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berry genomics

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https://www.readbyqxmd.com/read/27910897/genomic-variations-leading-to-alterations-in-cell-morphology-of-campylobacter-spp
#1
Diane Esson, Alison E Mather, Eoin Scanlan, Srishti Gupta, Stefan P W de Vries, David Bailey, Simon R Harris, Trevelyan J McKinley, Guillaume Méric, Sophia K Berry, Pietro Mastroeni, Samuel K Sheppard, Graham Christie, Nicholas R Thomson, Julian Parkhill, Duncan J Maskell, Andrew J Grant
Campylobacter jejuni, the most common cause of bacterial diarrhoeal disease, is normally helical. However, it can also adopt straight rod, elongated helical and coccoid forms. Studying how helical morphology is generated, and how it switches between its different forms, is an important objective for understanding this pathogen. Here, we aimed to determine the genetic factors involved in generating the helical shape of Campylobacter. A C. jejuni transposon (Tn) mutant library was screened for non-helical mutants with inconsistent results...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27903891/cloning-independent-markerless-gene-editing-in-streptococcus-sanguinis-novel-insights-in-type-iv-pilus-biology
#2
Ishwori Gurung, Jamie-Lee Berry, Alexander M J Hall, Vladimir Pelicic
Streptococcus sanguinis, a naturally competent opportunistic human pathogen, is a Gram-positive workhorse for genomics. It has recently emerged as a model for the study of type IV pili (Tfp)-exceptionally widespread and important prokaryotic filaments. To enhance genetic manipulation of Streptococcus sanguinis, we have developed a cloning-independent methodology, which uses a counterselectable marker and allows sophisticated markerless gene editing in situ We illustrate the utility of this methodology by answering several questions regarding Tfp biology by (i) deleting single or mutiple genes, (ii) altering specific bases in genes of interest, and (iii) engineering genes to encode proteins with appended affinity tags...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27869789/genome-guided-design-of-a-defined-mouse-microbiota-that-confers-colonization-resistance-against-salmonella-enterica-serovar-typhimurium
#3
Sandrine Brugiroux, Markus Beutler, Carina Pfann, Debora Garzetti, Hans-Joachim Ruscheweyh, Diana Ring, Manuel Diehl, Simone Herp, Yvonne Lötscher, Saib Hussain, Boyke Bunk, Rüdiger Pukall, Daniel H Huson, Philipp C Münch, Alice C McHardy, Kathy D McCoy, Andrew J Macpherson, Alexander Loy, Thomas Clavel, David Berry, Bärbel Stecher
Protection against enteric infections, also termed colonization resistance, results from mutualistic interactions of the host and its indigenous microbes. The gut microbiota of humans and mice is highly diverse and it is therefore challenging to assign specific properties to its individual members. Here, we have used a collection of murine bacterial strains and a modular design approach to create a minimal bacterial community that, once established in germ-free mice, provided colonization resistance against the human enteric pathogen Salmonella enterica serovar Typhimurium (S...
November 21, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27864912/inferring-contemporary-and-historical-genetic-connectivity-from-juveniles
#4
Pierre Feutry, Oliver Berry, Peter M Kyne, Richard D Pillans, Rich Hillary, Peter M Grewe, James R Marthick, Grant Johnson, Rasanthi M Gunasekera, Nicholas J Bax, Mark Bravington
Measuring population connectivity is a critical task in conservation biology. While genetic markers can provide reliable long-term historical estimates of population connectivity, scientists are still limited in their ability to determine contemporary patterns of gene flow, the most practical time frame for management. Here, we tackled this issue by developing a new approach that only requires juvenile sampling at a single time period. To demonstrate the usefulness of our method, we used the Speartooth shark (Glyphis glyphis), a critically endangered species of river sharks found only in tropical northern Australia and southern Papua New Guinea...
November 19, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27856586/genome-sequences-of-three-species-of-hanseniaspora-isolated-from-spontaneous-wine-fermentations
#5
Peter R Sternes, Danna Lee, Dariusz R Kutyna, Anthony R Borneman
Members of the genus Hanseniaspora represent a significant proportion of the normal flora of grape berries and play a significant role in wine fermentation. Here, we present genome sequences for three species of Hanseniaspora, H. opuntiae, H. osmophila, and H. uvarum, which were isolated from spontaneous Chardonnay wine fermentation.
November 17, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27853923/the-cognitive-and-behavioral-phenotypes-of-individuals-with-chrna7-duplications
#6
M A Gillentine, L N Berry, R P Goin-Kochel, M A Ali, J Ge, D Guffey, J A Rosenfeld, V Hannig, P Bader, M Proud, M Shinawi, B H Graham, A Lin, S R Lalani, J Reynolds, M Chen, T Greb, C G Minard, P Stankiewicz, A L Beaudet, C P Schaaf
Chromosome 15q11q13 is among the least stable regions in the genome due to its highly complex genomic architecture. Low copy repeat elements at 15q13.3 facilitate recurrent copy number variants (CNVs), with deletions established as pathogenic and CHRNA7 implicated as a candidate gene. However, the pathogenicity of duplications of CHRNA7 is unclear, as they are found in affected probands as well as in reportedly healthy parents and unaffected control individuals. We evaluated 18 children with microduplications involving CHRNA7, identified by clinical chromosome microarray analysis (CMA)...
November 16, 2016: Journal of Autism and Developmental Disorders
https://www.readbyqxmd.com/read/27832740/inter-and-intra-reproducibility-of-genotypes-from-sheep-technical-replicates-on-illumina-and-affymetrix-platforms
#7
Donagh P Berry, Aine O'Brien, Eamonn Wall, Kevin McDermott, Shane Randles, Paul Flynn, Stephen Park, Jenny Grose, Rebecca Weld, Noirin McHugh
BACKGROUND: Accurate genomic analyses are predicated upon access to accurate genotype input data. The objective of this study was to quantify the reproducibility of genotype data that are generated from the same genotype platform and from different genotyping platforms. METHODS: Genotypes based on 51,121 single nucleotide polymorphisms (SNPs) for 84 animals that were each genotyped on Illumina and Affymetrix platforms and for another 25 animals that were each genotyped twice on the same Illumina platform were compared...
November 10, 2016: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/27803702/comparative-profiling-of-mirnas-and-target-gene-identification-in-distant-grafting-between-tomato-and-lycium-goji-berry
#8
A B M Khaldun, Wenjun Huang, Haiyan Lv, Sihong Liao, Shaohua Zeng, Ying Wang
Local translocation of small RNAs between cells is proved. Long distance translocation between rootstock and scion is also well documented in the homo-grafting system, but the process in distant-grafting is widely unexplored where rootstock and scion belonging to different genera. Micro RNAs are a class of small, endogenous, noncoding, gene silencing RNAs that regulate target genes of a wide range of important biological pathways in plants. In this study, tomato was grafted onto goji (Lycium chinense Mill.) to reveal the insight of miRNAs regulation and expression patterns within a distant-grafting system...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27801843/comparative-transcriptomic-analysis-of-grape-berry-in-response-to-root-restriction-during-developmental-stages
#9
Feng Leng, Qiong Lin, Di Wu, Shiping Wang, Dengliang Wang, Chongde Sun
Root restriction improved berry quality by being involved in diverse aspects of grapevine life. However, the molecular mechanism driving this process is not understood very well. In this study, the 'Summer Black' grape berry (Vitis vinifera × V. labrusca) under root restriction was investigated, which showed an increase of total soluble solids (TSS), color index of red grapes (CIRG) value, anthocyanins accumulation, total phenolics and total procyanidins contents during berry development compared with those in control berries...
October 28, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27765014/distinct-transcriptome-responses-to-water-limitation-in-isohydric-and-anisohydric-grapevine-cultivars
#10
Silvia Dal Santo, Alberto Palliotti, Sara Zenoni, Giovanni Battista Tornielli, Marianna Fasoli, Paola Paci, Sergio Tombesi, Tommaso Frioni, Oriana Silvestroni, Andrea Bellincontro, Claudio d'Onofrio, Fabiola Matarese, Matteo Gatti, Stefano Poni, Mario Pezzotti
BACKGROUND: Grapevine (Vitis vinifera L.) is an economically important crop with a wide geographical distribution, reflecting its ability to grow successfully in a range of climates. However, many vineyards are located in regions with seasonal drought, and these are often predicted to be global climate change hotspots. Climate change affects the entire physiology of grapevine, with strong effects on yield, wine quality and typicity, making it difficult to produce berries of optimal enological quality and consistent stability over the forthcoming decades...
October 20, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27743245/a-review-of-the-genetics-of-intracranial-berry-aneurysms-and-implications-for-genetic-counseling
#11
Emma Hitchcock, William T Gibson
Here we review the current understanding of the genetic architecture of intracranial berry aneurysms (IBA) to aid in the genetic counseling of patients at risk for this condition. The familial subtype of IBA, familial intracranial aneurysms (FIA), is associated with increased frequency of IBA, increased risk of rupture, and increased morbidity and mortality after rupture. Family history is the strongest predictor for the development of IBA. However, a genetic test is not yet available to assess risk within a family...
October 14, 2016: Journal of Genetic Counseling
https://www.readbyqxmd.com/read/27729032/comparative-transcriptome-sequencing-and-de-novo-analysis-of-vaccinium-corymbosum-during-fruit-and-color-development
#12
Lingli Li, Hehua Zhang, Zhongshuai Liu, Xiaoyue Cui, Tong Zhang, Yanfang Li, Lingyun Zhang
BACKGROUND: Blueberry is an economically important fruit crop in Ericaceae family. The substantial quantities of flavonoids in blueberry have been implicated in a broad range of health benefits. However, the information regarding fruit development and flavonoid metabolites based on the transcriptome level is still limited. In the present study, the transcriptome and gene expression profiling over berry development, especially during color development were initiated. RESULTS: A total of approximately 13...
October 12, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27729005/an-assemblage-of-frankia-cluster-ii-strains-from-california-contains-the-canonical-nod-genes-and-also-the-sulfotransferase-gene-nodh
#13
Thanh Van Nguyen, Daniel Wibberg, Kai Battenberg, Jochen Blom, Brian Vanden Heuvel, Alison M Berry, Jörn Kalinowski, Katharina Pawlowski
BACKGROUND: The ability to establish root nodule symbioses is restricted to four different plant orders. Soil actinobacteria of the genus Frankia can establish a symbiotic relationship with a diverse group of plants within eight different families from three different orders, the Cucurbitales, Fagales and Rosales. Phylogenetically, Frankia strains can be divided into four clusters, three of which (I, II, III) contain symbiotic strains. Members of Cluster II nodulate the broadest range of host plants with species from four families from two different orders, growing on six continents...
October 12, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27696076/characterization-of-mirnas-responsive-to-exogenous-ethylene-in-grapevine-berries-at-whole-genome-level
#14
Fanggui Zhao, Chen Wang, Jian Han, Xudong Zhu, Xiaopeng Li, Xicheng Wang, Jinggui Fang
MicroRNAs (miRNAs) are critical regulators of various biological and metabolic processes of plants. Numerous miRNAs and their functions have been identified and analyzed in many plants. However, till now, the involvement of miRNAs in the response of grapevine berries to ethylene has not been reported yet. Here, Solexa technology was employed to deeply sequence small RNA libraries constructed from grapevine berries treated with and without ethylene. A total of 124 known and 78 novel miRNAs were identified. Among these miRNAs, 162 miRNAs were clearly responsive to ethylene, with 55 downregulated, 59 upregulated, and 14 unchanged miRNAs detected only in the control...
September 30, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27645994/selenoprotein-gene-nomenclature
#15
Vadim N Gladyshev, Elias S Arnér, Marla J Berry, Regina Brigelius-Flohé, Elspeth A Bruford, Raymond F Burk, Bradley A Carlson, Sergi Castellano, Laurent Chavatte, Marcus Conrad, Paul R Copeland, Alan M Diamond, Donna M Driscoll, Ana Ferreiro, Leopold Flohé, Fiona R Green, Roderic Guigó, Diane E Handy, Dolph L Hatfield, John Hesketh, Peter R Hoffmann, Arne Holmgren, Robert J Hondal, Michael T Howard, Kaixun Huang, Hwa-Young Kim, Ick Young Kim, Josef Köhrle, Alain Krol, Gregory V Kryukov, Byeong Jae Lee, Byung Cheon Lee, Xin Gen Lei, Qiong Liu, Alain Lescure, Alexei V Lobanov, Joseph Loscalzo, Matilde Maiorino, Marco Mariotti, K Sandeep Prabhu, Margaret P Rayman, Sharon Rozovsky, Gustavo Salinas, Edward E Schmidt, Lutz Schomburg, Ulrich Schweizer, Miljan Simonović, Roger A Sunde, Petra A Tsuji, Susan Tweedie, Fulvio Ursini, Philip D Whanger, Yan Zhang
The human genome contains 25 genes coding for selenocysteine-containing proteins (selenoproteins). These proteins are involved in a variety of functions, most notably redox homeostasis. Selenoprotein enzymes with known functions are designated according to these functions: TXNRD1, TXNRD2, and TXNRD3 (thioredoxin reductases), GPX1, GPX2, GPX3, GPX4, and GPX6 (glutathione peroxidases), DIO1, DIO2, and DIO3 (iodothyronine deiodinases), MSRB1 (methionine sulfoxide reductase B1), and SEPHS2 (selenophosphate synthetase 2)...
November 11, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27605106/thapmix-simulating-tumour-samples-through-haplotype-mixtures
#16
Sergii Ivakhno, Camilla Colombo, Stephen Tanner, Philip Tedder, Stefano Berri, Anthony J Cox
MOTIVATION: Large-scale rearrangements and copy number changes combined with different modes of clonal evolution create extensive somatic genome diversity, making it difficult to develop versatile and scalable variant calling tools and create well-calibrated benchmarks. RESULTS: We developed a new simulation framework tHapMix that enables the creation of tumour samples with different ploidy, purity and polyclonality features. It easily scales to simulation of hundreds of somatic genomes, while re-use of real read data preserves noise and biases present in sequencing platforms...
September 7, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27577962/genetic-and-phenotypic-characterization-of-grapevine-vein-clearing-virus-from-wild-vitis-rupestris-scheele
#17
Steve Bearch, Michael Kovens, LeAnn Hubbert, Shae Honesty, Qiang Guo, Daniel Pap, Ru Dai, Laszlo Kovacs, Wenping Qiu
Grapevine vein clearing virus (GVCV), a new member of the genus Badnavirus in the family Caulimoviridae, is associated with a vein clearing and vine decline disease that severely affects grape production and berry quality in commercial vineyards in the Midwest region of the USA. In this paper, the genetic and phenotypic characteristics of GVCV-VRU1 and GVCV-VRU2, two isolates from wild Vitis rupestris Scheele grapevines in their native habitat, are described. The GVCV-VRU1 genome is 7,755 bp long while the GVCV-VRU2 genome consists of 7,725 bp, both of which are different from the genome of the GVCV-CHA isolate (7,753 bp), which was originally discovered in the grape cultivar 'Chardonel'...
August 31, 2016: Phytopathology
https://www.readbyqxmd.com/read/27557446/an-integrative-transcriptomic-atlas-of-organogenesis-in-human-embryos
#18
Dave T Gerrard, Andrew A Berry, Rachel E Jennings, Karen Piper Hanley, Nicoletta Bobola, Neil A Hanley
Human organogenesis is when severe developmental abnormalities commonly originate. However, understanding this critical embryonic phase has relied upon inference from patient phenotypes and assumptions from in vitro stem cell models and non-human vertebrates. We report an integrated transcriptomic atlas of human organogenesis. By lineage-guided principal components analysis, we uncover novel relatedness of particular developmental genes across different organs and tissues and identified unique transcriptional codes which correctly predicted the cause of many congenital disorders...
2016: ELife
https://www.readbyqxmd.com/read/27544821/cellular-transduction-mechanisms-of-adeno-associated-viral-vectors
#19
Garrett Edward Berry, Aravind Asokan
Recombinant adeno-associated viral vectors (rAAV) are regarded as promising vehicles for therapeutic gene delivery. Continued development and new strategies are essential to improve the potency of AAV vectors and reduce the effective dose needed for clinical efficacy. In this regard, many studies have focused on understanding the cellular transduction mechanisms of rAAV, often with the goal of exploiting this knowledge to increase gene transfer efficiency. Here, we provide an overview of our evolving understanding of rAAV cellular trafficking pathways through the host cell, beginning with cellular entry and ending with transcription of the vector genome...
August 18, 2016: Current Opinion in Virology
https://www.readbyqxmd.com/read/27527408/predicting-non-small-cell-lung-cancer-prognosis-by-fully-automated-microscopic-pathology-image-features
#20
Kun-Hsing Yu, Ce Zhang, Gerald J Berry, Russ B Altman, Christopher Ré, Daniel L Rubin, Michael Snyder
Lung cancer is the most prevalent cancer worldwide, and histopathological assessment is indispensable for its diagnosis. However, human evaluation of pathology slides cannot accurately predict patients' prognoses. In this study, we obtain 2,186 haematoxylin and eosin stained histopathology whole-slide images of lung adenocarcinoma and squamous cell carcinoma patients from The Cancer Genome Atlas (TCGA), and 294 additional images from Stanford Tissue Microarray (TMA) Database. We extract 9,879 quantitative image features and use regularized machine-learning methods to select the top features and to distinguish shorter-term survivors from longer-term survivors with stage I adenocarcinoma (P<0...
August 16, 2016: Nature Communications
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