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Laboratory genetics

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https://www.readbyqxmd.com/read/28427845/development-of-a-micro-neutralization-assay-for-ebolaviruses-using-a-replication-competent-vesicular-stomatitis-hybrid-virus-and-a-quantitative-pcr-readout
#1
Stella S Lee, Kathryn Phy, Keith Peden, Li Sheng-Fowler
Development of vaccines against highly pathogenic viruses that could also be used as agents of bioterrorism is both a public health issue and a national security priority. Methods that can quantify neutralizing antibodies will likely be crucial in demonstrating vaccine effectiveness, as most licensed viral vaccines are effective due to their capacity to elicit neutralizing antibodies. Assays to determine whether antibodies are neutralizing traditionally involve infectious virus, and the assay most commonly used is the plaque-reduction neutralization test (PRNT)...
April 17, 2017: Vaccine
https://www.readbyqxmd.com/read/28426524/beyond-cascade-screening-detection-of-familial-hypercholesterolaemia-at-childhood-immunization-and-other-strategies
#2
Andrew C Martin, Damon A Bell, Tom Brett, Gerald F Watts
PURPOSE OF REVIEW: Familial hypercholesterolaemia is a common genetic disorder that accelerates premature coronary heart disease. Although effective treatments are available, the majority of individuals remain undiagnosed. We review new evidence for improving the detection of familial hypercholesterolaemia. RECENT FINDINGS: Recent studies have demonstrated that universal screening of children for familial hypercholesterolaemia may be highly effective at the time of immunization if combined with reverse cascade testing of adult family members, who have a more immediate risk of a coronary event...
April 19, 2017: Current Opinion in Lipidology
https://www.readbyqxmd.com/read/28423155/the-role-of-genetic-testing-in-patients-with-breast-cancer-a-review
#3
Olivia M Valencia, Selyne E Samuel, Rebecca K Viscusi, Taylor S Riall, Leigh A Neumayer, Hassan Aziz
Importance: In the United States from 2009 to 2013, the incidence of breast cancer was the highest of any cancer and the death rate was second to that of lung cancer. Approximately 5% to 10% of breast cancers are inheritable. Observations: BRCA1 and BRCA2 germline mutations account for up to 30% of inheritable breast cancers and are the most commonly assessed mutations in patients presenting with early-onset breast cancer, triple-negative breast cancer, bilateral breast cancer, and a family history of breast cancer...
April 19, 2017: JAMA Surgery
https://www.readbyqxmd.com/read/28422718/validation-and-optimization-of-the-ion-torrent-s5-xl-sequencer-and-oncomine-workflow-for-brca1-and-brca2-genetic-testing
#4
Saeam Shin, Yoonjung Kim, Seoung Chul Oh, Nae Yu, Seung-Tae Lee, Jong Rak Choi, Kyung-A Lee
In this study, we validated the analytical performance of BRCA1/2 sequencing using Ion Torrent's new bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. Using 43 samples that were previously validated by Illumina's MiSeq platform and/or by Sanger sequencing/multiplex ligation-dependent probe amplification, we amplified the target with the Oncomine™ BRCA Research Assay and sequenced on Ion Torrent S5 XL (Thermo Fisher Scientific, Waltham, MA, USA). We compared two bioinformatics pipelines for optimal processing of S5 XL sequence data: the Torrent Suite with a plug-in Torrent Variant Caller (Thermo Fisher Scientific), and commercial NextGENe software (Softgenetics, State College, PA, USA)...
April 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422281/wnk1-hsn2-founder-mutation-in-patients-with-hereditary-sensory-and-autonomic-neuropathy-a-japanese-cohort-study
#5
Jun-Hui Yuan, Akihiro Hashiguchi, Akiko Yoshimura, Norio Sakai, Masanori P Takahashi, Takehiro Ueda, Akira Taniguchi, Sayaka Okamoto, Nobuo Kanazawa, Yuki Yamamoto, Kazumasa Saigoh, Susumu Kusunoki, Masahiro Ando, Yu Hiramatsu, Yuji Okamoto, Hiroshi Takashima
The clinical and genetic spectrum of hereditary sensory and autonomic neuropathy (HSAN) is still unknown in Japan. We collected a broad cohort of 33 unrelated patients with predominant sensory and/or autonomic dysfunctions, who were referred to our genetic laboratory. A gene panel sequencing targeting 18 HSAN-related genes was performed using a next-generation sequencing system. A recurrent frame shift mutation in the WNK1/HSN2 gene, c.3237_3238insT (p.Asp1080*), was detected in five patients. This mutation was homozygous in four cases and of a compound heterozygous genotype in one case...
April 19, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28421066/unveiling-the-hybrid-genome-structure-of-escherichia-coli-rr1-hb101-reca
#6
Haeyoung Jeong, Young Mi Sim, Hyun Ju Kim, Sang Jun Lee
There have been extensive genome sequencing studies for Escherichia coli strains, particularly for pathogenic isolates, because fast determination of pathogenic potential and/or drug resistance and their propagation routes is crucial. For laboratory E. coli strains, however, genome sequence information is limited except for several well-known strains. We determined the complete genome sequence of laboratory E. coli strain RR1 (HB101 RecA(+)), which has long been used as a general cloning host. A hybrid genome sequence of K-12 MG1655 and B BL21(DE3) was constructed based on the initial mapping of Illumina HiSeq reads to each reference, and iterative rounds of read mapping, variant detection, and consensus extraction were carried out...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28420678/automated-analysis-of-high-content-microscopy-data-with-deep-learning
#7
Oren Z Kraus, Ben T Grys, Jimmy Ba, Yolanda Chong, Brendan J Frey, Charles Boone, Brenda J Andrews
Existing computational pipelines for quantitative analysis of high-content microscopy data rely on traditional machine learning approaches that fail to accurately classify more than a single dataset without substantial tuning and training, requiring extensive analysis. Here, we demonstrate that the application of deep learning to biological image data can overcome the pitfalls associated with conventional machine learning classifiers. Using a deep convolutional neural network (DeepLoc) to analyze yeast cell images, we show improved performance over traditional approaches in the automated classification of protein subcellular localization...
April 18, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28420081/spondyloarthritis-matrix-metalloproteinasesas-biomarkers-of-pathogenesis-and-response-to-tumor-necrosis-factor-tnf-inhibitors
#8
REVIEW
Stefania Moz, Ada Aita, Daniela Basso, Roberta Ramonda, Mario Plebani, Leonardo Punzi
The term spondyloarthritis (SpA) is used to describe a group of multifactorial chronic inflammatory diseases characterized by a predisposing genetic background and clinical manifestations typically involving the sacroiliac joint. The absence of pathognomonic clinical and/or laboratory findings generally results in a delay in diagnosis and, consequently, in treatment. In addition, 20-40% of SpA patients are non-responders to tumor necrosis factor (TNF) inhibitor therapies. Given these considerations, it is important to identify biomarkers that can facilitate the diagnosis and assessment of disease activity...
April 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28419853/listeria-monocytogenes-meningitis-in-the-netherlands-1985-2014-a-nationwide-surveillance-study
#9
Merel M Koopmans, Merijn W Bijlsma, Matthijs C Brouwer, Diederik van de Beek, Arie van der Ende
OBJECTIVES: Listeria monocytogenes can cause sepsis and meningitis. We report national surveillance data on L. monocytogenes meningitis in the Netherlands, describing incidence changes, genetic epidemiology and fatality rate. METHODS: We analyzed data from the Netherlands Reference Laboratory of Bacterial Meningitis for cases of Listeria monocytogenes meningitis. Strains were assessed by serotyping and bacterial population structure by multi-locus sequence typing...
April 15, 2017: Journal of Infection
https://www.readbyqxmd.com/read/28419427/how-i-manage-children-with-neutropenia
#10
REVIEW
David C Dale
Neutropenia, usually defined as a blood neutrophil count <1·5 × 10(9) /l, is a common medical problem for children and adults. There are many causes for neutropenia, and at each stage in life the clinical pattern of causes and consequences differs significantly. I recommend utilizing the age of the child and clinical observations for the preliminary diagnosis and primary management. In premature infants, neutropenia is quite common and contributes to the risk of sepsis with necrotizing enterocolitis...
April 17, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28419266/the-effect-of-parasitism-and-interpopulation-hybridization-on-aedes-albopictus-diptera-culicidae-fitness
#11
Michelle Tseng
Recent research in mosquito population genetics suggests that interpopulation hybridization has likely contributed to the rapid spread of the container-breeding mosquitoes. Here, I used laboratory experiments to investigate whether interpopulation Aedes (Stegomyia) albopictus (Skuse) F1 and F2 hybrids exhibit higher fitness than parental populations, and whether hybrid mosquito performance is related to infection by the coevolved protozoan parasite Ascogregarina taiwanensis (Lien and Levine). Overall, there were significant differences in development time, wing length, and survival between the two parental mosquito populations, but no difference in per capita growth rate r...
April 15, 2017: Journal of Medical Entomology
https://www.readbyqxmd.com/read/28419104/further-characterisation-of-differences-between-tl-and-ab-zebrafish-danio-rerio-gene-expression-physiology-and-behaviour-at-day-5-of-the-larval-stage
#12
Ruud van den Bos, Wouter Mes, Pietro Galligani, Anthony Heil, Jan Zethof, Gert Flik, Marnix Gorissen
Zebrafish (Danio rerio) have become popular as model organism in research. Many strains are readily available, which not only differ morphologically, but also genetically, physiologically and behaviourally. Here, we focus on the AB and Tupfel long-fin (TL) strain for which we have previously shown that adults differ in baseline hypothalamus-pituitary-interrenal (HPI)-axis activity (AB higher than TL) affecting inhibitory avoidance behaviour (absent in AB). To assess whether strain differences are already present in early life stages, we compared baseline HPI-axis related gene expression as well as cortisol levels, (neuro)development related as well as (innate) immune system related gene expression, and light-dark as well as startle behaviour in larvae 5 days post fertilisation...
2017: PloS One
https://www.readbyqxmd.com/read/28416939/a-systemic-onset-juvenile-idiopathic-arthritis-patient-with-reduced-anakinra-treatment-admitted-with-an-attack
#13
Dilek Yilmaz, Mediha Akcan, Semiha Terlemez, Ferah Sonmez, Abdullah Baris Akcan
Interleukin-1 plays an important role in the pathogenesis of systemic-onset juvenile idiopathic arthritis (SoJIA), and the use of anti-interleukin-1 therapy has been increasing. We report a case of a 14-year-old male patient with SoJIA. He was in remission with anakinra treatment for almost 2 years. When we extended the therapeutic range and decreased the dose (1 mg/kg twice a week), he developed symptoms mimicking pulmonary embolism and cardiac ischemia. Increased cardiac enzyme levels and echocardiographic findings were interpreted as myopericarditis...
February 2017: Eurasian Journal of Medicine
https://www.readbyqxmd.com/read/28416577/normal-and-neoplastic-stem-cells
#14
Melissa N McCracken, Benson M George, Kevin S Kao, Kristopher D Marjon, Tal Raveh, Irving L Weissman
A stem cell is broadly defined as a cell that retains the capacity to self-renew, a feature that confers the ability to continuously make identical daughter cells or additional cells that will differentiate into downstream progeny. This highly regulated genetic program to retain "stemness" is under active investigation. Research in our laboratory has explored similarities and differences in embryonic, tissue-specific, and neoplastic stem cells and their terminally differentiated counterparts. In this review, we will focus on the contributions of our laboratory, in particular on the studies that identified the mouse hematopoietic stem cell (HSC) and the human leukemic stem cell...
April 17, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28416012/congenital-cytomegalovirus-infection-advances-and-challenges-in-diagnosis-prevention-and-treatment
#15
REVIEW
Concetta Marsico, David W Kimberlin
Cytomegalovirus (CMV) is the most frequent cause of congenital infection worldwide, with an estimated incidence in developing countries of 0.6-0.7% of all live births. The burden of disease related to congenital CMV in substantial, as it is the leading non-genetic cause of sensorineural hearing loss and an important cause of neurodevelopmental disabilities in children. Despite its clinical significance, congenital CMV infection often goes undetected because the majority of infected infants are asymptomatic at birth and screening programs have not been substantially implemented...
April 17, 2017: Italian Journal of Pediatrics
https://www.readbyqxmd.com/read/28415976/smrt-genome-assembly-corrects-reference-errors-resolving-the-genetic-basis-of-virulence-in-mycobacterium-tuberculosis
#16
Afif Elghraoui, Samuel J Modlin, Faramarz Valafar
BACKGROUND: The genetic basis of virulence in Mycobacterium tuberculosis has been investigated through genome comparisons of virulent (H37Rv) and attenuated (H37Ra) sister strains. Such analysis, however, relies heavily on the accuracy of the sequences. While the H37Rv reference genome has had several corrections to date, that of H37Ra is unmodified since its original publication. RESULTS: Here, we report the assembly and finishing of the H37Ra genome from single-molecule, real-time (SMRT) sequencing...
April 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28414048/light-and-the-laboratory-mouse
#17
Stuart N Peirson, Laurence A Brown, Carina A Pothecary, Lindsay A Benson, Angus S Fisk
Light exerts widespread effects on physiology and behaviour. As well as the widely-appreciated role of light in vision, light also plays a critical role in many non-visual responses, including regulating circadian rhythms, sleep, pupil constriction, heart rate, hormone release and learning and memory. In mammals, responses to light are all mediated via retinal photoreceptors, including the classical rods and cones involved in vision as well as the recently identified melanopsin-expressing photoreceptive retinal ganglion cells (pRGCs)...
April 13, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28412695/cell-scientist-to-watch-robert-ernst
#18
(no author information available yet)
After obtaining his diploma in human biology at the Philipps-University Marburg, Germany, Robert Ernst joined the laboratory of Lutz Schmitt and obtained his PhD (summa cum laude) at Heinrich-Heine-University Düsseldorf in 2007. For his postdoctoral work, Robert worked with Hidde Ploegh at the Whitehead Institute for Biomedical Research, USA, supported by an EMBO long-term fellowship. Afterwards, he returned to Germany, to the laboratory of Kai Simons at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden...
April 15, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28412379/challenges-of-measles-and-rubella-laboratory-diagnostic-in-the-era-of-elimination
#19
REVIEW
Judith M Hübschen, Sonja M Bork, Kevin E Brown, Annette Mankertz, Sabine Santibanez, Myriam Ben Mamou, Mick N Mulders, Claude P Muller
The Member States of the WHO European Region adopted the goal of measles and rubella elimination more than 10 years ago, but so far only 21 of 53 countries have reached this target. Laboratory investigation of suspected cases is essential to support disease elimination efforts. Therefore WHO maintains a network of accredited laboratories providing high quality testing AIMS.: The present article reviews current measles and rubella laboratory diagnostic methods and describes specific challenges in elimination settings SOURCES...
April 13, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28409525/rare-pyrenophora-teres-hybridization-events-revealed-by-development-of-sequence-specific-pcr-markers
#20
Barsha Poudel, Simon R Ellwood, Alison C Testa, Mark McLean, Mark W Sutherland, Anke Martin
Pyrenophora teres f. teres and P. teres f. maculata cause net form and spot form, respectively, of net blotch on barley (Hordeum vulgare). The two forms reproduce sexually, producing hybrids with genetic and pathogenic variability. Phenotypic identification of hybrids is challenging because lesions induced by hybrids on host plants resemble lesions induced by either P. teres f. teres or P. teres f. maculata. In this study, 12 sequence-specific polymerase chain reaction markers were developed based on expressed regions spread across the genome...
April 14, 2017: Phytopathology
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