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https://www.readbyqxmd.com/read/28806749/defining-the-genetic-susceptibility-to-cervical-neoplasia-a-genome-wide-association-study
#1
Paul J Leo, Margaret M Madeleine, Sophia Wang, Stephen M Schwartz, Felicity Newell, Ulrika Kymmer, Kari Hemminki, Goran Hallmans, Sven Tiews, Winfried Steinberg, Janet S Rader, Felipe Castro, Mahboobeh Safaeian, Eduardo L Franco, François Coutlée, Claes Ohlsson, Adrian Cortes, Mhairi Marshall, Pamela Mukhopadhyay, Katie Cremin, Lisa G Johnson, Suzanne Garland, Sepehr N Tabrizi, Nicolas Wentzensen, Freddy Sitas, Julian Little, Maggie Cruickshank, Ian H Frazer, Allan Hildesheim, Matthew A Brown
A small percentage of women with cervical HPV infection progress to cervical neoplasia, and the risk factors determining progression are incompletely understood. We sought to define the genetic loci involved in cervical neoplasia and to assess its heritability using unbiased unrelated case/control statistical approaches. We demonstrated strong association of cervical neoplasia with risk and protective HLA haplotypes that are determined by the amino-acids carried at positions 13 and 71 in pocket 4 of HLA-DRB1 and position 156 in HLA-B...
August 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28806735/molecular-characterization-and-multi-locus-genotypes-of-enterocytozoon-bieneusi-from-captive-red-kangaroos-macropus-rfus-in-jiangsu-province-china
#2
Zhijun Zhong, Yinan Tian, Yuan Song, Lei Deng, Junxian Li, Zhihua Ren, Xiaoping Ma, Xiaobin Gu, Changliang He, Yi Geng, Guangneng Peng
Enterocytozoon bieneusi is the most common pathogen of microsporidian species infecting humans worldwide. Although E. bieneusi has been found in a variety of animal hosts, information on the presence of E. bieneusi in captive kangaroos in China is limited. The present study was aimed at determining the occurrence and genetic diversity of E. bieneusi in captive kangaroos. A total of 61 fecal specimens (38 from red kangaroos and 23 from grey kangaroos) were collected from Nanjing Hongshan Forest Zoo and Hongshan Kangaroo Breeding Research Base, Jiangsu province, China...
2017: PloS One
https://www.readbyqxmd.com/read/28806630/case-report-coincidental-inclusion-in-a-17-locus-y-str-mixture-wrongful-conviction-and-exoneration
#3
Greg Hampikian, Gianluca Peri, Shih-Shiang Lo, Mong-Hwa Chin, Kuo-Lan Liu
We report the case of a suspect (Suspect-3) who was convicted (and later exonerated) of participating in the multiple-attacker rape of two women. The forensic evidence against him was his inclusion in a 17-marker Y-STR mixture isolated from semen on one victim's clothing. The DNA inclusion produced a match statistic with a combined probability of inclusion of 1 in 741, and a Likelihood Ratio of 3296. While the defense team was told that Suspect-3 was included in the semen DNA mixture, they were not told that all of the Y-STR alleles could also be explained by just the other two accused attackers' haplotypes...
August 7, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28805909/genomewide-association-study-for-production-and-meat-quality-traits-in-canchim-beef-cattle
#4
G G Santiago, F Siqueira, F F Cardoso, L C A Regitano, R Ventura, B P Sollero, M D Souza, F B Mokry, A B R Ferreira, R A A Torres
The commercial value of the bovine carcass is determined by a set of traits, such as weight, yield, back fat thickness, and marbling; therefore, the genetic improvement of growth, meat, and carcass quality traits is an important tool to add value to the supply chain. Genomewide association studies (GWAS) enable the identification of loci that control phenotypic expression of quantitative traits (QTL). Therefore, the objective of this work was to perform a GWAS to identify genomic regions and genes associated with growth, carcass traits, and meat quality in Canchim beef cattle...
August 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28805827/transcriptional-risk-scores-link-gwas-to-eqtls-and-predict-complications-in-crohn-s-disease
#5
Urko M Marigorta, Lee A Denson, Jeffrey S Hyams, Kajari Mondal, Jarod Prince, Thomas D Walters, Anne Griffiths, Joshua D Noe, Wallace V Crandall, Joel R Rosh, David R Mack, Richard Kellermayer, Melvin B Heyman, Susan S Baker, Michael C Stephens, Robert N Baldassano, James F Markowitz, Mi-Ok Kim, Marla C Dubinsky, Judy Cho, Bruce J Aronow, Subra Kugathasan, Greg Gibson
Gene expression profiling can be used to uncover the mechanisms by which loci identified through genome-wide association studies (GWAS) contribute to pathology. Given that most GWAS hits are in putative regulatory regions and transcript abundance is physiologically closer to the phenotype of interest, we hypothesized that summation of risk-allele-associated gene expression, namely a transcriptional risk score (TRS), should provide accurate estimates of disease risk. We integrate summary-level GWAS and expression quantitative trait locus (eQTL) data with RNA-seq data from the RISK study, an inception cohort of pediatric Crohn's disease...
August 14, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28805816/selective-attention-within-the-foveola
#6
Martina Poletti, Michele Rucci, Marisa Carrasco
Efficient control of attentional resources and high-acuity vision are both fundamental for survival. Shifts in visual attention are known to covertly enhance processing at locations away from the center of gaze, where visual resolution is low. It is unknown, however, whether selective spatial attention operates where the observer is already looking-that is, within the high-acuity foveola, the small yet disproportionally important rod-free region of the retina. Using new methods for precisely controlling retinal stimulation, here we show that covert attention flexibly improves and speeds up both detection and discrimination at loci only a fraction of a degree apart within the foveola...
August 14, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28805283/closing-the-gap-avian-lineage-splits-at-a-young-narrow-seaway-imply-a-protracted-history-of-mixed-population-response
#7
S A Trewick, S Pilkington, L D Shepherd, G C Gibb, M Morgan-Richards
The evolutionary significance of spatial habitat gaps has been well recognised since Alfred Russel Wallace compared the faunas of Bali and Lombok. Gaps between islands influence population structuring of some species, and flightless birds are expected to show strong partitioning even where habitat gaps are narrow. We examined the population structure of the most numerous living flightless land bird in New Zealand and the world, Weka (Gallirallus australis). We surveyed Weka and their feather lice in native and introduced populations using genetic data gathered from DNA sequences of mitochondrial genes and nuclear β-fibrinogen and five microsatellite loci...
August 14, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28805257/three-representative-inter-and-intra-subspecific-crosses-reveal-the-genetic-architecture-of-reproductive-isolation-in-rice
#8
Guangwei Li, Xiaoting Li, Yuan Wang, Jiaming Mi, Feng Xing, Dahan Zhang, Qiyan Dong, Xianghua Li, Jinghua Xiao, Qifa Zhang, Yidan Ouyang
Systematic characterization of genetic and molecular mechanisms in formation of hybrid sterility is of fundamental importance in understanding reproductive isolation and speciation. Using ultra-high-density genetic maps, 43 single-locus QTLs and 223 digenic interactions for embryo-sac, pollen, and spikelet fertility are depicted from three crosses between representative varieties of japonica and two varietal groups of indica, which provide an extensive archive for investigating the genetic basis of reproductive isolation in rice...
August 14, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28805163/cryptosporidium-in-fish-alternative-sequencing-approaches-and-analyses-at-multiple-loci-to-resolve-mixed-infections
#9
Andrea Paparini, Rongchang Yang, Linda Chen, Kaising Tong, Susan Gibson-Kueh, Alan Lymbery, Una M Ryan
Currently, the systematics, biology and epidemiology of piscine Cryptosporidium species are poorly understood. Here, we compared Sanger ‒ and next-generation ‒ sequencing (NGS), of piscine Cryptosporidium, at the 18S rRNA and actin genes. The hosts comprised 11 ornamental fish species, spanning four orders and eight families. The objectives were: to (i) confirm the rich genetic diversity of the parasite and the high frequency of mixed infections; and (ii) explore the potential of NGS in the presence of complex genetic mixtures...
August 14, 2017: Parasitology
https://www.readbyqxmd.com/read/28804930/gaussian-covariance-graph-models-accounting-for-correlated-marker-effects-in-genome-wide-prediction
#10
C A Martínez, K Khare, S Rahman, M A Elzo
Several statistical models used in genome-wide prediction assume uncorrelated marker allele substitution effects, but it is known that these effects may be correlated. In statistics, graphical models have been identified as a useful tool for covariance estimation in high-dimensional problems and it is an area that has recently experienced a great expansion. In Gaussian covariance graph models (GCovGM), the joint distribution of a set of random variables is assumed to be Gaussian and the pattern of zeros of the covariance matrix is encoded in terms of an undirected graph G...
August 13, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28803920/open-chromatin-profiling-in-hipsc-derived-neurons-prioritizes-functional-noncoding-psychiatric-risk-variants-and-highlights-neurodevelopmental-loci
#11
Marc P Forrest, Hanwen Zhang, Winton Moy, Heather McGowan, Catherine Leites, Leonardo E Dionisio, Zihui Xu, Jianxin Shi, Alan R Sanders, William J Greenleaf, Chad A Cowan, Zhiping P Pang, Pablo V Gejman, Peter Penzes, Jubao Duan
Most disease variants lie within noncoding genomic regions, making their functional interpretation challenging. Because chromatin openness strongly influences transcriptional activity, we hypothesized that cell-type-specific open chromatin regions (OCRs) might highlight disease-relevant noncoding sequences. To investigate, we mapped global OCRs in neurons differentiating from hiPSCs, a cellular model for studying neurodevelopmental disorders such as schizophrenia (SZ). We found that the OCRs are highly dynamic and can stratify GWAS-implicated SZ risk variants...
August 4, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28803857/mapping-of-quantitative-trait-loci-for-temporal-growth-and-age-at-maturity-in-coho-salmon-evidence-for-genotype-by-sex-interactions
#12
Miyako Kodama, Jeffrey J Hard, Kerry A Naish
Phenotypic differences between males and females are ubiquitous throughout the animal kingdom. Therefore, investigating the extent to which sex-dependent genetic effects contribute to phenotypic variation is important in understanding the evolutionary response of each sex to natural and artificial selection. Sex-specific differences in growth patterns and age at sexual maturity have been observed in a number of anadromous salmonid fishes. In these species, faster growing individuals in a given cohort often mature earlier than conspecifics, and earlier maturing individuals are often males...
August 10, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28802691/the-genome-analysis-of-oleiphilus-messinensis-me102-dsm-13489-t-reveals-backgrounds-of-its-obligate-alkane-devouring-marine-lifestyle
#13
Stepan V Toshchakov, Alexei A Korzhenkov, Tatyana N Chernikova, Manuel Ferrer, Olga V Golyshina, Michail M Yakimov, Peter N Golyshin
Marine bacterium Oleiphilus messinensis ME102 (DSM 13489(T)) isolated from the sediments of the harbor of Messina (Italy) is a member of the order Oceanospirillales, class Gammaproteobacteria, representing the physiological group of marine obligate hydrocarbonoclastic bacteria (OHCB) alongside the members of the genera Alcanivorax, Oleispira, Thalassolituus, Cycloclasticus and Neptunomonas. These organisms play a crucial role in the natural environmental cleanup in marine systems. Despite having the largest genome (6...
August 9, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28802383/absence-of-kcnq4-mutation-in-bengali-families-with-adnshl-originated-from-west-bengal-india
#14
Bidisha Adhikary, Biswabandhu Bankura, Subhradev Biswas, Silpita Paul, Madhusudan Das
OBJECTIVE: Autosomal Dominant Non-Syndromic Hearing Loss (ADNSHL) is extremely heterogeneous in nature. More than 60 loci with 30 different genes have been identified linked to ADNSHL. Mutation in KCNQ4 is considered as one of the most common causative factor responsible for ADNSHL. No study focused on the genetic alteration of KCNQ4 gene among hearing loss patients in India. The present study for the first time was carried out to determine the mutation spectrum of KCNQ4 gene in ADNSHL patients of West Bengal state, India...
September 2017: International Journal of Pediatric Otorhinolaryngology
https://www.readbyqxmd.com/read/28802076/single-cell-sequencing-unveils-the-lifestyle-and-crispr-based-population-history-of-hydrotalea-sp-in-acid-mine-drainage
#15
J D Medeiros, L R Leite, V S Pylro, F S Oliveira, V M Almeida, G R Fernandes, A C M Salim, F M G Araújo, A C Volpini, G Oliveira, S Cuadros-Orellana
Acid mine drainage (AMD) is characterized by an acid and metal-rich runoff that originates from mining systems. Despite having been studied for many decades, much remains unknown about the microbial community dynamics in AMD sites, especially during their early development, when the acidity is moderate. Here, we describe draft genome assemblies from single cells retrieved from an early-stage AMD sample. These cells belong to the genus Hydrotalea, and is closely related to H. flava. The phylogeny and average nucleotide identity analysis suggest that all single-amplified genomes (SAGs) form two clades that may represent different strains...
August 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28801813/detection-of-qtl-for-greasy-fleece-weight-in-sheep-using-a-50%C3%A2-k-single-nucleotide-polymorphism-chip
#16
Fatemeh Ebrahimi, Mohsen Gholizadeh, Ghodrat Rahimi-Mianji, Ayoub Farhadi
Genome-wide association studies (GWAS) have introduced an influential tool in the search for quantitative trait loci (QTL) influencing economically important traits in sheep. To identify QTL associated with greasy fleece weight, a GWAS with 50 K single nucleotide polymorphisms (SNPs) was performed in a Baluchi sheep population. Association with greasy fleece weights was tested using the software Plink. The results of our GWAS provided three novel SNP markers and candidate genes associated with greasy fleece weight...
August 11, 2017: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/28801756/segregation-distortion-and-genome-wide-digenic-interactions-affect-transmission-of-introgressed-chromatin-from-wild-cotton-species
#17
Rahul Chandnani, Baohua Wang, Xavier Draye, Lisa K Rainville, Susan Auckland, Zhimin Zhuang, Edward L Lubbers, O Lloyd May, Peng W Chee, Andrew H Paterson
This study reports transmission genetics of chromosomal segments into Gossypium hirsutum from its most distant euploid relative, Gossypium mustelinum . Mutilocus interactions and structural rearrangements affect introgression and segregation of donor chromatin. Wild allotetraploid relatives of cotton are a rich source of genetic diversity that can be used in genetic improvement, but linkage drag and non-Mendelian transmission genetics are prevalent in interspecific crosses. These problems necessitate knowledge of transmission patterns of chromatin from wild donor species in cultivated recipient species...
August 11, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28801731/molecular-mapping-and-genomics-of-soybean-seed-protein-a-review-and-perspective-for-the-future
#18
REVIEW
Gunvant Patil, Rouf Mian, Tri Vuong, Vince Pantalone, Qijian Song, Pengyin Chen, Grover J Shannon, Tommy C Carter, Henry T Nguyen
Genetic improvement of soybean protein meal is a complex process because of negative correlation with oil, yield, and temperature. This review describes the progress in mapping and genomics, identifies knowledge gaps, and highlights the need of integrated approaches. Meal protein derived from soybean [Glycine max (L) Merr.] seed is the primary source of protein in poultry and livestock feed. Protein is a key factor that determines the nutritional and economical value of soybean. Genetic improvement of soybean seed protein content is highly desirable, and major quantitative trait loci (QTL) for soybean protein have been detected and repeatedly mapped on chromosomes (Chr...
August 11, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28801671/the-cpg-sites-of-the-cbx3-ubiquitous-chromatin-opening-element-are-critical-structural-determinants-for-the-anti-silencing-function
#19
Jessica Kunkiel, Natascha Gödecke, Mania Ackermann, Dirk Hoffmann, Axel Schambach, Nico Lachmann, Dagmar Wirth, Thomas Moritz
Suppression of therapeutic transgene expression from retroviral gene therapy vectors by epigenetic defence mechanisms represents a problem that is particularly encountered in pluripotent stem cells (PSCs) and their differentiated progeny. Transgene expression in these cells, however, can be stabilised by CpG-rich ubiquitous chromatin opening elements (UCOEs). In this context we recently demonstrated profound anti-silencing properties for the small (679 bp) CBX3-UCO element and we now confirmed this observation in the context of the defined murine chromosomal loci ROSA26 and TIGRE...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28801652/assessment-of-three-new-loci-from-genome-wide-association-study-in-essential-tremor-in-chinese-population
#20
Yuan Zhang, Yuwen Zhao, Xiaoting Zhou, Kai Li, Minhan Yi, Jifeng Guo, Xinxiang Yan, Beisha Tang, Qiying Sun
Essential tremor (ET) is the most common tremor disorder. Evidences indicated that genetics plays an essential role in the researches of etiology. A new genome-wide association study (GWAS) from European population identified three novel loci in ET, which were rs10937625 in STK32B, rs17590046 in PPARGC1A, and rs12764057, rs10822974 and rs7903491 in CTNNA3. Due to the different genetic background in different population, we performed a case-control study to investigate these variants in a cohort of 533 subjects in Chinese population...
August 11, 2017: Scientific Reports
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