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https://www.readbyqxmd.com/read/29146772/cre-dependent-cas9-expressing-pigs-enable-efficient-in-vivo-genome-editing
#1
Kepin Wang, Qin Jin, Degong Ruan, Yi Yang, Qishuai Liu, Han Wu, Zhiwei Zhou, Zhen Ouyang, Zhaoming Liu, Yu Zhao, Bentian Zhao, Quanjun Zhang, Jiangyun Peng, Chengdan Lai, Nana Fan, Yanhui Liang, Ting Lan, Nan Li, Xiaoshan Wang, Xinlu Wang, Yong Fan, Pieter A Doevendans, Joost P G Sluijter, Pentao Liu, Xiaoping Li, Liangxue Lai
Despite being time-consuming and costly, generating genome-edited pigs holds great promise for agricultural, biomedical, and pharmaceutical applications. To further facilitate genome editing in pigs, we report here establishment of a pig line with Cre-inducible Cas9 expression that allows a variety of ex vivo genome editing in fibroblast cells including single- and multigene modifications, chromosome rearrangements, and efficient in vivo genetic modifications. As a proof of principle, we were able to simultaneously inactivate five tumor suppressor genes (TP53, PTEN, APC, BRCA1, and BRCA2) and activate one oncogene (KRAS), achieved by delivering Cre recombinase and sgRNAs, which caused rapid lung tumor development...
November 16, 2017: Genome Research
https://www.readbyqxmd.com/read/29143596/genetic-testing-for-exercise-prescription-and-injury-prevention-ais-athlome-consortium-fims-joint-statement
#2
REVIEW
Nicole Vlahovich, David C Hughes, Lyn R Griffiths, Guan Wang, Yannis P Pitsiladis, Fabio Pigozzi, Nobert Bachl, Nir Eynon
BACKGROUND: There has been considerable growth in basic knowledge and understanding of how genes are influencing response to exercise training and predisposition to injuries and chronic diseases. On the basis of this knowledge, clinical genetic tests may in the future allow the personalisation and optimisation of physical activity, thus providing an avenue for increased efficiency of exercise prescription for health and disease. RESULTS: This review provides an overview of the current status of genetic testing for the purposes of exercise prescription and injury prevention...
November 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29140263/access-to-guideline-recommended-pharmacogenomic-tests-for-cancer-treatments-experience-of-providers-and-patients
#3
Ann Chen Wu, Kathleen M Mazor, Rachel Ceccarelli, Stephanie Loomer, Christine Y Lu
Genomic tests are the fastest growing sector in medicine and medical science, yet there remains a dearth of research on access to pharmacogenomic tests and medications. The objective of this study is to explore providers' and patients' experiences and views on test access as well as strategies used for gaining access. We interviewed clinicians who prescribed medications that should be guided by pharmacogenomic testing and patients who received those prescriptions. We organized the themes into the four dimensions suggested by the World Health Organization framework on access to medications and health technologies...
November 15, 2017: Journal of Personalized Medicine
https://www.readbyqxmd.com/read/29138689/clarifying-sub-genomic-positions-of-qtls-for-flowering-habit-and-fruit-quality-in-u-s-strawberry-fragaria%C3%A3-ananassa-breeding-populations-using-pedigree-based-qtl-analysis
#4
Sujeet Verma, Jason D Zurn, Natalia Salinas, Megan M Mathey, Beatrice Denoyes, James F Hancock, Chad E Finn, Nahla V Bassil, Vance M Whitaker
The cultivated strawberry (Fragaria×ananassa) is consumed worldwide for its flavor and nutritional benefits. Genetic analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this species. Although several quantitative trait loci (QTL) have been previously detected for fruit quality and flowering traits using low-density genetic maps, clarity on the sub-genomic locations of these QTLs was missing. Recent discoveries in allo-octoploid strawberry genomics led to the development of the IStraw90 single-nucleotide polymorphism (SNP) array, enabling high-density genetic maps and finer resolution QTL analysis...
2017: Horticulture Research
https://www.readbyqxmd.com/read/29137598/gff3sort-a-novel-tool-to-sort-gff3-files-for-tabix-indexing
#5
Tao Zhu, Chengzhen Liang, Zhigang Meng, Sandui Guo, Rui Zhang
BACKGROUND: The traditional method of visualizing gene annotation data in JBrowse is converting GFF3 files to JSON format, which is time-consuming. The latest version of JBrowse supports rendering sorted GFF3 files indexed by tabix, a novel strategy that is more convenient than the original conversion process. However, current tools available for GFF3 file sorting have some limitations and their sorting results would lead to erroneous rendering in JBrowse. RESULTS: We developed GFF3sort, a script to sort GFF3 files for tabix indexing...
November 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29136087/the-utility-and-perspectives-of-ngs-based-methods-in-bsl-3-and-bsl-4-laboratory-sequencing-and-analysis-strategies
#6
Tomasz Wolkowicz
Modern diagnostics is in general based on molecular biology methods. Nowadays sequencing-based methods, especially whole genome sequencing, are becoming increasingly important. Implementation of such methods into routine diagnostic of highly dangerous pathogens, like Bacillus anthracis, Francisella tularensis, Yersinia pestis, Ebola virus, MERS, Lassa virus etc. would be very helpful. The best diagnostic strategy would be the metagenomic sequencing directly from the clinical sample. Implementation of majority of currently available WGS platforms inside the BSL-3 or 4 laboratory is impractical because of the size of the equipment and time consuming wet lab part (e...
November 10, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29134551/the-dangers-of-direct-to-consumer-genetic%C3%A2-testing%C3%A2-for-alzheimer-s-disease-comment-on-personal-genomic-testing-genetic-inheritance-and-uncertainty
#7
Paul Lacaze, Jane Tiller, Joanne Ryan
The overarching issue with this case study is poor regulation and quality control over direct-to-consumer genetic testing, delivered in the absence of any medical oversight.
November 13, 2017: Journal of Bioethical Inquiry
https://www.readbyqxmd.com/read/29130778/lack-of-induced-mutagenesis-in-e-coli-or-human-lymphoblast-cell-line-upon-long-term-sub-culturing-in-medium-from-irradiated-meat
#8
Sachin N Hajare, Jyoti Tripathi, Satyendra Gautam
PURPOSE: Current study was aimed to enhance the confidence of consumers as well as entrepreneurs towards food irradiation program. MATERIALS AND METHODS: In this work, safety of high dose (25 kGy) irradiated meat samples (HDIMS) was ascertained by scoring mutation frequency through a long-term sub-culturing study in Escherichia coli MG1655 cells (ATCC 700926) up to 1500 generations (at 1%), 250 generations (at 5 and 10%) and human lymphoblast thymidine kinase heterozygote (TK6) cell line (ATCC CRL-8015) [at two gene loci, tk(-/+) (thymidine kinase) and hprt(+) (Hypoxanthine Phosphoribosyltransferase)] up to 156 generations using goat meat sample...
November 13, 2017: International Journal of Radiation Biology
https://www.readbyqxmd.com/read/29130150/predictors-of-adverse-psychological-experiences-surrounding-genome-wide-profiling-for-disease-risk
#9
K M Broady, K E Ormond, E J Topol, N J Schork, Cinnamon S Bloss
This study aimed to identify predictors of adverse psychological experiences among direct-to-consumer (DTC) genomic test consumers. We performed a secondary analysis on data from the Scripps Genomic Health Initiative (SGHI), which studied 2037 individuals tested with commercially available tests yielding personalized risk estimates for 23 common, genetically complex diseases. As part of the original study, the participants completed baseline and follow-up survey measures assessing demographics, personal and family health history, attitudes toward genetic testing, anxiety (State-Trait Anxiety Inventory (STAI)), test-related distress (Impact of Event Scale-Revised (IES-R)), and reactions to receipt of results...
November 13, 2017: Journal of Community Genetics
https://www.readbyqxmd.com/read/29126473/a-luminescent-probe-of-mismatched-dna-hybridization-location-and-number-of-mismatches
#10
Amira F El-Yazbi, Alysha Wong, Glen R Loppnow
The human genome is susceptible to change; base mismatches can arise from damaged DNA, replication errors, and spontaneous mutation, and have the potential to cause apoptosis, carcinogenesis, and mutagenesis. Many techniques have been developed for DNA mismatch detection, but many of these methods have complex, time-consuming procedures and are limited to the detection of specific types of DNA mismatches. In this work, we present a general method for the simple and sensitive nucleobase-sensitized luminescent detection of mismatches in double-stranded DNA (dsDNA) using terbium ions...
November 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29122835/multiple-hotspot-mutations-scanning-by-single-droplet-digital-pcr
#11
Charles Decraene, Amanda Silveira, François-Clément Bidard, Audrey Vallee, Marc Michel, Samia Melaabi, Anne Vincent-Salomon, Adrien Saliou, Alexandre Houy, Maud Milder, Olivier Lantz, Marc Ychou, Marc G Denis, Jean-Yves Pierga, Marc-Henri Stern, Charlotte Proudhon
BACKGROUND: Progress in the liquid biopsy field, combined with the development of droplet digital PCR (ddPCR)(12), has enabled noninvasive monitoring of mutations with high detection accuracy. However, current assays detect a restricted number of mutations per reaction. ddPCR is a recognized method for detecting alterations previously characterized in tumor tissues, but its use as a discovery tool when the mutation is unknown a priori remains limited. METHODS: We established 2 ddPCR assays detecting all genomic alterations within KRAS() exon 2 and EGFR exon 19 mutation hotspots, which are of clinical importance in colorectal and lung cancer, with use of a unique pair of TaqMan® oligoprobes...
November 9, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/29120619/a-rapid-throughput-method-to-extract-dna-from-formalin-fixed-paraffin-embedded-tissues-for-biomonitoring-carcinogenic-dna-adducts-in-humans
#12
Byeong Hwa Yun, Shun Xiao, Lihua Yao, Sesha Krishnamachari, Thomas A Rosenquist, Kathleen G Dickman, Arthur P Grollman, Paari Murugan, Christopher J Weight, Robert J Turesky
Formalin-fixed paraffin-embedded (FFPE) tissues are rarely used for screening DNA adducts of carcinogens because the harsh conditions required to reverse the formaldehyde-mediated DNA cross-links can destroy DNA adducts. We recently adapted a commercial silica-based column kit used in genomics to manually isolate DNA under mild conditions from FFPE tissues of rodents and humans and successfully measured DNA adducts of several carcinogens including aristolochic acid I (AA-I), 4-aminobiphenyl (4-ABP), and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) (Yun et al...
November 9, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/29118994/interval-mapping-for-red-green-skin-color-in-asian-pears-using-a-modified-qtl-seq-method
#13
Huabai Xue, Ting Shi, Fangfang Wang, Huangkai Zhou, Jian Yang, Long Wang, Suke Wang, Yanli Su, Zhen Zhang, Yushan Qiao, Xiugen Li
Pears with red skin are attractive to consumers and provide additional health benefits. Identification of the gene(s) responsible for skin coloration can benefit cultivar selection and breeding. The use of QTL-seq, a bulked segregant analysis method, can be problematic when heterozygous parents are involved. The present study modified the QTL-seq method by introducing a |Δ(SNP-index)| parameter to improve the accuracy of mapping the red skin trait in a group of highly heterozygous Asian pears. The analyses were based on mixed DNA pools composed of 28 red-skinned and 27 green-skinned pear lines derived from a cross between the 'Mantianhong' and 'Hongxiangsu' red-skinned cultivars...
2017: Horticulture Research
https://www.readbyqxmd.com/read/29118826/prevalence-of-hpv-infection-in-hypopharyngeal-and-laryngeal-squamous-cell-carcinoma-at-thailand-s-largest-tertiary-referral-center
#14
Warut Pongsapich, Nitathip Eakkasem, Sontana Siritantikorn, Paveena Pithuksurachai, Kshidej Bongsabhikul, Cheerasook Chongkolwatana
Background: Following the well-established relationship between human papillomavirus (HPV) and cervical carcinoma, the carcinogenicity of this virus has also been confirmed in subsets of head and neck carcinoma (HNCA), but mainly in the oropharynx. Other subsites of HNCA with less known association to HPV have never been studied in Thailand. Accordingly, the aim of this study was to investigate the prevalence of HPV DNA in hypopharyngeal and laryngeal squamous cell carcinoma in Thai population...
2017: Infectious Agents and Cancer
https://www.readbyqxmd.com/read/29113723/association-between-fruit-and-vegetable-consumption-and-risk-of-hypertension-in-middle-aged-and-older-korean-adults
#15
Jiwon Kim, Jihye Kim
BACKGROUND: High fruit and vegetable (F/V) intake may be beneficial for hypertension prevention. However, a prospective association has not been investigated in a Korean population, and differences exist between typical diets in Korea and those of Western populations. OBJECTIVE: The aim of this prospective study was to investigate the association between F/V intake and risk of incident hypertension in middle-aged and older Korean adults using the data from the Korean Genome and Epidemiology Study (KoGES)...
November 4, 2017: Journal of the Academy of Nutrition and Dietetics
https://www.readbyqxmd.com/read/29112135/rapid-construction-of-complex-plant-rna-virus-infectious-cdna-clones-for-agroinfection-using-a-yeast-e-coli-agrobacterium-shuttle-vector
#16
Kai Sun, Danyang Zhao, Yong Liu, Changjun Huang, Wei Zhang, Zhenghe Li
The availability of infectious full-length clone is indispensable for reverse genetics studies of virus biology, pathology and construction of viral vectors. However, for RNA viruses with large genome sizes or those exhibiting inherent cloning difficulties, procedure to generate biologically active circular DNA (cDNA) clones can be time-consuming or technically challenging. Here we have constructed a yeast-Escherichia coli-Agrobacterium shuttle vector that enables highly efficient homologous recombination in yeast for assembly of Agrobacterium compatible plant virus clones...
November 7, 2017: Viruses
https://www.readbyqxmd.com/read/29109180/isolation-of-aggressive-behavior-mutants-in-drosophila%C3%A2-using-a-screen-for-wing-damage
#17
Shaun M Davis, Amanda L Thomas, Lingzhi Liu, Ian M Campbell, Herman A Dierick
Aggression is a complex social behavior that is widespread in nature. To date only a limited number of genes that affect aggression have been identified, in large part because the complexity of the phenotype makes screening difficult and time consuming regardless of the species that is studied. We discovered that aggressive group-housed Drosophila melanogaster males inflict damage on each other's wings, and show that wing damage negatively affects their ability to fly and mate. Using this wing-damage phenotype, we screened males from ~1,400 chemically mutagenized strains and found ~40 mutant strains with substantial wing damage...
November 6, 2017: Genetics
https://www.readbyqxmd.com/read/29107015/ikcr-pseens-identify-lysine-crotonylation-sites-in-histone-proteins-with-pseudo-components-and-ensemble-classifier
#18
Wang-Ren Qiu, Bi-Qian Sun, Xuan Xiao, Zhao-Chun Xu, Jian-Hua Jia, Kuo-Chen Chou
Lysine crotonylation (Kcr) is an evolution-conserved histone posttranslational modification (PTM), occurring in both human somatic and mouse male germ cell genomes. It is important for male germ cell differentiation. Information of Kcr sites in proteins is very useful for both basic research and drug development. But it is time-consuming and expensive to determine them by experiments alone. Here, we report a novel predictor called iKcr-PseEns that is established by incorporating five tiers of amino acid pairwise couplings into the general pseudo amino acid composition...
October 26, 2017: Genomics
https://www.readbyqxmd.com/read/29105249/mimicking-microbial-interactions-under-nitrate-reducing-conditions-in-an-anoxic-bioreactor-enrichment-of-novel-nitrospirae-bacteria-distantly-related-to-thermodesulfovibrio
#19
Arslan Arshad, Paula Dalcin Martins, Jeroen Frank, Mike S M Jetten, Huub J M Op den Camp, Cornelia U Welte
Microorganisms are main drivers of the sulfur, nitrogen and carbon biogeochemical cycles. These element cycles are interconnected by the activity of different guilds in e.g. sediments or wastewater treatment systems. Here, we investigated a nitrate-reducing microbial community in a laboratory-scale bioreactor model that closely mimicked estuary or brackish sediment conditions. The bioreactor simultaneously consumed sulfide, methane and ammonium at the expense of nitrate. Ammonium oxidation occurred solely by the activity of anammox bacteria identified as Candidatus Scalindua brodae and Ca...
November 3, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29104933/heat-resistance-mediated-by-plm58-plasmid-borne-clpl-in-listeria-monocytogenes
#20
Anna Pöntinen, Mariella Aalto-Araneda, Miia Lindström, Hannu Korkeala
Listeria monocytogenes is one of the most heat-resistant non-spore-forming food-borne pathogens and poses a notable risk to food safety, particularly when mild heat treatments are used in food processing and preparation. While general heat stress properties and response mechanisms of L. monocytogenes have been described, accessory mechanisms providing particular L. monocytogenes strains with the advantage of enhanced heat resistance are unknown. Here, we report plasmid-mediated heat resistance of L. monocytogenes for the first time...
November 2017: MSphere
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