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https://www.readbyqxmd.com/read/28330108/identification-of-novel-snps-in-differentially-expressed-genes-and-its-association-with-horn-cancer-of-bos-indicus-bullocks-by-next-generation-sequencing
#1
P G Koringa, S J Jakhesara, D N Rank, C G Joshi
The use of polymorphic markers like SNPs promises to provide comprehensive tool for analysing genome and identifying genomic regions that contribute to cancer phenotype. Horn cancer is the most common cancer among Bos indicus animals. Increased expression of some genes due to polymorphisms increases risk of HC incidence. We successfully amplified 91 SNPs located in 69 genes in 52 samples, each of HC and HN. Equimolar concentration of amplicons from 69 PCR products of each sample was pooled and subjected to sequencing using Ion Torrent PGM...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329402/novel-orthopoxvirus-infection-in-an-alaska-resident
#2
Yuri P Springer, Christopher H Hsu, Zachary R Werle, Link E Olson, Michael P Cooper, Louisa J Castrodale, Nisha Fowler, Andrea M McCollum, Cynthia S Goldsmith, Ginny L Emerson, Kimberly Wilkins, Jeffrey B Doty, Jillybeth Burgado, JinXin Gao, Nishi Patel, Matthew R Mauldin, Mary G Reynolds, Panayampalli S Satheshkumar, Whitni Davidson, Yu Li, Joseph B McLaughlin
Background.: Human infection by orthopoxviruses is being reported with increasing frequency, attributed in part to the cessation of smallpox vaccination and concomitant waning of population-level immunity. In July 2015, a female resident of interior Alaska, presented to an urgent care clinic with a dermal lesion consistent with poxvirus infection. Laboratory testing of a virus isolated from the lesion confirmed infection by an Orthopoxvirus. Methods.: The virus isolate was characterized by using electron microscopy and nucleic acid sequencing...
March 15, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28327945/enhancing-knowledge-discovery-from-cancer-genomics-data-with-galaxy
#3
Marco A Albuquerque, Bruno M Grande, Elie J Ritch, Prasath Pararajalingam, Selin Jessa, Martin Krzywinski, Jasleen K Grewal, Sohrab P Shah, Paul C Boutros, Ryan D Morin
The field of cancer genomics has demonstrated the power of massively parallel sequencing techniques to inform on the genes and specific alterations that drive tumor onset and progression. Although large comprehensive sequence data sets continue to be made increasingly available, data analysis remains an ongoing challenge, particularly for laboratories lacking dedicated resources and bioinformatics expertise. To address this, we have produced a collection of Galaxy tools that represent many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data...
March 9, 2017: GigaScience
https://www.readbyqxmd.com/read/28327206/lessons-learned-from-additional-research-analyses-of-unsolved-clinical-exome-cases
#4
Mohammad K Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R Lalani, Christian P Schaaf, Michael F Wangler, Carlos A Bacino, Richard Alan Lewis, Lorraine Potocki, Brett H Graham, John W Belmont, Fernando Scaglia, Jordan S Orange, Shalini N Jhangiani, Theodore Chiang, Harsha Doddapaneni, Jianhong Hu, Donna M Muzny, Fan Xia, Arthur L Beaudet, Eric Boerwinkle, Christine M Eng, Sharon E Plon, V Reid Sutton, Richard A Gibbs, Jennifer E Posey, Yaping Yang, James R Lupski
BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease...
March 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28327131/transcriptome-analysis-of-pancreatic-cells-across-distant-species-highlights-novel-important-regulator-genes
#5
Estefania Tarifeño-Saldivia, Arnaud Lavergne, Alice Bernard, Keerthana Padamata, David Bergemann, Marianne L Voz, Isabelle Manfroid, Bernard Peers
BACKGROUND: Defining the transcriptome and the genetic pathways of pancreatic cells is of great interest for elucidating the molecular attributes of pancreas disorders such as diabetes and cancer. As the function of the different pancreatic cell types has been maintained during vertebrate evolution, the comparison of their transcriptomes across distant vertebrate species is a means to pinpoint genes under strong evolutionary constraints due to their crucial function, which have therefore preserved their selective expression in these pancreatic cell types...
March 21, 2017: BMC Biology
https://www.readbyqxmd.com/read/28326560/sex-chromosome-aneuploidy-detection-by-non-invasive-prenatal-testing-helpful-or-hazardous
#6
Rosemary E Reiss, Marie Discenza, Judith Foster, Lori Dobson, Louise Wilkins-Haug
OBJECTIVES: To assess the incidence of sex chromosome aneuploidy (SCA) predicted by non-invasive prenatal testing (NIPT), assess test performance, and compare it with nuchal translucency (NT) screening among patients seen in our prenatal diagnosis center. METHODS: We identified suspected cases of SCA by reviewing results from all NIPT samples sent from our center to commercial laboratories offering analysis by cell-free DNA between December 1, 2012 to July 31, 2015...
March 21, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28324847/species-identification-in-forensic-samples-using-the-spindel-approach-a-ghep-isfg-inter-laboratory-collaborative-exercise
#7
Cíntia Alves, Rui Pereira, Lourdes Prieto, Mercedes Aler, Cesar R L Amaral, Cristina Arévalo, Gabriela Berardi, Florencia Di Rocco, Mariela Caputo, Cristian Hernandez Carmona, Laura Catelli, Heloísa Afonso Costa, Pavla Coufalova, Sandra Furfuro, Óscar García, Anibal Gaviria, Ana Goios, Juan José Builes Gómez, Alexis Hernández, Eva Del Carmen Betancor Hernández, Luís Miranda, David Parra, Susana Pedrosa, Maria João Anjos Porto, Maria de Lurdes Rebelo, Matteo Spirito, María Del Carmen Villalobos Torres, António Amorim, Filipe Pereira
DNA is a powerful tool available for forensic investigations requiring identification of species. However, it is necessary to develop and validate methods able to produce results in degraded and or low quality DNA samples with the high standards obligatory in forensic research. Here, we describe a voluntary collaborative exercise to test the recently developed Species Identification by Insertions/Deletions (SPInDel) method. The SPInDel kit allows the identification of species by the generation of numeric profiles combining the lengths of six mitochondrial ribosomal RNA (rRNA) gene regions amplified in a single reaction followed by capillary electrophoresis...
March 7, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28324158/the-influence-of-sex-and-diet-on-the-characteristics-of-hibernation-in-syrian-hamsters
#8
Marie Trefna, Maaike Goris, Cynthia M C Thissen, Vera A Reitsema, Jojanneke J Bruintjes, Edwin L de Vrij, Hjalmar R Bouma, Ate S Boerema, Robert H Henning
Research on deep hibernators almost exclusively uses species captured from the wild or from local breeding. An exception is Syrian hamster (Mesocricetus auratus), the only standard laboratory animal showing deep hibernation. In deep hibernators, several factors influence hibernation quality, including body mass, sex and diet. We examined hibernation quality in commercially obtained Syrian hamsters in relation to body mass, sex and a diet enriched in polyunsaturated fatty acids. Animals (M/F:30/30, 12 weeks of age) were obtained from Harlan (IN, USA) and individually housed at 21 °C and L:D 14:10 until 20 weeks of age, followed by L:D 8:16 until 27 weeks...
March 21, 2017: Journal of Comparative Physiology. B, Biochemical, Systemic, and Environmental Physiology
https://www.readbyqxmd.com/read/28323278/acceptable-symbiont-cell-size-differs-among-cnidarian-species-and-may-limit-symbiont-diversity
#9
Elise Biquand, Nami Okubo, Yusuke Aihara, Vivien Rolland, David C Hayward, Masayuki Hatta, Jun Minagawa, Tadashi Maruyama, Shunichi Takahashi
Reef-building corals form symbiotic relationships with dinoflagellates of the genus Symbiodinium. Symbiodinium are genetically and physiologically diverse, and corals may be able to adapt to different environments by altering their dominant Symbiodinium phylotype. Notably, each coral species associates only with specific Symbiodinium phylotypes, and consequently the diversity of symbionts available to the host is limited by the species specificity. Currently, it is widely presumed that species specificity is determined by the combination of cell-surface molecules on the host and symbiont...
March 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28322587/development-and-validation-of-targeted-next-generation-sequencing-panels-for-detection-of-germline-variants-in-inherited-diseases
#10
Avni Santani, Jill Murrell, Birgit Funke, Zhenming Yu, Madhuri Hegde, Rong Mao, Andrea Ferreira-Gonzalez, Karl V Voelkerding, Karen E Weck
CONTEXT: - The number of targeted next-generation sequencing (NGS) panels for genetic diseases offered by clinical laboratories is rapidly increasing. Before an NGS-based test is implemented in a clinical laboratory, appropriate validation studies are needed to determine the performance characteristics of the test. OBJECTIVE: - To provide examples of assay design and validation of targeted NGS gene panels for the detection of germline variants associated with inherited disorders...
March 21, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/28321066/gilbert-syndrome-with-concomitant-hereditary-spherocytosis-presenting-with-moderate-unconjugated-hyperbilirubinemia
#11
Mitsuhiko Aiso, Minami Yagi, Atsushi Tanaka, Kotaro Miura, Ryo Miura, Toshihiko Arizumi, Yoriyuki Takamori, Sayuri Nakahara, Yoshihiro Maruo, Hajime Takikawa
We experienced a case of a 19-year-old man with Gilbert syndrome with concomitant hereditary spherocytosis. The patient presented with moderate unconjugated hyperbilirubinemia, and inherited etiology was strongly suspected. The diagnosis of Gilbert syndrome was confirmed by the genetic analysis of the UGT1A1 gene, demonstrating UGT1A1*28 and compound heterozygote UGT1A1*6. In addition, since the laboratory findings and imaging studies revealed lysemia as well as gallstone and splenomegaly, a diagnosis of hereditary spherocytosis was made as a comorbidity...
2017: Internal Medicine
https://www.readbyqxmd.com/read/28320949/discovery-of-scmr-as-a-global-regulator-of-secondary-metabolism-and-virulence-in-burkholderia-thailandensis-e264
#12
Dainan Mao, Leah B Bushin, Kyuho Moon, Yihan Wu, Mohammad R Seyedsayamdost
Bacteria produce a diverse array of secondary metabolites that have been invaluable in the clinic and in research. These metabolites are synthesized by dedicated biosynthetic gene clusters (BGCs), which assemble architecturally complex molecules from simple building blocks. The majority of BGCs in a given bacterium are not expressed under normal laboratory growth conditions, and our understanding of how they are silenced is in its infancy. Here, we have addressed this question in the Gram-negative model bacterium Burkholderia thailandensis E264 using genetic, transcriptomic, metabolomic, and chemical approaches...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28319856/systems-biology-solutions-for-biochemical-production-challenges
#13
REVIEW
Anne Sofie Lærke Hansen, Rebecca M Lennen, Nikolaus Sonnenschein, Markus J Herrgård
There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions...
March 16, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28319562/translating-biomarkers-from-research-to-clinical-use-in-pediatric-neurocritical-care-focus-on-traumatic-brain-injury-and-cardiac-arrest
#14
Andrew J Prout, Michael S Wolf, Ericka L Fink
PURPOSE OF REVIEW: Traumatic brain injury (TBI) and cardiac arrest are important causes of morbidity and mortality in children. Improved diagnosis and outcome prognostication using validated biomarkers could allow clinicians to better tailor therapies for optimal efficacy. RECENT FINDINGS: Contemporary investigation has yielded plentiful biomarker candidates of central nervous system (CNS) injury, including macromolecules, genetic, inflammatory, oxidative, and metabolic biomarkers...
March 17, 2017: Current Opinion in Pediatrics
https://www.readbyqxmd.com/read/28317805/prevalence-and-genetic-determinant-of-drug-resistant-tuberculosis-among-patients-completing-intensive-phase-of-treatment-in-a-tertiary-referral-center-in-nigeria
#15
Aminu Bashir Mohammad, Garba Iliyasu, Abdulrazaq Garba Habib
BACKGROUND: Drug-resistant tuberculosis (DR-TB) continues to be a challenge in developing countries with poor resources. Despite the high prevalence of primary DR-TB, its routine screening prior to the treatment is not performed in public hospitals in Nigeria. Data regarding drug resistance and its genetic determinant among follow-up patients with TB are lacking in Nigeria. Hence, the aim of this study was to determine the prevalence and genetic determinant of drug resistance among the follow-up patients with TB in a tertiary hospital in Nigeria...
January 2017: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28316114/a-single-haplotype-hyposensitive-to-light-and-requiring-strong-vernalization-dominates-arabidopsis-thaliana-populations-in-patagonia-argentina
#16
Luciana Kasulin, Beth Rowan, Rolando J C León, Verena J Schuenemann, Detlef Weigel, Javier F Botto
The growing collection of sequenced or genotyped Arabidopsis thaliana accessions includes mostly individuals from the native Eurasian and N. African range and introduced North American populations. Here, we describe the genetic and phenotypic diversity, along with habitats and life history, of A. thaliana plants collected at the southernmost end of its worldwide distribution. Seed samples were harvested from plants growing in four sites within a ~3500-km(2) -area in Patagonia, Argentina, and represent the first germplasm to be collected in South America for this species...
March 17, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28316093/morphology-heterogeneity-within-a-campylobacter-jejuni-helical-population-the-use-of-calcofluor-white-to-generate-rod-shaped-c-jejuni-81-176-clones-and-the-genetic-determinants-responsible-for-differences-in-morphology-within-11168-strains
#17
Emilisa Frirdich, Jacob Biboy, Steven Huynh, Craig T Parker, Waldemar Vollmer, Erin C Gaynor
Campylobacter jejuni helical shape is important for colonization and host interactions with straight mutants having altered biological properties. Passage on calcofluor white (CFW) resulted in C. jejuni 81-176 isolates with morphology changes: either a straight morphology from frameshift mutations and single nucleotide polymorphisms in peptidoglycan hydrolase genes pgp1 or pgp2 or a reduction in curvature due a frameshift mutation in cjj81176_1105, a putative peptidoglycan endopeptidase. Shape defects were restored by complementation...
March 18, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28315825/effects-of-florida-red-tides-on-histone-variant-expression-and-dna-methylation-in-the-eastern-oyster-crassostrea-virginica
#18
Rodrigo Gonzalez-Romero, Victoria Suarez-Ulloa, Javier Rodriguez-Casariego, Daniel Garcia-Souto, Gabriel Diaz, Abraham Smith, Juan Jose Pasantes, Gary Rand, Jose M Eirin-Lopez
Massive algal proliferations known as Harmful Algal Blooms (HABs) represent one of the most important threats to coastal areas. Among them, the so-called Florida Red Tides (FRTs, caused by blooms of the dinoflagellate Karenia brevis and associated brevetoxins) are particularly detrimental in the southeastern U.S., causing high mortality rates and annual losses in excess of $40 million. The ability of marine organisms to cope with environmental stressors (including those produced during HABs) is influenced by genetic and epigenetic mechanisms, the latter resulting in phenotypic changes caused by heritable modifications in gene expression, without involving changes in the genetic (DNA) sequence...
March 7, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28315651/what-goes-around-can-come-around-an-unexpected-deleterious-effect-of-using-mouse-running-wheels-for-environmental-enrichment
#19
Renee Y M Leduc, Gail Rauw, Glen B Baker, Heather E McDermid
Environmental enrichment items such as running wheels can promote the wellbeing of laboratory mice. Growing evidence suggests that wheel running simulates exercise effects in many mouse models of human conditions, but this activity also might change other aspects of mouse behavior. In this case study, we show that the presence of running wheels leads to pronounced and permanent circling behavior with route-tracing in a proportion of the male mice of a genetically distinct cohort. The genetic background of this cohort includes a mutation in Arhgap19, but genetic crosses showed that an unknown second-site mutation likely caused the induced circling behavior...
March 1, 2017: Journal of the American Association for Laboratory Animal Science: JAALAS
https://www.readbyqxmd.com/read/28306355/alpha-1-antitrypsin-deficiency-disease-management-and-learning-from-studies
#20
Timm Greulich
Alpha-1-antitrypsin deficiency (AATD) is one of the most frequent genetic causes of liver and lung diseases. Despite its known association with chronic obstructive pulmonary disease (COPD), AATD is largely unrecognised and underdiagnosed. Cases of AATD exist within every COPD or spirometry population but must be actively investigated. AATD is a laboratory diagnosis that must be confirmed by a blood test. A number of clinical 'clues' can raise suspicion of AATD, potentially facilitating earlier diagnosis and initiation of appropriate treatment...
March 15, 2017: COPD
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