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https://www.readbyqxmd.com/read/28749613/linked-selection-demography-and-the-evolution-of-correlated-genomic-landscapes-in-birds-and-beyond
#1
Reto Burri
Selection has a deep impact on the distribution of genetic diversity and population differentiation along the genome (the genomic landscapes of diversity and differentiation), reducing diversity and elevating differentiation not only at the sites it targets, but also at linked neutral sites. Fuelled by the high-throughput sequencing revolution, these genomic footprints of selection have been extensively exploited over the past decade with the aim to identify genomic regions involved in adaptation and speciation...
August 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28749054/the-precision-medicine-nation
#2
Maya Sabatello, Paul S Appelbaum
The United States' ambitious Precision Medicine Initiative proposes to accelerate exponentially the adoption of precision medicine, an approach to health care that tailors disease diagnosis, treatment, and prevention to individual variability in genes, environment, and lifestyle. It aims to achieve this by creating a cohort of volunteers for precision medicine research, accelerating biomedical research innovation, and adopting policies geared toward patients' empowerment. As strategies to implement the PMI are formulated, critical consideration of the initiative's ethical and sociopolitical dimensions is needed...
July 2017: Hastings Center Report
https://www.readbyqxmd.com/read/28748599/a-comparison-of-statistical-methods-for-the-study-of-etiologic-heterogeneity
#3
Emily C Zabor, Colin B Begg
Cancer epidemiologic research has traditionally been guided by the premise that certain diseases share an underlying etiology, or cause. However, with the rise of molecular and genomic profiling, attention has increasingly focused on identifying subtypes of disease. As subtypes are identified, it is natural to ask the question of whether they share a common etiology or in fact arise from distinct sets of risk factors. In this context, epidemiologic questions of interest include (1) whether a risk factor of interest has the same effect across all subtypes of disease and (2) whether risk factor effects differ across levels of each individual tumor marker of which the subtypes are comprised...
July 26, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28748462/in-vivo-rat-t-lymphocyte-pig-a-assay-detection-and-expansion-of-cells-deficient-in-the-gpi-anchored-cd48-surface-marker-for-analysis-of-mutation-in-the-endogenous-pig-a-gene
#4
Vasily N Dobrovolsky, Javier Revollo, Dayton M Petibone, Robert H Heflich
The Pig-a assay is being developed as an in vivo gene mutation assay for regulatory safety assessments. The assay is based on detecting mutation in the endogenous Pig-a gene of treated rats by using flow cytometry to measure changes in cell surface markers of peripheral blood cells. Here we present a methodology for demonstrating that phenotypically mutant rat T-cells identified by flow cytometry contain mutations in the Pig-a gene, an important step for validating the assay. In our approach, the mutant phenotype T-cells are sorted into individual wells of 96-well plates and expanded into clones...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28748394/association-mapping-analysis-of-fiber-yield-and-quality-traits-in-upland-cotton-gossypium-hirsutum-l
#5
Mulugeta Seyoum Ademe, Shoupu He, Zhaoe Pan, Junling Sun, Qinglian Wang, Hongde Qin, Jinhai Liu, Hui Liu, Jun Yang, Dongyong Xu, Jinlong Yang, Zhiying Ma, Jinbiao Zhang, Zhikun Li, Zhongmin Cai, Xuelin Zhang, Xin Zhang, Aifen Huang, Xianda Yi, Guanyin Zhou, Lin Li, Haiyong Zhu, Baoyin Pang, Liru Wang, Yinhua Jia, Xiongming Du
Fiber yield and quality are the most important traits for Upland cotton (Gossypium hirsutum L.). Identifying high yield and good fiber quality genes are the prime concern of researchers in cotton breeding. Association mapping offers an alternative and powerful method for detecting those complex agronomic traits. In this study, 198 simple sequence repeats (SSRs) were used to screen markers associated with fiber yield and quality traits with 302 elite Upland cotton accessions that were evaluated in 12 locations representing the Yellow River and Yangtze River cotton growing regions of China...
July 26, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28748348/impact-of-genetic-polymorphisms-on-phenytoin-pharmacokinetics-and-clinical-outcomes-in-the-middle-east-and-north-africa-region
#6
REVIEW
Renée Dagenais, Kyle John Wilby, Hazem Elewa, Mary H H Ensom
BACKGROUND: Genetic polymorphisms are known to influence outcomes with phenytoin yet effects in the Middle East and North Africa region are poorly understood. OBJECTIVES: The objective of this systematic review was to evaluate the impact of genetic polymorphisms on phenytoin pharmacokinetics and clinical outcomes in populations originating from the Middle East and North Africa region, and to characterize genotypic and allelic frequencies within the region for genetic polymorphisms assessed...
July 26, 2017: Drugs in R&D
https://www.readbyqxmd.com/read/28748222/an-improved-plasmodium-cynomolgi-genome-assembly-reveals-an-unexpected-methyltransferase-gene-expansion
#7
Erica M Pasini, Ulrike Böhme, Gavin G Rutledge, Annemarie Voorberg-Van der Wel, Mandy Sanders, Matt Berriman, Clemens Hm Kocken, Thomas Dan Otto
BACKGROUND: Plasmodium cynomolgi, a non-human primate malaria parasite species, has been an important model parasite since its discovery in 1907. Similarities in the biology of P. cynomolgi to the closely related, but less tractable, human malaria parasite P. vivax make it the model parasite of choice for liver biology and vaccine studies pertinent to P. vivax malaria. Molecular and genome-scale studies of P. cynomolgi have relied on the current reference genome sequence, which remains highly fragmented with 1,649 unassigned scaffolds and little representation of the subtelomeres...
2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28747977/use-of-c57bl-6n-mice-on-the-variety-of-immunological-researches
#8
REVIEW
Hyun Keun Song, Dae Youn Hwang
Inbred mice are an essential animal strain for research as they can improve the reproducibility and reliability of study results. The establishment of new inbred lines is continuing, and new inbred lines are being used in many research fields. C57BL/6 is a mouse laboratory animal that has been developed and used as an inbred strain since early stage of mouse strain development, and, in the 1950s, C57BL/6 was separated into substrains by the Jackson Laboratory (C57BL/6J) and the National Institutes of Health (C57BL/6N)...
June 2017: Laboratory Animal Research
https://www.readbyqxmd.com/read/28747380/identification-of-differentially-expressed-splice-variants-by-the-proteogenomic-pipeline-splicify
#9
Malgorzata A Komor, Thang Pham, Annemieke C Hiemstra, Sander R Piersma, Anne S Bolijn, Tim Schelfhorst, Pien M Delis-van Diemen, Marianne Tijssen, Robert P Sebra, Meredith Ashby, Gerrit A Meijer, Connie R Jimenez, Remond J A Fijneman
Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, we focus on this rich source of cancer specific biomarkers. To this end, we developed a proteogenomic pipeline, Splicify, which is able to detect differentially expressed protein isoforms. Splicify is based on integrating RNA massive parallel sequencing data and tandem mass spectrometry proteomics data to identify protein isoforms resulting from differential splicing between two conditions...
July 26, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28746760/de-extinction-and-conservation-genetics-in-the-anthropocene
#10
Ronald Sandler
One interesting feature of de-extinction-particularly with respect to long-extinct species such as the passenger pigeon, thylacine, and mammoth-is that it does not fit neatly into the primary rationales for adopting novel ecosystem-management and species-conservation technologies and strategies: efficiency and necessity. The efficiency rationale is that the new technology or strategy enables conservation biologists to do what they already do more effectively. Why should researchers embrace novel information technologies? Because they allow scientists to better track, monitor, map, aggregate, and analyze species behaviors, biological systems, and human-environment interactions...
July 2017: Hastings Center Report
https://www.readbyqxmd.com/read/28746715/identification-of-genetic-loci-jointly-influencing-schizophrenia-risk-and-the-cognitive-traits-of-verbal-numerical-reasoning-reaction-time-and-general-cognitive-function
#11
Olav B Smeland, Oleksandr Frei, Karolina Kauppi, W David Hill, Wen Li, Yunpeng Wang, Florian Krull, Francesco Bettella, Jon A Eriksen, Aree Witoelar, Gail Davies, Chun C Fan, Wesley K Thompson, Max Lam, Todd Lencz, Chi-Hua Chen, Torill Ueland, Erik G Jönsson, Srdjan Djurovic, Ian J Deary, Anders M Dale, Ole A Andreassen
Importance: Schizophrenia is associated with widespread cognitive impairments. Although cognitive deficits are one of the factors most strongly associated with functional outcome in schizophrenia, current treatment strategies largely fail to ameliorate these impairments. To develop more efficient treatment strategies in patients with schizophrenia, a better understanding of the pathogenesis of these cognitive deficits is needed. Accumulating evidence indicates that genetic risk of schizophrenia may contribute to cognitive dysfunction...
July 26, 2017: JAMA Psychiatry
https://www.readbyqxmd.com/read/28746411/selection-and-validation-of-reference-genes-for-quantitative-real-time-pcr-analysis-under-different-experimental-conditions-in-the-leafminer-liriomyza-trifolii-diptera-agromyzidae
#12
Ya-Wen Chang, Jing-Yun Chen, Ming-Xing Lu, Yuan Gao, Zi-Hua Tian, Wei-Rong Gong, Wei Zhu, Yu-Zhou Du
Liriomyza trifolii is a highly-invasive leafmining insect that causes significant damage to vegetables and horticultural crops worldwide. Relatively few studies have quantified gene expression in L. trifolii using real-time quantitative PCR (RT-qPCR), which is a reliable and sensitive technique for measuring gene expression. RT-qPCR requires the selection of reference genes to normalize gene expression data and control for internal differences between samples. In this study, nine housekeeping genes from L. trifolii were selected for their suitability in normalizing gene expression using geNorm, Normfinder, BestKeeper, the ΔCt method and RefFinder...
2017: PloS One
https://www.readbyqxmd.com/read/28745683/-genetic-aspects-of-schizophrenia
#13
A Yu Morozova, E A Zubkov, Ya A Zorkina, A M Reznik, G P Kostyuk, V P Chekhonin
Schizophrenia is a disease with a complex non-Mendelian inheritance mechanism in most cases involving the combined action of a large number of genes. Identifying of genomic variations associated with schizophrenia endophenotypes has a great potential. This review describes genetic markers of the disease, current methods of their analysis, including genome-wide association study (GWAS). Certain genes with mutations that increase the risk of schizophrenia are described. Functional polymorphisms with phenotypic expression, which are significantly associated with clinical manifestation of schizophrenia, can serve as useful genetic markers...
2017: Zhurnal Nevrologii i Psikhiatrii Imeni S.S. Korsakova
https://www.readbyqxmd.com/read/28745447/commentary-perspectives-on-alcohol-related-gene-and-environment-interplay-in-diverse-populations
#14
Marcia S Scott
BACKGROUND AND OBJECTIVES: Racial/ethnic groups comprise more than 20% of the U.S. population, but many experience disproportionately high risk for alcohol misuse, often resulting in higher rates of alcohol-associated consequences. Completion of mapping the human genome has launched rapidly evolving research methods aimed at improved understanding of genetic contribution to disease. Despite decades of research on the influence of genetic and environmental risks on alcohol use disorders and outcomes, few studies have included racial/ethnic subpopulations in sufficient numbers to allow for proper statistical analysis...
August 2017: American Journal on Addictions
https://www.readbyqxmd.com/read/28745211/the-lipid-lowering-effects-and-associated-mechanisms-of-dietary-phytosterol-supplementation
#15
Jerad H Dumolt, Todd C Rideout
Phytosterols (PS) are plant-based structural analogous of mammalian cholesterol that have been shown to lower blood cholesterol concentrations by ~10%, although inter-individual response to PS supplementation due to subject-specific metabolic and genetic factors is evident. Recent work further suggests that PS may act as effective triglyceride (TG)-lowering agents with maximal TG reductions observed in hypertriglyceridemic subjects. Although PS have been demonstrated to interfere with cholesterol and perhaps TG absorption within the intestine, they also have the capacity to modulate the expression of lipid regulatory genes through liver X receptor (LXR) activation...
July 25, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28745207/hiv-drug-resistance-testing-in-a-resource-limited-setting-with-high-viral-diversity-the-first-twenty-eight-months-experience
#16
Elodie Teclaire Ngo-Malabo, Paul Alain Ngoupo, Serge Alain Sadeuh-Mba, Emmanuel Akongnwi, Robert Banaï, Laure Ngono, Richard Njouom, Charles Felix Bilong-Bilong, Anfumbom Kfutwah
BACKGROUND: First line antiretroviral therapy in a resource-limited setting consists of nucleotide and non-nucleotide reverse transcriptase inhibitors. Protease inhibitors are the hub of second line therapy. The decision to change antiretroviral therapy for a patient is frequently presumptive because of the lack of genotypic resistance tests in routine follow-up. We describe here the resistance profiles observed in patients with varying terms of antiretroviral therapy in Cameroon after implementation of HIV genotypic resistance testing in routine practice...
July 25, 2017: Current HIV Research
https://www.readbyqxmd.com/read/28744713/genome-wide-analysis-of-gene-expression-profiling-revealed-that-cop9-signalosome-is-essential-for-correct-expression-of-fe-homeostasis-genes-in-arabidopsis
#17
Seckin Eroglu, Emre Aksoy
In plant cells, either excess or insufficient iron (Fe) concentration triggers stress responses, therefore it is strictly controlled. Proteasome-mediated degradation through ubiquitination of Fe homeostasis proteins has just become the focus of research in recent years. Deactivating ubiquitin ligases, COP9 signalosome has a central importance in the translational control of various stress responses. The aim of the study was to investigate COP9 signalosome in Fe deficiency response of Strategy I plants. In silico analysis of a set of Fe-deficiency-responsive genes was conducted against the transcriptome of Arabidopsis csn mutant lines using Genevestigator software...
July 25, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28744655/whose-turn-chromosome-research-and-the-study-of-the-human-genome
#18
Soraya de Chadarevian
A common account sees the human genome sequencing project of the 1990s as a "natural outgrowth" of the deciphering of the double helical structure of DNA in the 1950s. The essay aims to complicate this neat narrative by putting the spotlight on the field of human chromosome research that flourished at the same time as molecular biology. It suggests that we need to consider both endeavors - the human cytogeneticists who collected samples and looked down the microscope and the molecular biologists who probed the molecular mechanisms of gene function - to understand the rise of the human genome sequencing project and the current genomic practices...
July 25, 2017: Journal of the History of Biology
https://www.readbyqxmd.com/read/28744025/genetic-loci-associated-with-an-earlier-age-at-onset-in-multiplex-schizophrenia
#19
Annemarie L Woolston, Po-Chang Hsiao, Po-Hsiu Kuo, Shi-Heng Wang, Yin-Ju Lien, Chih-Min Liu, Hai-Gwo Hwu, Tzu-Pin Lu, Eric Y Chuang, Li-Ching Chang, Chien-Hsiun Chen, Jer-Yuarn Wu, Ming T Tsuang, Wei J Chen
An earlier age at onset (AAO) has been associated with greater genetic loadings in schizophrenia. This study aimed to identify modifier loci associated with an earlier AAO of schizophrenia. A genome-wide association analysis (GWAS) was conducted in 94 schizophrenia probands with the earliest AAO and 91 with the latest AAO. Candidate single nucleotide polymorphisms (SNPs) were then genotyped in the co-affected siblings and unrelated probands. Multi-SNP genetic risk scores (GRS) composed of the candidate loci were used to distinguish patients with an early or late AAO...
July 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28743673/genomic-landscape-of-copy-number-variation-and-copy-neutral-loss-of-heterozygosity-events-in-equine-sarcoids-reveals-increased-instability-of-the-sarcoid-genome
#20
Klaudia Pawlina, Artur Gurgul, Tomasz Szmatoła, Katarzyna Ropka-Molik, Ewelina Semik, Jolanta Klukowska-Rötzler, Christoph Koch, Kathrin Mählmann, Monika Bugno-Poniewierska
Although they are the most common neoplasms in equids, sarcoids are not fully characterized at the molecular level. Therefore, the objective of this study was to characterize the landscape of structural rearrangements, such as copy number variation (CNV) and copy neutral loss of heterozygosity (cnLOH), in the genomes of sarcoid tumor cells. This information will not only broaden our understanding of the characteristics of this genome but will also improve the general knowledge of this tumor and the mechanisms involved in its generation...
July 22, 2017: Biochimie
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