keyword
MENU ▼
Read by QxMD icon Read
search

berry genomics

keyword
https://www.readbyqxmd.com/read/28910288/genomics-enabled-analysis-of-the-emergent-disease-cotton-bacterial-blight
#1
Anne Z Phillips, Jeffrey C Berry, Mark C Wilson, Anupama Vijayaraghavan, Jillian Burke, J Imani Bunn, Tom W Allen, Terry Wheeler, Rebecca S Bart
Cotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistant germplasm for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Here, we report analysis of cotton variety planting statistics that indicate a steady increase in the percentage of susceptible cotton varieties grown each year since 2009. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv...
September 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28894154/n-terminomics-identifies-widespread-endoproteolysis-and-novel-methionine-excision-in-a-genome-reduced-bacterial-pathogen
#2
Iain J Berry, Veronica M Jarocki, Jessica L Tacchi, Benjamin B A Raymond, Michael Widjaja, Matthew P Padula, Steven P Djordjevic
Proteolytic processing alters protein function. Here we present the first systems-wide analysis of endoproteolysis in the genome-reduced pathogen Mycoplasma hyopneumoniae. 669 N-terminal peptides from 164 proteins were identified, demonstrating that functionally diverse proteins are processed, more than half of which 75 (53%) were accessible on the cell surface. Multiple cleavage sites were characterised, but cleavage with arginine in P1 predominated. Putative functions for a subset of cleaved fragments were assigned by affinity chromatography using heparin, actin, plasminogen and fibronectin as bait...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28894125/elongation-factor-tu-is-a-multifunctional-and-processed-moonlighting-protein
#3
Michael Widjaja, Kate Louise Harvey, Lisa Hagemann, Iain James Berry, Veronica Maria Jarocki, Benjamin Bernard Armando Raymond, Jessica Leigh Tacchi, Anne Gründel, Joel Ricky Steele, Matthew Paul Padula, Ian George Charles, Roger Dumke, Steven Philip Djordjevic
Many bacterial moonlighting proteins were originally described in medically, agriculturally, and commercially important members of the low G + C Firmicutes. We show Elongation factor Tu (Ef-Tu) moonlights on the surface of the human pathogens Staphylococcus aureus (SaEf-Tu) and Mycoplasma pneumoniae (MpnEf-Tu), and the porcine pathogen Mycoplasma hyopneumoniae (MhpEf-Tu). Ef-Tu is also a target of multiple processing events on the cell surface and these were characterised using an N-terminomics pipeline...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28843071/rna-seq-based-transcriptomic-analysis-of-cppu-treated-grape-berries-and-emission-of-volatile-compounds
#4
Wu Wang, Muhammad Khalil-Ur-Rehman, Jiao Feng, Jianmin Tao
Grapevine (Vitis vinifera L.) is considered to be one of the most popular and widespread fruit crops in the world. Numerous value added products are prepared from grape fruit and investments are being made to establish new viticulture region (Hoff et al., 2017; Imran et al., 2017). CPPU [forchlorfenuron N-(2-chloro-4-pyridyl)-N-phenylurea] is a synthetic cytokine-like plant regulator which promotes grape berry set and development. The influence of CPPU [forchlorfenuron N-(2-chloro-4-pyridyl)-N-phenylurea] on berry development of 'Shine Muscat' (Vitis labruscana Bailey×V vinifera L...
August 12, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28815698/altered-regulation-of-terminal-flower-1-causes-the-unique-vernalisation-response-in-an-arctic-woodland-strawberry-accession
#5
Elli A Koskela, Takeshi Kurokura, Tuomas Toivainen, Anita Sønsteby, Ola M Heide, Daniel J Sargent, Sachiko Isobe, Laura Jaakola, Hrannar Hilmarsson, Paula Elomaa, Timo Hytönen
Vernalisation requirement is an agriculturally important trait that postpones the development of cold-sensitive floral organs until the spring. The family Rosaceae includes many agriculturally important fruit and berry crops that suffer from crop losses caused by frost injury to overwintering flower buds. Recently, a vernalisation-requiring accession of the Rosaceae model woodland strawberry (Fragaria vesca) has been identified in northern Norway. Understanding the molecular basis of the vernalisation requirement in this accession would advance the development of strawberry cultivars better adapted to temperate climate...
August 16, 2017: New Phytologist
https://www.readbyqxmd.com/read/28811336/catastrophic-unbalanced-genome-rearrangements-cause-somatic-loss-of-berry-color-in-grapevine
#6
Pablo Carbonell-Bejerano, Carolina Royo, Rafael Torres-Pérez, Jérôme Grimplet, Lucie Fernandez, Jose M Franco-Zorrilla, Diego Lijavetzky, Elisa Baroja, Juana Martínez, Enrique García-Escudero, Javier Ibáñez, José M Martínez-Zapater
Grape color somatic variants that can be used to develop new grapevine cultivars occasionally appear associated to deletion events of uncertain origin. To understand the mutational mechanisms generating somatic structural variation in grapevine, we compared the Tempranillo Blanco (TB) white berry somatic variant to its black berry ancestor, Tempranillo Tinto. Whole-genome sequencing (WGS) uncovered a catastrophic genome rearrangement in TB that caused the hemizygous deletion of 313 genes, including the loss of the functional copy for the MYB transcription factors required for anthocyanin pigmentation in the berry skin...
August 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28791127/patterns-of-genomic-and-phenomic-diversity-in-wine-and-table-grapes
#7
Zoë Migicovsky, Jason Sawler, Kyle M Gardner, Mallikarjuna K Aradhya, Bernard H Prins, Heidi R Schwaninger, Carlos D Bustamante, Edward S Buckler, Gan-Yuan Zhong, Patrick J Brown, Sean Myles
Grapes are one of the most economically and culturally important crops worldwide, and they have been bred for both winemaking and fresh consumption. Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world's largest grape gene banks, the grape germplasm collection of the United States Department of Agriculture. We find that phenological events throughout the growing season are correlated, and quantify the marked difference in size between table and wine grapes...
2017: Horticulture Research
https://www.readbyqxmd.com/read/28780070/identification-of-cry48aa-cry49aa-toxin-ligands-in-the-midgut-of-culex-quinquefasciatus-larvae
#8
Tatiana Maria Teodoro Rezende, Tatiany Patrícia Romão, Michel Batista, Colin Berry, Michael J Adang, Maria Helena Neves Lobo Silva-Filha
A binary mosquitocidal toxin composed of a three-domain Cry-like toxin (Cry48Aa) and a binary-like toxin (Cry49Aa) was identified in Lysinibacillus sphaericus. Cry48Aa/Cry49Aa has action on Culex quinquefasciatus larvae, in particular, to those that are resistant to the Bin Binary toxin, which is the major insecticidal factor from L. sphaericus-based biolarvicides, indicating that Cry48Aa/Cry49Aa interacts with distinct target sites in the midgut and can overcome Bin toxin resistance. This study aimed to identify Cry48Aa/Cry49Aa ligands in C...
August 3, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28717173/liquid-phase-sequence-capture-and-targeted-re-sequencing-revealed-novel-polymorphisms-in-tomato-genes-belonging-to-the-mep-carotenoid-pathway
#9
Irma Terracciano, Concita Cantarella, Carlo Fasano, Teodoro Cardi, Giuseppe Mennella, Nunzio D'Agostino
Tomato (Solanum lycopersicum L.) plants are characterized by having a variety of fruit colours that reflect the composition and accumulation of diverse carotenoids in the berries. Carotenoids are extensively studied for their health-promoting effects and this explains the great attention these pigments received by breeders and researchers worldwide. In this work we applied Agilent's SureSelect liquid-phase sequence capture and Illumina targeted re-sequencing of 34 tomato genes belonging to the methylerythritol phosphate (MEP) carotenoid pathway on a panel of 48 genotypes which differ for carotenoid content calculated as the sum of β-carotene, cis- and trans-lycopene...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28712375/imputation-of-non-genotyped-sheep-from-the-genotypes-of-their-mates-and-resulting-progeny
#10
D P Berry, N McHugh, S Randles, E Wall, K McDermott, M Sargolzaei, A C O'Brien
Accurate genomic analyses are predicated on access to a large quantity of accurately genotyped and phenotyped animals. Because the cost of genotyping is often less than the cost of phenotyping, interest is increasing in generating genotypes for phenotyped animals. In some instances this may imply the requirement to genotype older animals with greater phenotypic information content. Biological material for these older informative animals may, however, no longer exist. The objective of the present study was to quantify the ability to impute 11 129 single nucleotide polymorphism (SNP) genotypes of non-genotyped animals (in this instance sires) from the genotypes of their progeny with or without including the genotypes of the progenys' dams (i...
July 17, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28652263/ripening-transcriptomic-program-in-red-and-white-grapevine-varieties-correlates-with-berry-skin-anthocyanin-accumulation
#11
Mélanie Massonnet, Marianna Fasoli, Giovanni Battista Tornielli, Mario Altieri, Marco Sandri, Paola Zuccolotto, Paola Paci, Massimo Gardiman, Sara Zenoni, Mario Pezzotti
Grapevine (Vitis vinifera) berry development involves a succession of physiological and biochemical changes reflecting the transcriptional modulation of thousands of genes. Although recent studies have investigated the dynamic transcriptome during berry development, most have focused on a single grapevine variety, so there is a lack of comparative data representing different cultivars. Here, we report, to our knowledge, the first genome-wide transcriptional analysis of 120 RNA samples corresponding to 10 Italian grapevine varieties collected at four growth stages...
August 2017: Plant Physiology
https://www.readbyqxmd.com/read/28645231/evolution-of-hormone-signaling-networks-in-plant-defense
#12
Matthias L Berens, Hannah M Berry, Akira Mine, Cristiana T Argueso, Kenichi Tsuda
Studies with model plants such as Arabidopsis thaliana have revealed that phytohormones are central regulators of plant defense. The intricate network of phytohormone signaling pathways enables plants to activate appropriate and effective defense responses against pathogens as well as to balance defense and growth. The timing of the evolution of most phytohormone signaling pathways seems to coincide with the colonization of land, a likely requirement for plant adaptations to the more variable terrestrial environments, which included the presence of pathogens...
August 4, 2017: Annual Review of Phytopathology
https://www.readbyqxmd.com/read/28633662/orthored-a-rapid-and-accurate-orthology-prediction-tool-with-low-computational-requirement
#13
Kai Battenberg, Ernest K Lee, Joanna C Chiu, Alison M Berry, Daniel Potter
BACKGROUND: Identifying orthologous genes is an initial step required for phylogenetics, and it is also a common strategy employed in functional genetics to find candidates for functionally equivalent genes across multiple species. At the same time, in silico orthology prediction tools often require large computational resources only available on computing clusters. Here we present OrthoReD, an open-source orthology prediction tool with accuracy comparable to published tools that requires only a desktop computer...
June 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28626454/a-syst-omics-approach-to-ensuring-food-safety-and-reducing-the-economic-burden-of-salmonellosis
#14
Jean-Guillaume Emond-Rheault, Julie Jeukens, Luca Freschi, Irena Kukavica-Ibrulj, Brian Boyle, Marie-Josée Dupont, Anna Colavecchio, Virginie Barrere, Brigitte Cadieux, Gitanjali Arya, Sadjia Bekal, Chrystal Berry, Elton Burnett, Camille Cavestri, Travis K Chapin, Alanna Crouse, France Daigle, Michelle D Danyluk, Pascal Delaquis, Ken Dewar, Florence Doualla-Bell, Ismail Fliss, Karen Fong, Eric Fournier, Eelco Franz, Rafael Garduno, Alexander Gill, Samantha Gruenheid, Linda Harris, Carol B Huang, Hongsheng Huang, Roger Johnson, Yann Joly, Maud Kerhoas, Nguyet Kong, Gisèle Lapointe, Line Larivière, Stéphanie Loignon, Danielle Malo, Sylvain Moineau, Walid Mottawea, Kakali Mukhopadhyay, Céline Nadon, John Nash, Ida Ngueng Feze, Dele Ogunremi, Ann Perets, Ana V Pilar, Aleisha R Reimer, James Robertson, John Rohde, Kenneth E Sanderson, Lingqiao Song, Roger Stephan, Sandeep Tamber, Paul Thomassin, Denise Tremblay, Valentine Usongo, Caroline Vincent, Siyun Wang, Joel T Weadge, Martin Wiedmann, Lucas Wijnands, Emily D Wilson, Thomas Wittum, Catherine Yoshida, Khadija Youfsi, Lei Zhu, Bart C Weimer, Lawrence Goodridge, Roger C Levesque
The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS), at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28624139/applying-rigor-and-reproducibility-standards-to-assay-donor-derived-cell-free-dna-as-a-non-invasive-method-for-detection-of-acute-rejection-and-graft-injury-after-heart-transplantation
#15
Sean Agbor-Enoh, Ilker Tunc, Iwijn De Vlaminck, Ulgen Fideli, Andrew Davis, Karen Cuttin, Kenneth Bhatti, Argit Marishta, Michael A Solomon, Annette Jackson, Grace Graninger, Bonnie Harper, Helen Luikart, Jennifer Wylie, Xujing Wang, Gerald Berry, Charles Marboe, Kiran Khush, Jun Zhu, Hannah Valantine
BACKGROUND: Use of new genomic techniques in clinical settings requires that such methods are rigorous and reproducible. Previous studies have shown that quantitation of donor-derived cell-free DNA (%ddcfDNA) by unbiased shotgun sequencing is a sensitive, non-invasive marker of acute rejection after heart transplantation. The primary goal of this study was to assess the reproducibility of %ddcfDNA measurements across technical replicates, manual vs automated platforms, and rejection phenotypes in distinct patient cohorts...
September 2017: Journal of Heart and Lung Transplantation
https://www.readbyqxmd.com/read/28618374/proteomic-profiling-of-german-dornfelder-grape-berries-using-data-independent-acquisition
#16
Matthias Riebel, Petra Fronk, Ute Distler, Stefan Tenzer, Heinz Decker
Grapevine is one of the most important fruit plants throughout the world. Sequencing of the grape genome in 2007 enabled in-depth analyses of the grape proteome. Whereas many studies addressed changes in proteomic composition of grapes during ripening, we focused on the proteome of mature grape berries from Dornfelder, a characteristic red wine grape for Germany. Current data-independent acquisition proteomics technology enables the analysis of proteomic compositions in a degree of accuracy that was unreachable only a few years ago...
June 7, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28559906/drawing-links-from-transcriptome-to-metabolites-the-evolution-of-aroma-in-the-ripening-berry-of-moscato-bianco-vitis-vinifera-l
#17
Laura Costantini, Christian D Kappel, Massimiliano Trenti, Juri Battilana, Francesco Emanuelli, Maddalena Sordo, Marco Moretto, Céline Camps, Roberto Larcher, Serge Delrot, Maria S Grando
Monoterpenes confer typical floral notes to "Muscat" grapevine varieties and, to a lesser extent, to other aromatic non-Muscat varieties. Previous studies have led to the identification and functional characterization of some enzymes and genes in this pathway. However, the underlying genetic map is still far from being complete. For example, the specific steps of monoterpene metabolism and its regulation are largely unknown. With the aim of identifying new candidates for the missing links, we applied an integrative functional genomics approach based on the targeted metabolic and genome-wide transcript profiling of Moscato Bianco ripening berries...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28553296/use-of-natural-diversity-and-biotechnology-to-increase-the-quality-and-nutritional-content-of-tomato-and-grape
#18
REVIEW
Quentin Gascuel, Gianfranco Diretto, Antonio J Monforte, Ana M Fortes, Antonio Granell
Improving fruit quality has become a major goal in plant breeding. Direct approaches to tackling fruit quality traits specifically linked to consumer preferences and environmental friendliness, such as improved flavor, nutraceutical compounds, and sustainability, have slowly been added to a breeder priority list that already includes traits like productivity, efficiency, and, especially, pest and disease control. Breeders already use molecular genetic tools to improve fruit quality although most advances have been made in producer and industrial quality standards...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28515004/animal-breeding-strategies-can-improve-meat-quality-attributes-within-entire-populations
#19
D P Berry, S Conroy, T Pabiou, A R Cromie
The contribution of animal breeding to changes in animal performance is well documented across a range of species. Once genetic variation in a trait exists, then breeding to improve the characteristics of that trait is possible, if so desired. Considerable genetic variation exists in a range of meat quality attributes across a range of species. The genetic variation that exists for meat quality is as large as observed for most performance traits; thus, within a well-structured breeding program, rapid genetic gain for meat quality could be possible...
April 21, 2017: Meat Science
https://www.readbyqxmd.com/read/28512461/transcriptional-responses-to-pre-flowering-leaf-defoliation-in-grapevine-berry-from-different-growing-sites-years-and-genotypes
#20
Sara Zenoni, Silvia Dal Santo, Giovanni B Tornielli, Erica D'Incà, Ilaria Filippetti, Chiara Pastore, Gianluca Allegro, Oriana Silvestroni, Vania Lanari, Antonino Pisciotta, Rosario Di Lorenzo, Alberto Palliotti, Sergio Tombesi, Matteo Gatti, Stefano Poni
Leaf removal is a grapevine canopy management technique widely used to modify the source-sink balance and/or microclimate around berry clusters to optimize fruit composition. In general, the removal of basal leaves before flowering reduces fruit set, hence achieving looser clusters, and improves grape composition since yield is generally curtailed more than proportionally to leaf area itself. Albeit responses to this practice seem quite consistent, overall vine performance is affected by genotype, environmental conditions, and severity of treatment...
2017: Frontiers in Plant Science
keyword
keyword
37593
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"