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Frontiers in Genetics

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https://www.readbyqxmd.com/read/30013594/polygenic-basis-and-variable-genetic-architectures-contribute-to-the-complex-nature-of-body-weight-a-genome-wide-study-in-four-chinese-indigenous-chicken-breeds
#1
Yangyang Yuan, Dezhi Peng, Xiaorong Gu, Yanzhang Gong, Zheya Sheng, Xiaoxiang Hu
Body weight (BW) is one of the most important economic traits for animal production and breeding, and it has been studied extensively for its phenotype-genotype associations. While mapping studies have mostly aimed at finding as many loci as possible that contributed to the variation in BW, the role of other factors in its genetic architecture, including their frequencies in the population and their interactions, have been largely overlooked. To comprehensively characterized the genetic architecture of BW, we performed a genome-wide association study (GWAS) both at the single-marker and haplotype level on birds from four indigenous Chinese chicken breeds (Chahua, Silkie, Langshan, and Beard), rather than studying crosses between two founder lines...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30013593/commentary-likelihood-ratio-as-weight-of-forensic-evidence-a-closer-look
#2
COMMENT
Colin Aitken, Anders Nordgaard, Franco Taroni, Alex Biedermann
No abstract text is available yet for this article.
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30013592/screening-of-the-lamb2-wt1-nphs1-and-nphs2-genes-in-pediatric-nephrotic-syndrome
#3
Aiysha Abid, Saba Shahid, Madiha Shakoor, Ali A Lanewala, Seema Hashmi, Shagufta Khaliq
Mutations in the NPHS1, NPHS2, LAMB2 , and the WT1 genes are responsible for causing nephrotic syndrome (NS) in two third of the early onset cases. This study was carried out to assess the frequencies of mutations in these genes in a cohort of pediatric NS patients. A total of 64 pediatric familial or sporadic SRNS cases were recruited. Among these, 74% had a disease onset of up to 3 years of age. We found one homozygous frameshift mutation in the NPHS1 gene in one CNS case and two homozygous mutations in the NPHS2 gene...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30008734/fast-growing-engineered-microbes-new-concerns-for-gain-of-function-research
#4
REVIEW
Lei Pei, Markus Schmidt
Research on fast-growing microbes holds promise for many industrial applications, including shortening test and trial times in research and development stages and reducing the operation costs for production. Such microbes can be obtained either by selecting naturally occurring variants or via metabolic engineering approaches, either eliminating 'unnecessary' or adding necessary pathways affecting growth speed in the cell. Here, we review recent research and development of engineered fast-growing strains in industrial biotechology, with a special focus on vaccine production using (synthetic biology) engineered pathogenic strains...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30002671/sample-size-for-successful-genome-wide-association-study-of-major-depressive-disorder
#5
Jo Nishino, Hidenori Ochi, Yuta Kochi, Tatsuhiko Tsunoda, Shigeyuki Matsui
Major depressive disorder (MDD) is a complex, heritable psychiatric disorder. Advanced statistical genetics for genome-wide association studies (GWASs) have suggested that the heritability of MDD is largely explained by common single nucleotide polymorphisms (SNPs). However, until recently, there has been little success in identifying MDD-associated SNPs. Here, based on an empirical Bayes estimation of a semi-parametric hierarchical mixture model using summary statistics from GWASs, we show that MDD has a distinctive polygenic architecture consisting of a relatively small number of risk variants (~17%), e...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29988524/equipped-for-migrations-across-high-latitude-regions-reduced-spur-length-and-outcrossing-rate-in-a-biennial-halenia-elliptica-gentianaceae-with-mixed-mating-system-along-a-latitude-gradient
#6
Ming-Liu Yang, Lin-Lin Wang, Guo-Peng Zhang, Li-Hua Meng, Yong-Ping Yang, Yuan-Wen Duan
Halenia (Gentianaceae) originated from the mountain regions of East Asia, and diversified in America following long migrations via Beringia. While Halenia elliptica , one species of the genus in China, migrated toward high latitudes in China. Spur length of H. elliptica is highly variable. We examined the relationship between spur length and mating pattern along a latitude gradient. Field experiments were performed in two populations of H. elliptica , and we found that this species could produce seeds via both autonomous selfing and the aid of pollinators, suggesting a mixed mating system...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29988451/association-of-interleukin-10-methylation-levels-with-gestational-diabetes-in-a-taiwanese-population
#7
Jessica Kang, Chien-Nan Lee, Hung-Yuan Li, Kai-Han Hsu, Shu-Huei Wang, Shin-Yu Lin
Objective: Gestational diabetes mellitus (GDM) is defined as glucose intolerance with onset during pregnancy, which is also associated with future metabolic diseases in both patients and their offspring. The mechanisms underlying this condition remain largely unknown and may be partly related to epigenetics. The aim of this study was to compare the methylation levels of the cytokine interleukin-10 (IL-10) in pregnant women and their fetuses under both hyperglycemic and euglycemic environments, as those levels may be a clue to the epigenetic mechanisms underlying pathogenesis of GDM...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29988410/functional-partitioning-of-genomic-variance-and-genome-wide-association-study-for-carcass-traits-in-korean-hanwoo-cattle-using-imputed-sequence-level-snp-data
#8
Mohammad S A Bhuiyan, Dajeong Lim, Mina Park, Soohyun Lee, Yeongkuk Kim, Cedric Gondro, Byoungho Park, Seunghwan Lee
Quantitative traits are usually controlled by numerous genomic variants with small individual effects, and variances associated with those traits are explained in a continuous manner. However, the relative contributions of genomic regions to observed genetic variations have not been well explored using sequence level single nucleotide polymorphism (SNP) information. Here, imputed sequence level SNP data (11,278,153 SNPs) of 2109 Hanwoo steers (Korean native cattle) were partitioned according to functional annotation, chromosome, and minor allele frequency (MAF)...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29988374/time-heals-all-wounds-but-scars-remain-can-personalized-medicine-help
#9
Saeid Amini-Nik
No abstract text is available yet for this article.
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29971094/editorial-metal-biology-takes-flight-the-study-of-metal-homeostasis-and-detoxification-in-insects
#10
EDITORIAL
Stephanie E Mohr, David W Killilea
No abstract text is available yet for this article.
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29971093/genetic-architecture-of-feeding-behavior-and-feed-efficiency-in-a-duroc-pig-population
#11
Rongrong Ding, Ming Yang, Xingwang Wang, Jianping Quan, Zhanwei Zhuang, Shenping Zhou, Shaoyun Li, Zheng Xu, Enqin Zheng, Gengyuan Cai, Dewu Liu, Wen Huang, Jie Yang, Zhenfang Wu
Increasing feed efficiency is a major goal of breeders as it can reduce production cost and energy consumption. However, the genetic architecture of feeding behavior and feed efficiency traits remains elusive. To investigate the genetic architecture of feed efficiency in pigs, three feeding behavior traits (daily feed intake, number of daily visits to feeder, and duration of each visit) and two feed efficiency traits (feed conversion ratio and residual feed intake) were considered. We performed genome-wide association studies (GWASs) of the five traits using a population of 1,008 Duroc pigs genotyped with an Illumina Porcine SNP50K BeadChip...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29971092/quantitative-evaluation-of-toxic-polyglycine-biosynthesis-and-aggregation-in-cell-models-expressing-expanded-cgg-repeats
#12
Magdalena Derbis, Patryk Konieczny, Agnieszka Walczak, Michal Sekrecki, Krzysztof Sobczak
Fragile X-associated tremor/ataxia syndrome (FXTAS) is a late-onset neurodegenerative disorder caused by expanded CGG (CGGexp ) trinucleotides in the 5'UTR of the FMR1 gene encoding fragile X mental retardation protein (FMRP). The patients, with the number of the repeats ranging from 55 to 200, show specific manifestation of clinical symptoms that include intention tremor, gait ataxia, cognitive deficits, and brain atrophy. Accumulation of toxic polyglycine (FMRpolyG), a by-product of the CGGexp repeat-associated non-ATG (RAN) translation, is considered to be one of the main factors triggering neurodegenerative processes in FXTAS patients...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29971091/editorial-the-least-cost-path-from-landscape-genetics-to-landscape-genomics-challenges-and-opportunities-to-explore-ngs-data-in-a-spatially-explicit-context
#13
EDITORIAL
Samuel A Cushman, Andrew J Shirk, Glenn T Howe, Melanie A Murphy, Rodney J Dyer, Stéphane Joost
No abstract text is available yet for this article.
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29971090/differential-integration-of-transcriptome-and-proteome-identifies-pan-cancer-prognostic-biomarkers
#14
Gregory W Schwartz, Jelena Petrovic, Yeqiao Zhou, Robert B Faryabi
High-throughput analysis of the transcriptome and proteome individually are used to interrogate complex oncogenic processes in cancer. However, an outstanding challenge is how to combine these complementary, yet partially disparate data sources to accurately identify tumor-specific gene products and clinical biomarkers. Here, we introduce inteGREAT for robust and scalable differential integration of high-throughput measurements. With inteGREAT, each data source is represented as a co-expression network, which is analyzed to characterize the local and global structure of each node across networks...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29971089/high-fructose-intake-during-pregnancy-in-rats-influences-the-maternal-microbiome-and-gut-development-in-the-offspring
#15
Stuart Astbury, Aleida Song, Mi Zhou, Brent Nielsen, Abha Hoedl, Benjamin P Willing, Michael E Symonds, Rhonda C Bell
Studies in pregnant women indicate the maternal microbiome changes during pregnancy so as to benefit the mother and fetus. In contrast, disruption of the maternal microbiota around birth can compromise normal bacterial colonisation of the infant's gastrointestinal tract. This may then inhibit development of the gut so as to increase susceptibility to inflammation and reduce barrier function. The impact of modulating fructose intake on the maternal microbiome through pregnancy is unknown, therefore we examined the effect of fructose supplementation on the maternal microbiome together with the immediate and next generation effects in the offspring...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29963077/passport-seq-a-novel-high-throughput-bioassay-to-functionally-test-polymorphisms-in-micro-rna-target-sites
#16
Joseph Ipe, Kimberly S Collins, Yangyang Hao, Hongyu Gao, Puja Bhatia, Andrea Gaedigk, Yunlong Liu, Todd C Skaar
Next-generation sequencing (NGS) studies have identified large numbers of genetic variants that are predicted to alter miRNA-mRNA interactions. We developed a novel high-throughput bioassay, PASSPORT-seq, that can functionally test in parallel 100s of these variants in miRNA binding sites (mirSNPs). The results are highly reproducible across both technical and biological replicates. The utility of the bioassay was demonstrated by testing 100 mirSNPs in HEK293, HepG2, and HeLa cells. The results of several of the variants were validated in all three cell lines using traditional individual luciferase assays...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29963076/revisiting-meiosis-in-sugarcane-chromosomal-irregularities-and-the-prevalence-of-bivalent-configurations
#17
Maria Lucia C Vieira, Carmelice B Almeida, Carlos A Oliveira, Luana O Tacuatiá, Carla F Munhoz, Luiz A Cauz-Santos, Luciana R Pinto, Claudia B Monteiro-Vitorello, Mauro A Xavier, Eliana R Forni-Martins
Traditional sugarcane cultivars ( Saccharum officinarum ) proved highly susceptible to diseases, and this led breeders to progress to interspecific crosses resulting in disease resistance. A backcrossing program to S. officinarum was then required to boost sucrose content. Clonal selection across generations and incorporation of other germplasm into cultivated backgrounds established the (narrow) genetic base of modern cultivars ( Saccharum spp.), which have a man-made genome. The genome complexity has inspired several molecular studies that have elucidated aspects of sugarcane genome constitution, architecture, and cytogenetics...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29963075/jointly-modelling-single-nucleotide-polymorphisms-with-longitudinal-and-time-to-event-trait-an-application-to-type-2-diabetes-and-fasting-plasma-glucose
#18
Mickaël Canouil, Beverley Balkau, Ronan Roussel, Philippe Froguel, Ghislain Rocheleau
In observational cohorts, longitudinal data are collected with repeated measurements at predetermined time points for many biomarkers, along with other variables measured at baseline. In these cohorts, time until a certain event of interest occurs is reported and very often, a relationship will be observed between some biomarker repeatedly measured over time and that event. Joint models were designed to efficiently estimate statistical parameters describing this relationship by combining a mixed model for the longitudinal biomarker trajectory and a survival model for the time until occurrence of the event, using a set of random effects to account for the relationship between the two types of data...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29963074/rare-case-of-ulnar-mammary-like-syndrome-with-left-ventricular-tachycardia-and-lack-of-tbx3-mutation
#19
Anna Zlotina, Artem Kiselev, Alexey Sergushichev, Elena Parmon, Anna Kostareva
"Heart-hand" type syndromes represent a group of rare congenital conditions that combine cardiac pathology (structural defect or arrhythmic disorder) and limb abnormality. Significant clinical variability and genetic heterogeneity typical for such syndromes complicate correct diagnosis, prognosis, and appropriate genetic counseling of the affected families. By now, only single genes have been unambiguously determined as a genetic cause of heart-hand syndromes and phenotypically similar conditions...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29963073/combining-pathway-identification-and-breast-cancer-survival-prediction-via-screening-network-methods
#20
Antonella Iuliano, Annalisa Occhipinti, Claudia Angelini, Italia De Feis, Pietro Liò
Breast cancer is one of the most common invasive tumors causing high mortality among women. It is characterized by high heterogeneity regarding its biological and clinical characteristics. Several high-throughput assays have been used to collect genome-wide information for many patients in large collaborative studies. This knowledge has improved our understanding of its biology and led to new methods of diagnosing and treating the disease. In particular, system biology has become a valid approach to obtain better insights into breast cancer biological mechanisms...
2018: Frontiers in Genetics
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