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https://www.readbyqxmd.com/read/27905883/carbohydrate-metabolism-in-oenococcus-oeni-a-genomic-insight
#1
Alice Cibrario, Claire Peanne, Marine Lailheugue, Hugo Campbell-Sills, Marguerite Dols-Lafargue
BACKGROUND: Oenococcus oeni is the bacterial species that drives malolactic fermentation in most wines. Several studies have described a high intraspecific diversity regarding carbohydrate degradation abilities but the link between the phenotypes and the genes and metabolic pathways has been poorly described. RESULTS: A collection of 41 strains whose genomic sequences were available and representative of the species genomic diversity was analyzed for growth on 18 carbohydrates relevant in wine...
December 1, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27902796/target-amplicon-sequencing-for-genotyping-genome-wide-single-nucleotide-polymorphisms-identified-by-whole-genome-resequencing-in-peanut
#2
Kenta Shirasawa, Chikara Kuwata, Manabu Watanabe, Masanobu Fukami, Hideki Hirakawa, Sachiko Isobe
Genome-wide genotyping data regarding breeding materials are essential resources for improving breeding efficiency, especially in plants with complex genomes with a high degree of polyploidy. Several current breeding efforts in cultivated peanut ( L.), which has a tetraploid genome, are devoted to developing high oleic acid cultivars. Genetic maps for such breeding programs have been developed using simple-sequence repeat (SSR) markers, the use of which requires time-consuming electrophoretic analyses. Next-generation sequencing (NGS) technology can overcome this technical hurdle...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27899345/ethics-of-genetic-testing-and-research-in-sport-a-position-statement-from-the-australian-institute-of-sport
#3
Nicole Vlahovich, Peter A Fricker, Matthew A Brown, David Hughes
As Australia's peak high-performance sport agency, the Australian Institute of Sport (AIS) has developed this position statement to address the implications of recent advances in the field of genetics and the ramifications for the health and well-being of athletes. Genetic testing has proven of value in the practice of clinical medicine. There are, however, currently no scientific grounds for the use of genetic testing for athletic performance improvement, sport selection or talent identification. Athletes and coaches should be discouraged from using direct-to-consumer genetic testing because of its lack of validation and replicability and the lack of involvement of a medical practitioner in the process...
November 29, 2016: British Journal of Sports Medicine
https://www.readbyqxmd.com/read/27898810/genomic-selection-for-processing-and-end-use-quality-traits-in-the-cimmyt-spring-bread-wheat-breeding-program
#4
Sarah D Battenfield, Carlos Guzmán, R Chris Gaynor, Ravi P Singh, Roberto J Peña, Susanne Dreisigacker, Allan K Fritz, Jesse A Poland
Wheat ( L.) cultivars must possess suitable end-use quality for release and consumer acceptability. However, breeding for quality traits is often considered a secondary target relative to yield largely because of amount of seed needed and expense. Without testing and selection, many undesirable materials are advanced, expending additional resources. Here, we develop and validate whole-genome prediction models for end-use quality phenotypes in the CIMMYT bread wheat breeding program. Model accuracy was tested using forward prediction on breeding lines ( = 5520) tested in unbalanced yield trials from 2009 to 2015 at Ciudad Obregon, Sonora, Mexico...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27895629/genome-wide-discovery-of-putative-srnas-in-paracoccus-denitrificans-expressed-under-nitrous-oxide-emitting-conditions
#5
Hannah Gaimster, Lisa Chalklen, Mark Alston, John T Munnoch, David J Richardson, Andrew J Gates, Gary Rowley
Nitrous oxide (N2O) is a stable, ozone depleting greenhouse gas. Emissions of N2O into the atmosphere continue to rise, primarily due to the use of nitrogen-containing fertilizers by soil denitrifying microbes. It is clear more effective mitigation strategies are required to reduce emissions. One way to help develop future mitigation strategies is to address the currently poor understanding of transcriptional regulation of the enzymes used to produce and consume N2O. With this ultimate aim in mind we performed RNA-seq on a model soil denitrifier, Paracoccus denitrificans, cultured anaerobically under high N2O and low N2O emitting conditions, and aerobically under zero N2O emitting conditions to identify small RNAs (sRNAs) with potential regulatory functions transcribed under these conditions...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27894783/comparison-of-speed-vacuum-method-and-heat-drying-method-to-measure-brain-water-content-of-small-brain-samples
#6
Anne Sebastiani, Tobias Hirnet, Antje Jahn-Eimermacher, Serge C Thal
BACKGROUND: A reliable measurement of brain water content (wet-to-dry ratio) is an important prerequisite for conducting research on mechanisms of brain edema formation. The conventionally used oven-drying method suffers from several limitations, especially in small samples. A technically demanding and time-consuming alternative is freeze-drying. NEW METHOD: Centrifugal vacuum concentrators (e.g. SpeedVac/speed-vacuum drying) are a combination of vacuum-drying and centrifugation, used to reduce the boiling temperature...
November 25, 2016: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/27881726/systems-genetics-identifies-a-novel-regulatory-domain-of-amylose-synthesis
#7
Vito M Butardo, Roslen Anacleto, Sabiha Parween, Irene Samson, Krishna de Guzman, Crisline Mae Alhambra, Gopal Misra, Nese Sreenivasulu
A deeper understanding of the regulation of starch biosynthesis in rice endosperm is crucial in tailoring digestibility without sacrificing grain quality. In this study, significant association peaks on chromosomes 6 and 7 were identified through genome-wide association study (GWAS) of debranched starch structure from grains of a 320 indica rice diversity panel using genotyping data from the high-density rice array. A systems genetics approach that interrelates starch structure data from GWAS to functional pathways from a gene regulatory network identified known and novel genes with high correlation to the proportion of amylose and amylopectin...
November 23, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27880996/oxidative-stress-induced-damage-to-paternal-genome-and-impact-of-meditation-and-yoga-can-it-reduce-incidence-of-childhood-cancer
#8
Dada Rima, Basant Kumar Shiv, Chawla Bhavna, Bisht Shilpa, Khan Saima
Background: Sperm DNA damage is underlying aetiology of poor implantation and pregnancy rates but also affects health of offspring and may also result in denovo mutations in germ line and post fertilization. This may result in complex diseases, polygenic disorders and childhood cancers. Childhood cancer like retinoblastoma (RB) is more prevalent in developing countries and the incidence of RB has increased more than three fold in India in the last decade. Recent studies have documented increased incidence of cancers in children born to fathers who consume alcohol in excess and tobacco or who were conceived by assisted conception...
January 9, 2016: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/27874090/a-novel-process-of-viral-vector-barcoding-and-library-preparation-enables-high-diversity-library-generation-and-recombination-free-paired-end-sequencing
#9
Marcus Davidsson, Paula Diaz-Fernandez, Oliver D Schwich, Marcos Torroba, Gang Wang, Tomas Björklund
Detailed characterization and mapping of oligonucleotide function in vivo is generally a very time consuming effort that only allows for hypothesis driven subsampling of the full sequence to be analysed. Recent advances in deep sequencing together with highly efficient parallel oligonucleotide synthesis and cloning techniques have, however, opened up for entirely new ways to map genetic function in vivo. Here we present a novel, optimized protocol for the generation of universally applicable, barcode labelled, plasmid libraries...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27872153/xpf-suppresses-mutagenic-consequences-of-bacterial-phagocytosis-in-dictyostelium
#10
Lucas B Pontel, Judith Langenick, Ivan V Rosado, Xiao-Yin Zhang, David Traynor, Robert R Kay, Ketan J Patel
As time passes, mutations accumulate in the genomes of all living organisms. These changes promote genetic diversity, but also precipitate ageing and the initiation of cancer. Food is a common source of mutagens, but little is known about how nutritional factors cause lasting genetic changes in the consuming organism. Here, we describe an unusual genetic interaction between DNA repair in the unicellular amoeba - Dictyostelium discoideum - and its natural bacterial food source. Dictyostelium deficient in the DNA repair nuclease Xpf displays a severe and specific growth defect when feeding on bacteria...
November 21, 2016: Journal of Cell Science
https://www.readbyqxmd.com/read/27871989/quality-by-design-qbd-approach-of-pharmacogenomics-in-drug-designing-and-formulation-development-for-optimization-of-drug-delivery-systems
#11
REVIEW
Sumeet Gupta, Vikas Jhawat
Conventional approaches of drug discovery are very complex, costly and time consuming. But after the completion of human genome project, applications of pharmacogenomics in this area completely revolutionize the drug discovery and development process to produce a quality by design (QbD) approach based products. The applications of two areas of pharmacogenomics i.e. structural and functional pharmacogenomics excel the drug discovery process by employing genomic data in drug target identification and evaluation, lead optimization via high throughput screening, evaluation of drug metabolizing enzymes, drug transporters and drug receptors using computer aided technique and bioinformatics library data base...
November 19, 2016: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/27867107/draft-genome-sequence-of-mentha-longifolia-l-and-development-of-resources-for-mint-cultivar-improvement
#12
Kelly J Vining, Sean R Johnson, Amirhossein Ahkami, Iris Lange, Amber N Parrish, Susan C Trapp, Rodney B Croteau, Shannon C K Straub, Iovanna Pandelova, B Markus Lange
The genus Mentha encompasses species cultivated for their essential oils, which are formulated into a vast array of consumer products. Desirable oil characteristics and resistance to the fungal disease Verticillium wilt are top priorities for the mint industry. However, cultivated mints have complex polyploid genomes and are sterile. Breeding efforts, therefore, require the development of genomic resources for fertile mint species. Here, we present draft de novo genome and plastome assemblies for a wilt-resistant South African accession of Mentha longifolia (L...
November 17, 2016: Molecular Plant
https://www.readbyqxmd.com/read/27866376/reduction-in-dietary-acrylamide-exposure-impact-of-potatoes-with-low-acrylamide-potential
#13
Nga L Tran, Leila M Barraj, Susan Collinge
Acrylamide forms primarily from a reaction between reducing sugars (e.g., glucose and fructose) and an amino acid (asparagine, Asn) formed naturally in foods, including potatoes. This reaction occurs when carbohydrate-rich foods are heated at temperatures above 120 °C. Multiple potato varieties were transformed with potato genomic DNA that results in down-regulation of the expression of the asparagine synthetase-1 gene (Asn1), significantly reducing synthesis of free Asn, and consequently lowering the potential to form acrylamide during cooking...
November 20, 2016: Risk Analysis: An Official Publication of the Society for Risk Analysis
https://www.readbyqxmd.com/read/27862524/sequence-capture-and-next-generation-sequencing-of-ultraconserved-elements-in-a-large-genome-salamander
#14
Catherine E Newman, Christopher C Austin
Amidst the rapid advancement in next-generation sequencing (NGS) technology over the last few years, salamanders have been left behind. Salamanders have enormous genomes - up to 40 times the size of the human genome - and this poses challenges to generating NGS data sets of quality and quantity similar to those of other vertebrates. However, optimization of laboratory protocols is time-consuming and often cost prohibitive, and continued omission of salamanders from novel phylogeographic research is detrimental to species facing decline...
November 14, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27857203/rapid-and-efficient-crispr-cas9-gene-inactivation-in-human-neurons-during-human-pluripotent-stem-cell-differentiation-and-direct-reprogramming
#15
Alicia Rubio, Mirko Luoni, Serena G Giannelli, Isabella Radice, Angelo Iannielli, Cinzia Cancellieri, Claudia Di Berardino, Giulia Regalia, Giovanna Lazzari, Andrea Menegon, Stefano Taverna, Vania Broccoli
The CRISPR/Cas9 system is a rapid and customizable tool for gene editing in mammalian cells. In particular, this approach has widely opened new opportunities for genetic studies in neurological disease. Human neurons can be differentiated in vitro from hPSC (human Pluripotent Stem Cells), hNPCs (human Neural Precursor Cells) or even directly reprogrammed from fibroblasts. Here, we described a new platform which enables, rapid and efficient CRISPR/Cas9-mediated genome targeting simultaneously with three different paradigms for in vitro generation of neurons...
November 18, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27856652/evolution-of-rosaceae-fruit-types-based-on-nuclear-phylogeny-in-the-context-of-geological-times-and-genome-duplication
#16
Yezi Xiang, Chien-Hsun Huang, Yi Hu, Jun Wen, Shisheng Li, Tingshuang Yi, Hongyi Chen, Jun Xiang, Hong Ma
Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ~3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution...
November 17, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27856232/improved-recombinant-antibody-production-by-cho-cells-using-a-production-enhancer-dna-element-with-repeated-transgene-integration-at-a-predetermined-chromosomal-site
#17
Yoshinori Kawabe, Takanori Inao, Shodai Komatsu, Guan Huang, Akira Ito, Takeshi Omasa, Masamichi Kamihira
Chinese hamster ovary (CHO) cells are one of the most useful host cell lines for the production of biopharmaceutical proteins. Although a series of production processes have been refined to improve protein productivity and cost performance, establishing producer cells is still time-consuming and labor-intensive. Recombinase-mediated site-specific gene integration into a predetermined chromosomal locus may enable predictable protein expression, reducing the laborious process of cell screening. We previously developed an accumulative site-specific gene integration system (AGIS) using Cre recombinase and mutated loxP sites for transgene integration and amplification in the CHO cell genome...
November 14, 2016: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/27854254/the-association-between-alcohol-consumption-and-%C3%AE-cell-function-and-insulin-sensitivity-in-korean-population
#18
Min-Gyu Yoo, Hyo-Jin Kim, Han Byul Jang, Hye-Ja Lee, Sang Ick Park
This cross-sectional study was performed to examine the association between alcohol consumption and insulin secretion and sensitivity using the Korean Genome and Epidemiology Study. Alcohol consumption levels were categorized into four groups: (i) abstainers, (ii) low (<5 g/day), (iii) intermediate (<30 g/day), and (iv) high (≥30 g/day) alcohol consumption. β-cell function and insulin sensitivity were estimated using the insulinogenic index (IGI60), and Matsuda insulin sensitivity index (ISI), respectively...
November 14, 2016: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/27853518/metagenomic-analysis-of-medicinal-cannabis-samples-pathogenic-bacteria-toxigenic-fungi-and-beneficial-microbes-grow-in-culture-based-yeast-and-mold-tests
#19
Kevin McKernan, Jessica Spangler, Yvonne Helbert, Ryan C Lynch, Adrian Devitt-Lee, Lei Zhang, Wendell Orphe, Jason Warner, Theodore Foss, Christopher J Hudalla, Matthew Silva, Douglas R Smith
Background: The presence of bacteria and fungi in medicinal or recreational Cannabis poses a potential threat to consumers if those microbes include pathogenic or toxigenic species. This study evaluated two widely used culture-based platforms for total yeast and mold (TYM) testing marketed by 3M Corporation and Biomérieux, in comparison with a quantitative PCR (qPCR) approach marketed by Medicinal Genomics Corporation. Methods: A set of 15 medicinal Cannabis samples were analyzed using 3M and Biomérieux culture-based platforms and by qPCR to quantify microbial DNA...
2016: F1000Research
https://www.readbyqxmd.com/read/27834660/private-and-efficient-query-processing-on-outsourced-genomic-databases
#20
Reza Ghasemi, Md Momin Al Aziz, Noman Mohammed, Massoud Hadian Dehkordi, Xiaoqian Jiang
Applications of genomic studies are spreading rapidly in many domains of science and technology such as healthcare, biomedical research, direct-to-consumer services, and legal and forensic. However, there are a number of obstacles that make it hard to access and process a big genomic database for these applications. First, sequencing genomic sequence is a timeconsuming and expensive process. Second, it requires large-scale computation and storage systems to processes genomic sequences. Third, genomic databases are often owned by different organizations and thus not available for public usage...
November 4, 2016: IEEE Journal of Biomedical and Health Informatics
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