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https://www.readbyqxmd.com/read/28817866/genomic-medicine-in-primary-care
#1
Catherine Hajek
Genomic medicine is a powerful tool with great potential to improve outcomes in the primary care setting. From a broad perspective, genomic medicine can be applied to rare disease, common disease and pharmacogenetics. There are applications in which it can be used to better identify rare disease, improve screening for common disease, reduce adverse drug effects and help to identify the right medication more quickly. This article provides specific examples of clinical applications for genomic medicine in the realm of cardiovascular disease to provide a better understanding of its potential use in primary care...
2017: South Dakota Medicine: the Journal of the South Dakota State Medical Association
https://www.readbyqxmd.com/read/28817824/parametric-linkage-analysis-identifies-five-novel-genome-wide-significant-loci-for-familial-lung-cancer
#2
Anthony M Musolf, Claire L Simpson, Mariza de Andrade, Diptasri Mandal, Colette Gaba, Ping Yang, Yafang Li, Ming You, Elena Y Kupert, Marshall W Anderson, Ann G Schwartz, Susan M Pinney, Christopher I Amos, Joan E Bailey-Wilson
OBJECTIVE: One of four American cancer patients dies of lung cancer. Environmental factors such as tobacco smoking are known to affect lung cancer risk. However, there is a genetic factor to lung cancer risk as well. Here, we perform parametric linkage analysis on family-based genotype data in an effort to find genetic loci linked to the disease. METHODS: 197 individuals from families with a high-risk history of lung cancer were recruited and genotyped using an Illumina array...
August 18, 2017: Human Heredity
https://www.readbyqxmd.com/read/28817787/evaluation-of-the-electron-transfer-flavoprotein-etf-as-an-antibacterial-target-in-burkholderia-cenocepacia
#3
Maria S Stietz, Christina Lopez, Osasumwen Osifo, Marcelo Tolmasky, Silvia T Cardona
There are hundreds of essential genes in multidrug resistant bacterial genomes, but only a few of their products are exploited as antibacterial targets. An example is the electron flavoprotein (ETF) which is required for growth and viability in <i>Burkholderia cenocepacia</i>. Here, we evaluated ETF as an antibiotic target for <i>Burkholderia cepacia</i> complex (Bcc). Depletion of the bacterial ETF during infection of <i>Caenorhabditis elegans</i> significantly extended survival of the nematodes, proving that ETF is essential for survival of <i>B...
August 17, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28817730/new-approach-to-generating-insights-for-aging-research-based-on-literature-mining-and-knowledge-integration
#4
Yeondae Kwon, Yukikazu Natori, Masaru Tanokura
The proportion of the elderly population in most countries worldwide is increasing dramatically. Therefore, social interest in the fields of health, longevity, and anti-aging has been increasing as well. However, the basic research results obtained from a reductionist approach in biology and a bioinformatic approach in genome science have limited usefulness for generating insights on future health, longevity, and anti-aging-related research on a case by case basis. We propose a new approach that uses our literature mining technique and bioinformatics, which lead to a better perspective on research trends by providing an expanded knowledge base to work from...
2017: PloS One
https://www.readbyqxmd.com/read/28817720/targeting-of-cdk9-with-indirubin-3-monoxime-safely-and-durably-reduces-hiv-viremia-in-chronically-infected-humanized-mice
#5
Sandra Medina-Moreno, Thomas C Dowling, Juan C Zapata, Nhut M Le, Edward Sausville, Joseph Bryant, Robert R Redfield, Alonso Heredia
Successful propagation of HIV in the human host requires entry into a permissive cell, reverse transcription of viral RNA, integration into the human genome, transcription of the integrated provirus, and assembly/release of new virus particles. Currently, there are antiretrovirals against each of these viral steps, except for provirus transcription. An inhibitor of HIV transcription could both increase potency of treatment and suppress drug-resistant strains. Cellular cyclin-dependent kinase 9 (CDK9) serves as a cofactor for the HIV Tat protein and is required for effective transcription of the provirus...
2017: PloS One
https://www.readbyqxmd.com/read/28817702/global-gene-expression-analysis-of-the-response-of-physic-nut-jatropha-curcas-l-to-medium-and-long-term-nitrogen-deficiency
#6
Qi Kuang, Sheng Zhang, Pingzhi Wu, Yaping Chen, Meiru Li, Huawu Jiang, Guojiang Wu
Jatropha curcas L. is an important biofuel plant with excellent tolerance of barren environments. However, studies on the regulatory mechanisms that operate in this plant in response to nitrogen (N) shortage are scarce. In this study, genome-wide transcriptional profiles of the roots and leaves of 8-week old physic nut seedlings were analyzed after 2 and 16 days of N starvation. Enrichment results showed that genes associated with N metabolism, processing and regulation of RNA, and transport predominated among those showing alterations in expression...
2017: PloS One
https://www.readbyqxmd.com/read/28817689/characterization-and-formulation-into-solid-dosage-forms-of-a-novel-bacteriophage-lytic-against-klebsiella-oxytoca
#7
Teagan L Brown, Steve Petrovski, Dannielle Hoyle, Hiu Tat Chan, Peter Lock, Joseph Tucci
AIM: To isolate and characterize bacteriophage lytic for the opportunistic pathogen Klebsiella oxytoca and their formulation into a range of solid dosage forms for in-vitro testing. METHODS AND RESULTS: We report the isolation, genomic and functional characterization of a novel bacteriophage lytic for Klebsiella oxytoca, which does not infect the closely related Klebsiella pneumoniae. This bacteriophage was formulated into suppositories and troches and shown to be released and lyse underlying Klebsiella oxytoca bacteria in an in-vitro model...
2017: PloS One
https://www.readbyqxmd.com/read/28817688/the-extremely-divergent-maternally-and-paternally-transmitted-mitochondrial-genomes-are-co-expressed-in-somatic-tissues-of-two-freshwater-mussel-species-with-doubly-uniparental-inheritance-of-mtdna
#8
Sophie Breton, Karim Bouvet, Gabrielle Auclair, Stéphanie Ghazal, Bernard E Sietman, Nathan Johnson, Stefano Bettinazzi, Donald T Stewart, Davide Guerra
Freshwater mussel species with doubly uniparental inheritance (DUI) of mtDNA are unique because they are naturally heteroplasmic for two extremely divergent mtDNAs with ~50% amino acid differences for protein-coding genes. The paternally-transmitted mtDNA (or M mtDNA) clearly functions in sperm in these species, but it is still unknown whether it is transcribed when present in male or female soma. In the present study, we used PCR and RT-PCR to detect the presence and expression of the M mtDNA in male and female somatic and gonadal tissues of the freshwater mussel species Venustaconcha ellipsiformis and Utterbackia peninsularis (Unionidae)...
2017: PloS One
https://www.readbyqxmd.com/read/28817683/genome-wide-association-analysis-of-cold-tolerance-at-germination-in-temperate-japonica-rice-oryza-sativa-l-varieties
#9
Ester Sales, Juan Viruel, Concha Domingo, Luis Marqués
A pool of 200 traditional, landraces and modern elite and old cultivars of rice, mainly japonica varieties adapted to temperate regions, have been used to perform a genome wide association study to detect chromosome regions associated to low temperature germination (LTG) regulation using a panel of 1672 SNP markers. Phenotyping was performed by determining growth rates when seeds were germinated at 25° and 15°C in order to separate the germination vigorousness from cold tolerance effects. As expected, the ability to produce viable seedlings varied widely among rice cultivars and also depended greatly on temperature...
2017: PloS One
https://www.readbyqxmd.com/read/28817678/family-based-exome-wide-association-study-of-childhood-acute-lymphoblastic-leukemia-among-hispanics-confirms-role-of-arid5b-in-susceptibility
#10
Natalie P Archer, Virginia Perez-Andreu, Ulrik Stoltze, Michael E Scheurer, Anna V Wilkinson, Ting-Nien Lin, Maoxiang Qian, Charnise Goodings, Michael D Swartz, Nalini Ranjit, Karen R Rabin, Erin C Peckham-Gregory, Sharon E Plon, Pedro A de Alarcon, Ryan C Zabriskie, Federico Antillon-Klussmann, Cesar R Najera, Jun J Yang, Philip J Lupo
We conducted an exome-wide association study of childhood acute lymphoblastic leukemia (ALL) among Hispanics to confirm and identify novel variants associated with disease risk in this population. We used a case-parent trio study design; unlike more commonly used case-control studies, this study design is ideal for avoiding issues with population stratification bias among this at-risk ethnic group. Using 710 individuals from 323 Guatemalan and US Hispanic families, two inherited SNPs in ARID5B reached genome-wide level significance: rs10821936, RR = 2...
2017: PloS One
https://www.readbyqxmd.com/read/28817636/uncovering-robust-patterns-of-microrna-co-expression-across-cancers-using-bayesian-relevance-networks
#11
Parameswaran Ramachandran, Daniel Sánchez-Taltavull, Theodore J Perkins
Co-expression networks have long been used as a tool for investigating the molecular circuitry governing biological systems. However, most algorithms for constructing co-expression networks were developed in the microarray era, before high-throughput sequencing-with its unique statistical properties-became the norm for expression measurement. Here we develop Bayesian Relevance Networks, an algorithm that uses Bayesian reasoning about expression levels to account for the differing levels of uncertainty in expression measurements between highly- and lowly-expressed entities, and between samples with different sequencing depths...
2017: PloS One
https://www.readbyqxmd.com/read/28817620/gtsp1-expression-in-non-smoker-and-non-drinker-patients-with-squamous-cell-carcinoma-of-the-head-and-neck
#12
Pamela de Oliveira Soares, Patrícia Maluf Cury, Rossana Verónica Mendoza López, Cláudio Roberto Cernea, Erika Erina Fukuyama, David Livingstone Alves Figueiredo, Francisco Gorgonio da Nobrega, Otavio Alberto Curioni, Fabio Daumas Nunes, Raquel Ajub Moyses, Maria Lúcia Bueno Garcia
INTRODUCTION: The main risk factors for head and neck squamous cell carcinoma (HNSCC) are tobacco and alcohol consumption and human papillomavirus (HPV) infection. However, in a subset of patients, no risk factors can be identified. Glutathione S-transferase π (GTSP1) is a carcinogen-detoxifying enzyme that is activated by exposure to carcinogens, and it is associated with a reduction in response to toxic therapies. We studied the expression of GTSP1 in tumor and non-tumor tissue samples from patients with and without these risks to identify whether GTSP1 expression differs according to exposure to carcinogens...
2017: PloS One
https://www.readbyqxmd.com/read/28817413/actn3-r577x-polymorphism-is-associated-with-the-incidence-and-severity-of-injuries-in-professional-football-players
#13
Massidda Myosotis, Voisin Sarah, Culigioni Claudia, Piras Francesco, Cugia Paolo, Yan Xu, Eynon Nir, Carla M Calò
OBJECTIVE: The ACTN3 R577X gene variant results in the absence of the α-actinin-3 protein in ∼18% of humans worldwide and has been associated with athletic performance and increased susceptibility to eccentric muscle damage. The aim of this study was to investigate the association between ACTN3 R577X variant and indirect muscle disorders/injuries in professional football players. DESIGN: A case-control, genotype-phenotype association study. INTERVENTION: Two hundred fifty-seven male professional Italian football players (from Serie A, Primavera, Allievi, and Giovanissimi; age = 21...
August 16, 2017: Clinical Journal of Sport Medicine: Official Journal of the Canadian Academy of Sport Medicine
https://www.readbyqxmd.com/read/28817303/chrna7-deletions-are-enriched-in-risperidone-treated-children-and-adolescents
#14
Madelyn A Gillentine, Janson J White, Christopher M Grochowski, James R Lupski, Christian P Schaaf, Chadi A Calarge
OBJECTIVE: Aggression is among the most common indications for referral to child and adolescent mental health services and is often challenging to treat. Understanding the biological underpinnings of aggression could help optimize treatment efficacy. Neuronal nicotinic acetylcholine receptors (nAChRs), specifically the α7 nAChR, encoded by the gene CHRNA7, have been implicated in aggressive behaviors in animal models as well as humans. Copy number variants (CNVs) of CHRNA7 are found in individuals with neuropsychiatric disorders, often with comorbid aggression...
August 17, 2017: Journal of Child and Adolescent Psychopharmacology
https://www.readbyqxmd.com/read/28817247/assessing-predictions-of-fitness-effects-of-missense-mutations-in-sumo-conjugating-enzyme-ube2i
#15
Jing Zhang, Lisa N Kinch, Qian Cong, Jochen Weile, Song Sun, Atina G Cote, Frederick P Roth, Nick V Grishin
The exponential growth of genomic variants uncovered by next-generation sequencing necessitates efficient and accurate computational analyses to predict their functional effects. A number of computational methods have been developed for the task, but few unbiased comparisons of their performance are available. To fill the gap, The Critical Assessment of Genome Interpretation (CAGI) comprehensively assesses phenotypic predictions on newly collected experimental datasets. Here, we present the results of the SUMO conjugase challenge where participants were predicting functional effects of missense mutations in human SUMO-conjugating enzyme UBE2I...
September 2017: Human Mutation
https://www.readbyqxmd.com/read/28817245/reports-from-cagi-the-critical-assessment-of-genome-interpretation
#16
Roger A Hoskins, Susanna Repo, Daniel Barsky, Gaia Andreoletti, John Moult, Steven E Brenner
No abstract text is available yet for this article.
September 2017: Human Mutation
https://www.readbyqxmd.com/read/28817238/stakeholders-in-psychiatry-and-their-attitudes-toward-receiving-pertinent-and-incident-findings-in-genomic-research
#17
Anna Sundby, Merete W Boolsen, Kristoffer S Burgdorf, Henrik Ullum, Thomas F Hansen, Anna Middleton, Ole Mors
Increasingly more psychiatric research studies use whole genome sequencing or whole exome sequencing. Consequently, researchers face difficult questions, such as which genomic findings to return to research participants and how. This study aims to gain more knowledge on the attitudes among potential research participants and health professionals toward receiving pertinent and incidental findings. A cross-sectional online survey was developed to investigate the attitudes among research participants toward receiving genomic findings...
August 17, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28817224/a-novel-post-hoc-method-for-detecting-index-switching-finds-no-evidence-for-increased-switching-on-the-illumina-hiseq-x
#18
Gregory L Owens, Marco Todesco, Emily B M Drummond, Sam Yeaman, Loren H Rieseberg
High throughput sequencing using the Illumina HiSeq platform is a pervasive and critical molecular ecology resource, and has provided the data underlying many recent advances. A recent study has suggested that 'index switching', where reads are misattributed to the wrong sample, may be higher in new versions of the HiSeq platform. This has the potential to invalidate both published and in-progress work across the field. Here, we test for evidence of index switching in an exemplar whole genome shotgun dataset sequenced on both the Illumina HiSeq 2500, which should not have the problem, and the Illumina HiSeq X, which may...
August 17, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28817186/a-prognostic-11genes-expression-model-for-ovarian-cancer
#19
Chuan-Di Men, Qiong-Na Liu, Qing Ren
The symptoms of ovarian cancer at early stages are usually absent which makes the diagnosis in its early stages exceedingly difficult. Previous research has proven that ovarian cancer is a genetic disease, which depends on the alteration of multi-cancer related genes and anti-cancer genes, multi-stages and multi-pathways, involving a variety of oncogene activation and anti-oncogene inactivation. For a better understanding of the prognostic classification of ovarian cancer, gene expression profiles were used to analyse the prognostic factors of ovarian cancer, and the prognostic model was used to classify the ovarian cancer samples...
August 17, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28817151/comprehensive-analysis-of-long-noncoding-rna-mrna-co-expression-patterns-in-thyroid-cancer
#20
Yaying Du, Wenfei Xia, Jinjun Zhang, Dongyi Wan, Zhifang Yang, Xingrui Li
Novel molecular-targeted treatments show great prospects for radioiodine-refractory and surgically inoperable thyroid carcinomas. While aberrations in protein-coding genes are a focus in molecular thyroid cancer medicine, the impact of oncogenes on the expression of long noncoding RNAs (lncRNAs) has been largely uncharacterized. We aimed to identify the expression patterns of lncRNAs and mRNAs in high-throughput molecular profiles of 18 papillary thyroid cancer (PTC) patients. We identified 452 mRNAs and 240 unannotated lncRNAs that were differentially expressed in PTC...
August 17, 2017: Molecular BioSystems
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