keyword
MENU ▼
Read by QxMD icon Read
search

linkage analysis

keyword
https://www.readbyqxmd.com/read/27913833/tight-repulsion-linkage-between-sr36-and-sr39-was-revealed-by-genetic-cytogenetic-and-molecular-analyses
#1
Bosco Chemayek, Urmil K Bansal, Naeela Qureshi, Peng Zhang, William W Wagoire, Harbans S Bariana
The shortening of Aegilops speltoides segment did not facilitate recombination between stem rust resistance genes Sr36 and Sr39 . Robustness of marker rwgs28 for marker-assisted selection of Sr39 was demonstrated. Stem rust resistance genes Sr39 and Sr36 were transferred from Aegilops speltoides and Triticum timopheevii, respectively, to chromosome 2B of wheat. Genetic stocks RL6082 and RWG1 carrying Sr39 on a large and a shortened Ae. speltoides segments, respectively, and the Sr36-carrying Australian wheat cultivar Cook were used in this study...
December 2, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27911494/determining-functional-aptamer-protein-interaction-by-biolayer-interferometry
#2
Xinhui Lou, Martin Egli, Xianbin Yang
Short single-stranded nucleic acids called aptamers are widely being explored as recognition molecules of high affinity and specificity for binding a wide range of target molecules, particularly protein targets. In biolayer interferometry (BLI), a simple Dip-and-Read approach in which the aptamer-coated biosensors are dipped into microplate wells is used to study the interactions between an aptamer and its target protein. Here we describe the protocol for the analysis of the interaction between a well-characterized anti-thrombin RNA aptamer with thrombin (Basic Protocol)...
December 1, 2016: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/27909454/linkage-and-association-analyses-of-schizophrenia-with-genetic-variations-on-chromosome-22q11-in-koreans
#3
Se Chang Yoon, Yong Lee Jang, Jong-Won Kim, Eun-Young Cho, Dong Yeon Park, Kyung Sue Hong, Yu Sang Lee
OBJECTIVE: Chromosome 22q11 has been implicated as a susceptibility locus of schizophrenia. It also contains various candidate genes for which evidence of association with schizophrenia has been reported. To determine whether genetic variations in chromosome 22q11 are associated with schizophrenia in Koreans, we performed a linkage analysis and case-control association study. METHODS: Three microsatellite markers within a region of 4.35 Mb on 22q11 were genotyped for 47 multiplex schizophrenia families, and a non-parametric linkage analysis was applied...
November 2016: Psychiatry Investigation
https://www.readbyqxmd.com/read/27909040/association-between-organisational-and-workplace-cultures-and-patient-outcomes-systematic-review-protocol
#4
J Braithwaite, J Herkes, K Ludlow, G Lamprell, L Testa
INTRODUCTION: Despite widespread interest in the topic, no current synthesis of research is available analysing the linkages between organisational or workplace cultures on the one hand, and patient outcomes on the other. This protocol proposes a systematic review to analyse and synthesise the literature to date on this topic. The resulting review will discuss characteristics of included studies in terms of the type of healthcare settings researched, the measurements of organisational and workplace culture, patient outcomes measured and the influence of these cultures on patient outcomes...
December 1, 2016: BMJ Open
https://www.readbyqxmd.com/read/27908108/dual-hydrogen-bonding-motifs-in-complexes-formed-between-tropolone-and-formic-acid
#5
Deacon J Nemchick, Michael K Cohen, Patrick H Vaccaro
The near-ultraviolet π(*)←π absorption system of weakly bound complexes formed between tropolone (TrOH) and formic acid (FA) under cryogenic free-jet expansion conditions has been interrogated by exploiting a variety of fluorescence-based laser-spectroscopic probes, with synergistic quantum-chemical calculations built upon diverse model chemistries being enlisted to unravel the structural and dynamical properties of the pertinent ground [X̃(1)A(')] and excited [Ã(1)A(')π(*)π] electronic states. For binary TrOH ⋅ FA adducts, the presence of dual hydrogen-bond linkages gives rise to three low-lying isomers designated (in relative energy order) as INT, EXT1, and EXT2 depending on whether docking of the FA ligand to the TrOH substrate takes place internal or external to the five-membered reaction cleft of tropolone...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27906986/cost-effectiveness-of-community-based-tb-hiv-screening-and-linkage-to-care-in-rural-south-africa
#6
Jennifer A Gilbert, Sheela V Shenoi, Anthony P Moll, Gerald H Friedland, A David Paltiel, Alison P Galvani
South Africa has one of the highest burdens of TB worldwide, driven by the country's widespread prevalence of HIV, and further complicated by drug resistance. Active case finding within the community, particularly in rural areas where healthcare access is limited, can significantly improve diagnosis and treatment coverage in high-incidence settings. We evaluated the potential health and economic consequences of implementing community-based TB/HIV screening and linkage to care. Using a dynamic model of TB and HIV transmission over a time horizon of 10 years, we compared status quo TB/HIV control to community-based TB/HIV screening at frequencies of once every two years, one year, and six months...
2016: PloS One
https://www.readbyqxmd.com/read/27906029/trends-in-clinical-characteristics-and-outcomes-of-pre-art-care-at-a-large-hiv-clinic-in-nairobi-kenya-a-retrospective-cohort-study
#7
Jared O Mecha, Elizabeth N Kubo, Lucy W Nganga, Peter N Muiruri, Lilian N Njagi, Immaculate N Mutisya, Justine J Odionyi, Syokau C Ilovi, Mary Wambui, Christopher Githu, Richard Ngethe, Elizabeth M Obimbo, Zipporah W Ngumi
BACKGROUND: The success of antiretroviral therapy in resource-scarce settings is an illustration that complex healthcare interventions can be successfully delivered even in fragile health systems. Documenting the success factors in the scale-up of HIV care and treatment in resource constrained settings will enable health systems to prepare for changing population health needs. This study describes changing demographic and clinical characteristics of adult pre-ART cohorts, and identifies predictors of pre-ART attrition at a large urban HIV clinic in Nairobi, Kenya...
November 14, 2016: AIDS Research and Therapy
https://www.readbyqxmd.com/read/27902806/orthology-guided-transcriptome-assembly-of-italian-ryegrass-and-meadow-fescue-for-single-nucleotide-polymorphism-discovery
#8
Štěpán Stočes, Tom Ruttink, Jan Bartoš, Bruno Studer, Steven Yates, Zbigniew Zwierzykowski, Michael Abrouk, Isabel Roldán-Ruiz, Tomasz Książczyk, Elodie Rey, Jaroslav Doležel, David Kopecký
Single-nucleotide polymorphisms (SNPs) represent natural DNA sequence variation. They can be used for various applications including the construction of high-density genetic maps, analysis of genetic variability, genome-wide association studies, and map-based cloning. Here we report on transcriptome sequencing in the two forage grasses, meadow fescue ( Huds.) and Italian ryegrass ( Lam.), and identification of various classes of SNPs. Using the Orthology Guided Assembly (OGA) strategy, we assembled and annotated a total of 18,952 and 19,036 transcripts for Italian ryegrass and meadow fescue, respectively...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902686/genomic-characterization-of-metformin-hepatic-response
#9
Marcelo R Luizon, Walter L Eckalbar, Yao Wang, Stacy L Jones, Robin P Smith, Megan Laurance, Lawrence Lin, Paul J Gallins, Amy S Etheridge, Fred Wright, Yihui Zhou, Cliona Molony, Federico Innocenti, Sook Wah Yee, Kathleen M Giacomini, Nadav Ahituv
Metformin is used as a first-line therapy for type 2 diabetes (T2D) and prescribed for numerous other diseases. However, its mechanism of action in the liver has yet to be characterized in a systematic manner. To comprehensively identify genes and regulatory elements associated with metformin treatment, we carried out RNA-seq and ChIP-seq (H3K27ac, H3K27me3) on primary human hepatocytes from the same donor treated with vehicle control, metformin or metformin and compound C, an AMP-activated protein kinase (AMPK) inhibitor (allowing to identify AMPK-independent pathways)...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27902594/combined-genotype-and-haplotype-distributions-of-mthfr-c677t-and-a1298c-polymorphisms-a-cross-sectional-descriptive-study-of-13-473-chinese-adult-women
#10
Shujun Fan, Boyi Yang, Xueyuan Zhi, Yanxun Wang, Quanmei Zheng, Guifan Sun
Methylenetetrahydrofolate reductase (MTHFR) C677T and A1298C polymorphisms are, independently and/or in combination, associated with many disorders. However, data on the combined genotype and haplotype distributions of the 2 polymorphisms in Chinese population were limited.We recruited 13,473 adult women from 9 Chinese provinces, collected buccal cell samples, and determined genotypes, to estimate the combined genotype and haplotype distributions of the MTHFR C677T and A1298C polymorphisms.In the total sample, the 6 common combined genotypes were CT/AA (29...
November 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27901114/genome-wide-diversity-and-association-mapping-for-capsaicinoids-and-fruit-weight-in-capsicum-annuum-l
#11
Padma Nimmakayala, Venkata L Abburi, Thangasamy Saminathan, Suresh B Alaparthi, Aldo Almeida, Brittany Davenport, Marjan Nadimi, Joshua Davidson, Krittika Tonapi, Lav Yadav, Sridhar Malkaram, Gopinath Vajja, Gerald Hankins, Robert Harris, Minkyu Park, Doil Choi, John Stommel, Umesh K Reddy
Accumulated capsaicinoid content and increased fruit size are traits resulting from Capsicum annuum domestication. In this study, we used a diverse collection of C. annuum to generate 66,960 SNPs using genotyping by sequencing. The study identified 1189 haplotypes containing 3413 SNPs. Length of individual linkage disequilibrium (LD) blocks varied along chromosomes, with regions of high and low LD interspersed with an average LD of 139 kb. Principal component analysis (PCA), Bayesian model based population structure analysis and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions are in agreement with capsaicin content (CA) and fruit weight (FW) classifications indicating the importance of these traits in shaping modern pepper genome...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27899648/genetic-selection-for-mistranslation-rescues-a-defective-co-chaperone-in-yeast
#12
Kyle S Hoffman, Matthew D Berg, Brian H Shilton, Christopher J Brandl, Patrick O'Donoghue
Despite the general requirement for translation fidelity, mistranslation can be an adaptive response. We selected spontaneous second site mutations that suppress the stress sensitivity caused by a Saccharomyces cerevisiae tti2 allele with a Leu to Pro mutation at residue 187, identifying a single nucleotide mutation at the same position (C70U) in four tRNA(Pro)UGG genes. Linkage analysis and suppression by SUF9G3:U70 expressed from a centromeric plasmid confirmed the causative nature of the suppressor mutation...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899575/ensembl-2017
#13
Bronwen L Aken, Premanand Achuthan, Wasiu Akanni, M Ridwan Amode, Friederike Bernsdorff, Jyothish Bhai, Konstantinos Billis, Denise Carvalho-Silva, Carla Cummins, Peter Clapham, Laurent Gil, Carlos García Girón, Leo Gordon, Thibaut Hourlier, Sarah E Hunt, Sophie H Janacek, Thomas Juettemann, Stephen Keenan, Matthew R Laird, Ilias Lavidas, Thomas Maurel, William McLaren, Benjamin Moore, Daniel N Murphy, Rishi Nag, Victoria Newman, Michael Nuhn, Chuang Kee Ong, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Daniel Sheppard, Helen Sparrow, Kieron Taylor, Anja Thormann, Alessandro Vullo, Brandon Walts, Steven P Wilder, Amonida Zadissa, Myrto Kostadima, Fergal J Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Daniel M Staines, Stephen J Trevanion, Fiona Cunningham, Andrew Yates, Daniel R Zerbino, Paul Flicek
Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access methods ensure uniform data analysis and distribution for all supported species...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898820/dissecting-the-genetic-basis-of-resistance-to-soybean-cyst-nematode-combining-linkage-and-association-mapping
#14
Ying-Hui Li, Xue-Hui Shi, Hui-Hui Li, Jochen C Reif, Jia-Jun Wang, Zhang-Xiong Liu, Sang He, Bai-Shuang Yu, Li-Juan Qiu
A set of 585 informative single-nucleotide polymorphism (SNP) loci was used to genotype both a panel of diverse accessions and a set of recombinant inbred lines (RILs) bred from the cross Zhongpin03-5373 (ZP; resistant to SCN) × Zhonghuang13 (ZH; susceptible). The SNP loci are mostly sited within genic sequence in regions of the soybean [ (L.) Merr.] genome thought to harbor genes determining resistance to the soybean cyst nematode (SCN, Ichinohe). The three strongest quantitative trait nucleotides (QTNs) identified by association mapping (AM) involved the genes (a component of the multigene locus ), and (an paralog), as well as some other loci with smaller effects...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898805/characterization-of-three-rice-multiparent-advanced-generation-intercross-magic-populations-for-quantitative-trait-loci-identification
#15
Lijun Meng, Longbiao Guo, Kimberly Ponce, Xiangqian Zhao, Guoyou Ye
Three new rice ( L.) multiparent advanced generation intercross (MAGIC) populations were developed using eight elite rice varieties from different breeding programs. These three populations were two recombinant inbred line (RIL) populations derived from two 4-way crosses, DC1 and DC2, and one RIL population derived from an 8-way cross. These populations were genotyped using an Illumina Infinium rice 6K SNP chip. The potential of the three MAGIC populations in identifying marker-trait associations was demonstrated using the plant height (PH) and heading date (HD) measured in 2014...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898759/establishment-and-optimization-of-genomic-selection-to-accelerate-the-domestication-and-improvement-of-intermediate-wheatgrass
#16
Xiaofei Zhang, Ahmad Sallam, Liangliang Gao, Traci Kantarski, Jesse Poland, Lee R DeHaan, Donald L Wyse, James A Anderson
Intermediate wheatgrass (IWG) is a perennial species and has edible and nutritious grain and desirable agronomic traits, including large seed size, high grain yield, and biomass. It also has the potential to provide ecosystem services and an economic return to farmers. However, because of its allohexaploidy and self-incompatibility, developing molecular markers for genetic analysis and molecular breeding has been challenging. In the present study, using genotyping-by-sequencing (GBS) technology, 3436 genome-wide markers discovered in a biparental population with 178 genets, were mapped to 21 linkage groups (LG) corresponding to 21 chromosomes of IWG...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27898757/expanding-maize-genetic-resources-with-predomestication-alleles-maize-teosinte-introgression-populations
#17
Zhengbin Liu, Jason Cook, Susan Melia-Hancock, Katherine Guill, Christopher Bottoms, Arturo Garcia, Oliver Ott, Rebecca Nelson, Jill Recker, Peter Balint-Kurti, Sara Larsson, Nicholas Lepak, Ed Buckler, Loren Trimble, William Tracy, Michael D McMullen, Sherry A Flint-Garcia
Teosinte ( subsp. H. H. Iltis & Doebley) has greater genetic diversity than maize inbreds and landraces ( subsp. ). There are, however, limited genetic resources to efficiently evaluate and tap this diversity. To broaden resources for genetic diversity studies in maize, we developed and evaluated 928 near-isogenic introgression lines (NILs) from 10 teosinte accessions in the B73 background. Joint linkage analysis of the 10 introgression populations identified several large-effect quantitative trait loci (QTL) for days to anthesis (DTA), kernel row number (KRN), and 50-kernel weight (Wt50k)...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27896743/analysis-of-quantitative-trait-loci
#18
David L Duffy
Although the term quantitative trait locus (QTL) strictly refers merely to a genetic variant that causes changes in a quantitative phenotype such as height, QTL analysis more usually describes techniques used to study oligogenic or polygenic traits where each identified locus contributes a relatively small amount to the genetic determination of the trait, which may be categorical in nature. Originally, too, it would be clear that it covered segregation and genetic linkage analysis, but now genetic association analysis in a genome-wide SNP or sequencing experiment would be the commonest application...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27895891/gene-specific-sex-effects-on-eosinophil-infiltration-in-leishmaniasis
#19
Martina Slapničková, Valeriya Volkova, Marie Čepičková, Tatyana Kobets, Matyáš Šíma, Milena Svobodová, Peter Demant, Marie Lipoldová
BACKGROUND: Sex influences susceptibility to many infectious diseases, including some manifestations of leishmaniasis. The disease is caused by parasites that enter to the skin and can spread to the lymph nodes, spleen, liver, bone marrow, and sometimes lungs. Parasites induce host defenses including cell infiltration, leading to protective or ineffective inflammation. These responses are often influenced by host genotype and sex. We analyzed the role of sex in the impact of specific gene loci on eosinophil infiltration and its functional relevance...
2016: Biology of Sex Differences
https://www.readbyqxmd.com/read/27895853/expression-of-liver-alpha-amylase-in-obese-mouse-hepatocytes
#20
Zohreh Afsartala, Sanaz Savabkar, Ehsan Nazemalhosseini Mojarad, Vahideh Assadollahi, Shima Tanha, Khosro Bijangi, Mohammadreza Gholami
AIM: The aim of this study is to demonstrate the relation between the expression of liver alpha-amylase and obesity. BACKGROUND: Alpha-amylase catalyses the hydrolysis of 1, 4-alpha-glucosidic linkages in polysaccharides and has three main subtypes, including: salivary, pancreatic, and hepatic. Hepatic alpha-amylase is involved in glycogen metabolism, and has a role in obesity and its management. In this study, we aimed to analyze the expression of liver alpha-amylase in overweight and obese mouse...
2016: Gastroenterology and Hepatology From Bed to Bench
keyword
keyword
95573
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"