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https://www.readbyqxmd.com/read/28446914/constructing-integrated-networks-for-identifying-new-secondary-metabolic-pathway-regulators-in-grapevine-recent-applications-and-future-opportunities
#1
Darren C J Wong, José Tomás Matus
Representing large biological data as networks is becoming increasingly adopted for predicting gene function while elucidating the multifaceted organization of life processes. In grapevine (Vitis vinifera L.), network analyses have been mostly adopted to contribute to the understanding of the regulatory mechanisms that control berry composition. Whereas, some studies have used gene co-expression networks to find common pathways and putative targets for transcription factors related to development and metabolism, others have defined networks of primary and secondary metabolites for characterizing the main metabolic differences between cultivars throughout fruit ripening...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28380529/characterization-of-an-x-chromosomal-non-mosaic-monosomy-59-x0-dairy-heifer-detected-using-routinely-available-single-nucleotide-polymorphism-genotype-data
#2
D P Berry, A Wolfe, J O'Donovan, N Byrne, R G Sayers, K G Dodds, J C McEwan, R E O'Connor, M McClure, D C Purfield
Evidence exists from a range of species on the impact of karyotype abnormalities on reproductive performance. Despite this, cytogenetic analyses of cattle, especially females, are not routinely undertaken. Genome-wide single nucleotide polymorphism (SNP) genotype data are now, however, routinely being generated in many species globally at a relatively low cost. The objective of the present study was to evaluate the potential of routinely available SNP genotype data to identify sex-chromosome aberrations using X chromosome monosomy 59,X0 as a case study for illustration...
March 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28370629/a-group-of-grapevine-myba-transcription-factors-located-in-chromosome-14-control-anthocyanin-synthesis-in-vegetative-organs-with-different-specificities-compared-to-the-berry-color-locus
#3
José Tomás Matus, Erika Cavallini, Rodrigo Loyola, Janine Höll, Laura Finezzo, Silvia Dal Santo, Sandrine Vialet, Mauro Commisso, Federica Roman, Andrea Schubert, José Antonio Alcalde, Jochen Bogs, Agnès Ageorges, Giovanni Battista Tornielli, Patricio Arce-Johnson
Grapevine organs accumulate anthocyanins in a cultivar-specific and environmentally induced manner. The MYBA1-A2 genes within the berry color locus in chromosome 2 represent the major genetic determinants of fruit color. The simultaneous occurrence of transposon insertions and point mutations in these genes is responsible for most white-skinned phenotypes. However, red pigmentation found in vegetative organs suggests the presence of additional regulators. This work describes a genomic region of chromosome 14 containing three closely related R2R3-MYB genes, named MYBA5, MYBA6 and MYBA7...
April 2, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28344990/inspiired-a-pipeline-for-quantitative-analysis-of-sites-of-new-dna-integration-in-cellular-genomes
#4
Eric Sherman, Christopher Nobles, Charles C Berry, Emmanuelle Six, Yinghua Wu, Anatoly Dryga, Nirav Malani, Frances Male, Shantan Reddy, Aubrey Bailey, Kyle Bittinger, John K Everett, Laure Caccavelli, Mary J Drake, Paul Bates, Salima Hacein-Bey-Abina, Marina Cavazzana, Frederic D Bushman
Integration of new DNA into cellular genomes mediates replication of retroviruses and transposons; integration reactions have also been adapted for use in human gene therapy. Tracking the distributions of integration sites is important to characterize populations of transduced cells and to monitor potential outgrow of pathogenic cell clones. Here, we describe a pipeline for quantitative analysis of integration site distributions named INSPIIRED (integration site pipeline for paired-end reads). We describe optimized biochemical steps for site isolation using Illumina paired-end sequencing, including new technology for suppressing recovery of unwanted contaminants, then software for alignment, quality control, and management of integration site sequences...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28344988/inspiired-quantification-and-visualization-tools-for-analyzing-integration-site-distributions
#5
Charles C Berry, Christopher Nobles, Emmanuelle Six, Yinghua Wu, Nirav Malani, Eric Sherman, Anatoly Dryga, John K Everett, Frances Male, Aubrey Bailey, Kyle Bittinger, Mary J Drake, Laure Caccavelli, Paul Bates, Salima Hacein-Bey-Abina, Marina Cavazzana, Frederic D Bushman
Analysis of sites of newly integrated DNA in cellular genomes is important to several fields, but methods for analyzing and visualizing these datasets are still under development. Here, we describe tools for data analysis and visualization that take as input integration site data from our INSPIIRED pipeline. Paired-end sequencing allows inference of the numbers of transduced cells as well as the distributions of integration sites in target genomes. We present interactive heatmaps that allow comparison of distributions of integration sites to genomic features and that support numerous user-defined statistical tests...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28341805/correction-the-high-polyphenol-content-of-grapevine-cultivar-tannat-berries-is-conferred-primarily-by-genes-that-are-not-shared-with-the-reference-genome
#6
https://www.readbyqxmd.com/read/28338755/red-blotch-disease-alters-grape-berry-development-and-metabolism-by-interfering-with-the-transcriptional-and-hormonal-regulation-of-ripening
#7
Barbara Blanco-Ulate, Helene Hopfer, Rosa Figueroa-Balderas, Zirou Ye, Rosa M Rivero, Alfonso Albacete, Francisco Pérez-Alfocea, Renata Koyama, Michael M Anderson, Rhonda J Smith, Susan E Ebeler, Dario Cantu
Grapevine red blotch-associated virus (GRBaV) is a major threat to the wine industry in the USA. GRBaV infections (aka red blotch disease) compromise crop yield and berry chemical composition, affecting the flavor and aroma properties of must and wine. In this study, we combined genome-wide transcriptional profiling with targeted metabolite analyses and biochemical assays to characterize the impact of the disease on red-skinned berry ripening and metabolism. Using naturally infected berries collected from two vineyards, we were able to identify consistent berry responses to GRBaV across different environmental and cultural conditions...
February 1, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28337183/are-oligotypes-meaningful-ecological-and-phylogenetic-units-a-case-study-of-microcystis-in-freshwater-lakes
#8
Michelle A Berry, Jeffrey D White, Timothy W Davis, Sunit Jain, Thomas H Johengen, Gregory J Dick, Orlando Sarnelle, Vincent J Denef
Oligotyping is a computational method used to increase the resolution of marker gene microbiome studies. Although oligotyping can distinguish highly similar sequence variants, the resulting units are not necessarily phylogenetically and ecologically informative due to limitations of the selected marker gene. In this perspective, we examine how oligotyping data is interpreted in recent literature, and we illustrate some of the method's constraints with a case study of the harmful bloom-forming cyanobacterium Microcystis...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28247243/grape-hexokinases-are-involved-in-the-expression-regulation-of-sucrose-synthase-and-cell-wall-invertase-encoding-genes-by-glucose-and-aba
#9
Xiu-Qin Wang, Li-Li Zheng, Hao Lin, Fei Yu, Li-Hui Sun, Li-Mei Li
Hexokinase (HXK, EC 2.7.1.1) is a multifunctional protein that both is involved in catalyzing the first step of glycolysis and plays an important role in sugar signaling. However, the supporting genetic evidence on hexokinases (CsHXKs) from grape (Vitis vinifera L. cv. Cabernet Sauvignon) berries has been lacking. Here, to investigate the role of CsHXK isoforms as glucose (Glc) and abscisic acid (ABA) sensors, we cloned two hexokinase isozymes, CsHXK1 and CsHXK2 with highly conserved genomic structure of nine exons and eight introns...
February 28, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28209818/complete-genome-sequence-of-the-who-international-standard-for-hepatitis-b-virus-dna
#10
Adrian Jenkins, Rehan Minhas, Clare Morris, Neil Berry
The World Health Organization (WHO) international standard (IS) for hepatitis B virus (HBV) DNA for use in nucleic acid amplification assays was characterized by determining the complete genome sequence, which was assigned genotype A. This information will aid the design, development, and evaluation of HBV DNA amplification assays.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28204924/genome-wide-analysis-of-transposable-elements-in-the-coffee-berry-borer-hypothenemus-hampei-coleoptera-curculionidae-description-of-novel-families
#11
Eric M Hernandez-Hernandez, Rita Daniela Fernández-Medina, Lucio Navarro-Escalante, Jonathan Nuñez, Pablo Benavides-Machado, Claudia M A Carareto
The coffee berry borer (CBB) Hypothenemus hampei is the most limiting pest of coffee production worldwide. The CBB genome has been recently sequenced; however, information regarding the presence and characteristics of transposable elements (TEs) was not provided. Using systematic searching strategies based on both de novo and homology-based approaches, we present a library of TEs from the draft genome of CBB sequenced by the Colombian Coffee Growers Federation. The library consists of 880 sequences classified as 66% Class I (LTRs: 46%, non-LTRs: 20%) and 34% Class II (DNA transposons: 8%, Helitrons: 16% and MITEs: 10%) elements, including families of the three main LTR (Gypsy, Bel-Pao and Copia) and non-LTR (CR1, Daphne, I/Nimb, Jockey, Kiri, R1, R2 and R4) clades and DNA superfamilies (Tc1-mariner, hAT, Merlin, P, PIF-Harbinger, PiggyBac and Helitron)...
February 15, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28198009/endoscopic-ultrasound-guided-fine-needle-aspirate-derived-preclinical-pancreatic-cancer-models-reveal-panitumumab-sensitivity-in-kras-wild-type-tumors
#12
William Berry, Elizabeth Algar, Beena Kumar, Christopher Desmond, Michael Swan, Brendan J Jenkins, Daniel Croagh
Pancreatic cancer (PC) is largely refractory to existing therapies used in unselected patient trials, thus emphasizing the pressing need for new approaches for patient selection in personalized medicine. KRAS mutations occur in 90% of PC patients and confer resistance to epidermal growth factor receptor (EGFR) inhibitors (e.g., panitumumab), suggesting that KRAS wild-type PC patients may benefit from targeted panitumumab therapy. Here, we use tumor tissue procured by endoscopic ultrasound-guided fine-needle aspirate (EUS-FNA) to compare the in vivo sensitivity in patient-derived xenografts (PDXs) of KRAS wild-type and mutant PC tumors to panitumumab, and to profile the molecular signature of these tumors in patients with metastatic or localized disease...
February 15, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28187155/in-silico-identification-and-annotation-of-non-coding-rnas-by-rna-seq-and-de-novo-assembly-of-the-transcriptome-of-tomato-fruits
#13
Daria Scarano, Rosa Rao, Giandomenico Corrado
The complexity of the tomato (Solanum lycopersicum) transcriptome has not yet been fully elucidated. To gain insights into the diversity and features of coding and non-coding RNA molecules of tomato fruits, we generated strand-specific libraries from berries of two tomato cultivars grown in two open-field conditions with different soil type. Following high-throughput Illumina RNA-sequencing (RNA-seq), more than 90% of the reads (over one billion, derived from twelve dataset) were aligned to the tomato reference genome...
2017: PloS One
https://www.readbyqxmd.com/read/28185084/-schistosomose-urog%C3%A3-nitale-et-cancer
#14
A Berry, X Iriart, J Fillaux, J-F Magnaval
The existence of a link between urinary schistosomiasis (US) and bladder carcinoma was first suspected by C. Goebel in 1905. In 1911, A.R Ferguson, who was a professor of Pathology and Microbiology at the Faculty of Medicine in Cairo, published a more detailed survey from 40 autopsies, and reported a likely association of bladder carcinoma with granulomas caused by US. Subsequently, published results from several studies reinforced Ferguson's hypothesis. Moreover, in most countries where US was endemic, association of high prevalence of bladder carcinoma with US had been pointed out...
February 10, 2017: Bulletin de la Société de Pathologie Exotique
https://www.readbyqxmd.com/read/28168224/lifestyle-and-horizontal-gene-transfer-mediated-evolution-of-mucispirillum-schaedleri-a-core-member-of-the-murine-gut-microbiota
#15
Alexander Loy, Carina Pfann, Michaela Steinberger, Buck Hanson, Simone Herp, Sandrine Brugiroux, João Carlos Gomes Neto, Mark V Boekschoten, Clarissa Schwab, Tim Urich, Amanda E Ramer-Tait, Thomas Rattei, Bärbel Stecher, David Berry
Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides...
January 2017: MSystems
https://www.readbyqxmd.com/read/28162992/adherence-to-clinic-recommendations-among-patients-with-phenylketonuria-in-the-united-states
#16
E R Jurecki, S Cederbaum, J Kopesky, K Perry, F Rohr, A Sanchez-Valle, K S Viau, M Y Sheinin, J L Cohen-Pfeffer
OBJECTIVE: Assess current management practices of phenylketonuria (PKU) clinics across the United States (US) based on the key treatment metrics of blood phenylalanine (Phe) concentrations and blood Phe testing frequency, as well as patient adherence to their clinic's management practice recommendations. METHODS: An online survey was conducted with medical professionals from PKU clinics across the US from July to September 2015. Forty-four clinics participated in the survey and account for approximately half of PKU patients currently followed in clinics in the US (Berry et al...
March 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/28139704/predictive-radiogenomics-modeling-of-egfr-mutation-status-in-lung-cancer
#17
Olivier Gevaert, Sebastian Echegaray, Amanda Khuong, Chuong D Hoang, Joseph B Shrager, Kirstin C Jensen, Gerald J Berry, H Henry Guo, Charles Lau, Sylvia K Plevritis, Daniel L Rubin, Sandy Napel, Ann N Leung
Molecular analysis of the mutation status for EGFR and KRAS are now routine in the management of non-small cell lung cancer. Radiogenomics, the linking of medical images with the genomic properties of human tumors, provides exciting opportunities for non-invasive diagnostics and prognostics. We investigated whether EGFR and KRAS mutation status can be predicted using imaging data. To accomplish this, we studied 186 cases of NSCLC with preoperative thin-slice CT scans. A thoracic radiologist annotated 89 semantic image features of each patient's tumor...
January 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28118385/rna-sequencing-reveals-biological-networks-during-table-grapevine-fujiminori-fruit-development
#18
Lingfei Shangguan, Qian Mu, Xiang Fang, Kekun Zhang, Haifeng Jia, Xiaoying Li, Yiqun Bao, Jinggui Fang
Grapevine berry development is a complex and genetically controlled process, with many morphological, biochemical and physiological changes occurring during the maturation process. Research carried out on grapevine berry development has been mainly concerned with wine grape, while barely focusing on table grape. 'Fujiminori' is an important table grapevine cultivar, which is cultivated in most provinces of China. In order to uncover the dynamic networks involved in anthocyanin biosynthesis, cell wall development, lipid metabolism and starch-sugar metabolism in 'Fujiminori' fruit, we employed RNA-sequencing (RNA-seq) and analyzed the whole transcriptome of grape berry during development at the expanding period (40 days after full bloom, 40DAF), véraison period (65DAF), and mature period (90DAF)...
2017: PloS One
https://www.readbyqxmd.com/read/28116755/gene-expression-atlas-for-the-food-security-crop-cassava
#19
Mark C Wilson, Andrew M Mutka, Aaron W Hummel, Jeffrey Berry, Raj Deepika Chauhan, Anupama Vijayaraghavan, Nigel J Taylor, Daniel F Voytas, Daniel H Chitwood, Rebecca S Bart
Cassava (Manihot esculenta) feeds c. 800 million people world-wide. Although this crop displays high productivity under drought and poor soil conditions, it is susceptible to disease, postharvest deterioration and the roots contain low nutritional content. Here, we provide molecular identities for 11 cassava tissue/organ types through RNA-sequencing and develop an open access, web-based interface for further interrogation of the data. Through this dataset, we consider the physiology of cassava. Specifically, we focus on identification of the transcriptional signatures that define the massive, underground storage roots used as a food source and the favored target tissue for transgene integration and genome editing, friable embryogenic callus (FEC)...
January 24, 2017: New Phytologist
https://www.readbyqxmd.com/read/28034300/frequency-of-influenza-h3n2-intra-subtype-reassortment-attributes-and-implications-of-reassortant-spread
#20
Irina Maljkovic Berry, Melanie C Melendrez, Tao Li, Anthony W Hawksworth, Gary T Brice, Patrick J Blair, Eric S Halsey, Maya Williams, Stefan Fernandez, In-Kyu Yoon, Leslie D Edwards, Robert Kuschner, Xiaoxu Lin, Stephen J Thomas, Richard G Jarman
BACKGROUND: Increasing evidence suggests that influenza reassortment not only contributes to the emergence of new human pandemics but also plays an important role in seasonal influenza epidemics, disease severity, evolution, and vaccine efficacy. We studied this process within 2091 H3N2 full genomes utilizing a combination of the latest reassortment detection tools and more conventional phylogenetic analyses. RESULTS: We found that the amount of H3N2 intra-subtype reassortment depended on the number of sampled genomes, occurred with a steady frequency of 3...
December 29, 2016: BMC Biology
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