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https://www.readbyqxmd.com/read/28538728/the-sunflower-genome-provides-insights-into-oil-metabolism-flowering-and-asterid-evolution
#1
Hélène Badouin, Jérôme Gouzy, Christopher J Grassa, Florent Murat, S Evan Staton, Ludovic Cottret, Christine Lelandais-Brière, Gregory L Owens, Sébastien Carrère, Baptiste Mayjonade, Ludovic Legrand, Navdeep Gill, Nolan C Kane, John E Bowers, Sariel Hubner, Arnaud Bellec, Aurélie Bérard, Hélène Bergès, Nicolas Blanchet, Marie-Claude Boniface, Dominique Brunel, Olivier Catrice, Nadia Chaidir, Clotilde Claudel, Cécile Donnadieu, Thomas Faraut, Ghislain Fievet, Nicolas Helmstetter, Matthew King, Steven J Knapp, Zhao Lai, Marie-Christine Le Paslier, Yannick Lippi, Lolita Lorenzon, Jennifer R Mandel, Gwenola Marage, Gwenaëlle Marchand, Elodie Marquand, Emmanuelle Bret-Mestries, Evan Morien, Savithri Nambeesan, Thuy Nguyen, Prune Pegot-Espagnet, Nicolas Pouilly, Frances Raftis, Erika Sallet, Thomas Schiex, Justine Thomas, Céline Vandecasteele, Didier Varès, Felicity Vear, Sonia Vautrin, Martin Crespi, Brigitte Mangin, John M Burke, Jérôme Salse, Stéphane Muños, Patrick Vincourt, Loren H Rieseberg, Nicolas B Langlade
The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs...
May 22, 2017: Nature
https://www.readbyqxmd.com/read/28538216/the-emerging-view-of-aging-as-a-reversible-epigenetic-process
#2
Micaela López-León, Rodolfo G Goya
The achievement of animal cloning and subsequent development of cell reprogramming technology are having a profound impact on our view of the mechanisms of aging in complex organisms. The experimental evidence showing that an adult somatic nucleus implanted into an enucleated oocyte can give rise to a whole new individual strongly suggests that the integrity of the genome of an adult nucleus is fully preserved. Here, we will review recent experimental evidence showing that pluripotency gene-based cell reprogramming can erase the epigenetic marks of aging and rejuvenate cells from old individuals reversing most signs of aging and that when induced pluripotent stem cells are differentiated back to the cell type of origin, the rejuvenated cells share many of the features of wild-type counterparts from young donors...
May 25, 2017: Gerontology
https://www.readbyqxmd.com/read/28535256/epigenetic-and-genetic-contributions-to-adaptation-in-chlamydomonas
#3
Ilkka Kronholm, Andrew Bassett, David Baulcombe, Sinéad Collins
Epigenetic modifications, such as DNA methylation or histone modifications, can be transmitted between cellular or organismal generations. However, there are no experiments measuring their role in adaptation, so here we use experimental evolution to investigate how epigenetic variation can contribute to adaptation. We manipulated DNA methylation and histone acetylation in the unicellular green alga Chlamydomonas reinhardtii both genetically and chemically to change the amount of epigenetic variation generated or transmitted in adapting populations in three different environments (salt stress, phosphate starvation, and high CO2) for two hundred asexual generations...
May 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28535255/tea-and-coffee-consumption-in-relation-to-dna-methylation-in-four-european-cohorts
#4
Weronica E Ek, Elmar W Tobi, Muhammad Ahsan, Erik Lampa, Erica Ponzi, Soterios A Kyrtopoulos, Panagiotis Georgiadis, L H Lumey, Bastiaan T Heijmans, Maria Botsivali, Ingvar A Bergdahl, Torgny Karlsson, Mathias Rask-Andersen, Domenico Palli, Erik Ingelsson, Åsa K Hedman, Lena M Nilsson, Paolo Vineis, Lars Lind, James M Flanagan, Åsa Johansson
Lifestyle factors, such as food choices and exposure to chemicals, can alter DNA methylation and lead to changes in gene activity. Two such exposures with pharmacologically active components are coffee and tea consumption. Both coffee and tea has been suggested to play an important role in modulating disease-risk in humans by suppressing tumour progression, decreasing inflammation and influencing estrogen metabolism. These mechanisms may be mediated by changes in DNA methylation.To investigate if DNA methylation in blood is associated with coffee and tea consumption we performed a genome-wide DNA methylation study for coffee and tea consumption in four European cohorts (N = 3,096)...
May 23, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28535155/elevated-apobec3b-expression-drives-a-kataegic-like-mutation-signature-and-replication-stress-related-therapeutic-vulnerabilities-in-p53-defective-cells
#5
Jenni Nikkilä, Rahul Kumar, James Campbell, Inger Brandsma, Helen N Pemberton, Fredrik Wallberg, Kinga Nagy, Ildikó Scheer, Beata G Vertessy, Artur A Serebrenik, Valentina Monni, Reuben S Harris, Stephen J Pettitt, Alan Ashworth, Christopher J Lord
BACKGROUND: Elevated APOBEC3B expression in tumours correlates with a kataegic pattern of localised hypermutation. We assessed the cellular phenotypes associated with high-level APOBEC3B expression and the influence of p53 status on these phenotypes using an isogenic system. METHODS: We used RNA interference of p53 in cells with inducible APOBEC3B and assessed DNA damage response (DDR) biomarkers. The mutational effects of APOBEC3B were assessed using whole-genome sequencing...
May 23, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28534044/hsp-and-deafness-neurocristopathy-caused-by-a-novel-mosaic-sox10-mutation
#6
Sandra Donkervoort, Diana Bharucha-Goebel, Pomi Yun, Ying Hu, Payam Mohassel, Ahmet Hoke, Wadih M Zein, Daniel Ezzo, Andrea M Atherton, Ann C Modrcin, Majed Dasouki, A Reghan Foley, Carsten G Bönnemann
OBJECTIVE: To identify the underlying genetic cause in 2 sisters affected with progressive lower extremity spasticity, neuropathy, and early-onset deafness. METHODS: Whole-exome sequencing was performed, and segregation testing of variants was investigated using targeted Sanger sequencing. An inherited paternal mosaic mutation was further evaluated through quantitative analysis of the ratio of mutant vs wild-type allele in genomic DNA from various tissues, including blood, dermal fibroblasts, and saliva...
June 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28533767/characterization-of-mycobacterium-chelonae-like-strains-by-comparative-genomics
#7
Christiane L Nogueira, Luiz G P de Almeida, Maria C Menendez, Maria J Garcia, Luciano A Digiampietri, Erica Chimara, Margo Cnockaert, Juan C Palomino, Françoise Portaels, Anandi Martin, Peter Vandamme, Sylvia C Leão
Isolates of the Mycobacterium chelonae-M. abscessus complex are subdivided into four clusters (CHI to CHIV) in the INNO-LiPA® Mycobacterium spp DNA strip assay. A considerable phenotypic variability was observed among isolates of the CHII cluster. In this study, we examined the diversity of 26 CHII cluster isolates by phenotypic analysis, drug susceptibility testing, whole genome sequencing and single-gene analysis. Pairwise genome comparisons were performed using several approaches, including average nucleotide identity (ANI) and genome-to-genome distance (GGD) among others...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28533441/trends-in-dna-methylation-with-age-replicate-across-diverse-human-populations
#8
Shyamalika Gopalan, Oana Carja, Maud Fagny, Etienne Patin, Justin W Myrick, Lisa M McEwen, Sarah M Mah, Michael S Kobor, Alain Froment, Marcus W Feldman, Lluis Quintana-Murci, Brenna M Henn
Aging is associated with widespread changes in genome-wide patterns of DNA methylation. Thousands of CpG sites whose tissue-specific methylation levels are strongly correlated with chronological age have been previously identified. However, the majority of these studies have focused primarily on cosmopolitan populations living in the developed world; it is not known if age-related patterns of DNA methylation at these loci are similar across a broad range of human genetic and ecological diversity. We investigated genome-wide methylation patterns using saliva- and whole blood-derived DNA from two traditionally hunting and gathering African populations: the Baka of the western Central African rainforest and the ≠Khomani San of the South African Kalahari Desert...
May 22, 2017: Genetics
https://www.readbyqxmd.com/read/28533337/development-of-a-medium-density-combined-species-snp-array-for-pacific-and-european-oysters-crassostrea-gigas-and-ostrea-edulis
#9
Alejandro P Gutierrez, Frances Turner, Karim Gharbi, Richard Talbot, Natalie R Lowe, Carolina Peñaloza, Mark McCullough, Paulo A Prodöhl, Tim P Bean, Ross D Houston
SNP arrays are enabling tools for high-resolution studies of the genetic basis of complex traits in farmed and wild animals. Oysters are of critical importance in many regions from both an ecological and economic perspective, and oyster aquaculture forms a key component of global food security. The aim of our study was to design a combined-species medium density SNP array for Pacific oyster (C. gigas) and European flat oyster (O. edulis), and to test the performance of this array on farmed and wild populations from multiple locations, with a focus on European populations...
May 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28533336/a-coding-variant-in-the-gene-bardet-biedl-syndrome-4-bbs4-is-associated-with-a-novel-form-of-canine-progressive-retinal-atrophy
#10
Tracy Chew, Bianca Haase, Roslyn Bathgate, Cali E Willet, Maria K Kaukonen, Lisa J Mascord, Hannes T Lohi, Claire M Wade
Progressive retinal atrophy is a common cause of blindness in the dog and affects over 100 breeds. It is characterized by gradual vision loss that occurs due to the degeneration of photoreceptor cells in the retina. Similar to the human counterpart retinitis pigmentosa, the canine disorder is clinically and genetically heterogeneous and the underlying cause remains unknown for many cases. We use a positional candidate gene approach to identify putative variants in the Hungarian Puli breed using genotyping data of 14 family-based samples (CanineHD BeadChip array, Illumina) and whole genome sequencing data of two proband and two parental samples (Illumina HiSeq 2000)...
May 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28533181/comparative-genome-analysis-of-lactobacillus-plantarum-gb-lp3-provides-candidates-of-survival-related-genetic-factors
#11
Soomin Jeon, Jaehoon Jung, Kwondo Kim, DongAhn Yoo, Chanho Lee, Jungsun Kang, Kyungjin Cho, Dae-Kyung Kang, Woori Kwak, Sook Hee Yoon, Heebal Kim, Seoae Cho
Lactobacillus plantarum is found in various environmental niches such as in the gastrointestinal tract of an animal host or a fermented food. This species isolated from a certain environment is known to possess a variety of properties according to inhabited environment's adaptation. However, a causal relationship of a genetic factor and phenotype affected by a specific environment has not been systematically comprehended. L. plantarum GB-LP3 strain was isolated from Korean traditional fermented vegetable and the whole genome of GB-LP3 was sequenced...
May 19, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28533157/characterization-of-the-cellulosomal-scaffolding-protein-cbpc-from-clostridium-cellulovorans-743b
#12
Daichi Nakajima, Toshiyuki Shibata, Reiji Tanaka, Kouichi Kuroda, Mitsuyoshi Ueda, Hideo Miyake
Clostridium cellulovorans 743B, an anaerobic and mesophilic bacterium, produces an extracellular enzyme complex called the cellulosome on the cell surface. Recently, we have reported the whole genome sequence of C. cellulovorans, which revealed that a total of 4 cellulosomal scaffolding proteins: CbpA, HbpA, CbpB, and CbpC were encoded in the C. cellulovorans genome. In particular, cbpC encoded a 429-residue polypeptide that includes a carbohydrate-binding module (CBM), an S-layer homology module, and a cohesin...
May 19, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28532976/microbiological-problems-and-biofilms-associated-with-mycobacterium-chimaera-in-heater-cooler-units-used-for-cardiopulmonary-bypass
#13
REVIEW
J Walker, G Moore, S Collins, S Parks, M I Garvey, T Lamagni, G Smith, L Dawkin, S Goldenberg, M Chand
The role of heater-cooler units (HCUs) in the transmission of Mycobacterium chimaera during open heart surgery has been recognized since 2013. Subsequent investigations uncovered a remarkable global outbreak reflecting the wide distribution of implicated devices. HCUs are an essential component of cardiopulmonary bypass operations and their withdrawal would severely affect capacity for life-saving cardiac surgery. However, studies have demonstrated that many HCUs are contaminated with a wide range of micro-organisms, including M...
April 26, 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/28532787/evolution-of-avian-encephalomyelitis-virus-during-embryo-adaptation
#14
Rüdiger Hauck, C Gabriel Sentíes-Cué, Ying Wang, Colin Kern, H L Shivaprasad, Huaijun Zhou, Rodrigo A Gallardo
Wild-type avian encephalomyelitis virus (AEV) causes neurological signs in young chicks but no disease in pullets after oral or intracutaneous infection. However, if the virus gets embryo-adapted by serial passaging in chicken embryos, it will cause AE after intracutaneous infection in chickens of all ages. Recently, several cases of AE in layer pullets occurring shortly after intracutaneous vaccination were described. The present investigation was initiated to determine if vaccines that had inadvertently been embryo-adapted were responsible for these outbreaks...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28532434/hierarchical-genomic-analysis-of-carried-and-invasive-serogroup-a-neisseria-meningitidis-during-the-2011-epidemic-in-chad
#15
Kanny Diallo, Kadija Gamougam, Doumagoum M Daugla, Odile B Harrison, James E Bray, Dominique A Caugant, Jay Lucidarme, Caroline L Trotter, Musa Hassan-King, James M Stuart, Olivier Manigart, Brian M Greenwood, Martin C J Maiden
BACKGROUND: Serogroup A Neisseria meningitidis (NmA) was the cause of the 2011 meningitis epidemics in Chad. This bacterium, often carried asymptomatically, is considered to be an "accidental pathogen"; however, the transition from carriage to disease phenotype remains poorly understood. This study examined the role genetic diversity might play in this transition by comparing genomes from geographically and temporally matched invasive and carried NmA isolates. RESULTS: All 23 NmA isolates belonged to the ST-5 clonal complex (cc5)...
May 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28532386/extremely-low-coverage-whole-genome-sequencing-in-south-asians-captures-population-genomics-information
#16
Navin Rustagi, Anbo Zhou, W Scott Watkins, Erika Gedvilaite, Shuoguo Wang, Naveen Ramesh, Donna Muzny, Richard A Gibbs, Lynn B Jorde, Fuli Yu, Jinchuan Xing
BACKGROUND: The cost of Whole Genome Sequencing (WGS) has decreased tremendously in recent years due to advances in next-generation sequencing technologies. Nevertheless, the cost of carrying out large-scale cohort studies using WGS is still daunting. Past simulation studies with coverage at ~2x have shown promise for using low coverage WGS in studies focused on variant discovery, association study replications, and population genomics characterization. However, the performance of low coverage WGS in populations with a complex history and no reference panel remains to be determined...
May 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28531898/plasma-et-1-concentrations-are-elevated-in-patients-with-hypertension-meta-analysis-of-clinical-studies
#17
Mei Xu, Yong-Ping Lu, Ahmed Abdallah Hasan, Berthold Hocher
BACKGROUND/AIMS: A recent study revealed that global overexpression of ET-1 causes a slight reduction in systemic blood pressure. Moreover, heterozygous ET-1 knockout mice are hypertensive. The role of ET-1 in human hypertension was so far not addressed by a strict meta-analysis of published human clinical studies. METHODS: We included studies published between January 1, 1990 and February 28, 2017. We included case control studies analyzing untreated essential hypertension or hypertensive patients where antihypertensive medication was discontinued for at least two weeks...
May 26, 2017: Kidney & Blood Pressure Research
https://www.readbyqxmd.com/read/28531216/impact-of-mutations-in-toll-like-receptor-pathway-genes-on-esophageal-carcinogenesis
#18
Daffolyn Rachael Fels Elliott, Juliane Perner, Xiaodun Li, Martyn F Symmons, Brett Verstak, Matthew Eldridge, Lawrence Bower, Maria O'Donovan, Nick J Gay, Rebecca C Fitzgerald
Esophageal adenocarcinoma (EAC) develops in an inflammatory microenvironment with reduced microbial diversity, but mechanisms for these influences remain poorly characterized. We hypothesized that mutations targeting the Toll-like receptor (TLR) pathway could disrupt innate immune signaling and promote a microenvironment that favors tumorigenesis. Through interrogating whole genome sequencing data from 171 EAC patients, we showed that non-synonymous mutations collectively affect the TLR pathway in 25/171 (14...
May 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28531208/phylogenetic-analysis-of-emergent-streptococcus-pneumoniae-serotype-22f-causing-invasive-pneumococcal-disease-using-whole-genome-sequencing
#19
Walter H B Demczuk, Irene Martin, Linda Hoang, Paul Van Caeseele, Brigitte Lefebvre, Greg Horsman, David Haldane, Jonathan Gubbay, Sam Ratnam, Gregory German, Jennifer Daley Bernier, Lori Strudwick, Allison McGeer, George G Zhanel, Gary Van Domselaar, Morag Graham, Michael R Mulvey
Since implementation of the 13-valent polyvalent conjugate vaccine (PCV13) in Canada during 2010, the proportion of PCV13 serotypes causing invasive pneumococcal disease (IPD) has declined from 55% (n = 1492) in 2010 to 31% (n = 764) in 2014. A concurrent increase of non-PCV13 serotypes has occurred and 22F has become the most prevalent serotype in Canada increasing from 7% (n = 183) to 11% (n = 283). Core single nucleotide variant phylogenetic analysis was performed on 137 Streptococcus pneumoniae serotype 22F isolates collected across Canada from 2005-2015...
2017: PloS One
https://www.readbyqxmd.com/read/28531189/tandem-duplications-lead-to-novel-expression-patterns-through-exon-shuffling-in-drosophila-yakuba
#20
Rebekah L Rogers, Ling Shao, Kevin R Thornton
One common hypothesis to explain the impacts of tandem duplications is that whole gene duplications commonly produce additive changes in gene expression due to copy number changes. Here, we use genome wide RNA-seq data from a population sample of Drosophila yakuba to test this 'gene dosage' hypothesis. We observe little evidence of expression changes in response to whole transcript duplication capturing 5' and 3' UTRs. Among whole gene duplications, we observe evidence that dosage sharing across copies is likely to be common...
May 22, 2017: PLoS Genetics
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