scholarly journals A Genome-Wide Perspective of Human Diversity and Its Implications in Infectious Disease

2013 ◽  
Vol 3 (1) ◽  
pp. a012450-a012450 ◽  
Author(s):  
J. Manry ◽  
L. Quintana-Murci
Keyword(s):  
Infectious Disease ◽  
Human Diversity ◽  
Genome Wide ◽  
A Genome ◽  
Wide Perspective

scholarly journals A Genome-Wide Perspective of miRNAome in Response to High Temperature, Salinity and Drought Stresses in Brassica juncea (Czern) L

PLoS ONE ◽  
2014 ◽  
Vol 9 (3) ◽  
pp. e92456 ◽  
Author(s):  
Ankur R. Bhardwaj ◽  
Gopal Joshi ◽  
Ritu Pandey ◽  
Bharti Kukreja ◽  
Shailendra Goel ◽  
...  
Keyword(s):  
High Temperature ◽  
Brassica Juncea ◽  
Genome Wide ◽  
A Genome ◽  
Wide Perspective

scholarly journals Omics versus Questionnaires: Using methylation data to assess the environmental impact of smoking on obesity-related traits

2020 ◽  
Author(s):  
Carmen Amador ◽  
Yanni Zeng ◽  
Rosie Walker ◽  
Archie Campbell ◽  
Andrew M. McIntosh ◽  
...  
Keyword(s):  
Complex Traits ◽  
Environmental Changes ◽  
Methylation Data ◽  
Total Contribution ◽  
Socioeconomic Changes ◽  
Genome Wide ◽  
A Genome ◽  
Wide Perspective ◽  
Environmental Measures ◽  
Reported Data

ABSTRACTVariation in complex traits related to obesity, such as body weight and body mass index, has a genetic basis with heritabilities between 40 and 70%. Nonetheless, the so-called global obesity pandemic is usually associated with environmental changes related to diet, lifestyle, and sociocultural and socioeconomic changes. However, most genetic studies do not include all relevant environmental covariates so their contribution, alongside genetics, to variation in obesity-related traits can not be assessed. Similarly, some studies have described interactions between a few individual genes linked to obesity and different environmental variables but the total contribution to differences between individuals is unknown. In this study we explored the effect of smoking and gene-by-smoking interactions on obesity related traits from a genome-wide perspective to estimate the amount of variance they explain by modelling them using self-reported data and a proxy created using methylation data. Our results indicate that exploiting omic measures as proxies for environmental variation can improve our models for complex traits such as obesity and can be used as a substitute of environmental measures when they are not available or jointly to improve their accuracy.

scholarly journals Genome-wide methylation data improves dissection of the effect of smoking on body mass index

PLoS Genetics ◽  
2021 ◽  
Vol 17 (9) ◽  
pp. e1009750
Author(s):  
Carmen Amador ◽  
Yanni Zeng ◽  
Michael Barber ◽  
Rosie M. Walker ◽  
Archie Campbell ◽  
...  
Keyword(s):  
Complex Traits ◽  
Genetic Basis ◽  
Environmental Changes ◽  
Total Contribution ◽  
Genetic Studies ◽  
Socioeconomic Changes ◽  
Genome Wide ◽  
A Genome ◽  
Causes Of Disease ◽  
Wide Perspective

Variation in obesity-related traits has a genetic basis with heritabilities between 40 and 70%. While the global obesity pandemic is usually associated with environmental changes related to lifestyle and socioeconomic changes, most genetic studies do not include all relevant environmental covariates, so the genetic contribution to variation in obesity-related traits cannot be accurately assessed. Some studies have described interactions between a few individual genes linked to obesity and environmental variables but there is no agreement on their total contribution to differences between individuals. Here we compared self-reported smoking data and a methylation-based proxy to explore the effect of smoking and genome-by-smoking interactions on obesity related traits from a genome-wide perspective to estimate the amount of variance they explain. Our results indicate that exploiting omic measures can improve models for complex traits such as obesity and can be used as a substitute for, or jointly with, environmental records to better understand causes of disease.

scholarly journals A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds

2016 ◽  
Vol 48 (1) ◽  
Author(s):  
Arianna Manunza ◽  
Antonia Noce ◽  
Juan Manuel Serradilla ◽  
Félix Goyache ◽  
Amparo Martínez ◽  
...  
Keyword(s):  
Demographic History ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Wide Perspective ◽  
Spanish Goat

scholarly journals Genome-Wide Mutagenesis Links Multiple Metabolic Pathways with Actinorhodin Production inStreptomyces coelicolor

2019 ◽  
Vol 85 (7) ◽  
Author(s):  
Zhong Xu ◽  
Yuanyuan Li ◽  
Yemin Wang ◽  
Zixin Deng ◽  
Meifeng Tao
Keyword(s):  
Metabolic Pathways ◽  
Antibiotic Production ◽  
Streptomyces Coelicolor ◽  
Acid Biosynthesis ◽  
Content Type ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Wide Perspective ◽  
Actinorhodin Production

ABSTRACTStreptomycesspecies are important antibiotic-producing organisms that tightly regulate their antibiotic production. Actinorhodin is a typical antibiotic produced by the model actinomyceteStreptomyces coelicolor. To discover the regulators of actinorhodin production, we constructed a library of 50,000 independent mutants with hyperactive Tn5transposase-based transposition systems. Five hundred fifty-one genes were found to influence actinorhodin production in 988 individual mutants. Genetic complementation suggested that most of the insertions (76%) were responsible for the changes in antibiotic production. Genes involved in diverse cellular processes such as amino acid biosynthesis, carbohydrate metabolism, cell wall homeostasis, and DNA metabolism affected actinorhodin production. Genome-wide mutagenesis can identify novel genes and pathways that impact antibiotic levels, potentially aiding in engineering strains to optimize the production of antibiotics inStreptomyces.IMPORTANCEPrevious studies have shown that various genes can influence antibiotic production inStreptomycesand that intercommunication between regulators can complicate antibiotic production. Therefore, to gain a better understanding of antibiotic regulation, a genome-wide perspective on genes that influence antibiotic production was needed. We searched for genes that affected production of the antibiotic actinorhodin using a genome-wide gene disruption system. We identified 551 genes that altered actinorhodin levels, and more than half of these genes were newly identified effectors. Some of these genes may be candidates for engineeringStreptomycesstrains to improve antibiotic production levels.

scholarly journals A major quantitative trait locus affecting resistance to Tilapia lake virus in farmed Nile tilapia (Oreochromis niloticus)

Heredity ◽  
2021 ◽  
Author(s):  
Agustin Barría ◽  
Trọng Quốc Trịnh ◽  
Mahirah Mahmuddin ◽  
Carolina Peñaloza ◽  
Athina Papadopoulou ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Host Resistance ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Genome Wide ◽  
A Genome ◽  
The Gift ◽  
Trait Locus

AbstractEnhancing host resistance to infectious disease has received increasing attention in recent years as a major goal of farm animal breeding programs. Combining field data with genomic tools can provide opportunities to understand the genetic architecture of disease resistance, leading to new opportunities for disease control. In the current study, a genome-wide association study was performed to assess resistance to the Tilapia lake virus (TiLV), one of the biggest threats affecting Nile tilapia (Oreochromis niloticus); a key aquaculture species globally. A pond outbreak of TiLV in a pedigreed population of the GIFT strain was observed, with 950 fish classified as either survivor or mortality, and genotyped using a 65 K SNP array. A significant QTL of large effect was identified on chromosome Oni22. The average mortality rate of tilapia homozygous for the resistance allele at the most significant SNP (P value = 4.51E−10) was 11%, compared to 43% for tilapia homozygous for the susceptibility allele. Several candidate genes related to host response to viral infection were identified within this QTL, including lgals17, vps52, and trim29. These results provide a rare example of a major QTL affecting a trait of major importance to a farmed animal. Genetic markers from the QTL region have potential in marker-assisted selection to improve host resistance, providing a genetic solution to an infectious disease where few other control or mitigation options currently exist.

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