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https://www.readbyqxmd.com/read/28219347/aquaculture-genomics-genetics-and-breeding-in-the-united-states-current-status-challenges-and-priorities-for-future-research
#1
EDITORIAL
Hisham Abdelrahman, Mohamed ElHady, Acacia Alcivar-Warren, Standish Allen, Rafet Al-Tobasei, Lisui Bao, Ben Beck, Harvey Blackburn, Brian Bosworth, John Buchanan, Jesse Chappell, William Daniels, Sheng Dong, Rex Dunham, Evan Durland, Ahmed Elaswad, Marta Gomez-Chiarri, Kamal Gosh, Ximing Guo, Perry Hackett, Terry Hanson, Dennis Hedgecock, Tiffany Howard, Leigh Holland, Molly Jackson, Yulin Jin, Karim Kahlil, Thomas Kocher, Tim Leeds, Ning Li, Lauren Lindsey, Shikai Liu, Zhanjiang Liu, Kyle Martin, Romi Novriadi, Ramjie Odin, Yniv Palti, Eric Peatman, Dina Proestou, Guyu Qin, Benjamin Reading, Caird Rexroad, Steven Roberts, Mohamed Salem, Andrew Severin, Huitong Shi, Craig Shoemaker, Sheila Stiles, Suxu Tan, Kathy F J Tang, Wilawan Thongda, Terrence Tiersch, Joseph Tomasso, Wendy Tri Prabowo, Roger Vallejo, Hein van der Steen, Khoi Vo, Geoff Waldbieser, Hanping Wang, Xiaozhu Wang, Jianhai Xiang, Yujia Yang, Roger Yant, Zihao Yuan, Qifan Zeng, Tao Zhou
Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28218837/rapid-and-efficient-genome-editing-in-staphylococcus-aureus-by-using-an-engineered-crispr-cas9-system
#2
Weizhong Chen, Yifei Zhang, Won-Sik Yeo, Taeok Bae, Quanjiang Ji
Staphylococcus aureus, a major human pathogen, has been the cause of serious infectious diseases with a high mortality rate. Although genetics is a key means to study S. aureus physiology, such as drug resistance and pathogenesis, genetic manipulation in S. aureus is always time consuming and labor intensive. Here, we report a CRISPR/Cas9 system (pCasSA) for rapid and efficient genome editing, including gene deletion, insertion and single-base substitution mutation in S. aureus. The designed pCasSA system is amenable to assembly of spacers and repair arms by Golden Gate assembly and Gibson assembly, respectively, enabling rapid construction of the plasmids for editing...
February 20, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28217441/genome-sequence-of-the-acid-tolerant-desulfovibrio-sp-dv-isolated-from-the-sediments-of-a-pb-zn-mine-tailings-dam-in-the-chita-region-russia
#3
Anastasiia Kovaliova, Vitaly V Kadnikov, Dmitrii V Antsiferov, Alexey V Beletsky, Ehrzena V Danilova, Marat R Avakyan, Andrey V Mardanov, Olga V Karnachuk
Here we report the draft genome sequence of the acid-tolerant Desulfovibrio sp. DV isolated from the sediments of a Pb-Zn mine tailings dam in the Chita region, Russia. The draft genome has a size of 4.9 Mb and encodes multiple K(+)-transporters and proton-consuming decarboxylases. The phylogenetic analysis based on concatenated ribosomal proteins revealed that strain DV clusters together with the acid-tolerant Desulfovibrio sp. TomC and Desulfovibrio magneticus. The draft genome sequence and annotation have been deposited at GenBank under the accession number MLBG00000000...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28216063/the-nad-precursor-nicotinic-acid-improves-genomic-integrity-in-human-peripheral-blood-mononuclear-cells-after-x-irradiation
#4
Kathrin Weidele, Sascha Beneke, Alexander Bürkle
NAD(+) is an essential cofactor for enzymes catalyzing redox-reactions as well as an electron carrier in energy metabolism. Aside from this, NAD(+) consuming enzymes like poly(ADP-ribose) polymerases and sirtuins are important regulators involved in chromatin-restructuring processes during repair and epigenetics/transcriptional adaption. In order to replenish cellular NAD(+) levels after cleavage, synthesis starts from precursors such as nicotinamide, nicotinamide riboside or nicotinic acid to match the need for this essential molecule...
February 13, 2017: DNA Repair
https://www.readbyqxmd.com/read/28214915/evaluation-of-the-gard-assay-in-a-blind-cosmetics-europe-study
#5
Henrik Johansson, Robin Gradin, Andy Forreryd, Maria Agemark, Kathrin Zeller, Angelica Johansson, Olivia Larne, Erwin van Vliet, Carl Borrebaeck, Malin Lindstedt
Chemical hypersensitivity is an immunological response towards foreign substances, commonly referred to as sensitizers, which gives rise primarily to the clinical symptoms known as allergic contact dermatitis. For the purpose of mitigating risks associated with consumer products, chemicals are screened for sensitizing effects. Historically, such predictive screenings have been performed using animal models. However, due to industrial and regulatory demand, animal models for the purpose of sensitization assessment are being replaced by animal-free testing methods, a global trend that is spreading across industries and market segments...
February 17, 2017: ALTEX
https://www.readbyqxmd.com/read/28212417/splitax-a-novel-method-to-assess-the-function-of-engineered-nucleases
#6
Richard A Axton, Sharmin S Haideri, Martha Lopez-Yrigoyen, Helen A Taylor, Lesley M Forrester
Engineered nucleases have been used to generate knockout or reporter cell lines and a range of animal models for human disease. These new technologies also hold great promise for therapeutic genome editing. Current methods to evaluate the activity of these nucleases are time consuming, require extensive optimization and are hampered by readouts with low signals and high background. We have developed a simple and easy to perform method (SplitAx) that largely addresses these issues and provides a readout of nuclease activity...
2017: PloS One
https://www.readbyqxmd.com/read/28202802/multi-laboratory-survey-to-evaluate-salmonella-prevalence-in-diarrheic-and-non-diarrheic-dogs-and-cats-in-the-usa-between-2012-and-2014
#7
Renate Reimschuessel, Michael Grabenstein, Jake Guag, Sarah M Nemser, Kyunghee Song, Junshan Qiu, Kristin A Clothier, Barbara A Byrne, Stanley L Marks, Kyran Cadmus, Kristy Pabilonia, Susan Sanchez, Sreekumari Rajeev, Steve Ensley, Timothy S Frana, Albert E Jergens, Kimberly H Chappell, Siddhartha Thakur, Beverly Byrum, Jing Cui, Yan Zhang, Matthew M Erdman, Shelley C Rankin, Russell Daly, Seema Das, Laura Ruesch, Sara D Lawhon, Shuping Zhang, Timothy Baszler, Dubraska Diaz-Campos, Faye Hartmann, Ogi Okwumabua
Eleven laboratories collaborated to determine the periodic prevalence of Salmonella in a population of dogs and cats in the USA visiting veterinary clinics. Fecal samples (2965) solicited from 11 geographically dispersed veterinary testing laboratories were collected in 36 states between January 2012 and April 2014 and tested using a harmonized method. The overall study prevalence of Salmonella in cats (3 of 542) was <1%. Prevalence in dogs (60 of 2422) was 2.5%. Diarrhea was present in only 55% of positive dogs; however 3...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28188449/xylitol-production-by-genetically-modified-industrial-strain-of-saccharomyces-cerevisiae-using-glycerol-as-co-substrate
#8
Anushree B Kogje, Anand Ghosalkar
Xylitol is commercially used in chewing gum and dental care products as a low calorie sweetener having medicinal properties. Industrial yeast strain of S. cerevisiae was genetically modified to overexpress an endogenous aldose reductase gene GRE3 and a xylose transporter gene SUT1 for the production of xylitol. The recombinant strain (XP-RTK) carried the expression cassettes of both the genes and the G418 resistance marker cassette KanMX integrated into the genome of S. cerevisiae. Short segments from the 5' and 3' delta regions of the Ty1 retrotransposons were used as homology regions for integration of the cassettes...
February 10, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28188208/quantitative-detection-of-burkholderia-pseudomallei-in-soil-samples-using-multiple-gene-targets-in-real-time-pcr
#9
A Göhler, T T Trung, V Hopf, C Kohler, J Hartleib, V Wuthiekanun, S J Peacock, D Limmathurotsakul, A Tuanyok, I Steinmetz
Burkholderia pseudomallei is present in the environment in many parts of the world and causes the often-fatal disease melioidosis. The sensitive detection and quantification of B. pseudomallei in the environment is a prerequisite to assess the risk of infection. We recently reported the direct detection of B. pseudomallei in soil samples using a qPCR targeting a single type three secretion system 1 (TTSS1) gene. Here, we extend the qPCR-based analysis of B. pseudomallei in soil by validating novel qPCR gene targets selected from comparative genomic analysis...
February 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28187714/tipmt-identification-of-pcr-based-taxon-specific-markers
#10
Gabriela F Rodrigues-Luiz, Mariana S Cardoso, Hugo O Valdivia, Edward V Ayala, Célia M F Gontijo, Thiago de S Rodrigues, Ricardo T Fujiwara, Robson S Lopes, Daniella C Bartholomeu
BACKGROUND: Molecular genetic markers are one of the most informative and widely used genome features in clinical and environmental diagnostic studies. A polymerase chain reaction (PCR)-based molecular marker is very attractive because it is suitable to high throughput automation and confers high specificity. However, the design of taxon-specific primers may be difficult and time consuming due to the need to identify appropriate genomic regions for annealing primers and to evaluate primer specificity...
February 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28187376/genome-wide-analysis-of-excretory-secretory-proteins-in-root-knot-nematode-meloidogyne-incognita-provides-potential-targets-for-parasite-control
#11
Shachi Gahoi, Budhayash Gautam
The root-knot nematode, Meloidogyne incognita causes significant damage to various economically important crops. Infection is associated with secretion of effector proteins into host cytoplasm and interference with host innate immunity. To combat this infection, the identification and functional annotations of Excretory/Secretory (ES) proteins serve as a key to produce durable control measures. The identification of ES proteins through experimental methods are expensive and time consuming while bioinformatics approaches are cost-effective by prioritizing the experimental analysis of potential drug targets for parasitic diseases...
February 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28174040/solid-state-fermentative-production-of-aroma-esters-by-myroides-sp-zb35-and-its-complete-genome-sequence
#12
Zijun Xiao, Wenlong Liang, Xiankun Zhu, Jing-Yi Zhao
Consumers prefer biotechnological food products with high nutritional values and good flavors. Solid-state fermentation is a commonly used technique with a long history. In the present study, Myroides sp. ZB35 was used in solid-state fermentative production of aroma volatiles on a rice medium. Using the headspace solid phase microextraction coupled with gas chromatography-mass spectrometry technique and authentic standards, 22 esters with molecular weight ranging from 102 to 172 were identified. At 192h, the esters reached a total concentration of 1774μg/kg...
February 4, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28163590/development-of-genome-wide-pcr-based-markers-from-insertion-deletion-and-single-nucleotide-polymorphisms-for-closely-related-japanese-rice-cultivars-and-identification-of-qtls-for-the-appearance-of-cooked-rice-and-polished-rice
#13
Noriko Kinoshita, Sho Takano, Naomi Shimoda, Itsuro Takamure, Takashi Sato, Kiyoaki Kato
Appearance of rice grain is an important property, affecting its acceptance by consumers. Moreover, appearance is a complex characteristic involving many components, including glossiness and whiteness. The genetic bases for the glossiness of cooked rice and the whiteness of polished rice (WPR) were determined using 133 recombinant inbred lines (RILs) derived from a cross between two closely related cultivars from Hokkaido, Joiku462, with high glossiness and whiteness, and Yukihikari, an ancestor of Joiku462 with low glossiness and whiteness...
December 2016: Breeding Science
https://www.readbyqxmd.com/read/28155718/improved-protein-protein-interactions-prediction-via-weighted-sparse-representation-model-combining-continuous-wavelet-descriptor-and-pseaa-composition
#14
Yu-An Huang, Zhu-Hong You, Xing Chen, Gui-Ying Yan
BACKGROUND: Protein-protein interactions (PPIs) are essential to most biological processes. Since bioscience has entered into the era of genome and proteome, there is a growing demand for the knowledge about PPI network. High-throughput biological technologies can be used to identify new PPIs, but they are expensive, time-consuming, and tedious. Therefore, computational methods for predicting PPIs have an important role. For the past years, an increasing number of computational methods such as protein structure-based approaches have been proposed for predicting PPIs...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28155639/inferring-new-indications-for-approved-drugs-via-random-walk-on-drug-disease-heterogenous-networks
#15
Hui Liu, Yinglong Song, Jihong Guan, Libo Luo, Ziheng Zhuang
BACKGROUND: Since traditional drug research and development is often time-consuming and high-risk, there is an increasing interest in establishing new medical indications for approved drugs, referred to as drug repositioning, which provides a relatively low-cost and high-efficiency approach for drug discovery. With the explosive growth of large-scale biochemical and phenotypic data, drug repositioning holds great potential for precision medicine in the post-genomic era. It is urgent to develop rational and systematic approaches to predict new indications for approved drugs on a large scale...
December 23, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28143888/divergent-mechanisms-leading-to-signaling-dysfunction-in-embryonic-muscle-by-bisphenol-a-and-tetrabromobisphenol-a
#16
Rui Zhang, Isaac N Pessah
Bisphenol A (BPA) and its brominated derivative tetrabromobisphenol A (TBBPA) are high production volume chemicals utilized in the manufacture of various consumer products. Although regarded as endocrine disruptors, these chemicals are suspected to exert non-genomic actions on muscle function that are not well understood. Using skeletal muscle microsomes, we examined the effects of BPA and TBBPA on ryanodine receptor type 1 (RyR1), dihydropyridine receptor (DHPR), and sarco/endoplasmic reticulum Ca(2+) ATPase (SERCA)...
January 31, 2017: Molecular Pharmacology
https://www.readbyqxmd.com/read/28126817/a-chemical-genetic-roadmap-to-improved-tomato-flavor
#17
Denise Tieman, Guangtao Zhu, Marcio F R Resende, Tao Lin, Cuong Nguyen, Dawn Bies, Jose Luis Rambla, Kristty Stephanie Ortiz Beltran, Mark Taylor, Bo Zhang, Hiroki Ikeda, Zhongyuan Liu, Josef Fisher, Itay Zemach, Antonio Monforte, Dani Zamir, Antonio Granell, Matias Kirst, Sanwen Huang, Harry Klee
Modern commercial tomato varieties are substantially less flavorful than heirloom varieties. To understand and ultimately correct this deficiency, we quantified flavor-associated chemicals in 398 modern, heirloom, and wild accessions. A subset of these accessions was evaluated in consumer panels, identifying the chemicals that made the most important contributions to flavor and consumer liking. We found that modern commercial varieties contain significantly lower amounts of many of these important flavor chemicals than older varieties...
January 27, 2017: Science
https://www.readbyqxmd.com/read/28126051/loop-mediated-isothermal-amplification-lamp-assay-for-rapid-detection-of-streptococcus-agalactiae-group-b-streptococcus-gbs-in-vaginal-swabs-a-proof-of-concept-study
#18
James Patrick McKenna, Ciara Cox, Derek John Fairley, Rachael Burke, Michael D Shields, Alison Watt, Peter Valentine Coyle
PURPOSE: Neonatal infection with Streptococcus agalactiae (Group B streptococcus - GBS) is a life threatening condition which is preventable if colonised mothers are identified and given antibiotic prophylaxis during labour. Conventional culture is time consuming and unreliable, and many available non-culture diagnostics are too complex to implement routinely at point of care. Loop-mediated isothermal amplification (LAMP) is a method which enables the rapid and specific detection of target nucleic acid sequences in clinical material without requirements for extensive sample preparation...
January 24, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28119845/identification-of-a-heterozygous-spg11-mutation-by-clinical-exome-sequencing-in-a-patient-with-hereditary-spastic-paraplegia-a-case-report
#19
Ja-Young Oh, Hyun Jung Do, Seungok Lee, Ja-Hyun Jang, Eun-Hae Cho, Dae-Hyun Jang
Next-generation sequencing, such as whole-genome sequencing, whole-exome sequencing, and targeted panel sequencing have been applied for diagnosis of many genetic diseases, and are in the process of replacing the traditional methods of genetic analysis. Clinical exome sequencing (CES), which provides not only sequence variation data but also clinical interpretation, aids in reaching a final conclusion with regards to genetic diagnosis. Sequencing of genes with clinical relevance rather than whole exome sequencing might be more suitable for the diagnosis of known hereditary disease with genetic heterogeneity...
December 2016: Annals of Rehabilitation Medicine
https://www.readbyqxmd.com/read/28117820/from-a-natural-product-to-its-biosynthetic-gene-cluster-a-demonstration-using-polyketomycin-from-streptomyces-diastatochromogenes-t%C3%A3-6028
#20
Anja Greule, Songya Zhang, Thomas Paululat, Andreas Bechthold
Streptomyces strains are known for their capability to produce a lot of different compounds with various bioactivities. Cultivation under different conditions often leads to the production of new compounds. Therefore, production cultures of the strains are extracted with ethyl acetate and the crude extracts are analyzed by HPLC. Furthermore, the extracts are tested for their bioactivity by different assays. For structure elucidation the compound of interest is purified by a combination of different chromatography methods...
January 13, 2017: Journal of Visualized Experiments: JoVE
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