keyword
MENU ▼
Read by QxMD icon Read
search

population genomics

keyword
https://www.readbyqxmd.com/read/28350798/research-priorities-for-harnessing-plant-microbiomes-in-sustainable-agriculture
#1
Posy E Busby, Chinmay Soman, Maggie R Wagner, Maren L Friesen, James Kremer, Alison Bennett, Mustafa Morsy, Jonathan A Eisen, Jan E Leach, Jeffery L Dangl
Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes-i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance-into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28348855/emergence-of-a-novel-lineage-containing-a-prophage-in-emm-m3-group-a-streptococcus-associated-with-upsurge-in-invasive-disease-in-the-uk
#2
Ali Al-Shahib, Anthony Underwood, Baharak Afshar, Claire E Turner, Theresa Lamagni, Shiranee Sriskandan, Androulla Efstratiou
A sudden increase in invasive Group A Streptococcus (iGAS) infections associated with emm/M3 isolates during the winter of 2008/09 prompted the initiation of enhanced surveillance in England. In order to characterise the population of emm/M3 GAS within the UK and determine bacterial factors that might be responsible for this upsurge, 442 emm/M3 isolates from cases of invasive and non-invasive infections during the period 2001-2013 were subjected to whole genome sequencing. MLST analysis differentiated emm/M3 isolates into three sequence types (STs): ST15, ST315 and ST406...
June 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28346895/wheat-genomics-comes-of-age
#3
REVIEW
Cristobal Uauy
Advances in wheat genomics have lagged behind other major cereals (e.g., rice and maize) due to its highly repetitive and large polyploid genome. Recent technological developments in sequencing and assembly methods, however, have largely overcome these barriers. The community now moves to an era centred on functional characterisation of the genome. This includes understanding sequence and structural variation as well as how information is integrated across multiple homoeologous genomes. This understanding promises to uncover variation previously hidden from natural and human selection due to the often observed functional redundancy between homoeologs...
March 24, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28346890/high-throughput-system-wide-engineering-and-screening-for-microbial-biotechnology
#4
REVIEW
Yannick Vervoort, Alicia Gutiérrez Linares, Miguel Roncoroni, Chengxun Liu, Jan Steensels, Kevin J Verstrepen
Genetic engineering and screening of large number of cells or populations is a crucial bottleneck in today's systems biology and applied (micro)biology. Instead of using standard methods in bottles, flasks or 96-well plates, scientists are increasingly relying on high-throughput strategies that miniaturize their experiments to the nanoliter and picoliter scale and the single-cell level. In this review, we summarize different high-throughput system-wide genome engineering and screening strategies for microbes...
March 24, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28346444/genetic-variants-associated-with-mosaic-y-chromosome-loss-highlight-cell-cycle-genes-and-overlap-with-cancer-susceptibility
#5
Daniel J Wright, Felix R Day, Nicola D Kerrison, Florian Zink, Alexia Cardona, Patrick Sulem, Deborah J Thompson, Svanhvit Sigurjonsdottir, Daniel F Gudbjartsson, Agnar Helgason, J Ross Chapman, Steve P Jackson, Claudia Langenberg, Nicholas J Wareham, Robert A Scott, Unnur Thorsteindottir, Ken K Ong, Kari Stefansson, John R B Perry
The Y chromosome is frequently lost in hematopoietic cells, which represents the most common somatic alteration in men. However, the mechanisms that regulate mosaic loss of chromosome Y (mLOY), and its clinical relevance, are unknown. We used genotype-array-intensity data and sequence reads from 85,542 men to identify 19 genomic regions (P < 5 × 10(-8)) that are associated with mLOY. Cumulatively, these loci also predicted X chromosome loss in women (n = 96,123; P = 4 × 10(-6)). Additional epigenome-wide methylation analyses using whole blood highlighted 36 differentially methylated sites associated with mLOY...
March 27, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28345837/association-of-the-asp1312gly-thyroglobulin-gene-polymorphism-with-susceptibility-to-differentiated-thyroid-cancer-in-an-iranian-population
#6
Maryam Abidi, Shima Fayaz, Pezhman Fard Esfahani
Background and aim: While the causes of thyroid cancer in most patients remain largely unknown, it has recently been reported that there may be links to particular chromosome regions. In particular, polymorphisms (SNPs) in the thyroglobulin (TG) gene could be susceptibility factors. Methods: In this case-control study, any association of the Asp1312Gly single nucleotide polymorphism (SNP) in the TG gene (rs2069556) with susceptibility to differentiated thyroid cancer (DTC) was investigated among 103 Iranian patients and 100 controls who had no history of any type of cancer...
February 1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28345409/osteoarthritis-in-football
#7
Gian M Salzmann, Stefan Preiss, Marcy Zenobi-Wong, Laurent P Harder, Dirk Maier, Jirí Dvorák
Football is currently the most popular sporting activity in the world. Multiple reports have shown that a high incidence of osteoarthritis is found in football players. Evidence clearly shows that traumatic injury significantly predisposes players for such pathophysiology. Injuries are frequent in amateur as well as professional football players, with knee and ankle accounting for the most severe injuries. Many professional athletes lose playing time due to injuries and many are forced into early retirement...
April 2017: Cartilage
https://www.readbyqxmd.com/read/28345200/all-roads-lead-to-weediness-patterns-of-genomic-divergence-reveal-extensive-recurrent-weedy-rice-origins-from-south-asian-oryza
#8
Zhongyun Huang, Nelson D Young, Michael Reagon, Katie E Hyma, Kenneth M Olsen, Yulin Jia, Ana L Caicedo
Weedy rice (Oryza spp.), a weedy relative of cultivated rice (O. sativa), infests and persists in cultivated rice fields worldwide. Many weedy rice populations have evolved similar adaptive traits, considered part of the "agricultural weed syndrome," making this an ideal model to study the genetic basis of parallel evolution. Understanding parallel evolution hinges on accurate knowledge of the genetic background and origins of existing weedy rice groups. Using population structure analyses of South Asian and US weedy rice, we show that weeds in South Asia have highly heterogeneous genetic backgrounds, with ancestry contributions both from cultivated varieties (aus and indica) and wild rice...
March 27, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28345182/can-genomic-data-alone-tell-us-whether-speciation-happened-with-gene-flow
#9
Ming Yang, Ziwen He, Suhua Shi, Chung-I Wu
The allopatric model, which requires a period of geographical isolation for speciation to complete, has been the standard model in the modern era. Recently, "speciation with gene flow" has been widely discussed in relation to the model of "strict allopatry" and the level of DNA divergence across genomic regions. We wish to caution that genomic data by themselves may only permit the rejection of the simplest form of allopatry. Even a slightly more complex and realistic model that starts with sub-divided populations would be impossible to reject by the genomic data alone...
March 27, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28345074/single-cell-rna-seq-and-computational-analysis-using-temporal-mixture-modelling-resolves-th1-tfh-fate-bifurcation-in-malaria
#10
Tapio Lönnberg, Valentine Svensson, Kylie R James, Daniel Fernandez-Ruiz, Ismail Sebina, Ruddy Montandon, Megan S F Soon, Lily G Fogg, Arya Sheela Nair, Urijah Liligeto, Michael J T Stubbington, Lam-Ha Ly, Frederik Otzen Bagger, Max Zwiessele, Neil D Lawrence, Fernando Souza-Fonseca-Guimaraes, Patrick T Bunn, Christian R Engwerda, William R Heath, Oliver Billker, Oliver Stegle, Ashraful Haque, Sarah A Teichmann
Differentiation of naïve CD4(+) T cells into functionally distinct T helper subsets is crucial for the orchestration of immune responses. Due to extensive heterogeneity and multiple overlapping transcriptional programs in differentiating T cell populations, this process has remained a challenge for systematic dissection in vivo. By using single-cell transcriptomics and computational analysis using a temporal mixtures of Gaussian processes model, termed GPfates, we reconstructed the developmental trajectories of Th1 and Tfh cells during blood-stage Plasmodium infection in mice...
March 3, 2017: Science Immunology
https://www.readbyqxmd.com/read/28344990/inspiired-a-pipeline-for-quantitative-analysis-of-sites-of-new-dna-integration-in-cellular-genomes
#11
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
#12
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/28344773/escherichia-coli-st131-a-multidrug-resistant-clone-primed-for-global-domination
#13
REVIEW
Johann D D Pitout, Rebekah DeVinney
A single extra-intestinal pathogenic Escherichia coli (ExPEC) clone, named sequence type (ST) 131, is responsible for millions of global antimicrobial-resistant (AMR) infections annually. Population genetics indicate that ST131 consists of different clades (i.e. A, B, and C); however, clade C is the most dominant globally. A ST131 subclade, named C1-M27, is emerging in Japan and has been responsible for the recent increase in AMR ExPEC in that country. The sequential acquisition of several virulence and AMR genes associated with mobile genetic elements during the 1960s to 1980s primed clade C (and its subclades C1 and C2) for success in the 1990s to 2000s...
2017: F1000Research
https://www.readbyqxmd.com/read/28344482/the-genetic-profiles-of-cyp1a1-cyp1a2-and-cyp2e1-enzymes-as-susceptibility-factor-in-xenobiotic-toxicity-in-turkish-population
#14
Merve Arici, Gül Özhan
Evaluation and sequencing of heritable alterations in the human genome and the large-scale identification of gene polymorphism for understanding the genetic background of individuals in response to potential toxicants are provided by toxicogenetics. Cytochrome P450 (CYP) enzymes play role not only phase I-dependent metabolism of xenobiotics but also metabolism of endogenous compounds. CYP1A1, CYP1A2 and CYP2E1 enzymes, which are in phase I enzymes, are responsible for metabolic activation and detoxification of several chemical compounds...
February 2017: Saudi Pharmaceutical Journal: SPJ: the Official Publication of the Saudi Pharmaceutical Society
https://www.readbyqxmd.com/read/28344472/prevalence-of-udp-glucuronosyltransferase-polymorphisms-ugt1a6%C3%A2-2-1a7%C3%A2-12-1a8%C3%A2-3-1a9%C3%A2-3-2b7%C3%A2-2-and-2b15%C3%A2-2-in-a-saudi-population
#15
Khalid M Alkharfy, Basit L Jan, Sibtain Afzal, Fahad I Al-Jenoobi, Abdullah M Al-Mohizea, Saleh Al-Muhsen, Rabih Halwani, Mohammad K Parvez, Mohammed S Al-Dosari
Glucuronidation is an important phase II pathway responsible for many endogenous substances and drug metabolism. The present work evaluated allele frequencies of certain UDP-glucuronosyl-transferases (UGT 1A6∗2, A7∗12, A8∗3, A9∗3, 2B7∗2, and 2B15∗2) in Saudi Arabians that could provide essential ethnic information. Blood samples from 192 healthy unrelated Saudi males of various geographic regions were collected. Genomic DNA was isolated and genotyping of various UGTs was carried out using polymerase chain reaction (PCR) followed by direct sequencing...
February 2017: Saudi Pharmaceutical Journal: SPJ: the Official Publication of the Saudi Pharmaceutical Society
https://www.readbyqxmd.com/read/28344127/replicated-association-between-the-european-gwas-locus-rs10503253-at-csmd1-and-schizophrenia-in-asian-population
#16
Weiqing Liu, Fang Liu, Xiufeng Xu, Yan Bai
Schizophrenia is one of the most severe mental disorders with significant heritability. Recent genetic association studies including genome-wide association studies (GWAS) have identified multiple common variants conferring risk of schizophrenia. An intronic SNP within CSMD1, rs10503253, is one of the top risk SNPs for schizophrenia in Europeans discovered through large GWAS. However, whether rs10503253 is also a risk SNP for schizophrenia in other populations, such as Asians, is still unknown. To answer this question, we examined the association of rs10503253 with schizophrenia in a total of 7,514 schizophrenia patients, 9,058 healthy controls and 1,115 nuclear families originated from Asia using a meta-analytic approach...
March 23, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28343740/pediatric-oncology-enters-an-era-of-precision-medicine
#17
Nita L Seibel, Katherine Janeway, Carl E Allen, Susan N Chi, Yoon-Jae Cho, Julia L Glade Bender, AeRang Kim, Theodore W Laetsch, Meredith S Irwin, Naoko Takebe, James V Tricoli, Donald Williams Parsons
With the use of high-throughput molecular profiling technologies, precision medicine trials are ongoing for adults with cancer. Similarly, there is an interest in how these techniques can be applied to tumors in children and adolescents to expand our understanding of the biology of pediatric cancers and evaluate the clinical implications of genomic testing for these patients. This article reviews the early studies in pediatric oncology showing the feasibility of this approach, describe the future plans to evaluate the clinical implications in a multicenter clinical trial and identify the challenges of applying genomics in this patient population...
February 1, 2017: Current Problems in Cancer
https://www.readbyqxmd.com/read/28343239/improved-full-length-killer-cell-immunoglobulin-like-receptor-transcript-discovery-in-mauritian-cynomolgus-macaques
#18
Trent M Prall, Michael E Graham, Julie A Karl, Roger W Wiseman, Adam J Ericsen, Muthuswamy Raveendran, R Alan Harris, Donna M Muzny, Richard A Gibbs, Jeffrey Rogers, David H O'Connor
Killer cell immunoglobulin-like receptors (KIRs) modulate disease progression of pathogens including HIV, malaria, and hepatitis C. Cynomolgus and rhesus macaques are widely used as nonhuman primate models to study human pathogens, and so, considerable effort has been put into characterizing their KIR genetics. However, previous studies have relied on cDNA cloning and Sanger sequencing that lack the throughput of current sequencing platforms. In this study, we present a high throughput, full-length allele discovery method utilizing Pacific Biosciences circular consensus sequencing (CCS)...
March 25, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28343093/influence-of-genetic-variants-of-cyp2d6-cyp2c9-cyp2c19-and-cyp3a4-on-antiepileptic-drug-metabolism-in-pediatric-patients-with-refractory-epilepsy
#19
Miguel A López-García, Iris A Feria-Romero, Héctor Serrano, Darío Rayo-Mares, Pietro Fagiolino, Marta Vázquez, Consuelo Escamilla-Núñez, Israel Grijalva, David Escalante-Santiago, Sandra Orozco-Suarez
BACKGROUND: Identified the polymorphisms of CYP2D6, CYP2C9, CYP2C19 and CYP3A4, within a rigorously selected population of pediatric patients with drug-resistant epilepsy. METHOD: The genomic DNA of 23 drug-resistant epilepsy patients and 7 patients with good responses were analyzed. Ten exons in these four genes were genotyped, and the drug concentrations in saliva and plasma were determined. RESULTS: The relevant SNPs with pharmacogenomics relations were CYP2D6*2 (rs16947) decreased your activity and CYP2D6*4 (rs1065852), CYP2C19*2 (rs4244285) and CYP3A4*1B (rs2740574) by association with poor metabolizer...
January 19, 2017: Pharmacological Reports: PR
https://www.readbyqxmd.com/read/28342108/fine-mapping-of-a-quantitative-resistance-gene-for-gray-leaf-spot-of-maize-zea-mays-l-derived-from-teosinte-z-mays-ssp-parviglumis
#20
Xinye Zhang, Qin Yang, Elizabeth Rucker, Wade Thomason, Peter Balint-Kurti
In this study we mapped the QTL Qgls8 for gray leaf spot (GLS) resistance in maize to a ~130 kb region on chromosome 8 including five predicted genes. In previous work, using near isogenic line (NIL) populations in which segments of the teosinte (Zea mays ssp. parviglumis) genome had been introgressed into the background of the maize line B73, we had identified a QTL on chromosome 8, here called Qgls8, for gray leaf spot (GLS) resistance. We identified alternate teosinte alleles at this QTL, one conferring increased GLS resistance and one increased susceptibility relative to the B73 allele...
March 24, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
keyword
keyword
84104
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"