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https://www.readbyqxmd.com/read/29343764/genome-wide-association-study-in-79-366-european-ancestry-individuals-informs-the-genetic-architecture-of-25-hydroxyvitamin-d-levels
#1
Xia Jiang, Paul F O'Reilly, Hugues Aschard, Yi-Hsiang Hsu, J Brent Richards, Josée Dupuis, Erik Ingelsson, David Karasik, Stefan Pilz, Diane Berry, Bryan Kestenbaum, Jusheng Zheng, Jianan Luan, Eleni Sofianopoulou, Elizabeth A Streeten, Demetrius Albanes, Pamela L Lutsey, Lu Yao, Weihong Tang, Michael J Econs, Henri Wallaschofski, Henry Völzke, Ang Zhou, Chris Power, Mark I McCarthy, Erin D Michos, Eric Boerwinkle, Stephanie J Weinstein, Neal D Freedman, Wen-Yi Huang, Natasja M Van Schoor, Nathalie van der Velde, Lisette C P G M de Groot, Anke Enneman, L Adrienne Cupples, Sarah L Booth, Ramachandran S Vasan, Ching-Ti Liu, Yanhua Zhou, Samuli Ripatti, Claes Ohlsson, Liesbeth Vandenput, Mattias Lorentzon, Johan G Eriksson, M Kyla Shea, Denise K Houston, Stephen B Kritchevsky, Yongmei Liu, Kurt K Lohman, Luigi Ferrucci, Munro Peacock, Christian Gieger, Marian Beekman, Eline Slagboom, Joris Deelen, Diana van Heemst, Marcus E Kleber, Winfried März, Ian H de Boer, Alexis C Wood, Jerome I Rotter, Stephen S Rich, Cassianne Robinson-Cohen, Martin den Heijer, Marjo-Riitta Jarvelin, Alana Cavadino, Peter K Joshi, James F Wilson, Caroline Hayward, Lars Lind, Karl Michaëlsson, Stella Trompet, M Carola Zillikens, Andre G Uitterlinden, Fernando Rivadeneira, Linda Broer, Lina Zgaga, Harry Campbell, Evropi Theodoratou, Susan M Farrington, Maria Timofeeva, Malcolm G Dunlop, Ana M Valdes, Emmi Tikkanen, Terho Lehtimäki, Leo-Pekka Lyytikäinen, Mika Kähönen, Olli T Raitakari, Vera Mikkilä, M Arfan Ikram, Naveed Sattar, J Wouter Jukema, Nicholas J Wareham, Claudia Langenberg, Nita G Forouhi, Thomas E Gundersen, Kay-Tee Khaw, Adam S Butterworth, John Danesh, Timothy Spector, Thomas J Wang, Elina Hyppönen, Peter Kraft, Douglas P Kiel
Vitamin D is a steroid hormone precursor that is associated with a range of human traits and diseases. Previous GWAS of serum 25-hydroxyvitamin D concentrations have identified four genome-wide significant loci (GC, NADSYN1/DHCR7, CYP2R1, CYP24A1). In this study, we expand the previous SUNLIGHT Consortium GWAS discovery sample size from 16,125 to 79,366 (all European descent). This larger GWAS yields two additional loci harboring genome-wide significant variants (P = 4.7×10-9 at rs8018720 in SEC23A, and P = 1...
January 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29335436/deregulated-pp1%C3%AE-phosphatase-activity-towards-mapk-activation-is-antagonized-by-a-tumor-suppressive-failsafe-mechanism
#2
Ming Chen, Lixin Wan, Jiangwen Zhang, Jinfang Zhang, Lourdes Mendez, John G Clohessy, Kelsey Berry, Joshua Victor, Qing Yin, Yuan Zhu, Wenyi Wei, Pier Paolo Pandolfi
The mitogen-activated protein kinase (MAPK) pathway is frequently aberrantly activated in advanced cancers, including metastatic prostate cancer (CaP). However, activating mutations or gene rearrangements among MAPK signaling components, such as Ras and Raf, are not always observed in cancers with hyperactivated MAPK. The mechanisms underlying MAPK activation in these cancers remain largely elusive. Here we discover that genomic amplification of the PPP1CA gene is highly enriched in metastatic human CaP. We further identify an S6K/PP1α/B-Raf signaling pathway leading to activation of MAPK signaling that is antagonized by the PML tumor suppressor...
January 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29226179/virus-binding-and-internalization-assay-for-adeno-associated-virus
#3
Garrett E Berry, Longping V Tse
The binding and internalization of adeno-associated virus (AAV) is an important determinant of viral infectivity and tropism. The ability to dissect these two tightly connected cellular processes would allow better understanding and provide insight on virus entry and trafficking. In the following protocol, we describe a quantitative PCR (qPCR) based method to determine the amount of vector bound to the cell surface and the amount of subsequent virus internalization based on viral genome quantification. This protocol is optimized for studying AAV...
January 20, 2017: Bio-protocol
https://www.readbyqxmd.com/read/29224864/breeding-a-better-cow-will-she-be-adaptable
#4
D P Berry
Adaption is a process that makes an individual or population more suited to their environment. Long-term adaptation is predicated on ample usable genetic variation. Evolutionary forces influencing the extent and dynamics of genetic variation in a population include random drift, mutation, recombination, selection, and migration; the relative importance of each differs by population (i.e., drift is likely to be more influential in smaller populations) and number of generations exposed to selection (i.e., mutation is expected to contribute substantially to genetic variability following many generations of selection)...
December 7, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29220350/deep-sequencing-of-near-full-length-hiv-1-genomes-from-plasma-identifies-circulating-subtype-c-and-infrequent-occurrence-of-ac-recombinant-form-in-southern-india
#5
Shuba Varshini Alampalli, Michael M Thomson, Raghavan Sampathkumar, Karthi Sivaraman, Anto Jesuraj U K J, Chirag Dhar, George D Souza, Neil Berry, Annapurna Vyakarnam
India has the third largest number of HIV-1-infected individuals accounting for approximately 2.1 million people, with a predominance of circulating subtype C strains and a low prevalence of subtype A and A1C and BC recombinant forms, identified over the past two decades. Recovery of near full-length HIV-1 genomes from a plasma source coupled with advances in next generation sequencing (NGS) technologies and development of universal methods for amplifying whole genomes of HIV-1 circulating in a target geography or population provides the opportunity for a detailed analysis of HIV-1 strain identification, evolution and dynamics...
2017: PloS One
https://www.readbyqxmd.com/read/29217530/the-impact-of-smoking-and-tp53-mutations-in-lung-adenocarcinoma-patients-with-targetable-mutations-the-lung-cancer-mutation-consortium-lcmc2
#6
Dara L Aisner, Lynette M Sholl, Lynne Berry, Michael Rossi, Heidi Chen, Junya Fujimoto, Andre L Moreira, Suresh Ramalingam, Liza C Villaruz, Gregory A Otterson, Eric B Haura, Katerina Politi, Bonnie S Glisson, Jeremy Cetnar, Edward Garon, Joan Schiller, Saiama Waqar, Lecia V Sequist, Julie R Brahmer, Yu Shyr, Kelly Kugler, Ignacio Ivan Wistuba, Bruce E Johnson, John D Minna, Mark G Kris, Paul A Bunn, David J Kwiatkowski
PURPOSE Multiplex genomic profiling is standard of care for patients with advanced lung adenocarcinomas. The Lung Cancer Mutation Consortium (LCMC) is a multi-institutional effort to identify and treat oncogenic driver events in patients with lung adenocarcinomas. PATIENTS AND METHODS Sixteen U.S. institutions enrolled 1367 lung cancer patients in LCMC2; 904 were deemed eligible and had at least one of 14 cancer-related genes profiled using validated methods including genotyping, massively parallel sequencing, and immunohistochemistry...
December 7, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29162903/the-lateral-organ-boundaries-domain-gene-family-in-grapevine-genome-wide-characterization-and-expression-analyses-during-developmental-processes-and-stress-responses
#7
Jérôme Grimplet, Diana Pimentel, Patricia Agudelo-Romero, Jose Miguel Martinez-Zapater, Ana Margarida Fortes
LATERAL ORGAN BOUNDARIES (LOB) DOMAIN (LBD) constitute a family of plant-specific transcription factors with key roles in the regulation of plant organ development, pollen development, plant regeneration, pathogen response, and anthocyanin and nitrogen metabolisms. However, the role of LBDs in fruit ripening and in grapevine (Vitis vinifera L.) development and stress responses is poorly documented. By performing a model curation of LBDs in the latest genome annotation 50 genes were identified. Phylogenetic analysis showed that LBD genes can be grouped into two classes mapping on 16 out of the 19 V...
November 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29153840/association-of-omics-features-with-histopathology-patterns-in-lung-adenocarcinoma
#8
Kun-Hsing Yu, Gerald J Berry, Daniel L Rubin, Christopher Ré, Russ B Altman, Michael Snyder
Adenocarcinoma accounts for more than 40% of lung malignancy, and microscopic pathology evaluation is indispensable for its diagnosis. However, how histopathology findings relate to molecular abnormalities remains largely unknown. Here, we obtained H&E-stained whole-slide histopathology images, pathology reports, RNA sequencing, and proteomics data of 538 lung adenocarcinoma patients from The Cancer Genome Atlas and used these to identify molecular pathways associated with histopathology patterns. We report cell-cycle regulation and nucleotide binding pathways underpinning tumor cell dedifferentiation, and we predicted histology grade using transcriptomics and proteomics signatures (area under curve >0...
November 13, 2017: Cell Systems
https://www.readbyqxmd.com/read/29153091/detection-of-complex-genomic-signatures-associated-with-risk-in-plasma-cell-disorders
#9
Nadine K Berry, Amanda Dixon-McIver, Rodney J Scott, Philip Rowlings, Anoop K Enjeti
Plasma cell disorders (PCD) range from benign to highly malignant disease. The ability to detect risk-stratifying aberrations based on cytogenetic and molecular genetic assays plays an increasing role in therapeutic decision making. In this study, 58 patients were chosen for screening by comparative genomic hybridisation microarray (aCGH) to identify the new high-risk prognostic markers of chromothripsis and chromoanasynthesis. All patients had an unequivocal clinical diagnosis of a plasma cell disorder (plasma cell myeloma (PCM)(n = 51) or monoclonal gammopathy of undetermined significance (MGUS)(n = 7)) and an abnormal FISH result...
December 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29126148/consensus-coding-sequence-ccds-database-a-standardized-set-of-human-and-mouse-protein-coding-regions-supported-by-expert-curation
#10
Shashikant Pujar, Nuala A O'Leary, Catherine M Farrell, Jane E Loveland, Jonathan M Mudge, Craig Wallin, Carlos G Girón, Mark Diekhans, If Barnes, Ruth Bennett, Andrew E Berry, Eric Cox, Claire Davidson, Tamara Goldfarb, Jose M Gonzalez, Toby Hunt, John Jackson, Vinita Joardar, Mike P Kay, Vamsi K Kodali, Fergal J Martin, Monica McAndrews, Kelly M McGarvey, Michael Murphy, Bhanu Rajput, Sanjida H Rangwala, Lillian D Riddick, Ruth L Seal, Marie-Marthe Suner, David Webb, Sophia Zhu, Bronwen L Aken, Elspeth A Bruford, Carol J Bult, Adam Frankish, Terence Murphy, Kim D Pruitt
The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID)...
November 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29104938/vitamin-and-amino-acid-auxotrophy-in-anaerobic-consortia-operating-under-methanogenic-conditions
#11
Valerie Hubalek, Moritz Buck, BoonFei Tan, Julia Foght, Annelie Wendeberg, David Berry, Stefan Bertilsson, Alexander Eiler
Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions...
September 2017: MSystems
https://www.readbyqxmd.com/read/29104582/vvvhp1-2-is-transcriptionally-activated-by-vvmyba1-and-promotes-anthocyanin-accumulation-of-grape-berry-skins-via-glucose-signal
#12
Tianyu Sun, Lili Xu, Hong Sun, Qianyu Yue, Heng Zhai, Yuxin Yao
In this work, four vacuolar H(+)-PPase (VHP) genes were identified in the grape genome. Among them, VvVHP1; 2 was strongly expressed in berry skin and its expression exhibited high correlations to anthocyanin content of berry skin during berry ripening and under ABA and UVB treatments. VvVHP1; 2 was transcriptionally activated directly by VvMYBA1, and VvVHP1; 2 overexpression promoted anthocyanin accumulation in berry skins and Arabidopsis leaves; therefore, VvVHP1; 2 mediated VvMYBA1-regulated berry pigmentation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29080323/seascape-genomics-reveals-fine-scale-patterns-of-dispersal-for-a-reef-fish-along-the-ecologically-divergent-coast-of-northwestern-australia
#13
Joseph D DiBattista, Michael J Travers, Glenn I Moore, Richard D Evans, Stephen J Newman, Ming Feng, Samuel D Moyle, Rebecca J Gorton, Thor Saunders, Oliver Berry
Understanding the drivers of dispersal among populations is a central topic in marine ecology and fundamental for spatially explicit management of marine resources. The extensive coast of Northwestern Australia provides an emerging frontier for implementing new genomic tools to comparatively identify patterns of dispersal across diverse and extreme environmental conditions. Here, we focused on the stripey snapper (Lutjanus carponotatus), which is important to recreational, charter-based and customary fishers throughout the Indo-West Pacific...
October 28, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29058421/authentication-of-zanthoxylum-species-based-on-integrated-analysis-of-complete-chloroplast-genome-sequences-and-metabolite-profiles
#14
Hyeon Ju Lee, Hyun Jo Koo, Jonghoon Lee, Dong Young Lee, Vo Ngoc Linh Giang, Minjung Kim, Hyeonah Shim, Jee Young Park, Ki-Oug Yoo, Sang Hyun Sung, Tae-Jin Yang
We performed chloroplast genome sequencing and comparative analysis of two Rutaceae species, Zanthoxylum schinifolium (Korean pepper tree) and Z. piperitum (Japanese pepper tree), which are medicinal and culinary crops in Asia. We identified more than 837 single nucleotide polymorphisms and 103 insertions/deletions (InDels) based on a comparison of the two chloroplast genomes and developed seven DNA markers derived from five tandem repeats and two InDel variations that discriminated between Korean Zanthoxylum species...
October 23, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29049475/potential-of-aqueous-humor-as-a-surrogate-tumor-biopsy-for-retinoblastoma
#15
Jesse L Berry, Liya Xu, A Linn Murphree, Subramanian Krishnan, Kevin Stachelek, Emily Zolfaghari, Kathleen McGovern, Thomas C Lee, Anders Carlsson, Peter Kuhn, Jonathan W Kim, David Cobrinik, James Hicks
Importance: Retinoblastoma (Rb) is one of the first tumors to have a known genetic etiology. However, because biopsy of this tumor is contraindicated, it has not been possible to define the effects of secondary genetic changes on the disease course. Objective: To investigate whether the aqueous humor (AH) of Rb eyes has sufficient tumor-derived DNA to perform genetic analysis of the tumor, including DNA copy number alterations. Design, Setting, and Participants: This investigation was a case series study at a tertiary care hospital (Children's Hospital Los Angeles) with a large Rb treatment center...
November 1, 2017: JAMA Ophthalmology
https://www.readbyqxmd.com/read/29048594/neptune-a-bioinformatics-tool-for-rapid-discovery-of-genomic-variation-in-bacterial-populations
#16
Eric Marinier, Rahat Zaheer, Chrystal Berry, Kelly A Weedmark, Michael Domaratzki, Philip Mabon, Natalie C Knox, Aleisha R Reimer, Morag R Graham, Linda Chui, Laura Patterson-Fortin, Jian Zhang, Franco Pagotto, Jeff Farber, Jim Mahony, Karine Seyer, Sadjia Bekal, Cécile Tremblay, Judy Isaac-Renton, Natalie Prystajecky, Jessica Chen, Peter Slade, Gary Van Domselaar
The ready availability of vast amounts of genomic sequence data has created the need to rethink comparative genomics algorithms using 'big data' approaches. Neptune is an efficient system for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches. Neptune's loci discovery process identifies sequences that are sufficiently common to a group of target sequences and sufficiently absent from non-targets using probabilistic models...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29039721/a-recurrent-splice-site-mutation-in-epha2-causing-congenital-posterior-nuclear-cataract
#17
Vanita Berry, Nikolas Pontikos, Monica Albarca-Aguilera, Vincent Plagnol, Andreas Massouras, DeQuincy Prescott, Anthony T Moore, Gavin Arno, Michael E Cheetham, Michel Michaelides
Intoduction: Inherited cataract, opacification of the lens, is the most common worldwide cause of blindness in children. We aimed to identify the genetic cause of autosomal dominant (AD) posterior nuclear cataract in a four generation British family. METHODS: Whole genome sequence (WGS) was performed on two affected and one unaffected individual of the family and further validated by direct sequencing. Haplotype analysis was performed via genotying. RESULTS: A splice-site mutation c...
October 17, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/29027367/the-parasporal-crystals-of-bacillus-pumilus-strain-15-1-a-potential-virulence-factor
#18
Diana C Garcia-Ramon, Colin Berry, Carmen Tse, Alberto Fernández-Fernández, Antonio Osuna, Susana Vílchez
Bacillus pumilus strain 15.1 was previously found to cause larval mortality in the Med-fly Ceratitis capitata and was shown to produce crystals in association with the spore. As parasporal crystals are well-known as invertebrate-active toxins in entomopathogenic bacteria such as Bacillus thuringiensis (Cry and Cyt toxins) and Lysinibacillus sphaericus (Bin and Cry toxins), the B. pumilus crystals were characterized. The crystals were composed of a 45 kDa protein that was identified as an oxalate decarboxylase by peptide mass fingerprinting, N-terminal sequencing and by comparison with the genome sequence of strain 15...
October 12, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/29020009/genome-sequences-of-lower-great-lakes-microcystis-sp-reveal-strain-specific-genes-that-are-present-and-expressed-in-western-lake-erie-blooms
#19
Kevin Anthony Meyer, Timothy W Davis, Susan B Watson, Vincent J Denef, Michelle A Berry, Gregory J Dick
Blooms of the potentially toxic cyanobacterium Microcystis are increasing worldwide. In the Laurentian Great Lakes they pose major socioeconomic, ecological, and human health threats, particularly in western Lake Erie. However, the interpretation of "omics" data is constrained by the highly variable genome of Microcystis and the small number of reference genome sequences from strains isolated from the Great Lakes. To address this, we sequenced two Microcystis isolates from Lake Erie (Microcystis aeruginosa LE3 and M...
2017: PloS One
https://www.readbyqxmd.com/read/29019092/rapid-detection-of-human-norovirus-in-frozen-raspberries
#20
Maija Summa, Leena Maunula
Raspberries have lately caused several human norovirus (HuNoV) outbreaks in Europe. In this study, we developed and evaluated for HuNoV reverse transcription (RT)-PCR detection in frozen raspberries extraction methods that have equal sensitivity but are less time-consuming than widely used methods based on polyethylene glycol (PEG) precipitation and chloroform-butanol purification. One method was applied to stored frozen raspberries linked to previous HuNoV outbreaks and berries on sale. In the virus elution-based Method 1, sparkling water eluted viruses most efficiently from the berries...
October 10, 2017: Food and Environmental Virology
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