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population genome

Slim Ben Jemaa, Nejia Thamri, Sofiane Mnara, Emmanuelle Rebours, Dominique Rocha, Mekki Boussaha
To carry out effective genome-wide association studies, information about linkage disequilibrium (LD) is essential. Here, we used medium-density SNP chips to provide estimates of LD in native Tunisian cattle. The two measures of LD that were used, mean r2 and D', decreased from 0.26 to 0.05 and from 0.73 to 0.40, respectively, when the distance between markers increased from less than 20 Kb to 200 Kb. The decay in LD over physical distance occurred at a faster rate than that reported for European and other indigenous breeds, and reached background levels at less than 500 Kb distance...
February 18, 2019: Genetics and Molecular Biology
Liang Sun, Upinder S Gill, Raja Sekhar Nandety, Soonil Kwon, Perdeep Mehta, Rebecca Dickstein, Michael K Udvardi, Kirankumar S Mysore, Jiangqi Wen
From a single transgenic line harboring five Tnt1 transposon insertions, we generated a near-saturated insertion population in Medicago truncatula. Using thermal asymmetric interlaced (TAIL) PCR followed by sequencing, we recovered 388,888 flanking sequence tags (FSTs) from 21,741 insertion lines in this population. FST recovery from 14 Tnt1 lines using the whole genome sequencing and/or Tnt1-capture sequencing approaches suggests an average of 80 insertions per line, which is more than previous estimation of 25 insertions...
February 18, 2019: Plant Journal: for Cell and Molecular Biology
José Vargas-Asencio, Harris Liou, Keith L Perry, Jeremy R Thompson
Grapevine red blotch virus (GRBV) is type member of the newly identified genus Grablovirus. It possesses a single-stranded circular DNA genome of around 3200 nucleotides encoding three open reading frames (ORFs) in both the virion sense, the V1 (CP), V2 and V3, and complementary sense, C1 (RepA), C2 and C3. As shown for members of the genus Mastrevirus, the C1 and C2 ORFs are predicted to fuse through splicing to form a replication-associated protein (Rep). Data obtained using high-throughput sequencing (RNA-Seq) of three RNA-enriched populations, extracted from GRBV-infected grapevine (Vitis vinifera), confirmed the presence of the predicted C1-C2 intron (nts 2288-2450), but in addition identified a larger virion-sense intron (nts 251-589) spanning the V2 ORF...
February 18, 2019: Journal of General Virology
Fei Luo, Yu-Zhuo Wang, Dong Lin, Jian Li, Kuo Yang
Prostate cancer (PCa) is the most prevalent malignancy and the second leading cause of cancer-related deaths in the male population in western countries, and we explored the association between exonuclease 1 (EXO1) expression and clinical progression, metastasis (Met), and survival prognosis of PCa. EXO1 expression of high/low-metastatic patient-derived xenografts model was investigated and clinical correlation and prognosis outcomes were validated. EXO1 in high-metastatic models was significantly increased compared with low-metastatic lines...
February 18, 2019: Journal of Cellular Biochemistry
David J Duffy, Mark Q Martindale
Our recent Communications Biology research article revealed the genomic drivers and therapeutic vulnerabilities of sea turtle fibropapillomatosis tumors. Fibropapillomatosis is a debilitating tumorous disease afflicting populations of green sea turtles globally. While a virus is involved in the development of this disease, it is increasingly understood that the key trigger is linked to anthropogenic disturbances of the environment. The specific environmental co-trigger(s) has yet to be functionally confirmed...
2019: Communications biology
Yashoda Ghanekar, Subhashini Sadasivam
Background: Sequencing studies across multiple cancers continue to reveal mutations and genes involved in the pathobiology of these cancers. Exome sequencing of oral cancers, a subset of Head and Neck Squamous cell Carcinomas (HNSCs) common among tobacco-chewing populations, revealed that ∼34% of the affected patients harbor mutations in the CASP8 gene . Uterine Corpus Endometrial Carcinoma (UCEC) is another cancer where ∼10% cases harbor CASP8 mutations. Caspase-8, the protease encoded by CASP8 gene, plays a dual role in programmed cell death, which in turn has an important role in tumor cell death and drug resistance...
2019: PeerJ
Mike W Humphreys, John H Doonan, Roger Boyle, Anyela C Rodriguez, Christina L Marley, Kevin Williams, Markku S Farrell, Jason Brook, Dagmara Gasior, Dimitra Loka, Rosemary P Collins, Athole H Marshall, Debbie K Allen, Rattan S Yadav, Jennifer A J Dungait, Phil Murray, John A Harper
The incorporation of new sophisticated phenotyping technologies within a crop improvement program allows for a plant breeding strategy that can include selections for major root traits previously inaccessible due to the challenges in their phenotype assessment. High-throughput precision phenotyping technology is employed to evaluate root ontogeny and progressive changes to root architecture of both novel amphiploid and introgression lines of Festulolium over four consecutive months of the growing season and these compared under the same time frame to that of closely related perennial ryegrass ( L...
November 2018: Food and Energy Security
Filipe Couto Alves, Ítalo Stefanine Correa Granato, Giovanni Galli, Danilo Hottis Lyra, Roberto Fritsche-Neto, Gustavo de Los Campos
Background: The selection of hybrids is an essential step in maize breeding. However, evaluating a large number of hybrids in field trials can be extremely costly. However, genomic models can be used to predict the expected performance of un-tested genotypes. Bayesian models offer a very flexible framework for hybrid prediction. The Bayesian methodology can be used with parametric and semi-parametric assumptions for additive and non-additive effects. Furthermore, samples from the posterior distribution of Bayesian models can be used to estimate the variance due to general and specific combining abilities even in cases where additive and non-additive effects are not mutually orthogonal...
2019: Plant Methods
Arash Assadsangabi, Caroline A Evans, Bernard M Corfe, Alan Lobo
Inflammatory bowel disease (IBD) is a chronic relapsing/remitting inflammatory illness of the gastrointestinal tract of unknown aetiology. Despite recent advances in decoding the pathophysiology of IBD, many questions regarding disease pathogenesis remain. Genome-wide association studies (GWAS) and knockout mouse models have significantly advanced our understanding of genetic susceptibility loci and inflammatory pathways involved in IBD pathogenesis. Despite their important contribution to a better delineation of the disease process in IBD, these genetic findings have had little clinical impact to date...
2019: Gastroenterology Research and Practice
Yanming Meng, Heng Xu, Shouyue Zhang, Junlong Zhang, Lu Wang, Honghu Tang, Yongkang Wu
OBJECTIVE: Interleukin-21 (IL-21) contributes to expansion, differentiation, and modulation of various immunocompetent cells. Deregulated production of IL-21 plays a role of cardinal significance in the pathogenesis of systemic lupus erythematosus (SLE). We aimed to determine whether single nucleotide polymorphisms (SNP) near the IL-21 gene have significant association with SLE susceptibility and the T helper-related inflammatory cytokine profile of SLE patients. METHODS: We enrolled 460 SLE patients and 460 healthy controls...
February 18, 2019: Lupus
Alicia Grealy, Michael Bunce, Clare Holleley
Avian eggshell is a bio-ceramic material with exceptional properties for preserving DNA within its crystalline structure, presenting an opportunity to retrieve genomic information from extinct or historic populations of birds. However, intracrystalline DNA has only been recovered from the large, thick eggshell of palaeognaths; members of their more-diverse sister group (neognaths) lay smaller, thinner eggs that may not exhibit the same propensity for DNA preservation. Here, we use three 40-60 year-old museum eggshell specimens of Australian neognath birds to determine the minimum mass of eggshell from which intracrystalline DNA can be retrieved, and to characterise the yield and quality of such DNA...
February 17, 2019: Molecular Ecology Resources
Lei Zhang, Yining Bao, Moeen Riaz, Jane Tiller, Danny Liew, Xun Zhuang, David J Amor, Aamira Huq, Lara Petelin, Mark Nelson, Paul A James, Ingrid Winship, John J McNeil, Paul Lacaze
PURPOSE: To consider the impact and cost-effectiveness of offering preventive population genomic screening to all young adults in a single-payer health-care system. METHODS: We modeled screening of 2,688,192 individuals, all adults aged 18-25 years in Australia, for pathogenic variants in BRCA1/BRCA2/MLH1/MSH2 genes, and carrier screening for cystic fibrosis (CF), spinal muscular atrophy (SMA), and fragile X syndrome (FXS), at 71% testing uptake using per-test costs ranging from AUD$200 to $1200 (~USD$140 to $850)...
February 18, 2019: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Jiwen Liu, Chun-Xu Xue, Hao Sun, Yanfen Zheng, Zhe Meng, Xiao-Hua Zhang
Flavobacteriia are abundant in many marine environments including hadal waters, as demonstrated recently. However, it is unclear how this flavobacterial population adapts to hadal conditions. In this study, extensive comparative genomic analyses were performed for the flavobacterial strain Euzebyella marina RN62 isolated from the Mariana Trench hadal water in low abundance. The complete genome of RN62 possessed a considerable number of carbohydrate-active enzymes with a different composition. There was a predominance of GH family 13 proteins compared to closely related relatives, suggesting that RN62 has preserved a certain capacity for carbohydrate utilization and that the hadal ocean may hold an organic matter reservoir distinct from the surface ocean...
January 29, 2019: Systematic and Applied Microbiology
Kelsey E Grinde, Lisa A Brown, Alexander P Reiner, Timothy A Thornton, Sharon R Browning
Admixture mapping studies have become more common in recent years, due in part to technological advances and growing international efforts to increase the diversity of genetic studies. However, many open questions remain about appropriate implementation of admixture mapping studies, including how best to control for multiple testing, particularly in the presence of population structure. In this study, we develop a theoretical framework to characterize the correlation of local ancestry and admixture mapping test statistics in admixed populations with contributions from any number of ancestral populations and arbitrary population structure...
February 4, 2019: American Journal of Human Genetics
W P T James, R J Johnson, J R Speakman, D C Wallace, G Frühbeck, P O Iverson, P J Stover
Our understanding of human evolution has improved rapidly over recent decades, facilitated by large-scale cataloguing of genomic variability amongst both modern and archaic humans. It seems clear that the evolution of the ancestors of chimpanzees and hominins separated 7-9 million years ago with some migration out of Africa by the earlier hominins; Homo sapiens slowly emerged as climate change resulted in drier, less forested African conditions. The African populations expanded and evolved in many different conditions with slow mutation and selection rates in the human genome, but with much more rapid mutation occurring in mitochondrial DNA...
February 17, 2019: Journal of Internal Medicine
P Comizzoli, W V Holt
Because of higher extinction rates due to human and natural factors, more basic and applied research in reproductive biology is required to preserve wild species and design proper strategies leading to sustainable populations. The objective of the review is to highlight recent, inspiring breakthroughs in wildlife reproduction science that will set directions for future research and lead to more successes in conservation biology. Despite new tools and approaches allowing a better and faster understanding of key mechanisms, we still know little about reproduction in endangered species...
February 17, 2019: Biology of Reproduction
Rui-Qian Zhang, Jun-Jie Wang, Teng Zhang, Hong-Li Zhai, Wei Shen
Copy number variation (CNV), as an important component of genomic structural variation (SV), plays essential roles in phenotypic variability, disease susceptibility and species evolution. To investigate whether critical CNVs exist in dairy goats with differing fecundity, we performed genome-wide sequencing of two populations of Laoshan dairy goats with large differences in litter size. After reference genome aligning, CNV calling, and annotation, we screened identified CNVs in the high-fecundity (HF) and low-fecundity (LF) groups to identify discrepant CNVs and their distribution within the genome...
February 14, 2019: Gene
Calvin Rodrigues, Chitra Pattabiraman, Anjali Vijaykumar, Reety Arora, Suma Mysore Narayana, Rekha V Kumar, Dimple Notani, Patrick Varga-Weisz, Sudhir Krishna
Metastatic progression is a major cause of mortality in cervical cancers, but factors regulating migratory and pre-metastatic cell populations remain poorly understood. Here, we sought to assess whether a SUV39H1-low chromatin state promotes migratory cell populations in cervical cancers, using meta-analysis of data from The Cancer Genome Atlas (TCGA), immunohistochemistry, genomics and functional assays. Cervical cancer cells sorted based on migratory ability in vitro have low levels of SUV39H1 protein, and SUV39H1 knockdown in vitro enhanced cervical cancer cell migration...
February 14, 2019: Experimental Cell Research
Andrew J Colebatch, Peter Ferguson, Felicity Newell, Stephen H Kazakoff, Tom Witkowski, Alexander Dobrovic, Peter A Johansson, Robyn Pm Saw, Jonathan R Stretch, Grant A McArthur, Georgina V Long, John F Thompson, John V Pearson, Graham J Mann, Nicholas K Hayward, Nicola Waddell, Richard A Scolyer, James S Wilmott
The benign melanocytic nevus is the commonest tumor in humans and rarely transforms into cutaneous melanoma. Elucidation of the nevus genome is required to better understand the molecular steps of progression to melanoma. We performed whole genome sequencing on a series of 14 benign melanocytic nevi, consisting of both congenital and acquired types. All nevi had driver mutations in the MAPK signalling pathway, either BRAF V600E or NRAS Q61R/L. No additional definite driver mutations were identified. Somatic mutations in nevi with higher mutation loads showed a predominance of mutational signatures 7a and 7b, consistent with ultraviolet radiation exposure, whereas nevi with lower mutation loads (including all three congenital nevi) had a predominance of the ubiquitous signatures 1 and 5...
February 14, 2019: Journal of Investigative Dermatology
Martine Paquette, Sophie Bernard, Alexis Baass
BACKGROUND AND AIMS: Several clinical and genetic factors have been shown to modulate the cardiovascular risk in subjects affected by familial hypercholesterolemia (FH). Genome wide association studies (GWAS) in the general population have identified several single nucleotide polymorphisms (SNPs) significantly associated with the risk of cardiovascular disease (CVD). This include the rs2048327 variant in the SLC22A3 gene. However, the effect of this SNP in FH subjects is unknown. The objectives of this study are to investigate the association between rs2048327 and the prevalence of CVD as well as with the concentration of lipoprotein (a) (Lp (a)), in a cohort of genetically-confirmed heterozygous FH patients...
February 14, 2019: Clinical Biochemistry
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