in humans. Yet, selection pressures driving DENV microevolution within human hosts (intrahost) remain unknown. We employed a whole-genome segmented amplification approach coupled with deep sequencing to profile DENV-3 intrahost diversity in peripheral blood mononuclear cell (PBMC) and plasma samples from 77 dengue patients. DENV-3 intrahost diversity appears to be driven by immune pressures as well as replicative success in PBMCs and potentially other replication sites...
September 13, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/28910305/aspirin-increases-metabolism-through-germline-signalling-to-extend-the-lifespan-of-caenorhabditis-elegans
#13
Xiao-Bing Huang, Xiao-Hui Mu, Qin-Li Wan, Xiao-Ming He, Gui-Sheng Wu, Huai-Rong Luo
Aspirin is a prototypic cyclooxygenase inhibitor with a variety of beneficial effects on human health. It prevents age-related diseases and delays the aging process. Previous research has shown that aspirin might act through a dietary restriction-like mechanism to extend lifespan. To explore the mechanism of action of aspirin on aging, we determined the whole-genome expression profile of Caenorhabditis elegans treated with aspirin. Transcriptome analysis revealed the RNA levels of genes involved in metabolism were primarily increased...
2017: PloS One
https://www.readbyqxmd.com/read/28904649/harnessing-whole-genome-sequencing-in-medical-mycology
#14
REVIEW
Christina A Cuomo
PURPOSE OF REVIEW: Comparative genome sequencing studies of human fungal pathogens enable identification of genes and variants associated with virulence and drug resistance. This review describes current approaches, resources, and advances in applying whole genome sequencing to study clinically important fungal pathogens. RECENT FINDINGS: Genomes for some important fungal pathogens were only recently assembled, revealing gene family expansions in many species and extreme gene loss in one obligate species...
2017: Current Fungal Infection Reports
https://www.readbyqxmd.com/read/28904385/rapid-discovery-of-de-novo-deleterious-mutations-in-cattle-enhances-the-value-of-livestock-as-model-species
#15
E Bourneuf, P Otz, H Pausch, V Jagannathan, P Michot, C Grohs, G Piton, S Ammermüller, M-C Deloche, S Fritz, H Leclerc, C Péchoux, A Boukadiri, C Hozé, R Saintilan, F Créchet, M Mosca, D Segelke, F Guillaume, S Bouet, A Baur, A Vasilescu, L Genestout, A Thomas, A Allais-Bonnet, D Rocha, M-A Colle, C Klopp, D Esquerré, C Wurmser, K Flisikowski, H Schwarzenbacher, J Burgstaller, M Brügmann, E Dietschi, N Rudolph, M Freick, S Barbey, G Fayolle, C Danchin-Burge, L Schibler, B Bed'Hom, B J Hayes, H D Daetwyler, R Fries, D Boichard, D Pin, C Drögemüller, A Capitan
In humans, the clinical and molecular characterization of sporadic syndromes is often hindered by the small number of patients and the difficulty in developing animal models for severe dominant conditions. Here we show that the availability of large data sets of whole-genome sequences, high-density SNP chip genotypes and extensive recording of phenotype offers an unprecedented opportunity to quickly dissect the genetic architecture of severe dominant conditions in livestock. We report on the identification of seven dominant de novo mutations in CHD7, COL1A1, COL2A1, COPA, and MITF and exploit the structure of cattle populations to describe their clinical consequences and map modifier loci...
September 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28903777/modest-heterologous-protection-after-plasmodium-falciparum-sporozoite-immunization-a-double-blind-randomized-controlled-clinical-trial
#16
Jona Walk, Isaie J Reuling, Marije C Behet, Lisette Meerstein-Kessel, Wouter Graumans, Geert-Jan van Gemert, Rianne Siebelink-Stoter, Marga van de Vegte-Bolmer, Thorsten Janssen, Karina Teelen, Johannes H W de Wilt, Quirijn de Mast, André J van der Ven, Ernest Diez Benavente, Susana Campino, Taane G Clark, Martijn A Huynen, Cornelus C Hermsen, Else M Bijker, Anja Scholzen, Robert W Sauerwein
BACKGROUND: A highly efficacious vaccine is needed for malaria control and eradication. Immunization with Plasmodium falciparum NF54 parasites under chemoprophylaxis (chemoprophylaxis and sporozoite (CPS)-immunization) induces the most efficient long-lasting protection against a homologous parasite. However, parasite genetic diversity is a major hurdle for protection against heterologous strains. METHODS: We conducted a double-blind, randomized controlled trial in 39 healthy participants of NF54-CPS immunization by bites of 45 NF54-infected (n = 24 volunteers) or uninfected mosquitoes (placebo; n = 15 volunteers) against a controlled human malaria infection with the homologous NF54 or the genetically distinct NF135...
September 13, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28902847/first-insights-in-the-variability-of-borrelia-recurrentis-genomes
#17
Durdica Marosevic, Gabriele Margos, Reinhard Wallich, Andreas Wieser, Andreas Sing, Volker Fingerle
BACKGROUND: Borrelia recurrentis is the causative agent of louse-borne relapsing fever, endemic to the Horn of Africa. New attention was raised in Europe, with the highest number of cases (n = 45) reported among migrants in 2015 in Germany and sporadically from other European countries. So far only one genome was sequenced, hindering the development of specific molecular diagnostic and typing tools. Here we report on modified culture conditions for B. recurrentis and the intraspecies genome variability of six isolates isolated and cultured in different years in order to explore the possibility to identify new targets for typing and examine the molecular epidemiology of the pathogen...
September 13, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28901446/a-support-vector-machine-classifier-for-the-prediction-of-osteosarcoma-metastasis-with-high-accuracy
#18
Yunfei He, Jun Ma, Xiaojian Ye
In this study, gene expression profiles of osteosarcoma (OS) were analyzed to identify critical genes associated with metastasis. Five gene expression datasets were screened and downloaded from Gene Expression Omnibus (GEO). Following assessment by MetaQC, the dataset GSE9508 was excluded for poor quality. Subsequently, differentially expressed genes (DEGs) between metastatic and non-metastatic OS were identified using meta‑analysis. A protein-protein interaction (PPI) network was constructed with information from Human Protein Reference Database (HPRD) for the DEGs...
September 7, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28900766/diversity-and-distribution-of-cyp-gene-family-in-bactrian-camel
#19
Surong Hasi, Jirimutu Yao, Siriguleng Yu, Yanan Tian
Cytochrome P450 (CYP) enzymes belong to a superfamily of monooxygenases which are phase I enzymes responsible for the first pass metabolism of about 90% of drugs in animals. However, these enzymes are often polymorphic and metabolism of the same drug in different species or different individuals is influenced by genetic and non-genetic factors. Bactrian camels are capable of survival in harsh living environments, being able to consume diets that are often toxic to other mammals and can tolerate extreme water and food deprivation...
September 12, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28900628/gene-expression-profiling-identifies-downregulation-of-the-neurotrophin-mapk-signaling-pathway-in-female-diabetic-peripheral-neuropathy-patients
#20
Lin Luo, Wen-Hua Zhou, Jiang-Jia Cai, Mei Feng, Mi Zhou, Su-Pei Hu, Jin Xu, Lin-Dan Ji
Diabetic peripheral neuropathy (DPN) is a common complication of diabetes mellitus (DM). It is not diagnosed or managed properly in the majority of patients because its pathogenesis remains controversial. In this study, human whole genome microarrays identified 2898 and 4493 differentially expressed genes (DEGs) in DM and DPN patients, respectively. A further KEGG pathway analysis indicated that DPN and DM share four pathways, including apoptosis, B cell receptor signaling pathway, endocytosis, and Toll-like receptor signaling pathway...
2017: Journal of Diabetes Research
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