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https://www.readbyqxmd.com/read/28231383/the-pangenome-of-hexaploid-bread-wheat
#1
Juan D Montenegro, Agnieszka A Golicz, Philipp E Bayer, Bhavna Hurgobin, HueyTyng Lee, Chon-Kit Kenneth Chan, Paul Visendi, Kaitao Lai, Jaroslav Doležel, Jacqueline Batley, David Edwards
There is an increasing understanding that gene presence absence variation plays an important role in the heritability of agronomic traits, however there have been relatively few studies on gene presence absence variation in crop species. Hexaploid wheat is one of the most important food crops in the world and intensive breeding has reduced the genetic diversity of elite cultivars. Major efforts have produced draft genome assemblies for the cultivar Chinese Spring, but it is unknown how well this represents the genome diversity found in current modern elite cultivars...
February 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28231382/accurate-measurement-of-transgene-copy-number-in-crop-plants-using-droplet-digital-pcr
#2
Ray Collier, Kasturi Dasgupta, Yan-Ping Xing, Bryan Tarape Hernandez, Min Shao, Dominica Rohozinski, Emma Kovak, Jeanie Lin, Maria Luiza P de Oliveira, Ed Stover, Kent F McCue, Frank G Harmon, Ann Blechl, James G Thomson, Roger Thilmony
Genetic transformation is a powerful means for the improvement of crop plants, but requires labor and resource intensive methods. An efficient method for identifying single copy transgene insertion events from a population of independent transgenic lines is desirable. Currently transgene copy number is estimated by either Southern blot hybridization analyses or quantitative polymerase chain reaction (qPCR) experiments. Southern hybridization is a convincing and reliable method, but it also is expensive, time-consuming and often requires a large amount of genomic DNA and radioactively labeled probes...
February 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28231338/genes-encoding-two-theileria-parva-antigens-recognized-by-cd8-t-cells-exhibit-sequence-diversity-in-south-sudanese-cattle-populations-but-the-majority-of-alleles-are-similar-to-the-muguga-component-of-the-live-vaccine-cocktail
#3
Diaeldin A Salih, Roger Pelle, Joram M Mwacharo, Moses N Njahira, Wani L Marcellino, Henry Kiara, Agol K Malak, Abdel Rahim M El Hussein, Richard Bishop, Robert A Skilton
East Coast fever (ECF), caused by Theileria parva infection, is a frequently fatal disease of cattle in eastern, central and southern Africa, and an emerging disease in South Sudan. Immunization using the infection and treatment method (ITM) is increasingly being used for control in countries affected by ECF, but not yet in South Sudan. It has been reported that CD8+ T-cell lymphocytes specific for parasitized cells play a central role in the immunity induced by ITM and a number of T. parva antigens recognized by parasite-specific CD8+ T-cells have been identified...
2017: PloS One
https://www.readbyqxmd.com/read/28231034/upscaling-of-hips-cell-derived-neurons-for-high-throughput-screening
#4
Stefanie Traub, Heiko Stahl, Holger Rosenbrock, Eric Simon, Ralf Heilker
The advent of human-induced pluripotent stem (hiPS) cell-derived neurons promised to provide better model cells for drug discovery in the context of the central nervous system. This work demonstrates both the upscaling of cellular expansion and the acceleration of neuronal differentiation to accommodate the immense material needs of a high-throughput screening (HTS) approach. Using GRowth factor-driven expansion and INhibition of NotCH (GRINCH) during maturation, the derived cells are here referred to as GRINCH neurons...
March 2017: SLAS Discov
https://www.readbyqxmd.com/read/28230851/using-hiclip-to-identify-rna-duplexes-that-interact-with-a-specific-rna-binding-protein
#5
Yoichiro Sugimoto, Anob M Chakrabarti, Nicholas M Luscombe, Jernej Ule
The structure of RNA molecules has a critical role in regulating gene expression, largely through influencing their interactions with RNA-binding proteins (RBPs). RNA hybrid and individual-nucleotide resolution UV cross-linking and immunoprecipitation (hiCLIP) is a transcriptome-wide method of monitoring these interactions by identifying RNA duplexes bound by a specific RBP. The hiCLIP protocol consists of the following steps: in vivo cross-linking of RBPs to their bound RNAs; partial RNA digestion and purification of RNA duplexes interacting with the specific RBP using immunoprecipitation; ligation of the two arms of RNA duplexes via a linker; reverse transcription; cDNA library amplification; and finally high-throughput DNA sequencing...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28229513/pathogenic-asxl1-somatic-variants-in-reference-databases-complicate-germline-variant-interpretation-for-bohring-opitz-syndrome
#6
Colleen M Carlston, Anne H O'Donnell-Luria, Hunter R Underhill, Beryl B Cummings, Ben Weisburd, Eric V Minikel, Daniel P Birnbaum, Tatiana Tvrdik, Daniel G MacArthur, Rong Mao
The clinical interpretation of genetic variants has come to rely heavily on reference population databases such as the Exome Aggregation Consortium (ExAC) database. Pathogenic variants in genes associated with severe, pediatric-onset, highly penetrant, autosomal dominant conditions are assumed to be absent or rare in these databases. Exome sequencing of a six-year-old female patient with seizures, developmental delay, dysmorphic features and failure to thrive identified an ASXL1 variant previously reported as causative of Bohring-Opitz syndrome (BOS)...
February 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28229023/toxgen-an-improved-reference-database-for-the-identification-of-type-b-trichothecene-genotypes-in-fusarium
#7
Tomasz Kulik, Kessy Abarenkov, Maciej Buśko, Katarzyna Bilska, Anne D van Diepeningen, Anna Ostrowska-Kołodziejczak, Katarzyna Krawczyk, Balázs Brankovics, Sebastian Stenglein, Jakub Sawicki, Juliusz Perkowski
Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol), 15ADON (15-acetyldeoxynivalenol) and NIV (nivalenol), named after these three major mycotoxin compounds. Correct identification of these genotypes is elementary for all studies relating to population surveys, fungal ecology and mycotoxicology. Trichothecene producers exhibit enormous strain-dependent chemical diversity, which may result in variation in levels of the genotype's determining toxin and in the production of low to high amounts of atypical compounds...
2017: PeerJ
https://www.readbyqxmd.com/read/28229018/-genomic-data-mining-of-the-marine-actinobacteria-streptomyces-sp-h-kf8-unveils-insights-into-multi-stress-related-genes-and-metabolic-pathways-involved-in-antimicrobial-synthesis
#8
Agustina Undabarrena, Juan A Ugalde, Michael Seeger, Beatriz Cámara
Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs...
2017: PeerJ
https://www.readbyqxmd.com/read/28228222/-surgical-treatment-and-prognosis-for-patients-with-%C3%A2-synchronous-multiple-primary-lung-adenocarcinomas
#9
Yue Peng, Hui Wang, Hounai Xie, Wangang Ren, Zhen Feng, Meng Li, Zhongmin Peng
BACKGROUND: With the popularization of high-resolution computed tomography (HRCT), there is a rising trend of the detection of multiple primary lung cancers (MPLC). Adenocarcinomas is the major pathological type of MPLC. At present, reports on MPLC are relatively common, but few study focused on synchronous multiple primary lung adenocarcinomas (SMPLA). We carried out this study in an attempt to enhance our understanding about SMPLA. METHODS: Data from 38 patients undergoing surgery for SMPLA in our institution frrom December 2012 and July 2016 were retrospectively collected...
February 20, 2017: Zhongguo Fei Ai za Zhi, Chinese Journal of Lung Cancer
https://www.readbyqxmd.com/read/28228068/stress-in-gastrointestinal-tract-and-stable-gastric-pentadecapeptide-bpc-157-finally-do-we-have-a-solution
#10
Predrag Sikiric, Sven Seiwerth, Rudolf Rucman, Domagoj Drmic, Mirjana Stupnisek, Antonio Kokot, Marko Sever, Ivan Zoricic, Zoran Zoricic, Lovorka Batelja, Tihomil Ziger, Josipa Vlainic, Zarko Rasic, Martina Lovric Bencic
Selye's syndrome produced by diverse nocuous agents and "response to damage as such" means Selye's stress triad in stress coping response to reestablish homeostasis. Logically, from the gastrointestinal tract viewpoint, such organoprotective/healing response implies the angiogenic growth factors that commonly signify the healing. Thereby, the gastric pentadecapeptide BPC 157-organoprotection (huge range of beneficial effects) signifies the Selye's stress concept/stress coping response implemented in and from gastrointestinal tract, and BPC 157 as an integrative mediator that integrates the adaptive bodily response to stress...
February 20, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28226237/novel-insights-into-tree-biology-and-genome-evolution-as-revealed-through-genomics
#11
David B Neale, Pedro J Martínez-García, Amanda R De La Torre, Sara Montanari, Xiao-Xin Wei
Reference genome sequences are the key to the discovery of genes and gene families that determine traits of interest. Recent progress in sequencing technologies has enabled a rapid increase in genome sequencing of tree species, allowing the dissection of complex characters of economic importance, such as fruit and wood quality and resistance to biotic and abiotic stresses. Although the number of reference genome sequences for trees lags behind those for other plant species, it is not too early to gain insight into the unique features that distinguish trees from nontree plants...
February 6, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28225826/assessing-mycoplasma-contamination-of-cell-cultures-by-qpcr-using-a-set-of-universal-primer-pairs-targeting-a-1-5-kb-fragment-of-16s-rrna-genes
#12
Audrey Jean, Florence Tardy, Omran Allatif, Isabelle Grosjean, Bariza Blanquier, Denis Gerlier
Mycoplasmas (a generic name for Mollicutes) are a predominant bacterial contaminant of cell culture and cell derived products including viruses. This prokaryote class is characterized by very small size and lack of a cell wall. Consequently, mycoplasmas escape ultrafiltration and visualization under routine microscopic examination, hence the ease with which cells in culture can be contaminated, with routinely more than 10% of cell lines being contaminated. Mycoplasma are a formidable threat both in fundamental research by perverting a whole range of cell properties and functions and in the pharmacological use of cells and cell derived products...
2017: PloS One
https://www.readbyqxmd.com/read/28224032/prevalence-of-intestinal-parasites-in-referred-individuals-to-the-medical-centers-of-tonekabon-city-mazandaran-province
#13
Samira Shahdoust, Maryam Niyyati, Ali Haghighi, Eznoallah Azargashb, Mohammad Reza Khataminejad
AIM: The aim of the present study was to determine the prevalence of intestinal parasites and their relation with socio-demographic data in referred individuals to the medical centers in Tonekabon, Mazandaran province, 2015. BACKGROUND: Due to the climatic and ecological conditions in Mazandaran province, determination of the status of intestinal parasites among referred individuals to the medical centers of Tonekabon city can help researchers and healthcare services to prevent and/or control of parasitic infection in this region...
December 2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28224028/evaluation-of-antimicrobial-susceptibility-and-integron-carriage-in-helicobacter-pylori-isolates-from-patients
#14
Mehdi Goudarzi, Mohsen Heidary, Mehdi Azad, Maryam Fazeli, Hossein Goudarzi
AIM: The purpose of this study was to determine the antibiotic susceptibility pattern and distribution of integron in H. pylori isolates collected from patients referred to private health care centers in Tehran, Iran. BACKGROUND: Antibiotic resistance is the main reason for failure of Helicobacter pylori therapy. Integrons as genetic reservoirs play main roles in the dissemination of antimicrobial resistance gene. METHODS: During a 12-month cross-sectional study period, 65 H...
December 2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28224000/co-inoculation-effect-of-rhizobia-and-plant-growth-promoting-rhizobacteria-on-common-bean-growth-in-a-low-phosphorus-soil
#15
Hezekiah Korir, Nancy W Mungai, Moses Thuita, Yosef Hamba, Cargele Masso
Nitrogen (N) fixation through legume-Rhizobium symbiosis is important for enhancing agricultural productivity and is therefore of great economic interest. Growing evidence indicates that other soil beneficial bacteria can positively affect symbiotic performance of rhizobia. Nodule endophytic plant growth promoting rhizobacteria (PGPR) were isolated from common bean nodules from Nakuru County in Kenya and characterized 16S rDNA partial gene sequencing. The effect of co-inoculation of rhizobium and PGPR, on nodulation and growth of common bean (Phaseolus vulgaris L...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28223462/fallacy-of-the-unique-genome-sequence-diversity-within-single-helicobacter-pylori-strains
#16
Jenny L Draper, Lori M Hansen, David L Bernick, Samar Abedrabbo, Jason G Underwood, Nguyet Kong, Bihua C Huang, Allison M Weis, Bart C Weimer, Arnoud H M van Vliet, Nader Pourmand, Jay V Solnick, Kevin Karplus, Karen M Ottemann
Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra- and intergenomic variability. Using high sequence coverage depth and experimental validation, we detected extensive genome plasticity within these H. pylori isolates, including movement of the transposable element IS607, large and small inversions, multiple single nucleotide polymorphisms, and variation in cagA copy number...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28223374/enterobacter-cloacae-complex-isolates-harboring-blanmc-a-or-blaimi-type-class-a-carbapenemase-genes-on-novel-chromosomal-integrative-elements-and-plasmids
#17
David A Boyd, Laura F Mataseje, Ross Davidson, Johannes A Delport, Jeff Fuller, Linda Hoang, Brigitte Lefebvre, Paul Levett, Diane L Roscoe, Barbara M Willey, Michael R Mulvey
Carbapenem-resistant Enterobacter cloacae complex isolates submitted to a reference laboratory from 2010 to 2015 were screened by PCR for seven common carbapenemase gene groups, namely, KPC, NDM, OXA-48, VIM, IMP, GES, and NMC-A/IMI. Nineteen of the submitted isolates (1.7%) were found to harbor Ambler class A blaNMC-A or blaIMI-type carbapenemases. All 19 isolates were resistant to at least one carbapenem but susceptible to aminoglycosides, trimethoprim-sulfamethoxazole, tigecycline, and ciprofloxacin. Most isolates (17/19) gave positive results with the Carba-NP test for phenotypic carbapenemase detection...
February 21, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28223208/characterizing-the-poagome-a-bioinformatics-driven-approach-to-primary-open-angle-glaucoma
#18
REVIEW
Ian D Danford, Lana D Verkuil, Daniel J Choi, David W Collins, Harini V Gudiseva, Katherine E Uyhazi, Marisa K Lau, Levi N Kanu, Gregory R Grant, Venkata R M Chavali, Joan M O'Brien
Primary open-angle glaucoma (POAG) is a genetically, physiologically, and phenotypically complex neurodegenerative disorder. This study addressed the expanding collection of genes associated with POAG, referred to as the "POAGome." We used bioinformatics tools to perform an extensive, systematic literature search and compiled 522 genes with confirmed associations with POAG and its related phenotypes (normal tension glaucoma, ocular hypertension, juvenile open-angle glaucoma, and primary congenital glaucoma)...
February 18, 2017: Progress in Retinal and Eye Research
https://www.readbyqxmd.com/read/28223147/comparative-performance-study-of-six-commercial-molecular-assays-for-rapid-detection-of-toxigenic-clostridium-difficile
#19
Yossi Paitan, Tamar Miller Roll, Amos Adler
OBJECTIVES: Rapid and accurate detection of C. difficile in stool impacts patient treatment and containment efforts. Detection of C. difficile toxin genes using nucleic acid amplification techniques (NAAT) is part of a multistep algorithm. Our objective was to directly compare the diagnostic accuracy and applicability of 6 commercial C. difficile NAAT assays. METHODS: In this study, 210 specimens were analysed in parallel by 6 commercial NAAT. Toxigenic culture was used as a reference method...
February 18, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28222685/evaluation-of-the-accuracy-of-imputed-sequence-variant-genotypes-and-their-utility-for-causal-variant-detection-in-cattle
#20
Hubert Pausch, Iona M MacLeod, Ruedi Fries, Reiner Emmerling, Phil J Bowman, Hans D Daetwyler, Michael E Goddard
BACKGROUND: The availability of dense genotypes and whole-genome sequence variants from various sources offers the opportunity to compile large datasets consisting of tens of thousands of individuals with genotypes at millions of polymorphic sites that may enhance the power of genomic analyses. The imputation of missing genotypes ensures that all individuals have genotypes for a shared set of variants. RESULTS: We evaluated the accuracy of imputation from dense genotypes to whole-genome sequence variants in 249 Fleckvieh and 450 Holstein cattle using Minimac and FImpute...
February 21, 2017: Genetics, Selection, Evolution: GSE
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