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https://www.readbyqxmd.com/read/28646443/recent-discoveries-in-monogenic-disorders-of-childhood-bone-fragility
#1
REVIEW
Riikka E Mäkitie, Anders J Kämpe, Fulya Taylan, Outi Mäkitie
PURPOSE OF REVIEW: This review summarizes our current knowledge on primary osteoporosis in children with focus on recent genetic findings. RECENT FINDINGS: Advances in genetic research, particularly next-generation sequencing, have found several genetic loci that associate with monogenic forms of inherited osteoporosis, widening the scope of primary osteoporosis beyond classical osteogenesis imperfecta. New forms of primary osteoporosis, such as those related to WNT1, PLS3, and XYLT2, have identified defects outside the extracellular matrix components and collagen-related pathways, in intracellular cascades directly affecting bone cell function...
June 23, 2017: Current Osteoporosis Reports
https://www.readbyqxmd.com/read/28645872/two-obesity-susceptibility-loci-in-lyplal1-and-etv5-independently-associated-with-childhood-hypertension-in-chinese-population
#2
Duo Lv, Dan Zhou, Yan Zhang, Shuai Zhang, Yi-Min Zhu
AIMS: Genome-wide association studies have identified novel obesity-associated susceptibility loci. Associations of these variants with childhood obesity have been studied in our previous research. The purpose of this study is to investigate if these loci are associated with hypertension being independent of obesity in Chinese children and adolescents. METHODS: Nineteen candidate SNPs were genotyped using Sequenom MassARRAY platform among Chinese children (N=2954, 514 hypertension and 2440 controls, aged 7-17years)...
June 20, 2017: Gene
https://www.readbyqxmd.com/read/28645767/assessing-the-potential-of-rad-sequencing-to-resolve-phylogenetic-relationships-within-species-radiations-the-fly-genus-chiastocheta-diptera-anthomyiidae-as-a-case-study
#3
Tomasz Suchan, Anahí Espíndola, Sereina Rutschmann, Brent C Emerson, Kevin Gori, Christophe Dessimoz, Nils Arrigo, Michał Ronikier, Nadir Alvarez
Determining phylogenetic relationships among recently diverged species has long been a challenge in evolutionary biology. Cytoplasmic markers, which have been widely used notably in the context of molecular barcoding, have not always proved successful in resolving such phylogenies, but phylogenies for closely related species have been resolved at a much higher detail in the last couple of years with the advent of next-generation-sequencing technologies and associated techniques of reduced genome representation...
June 20, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28644860/time-dependent-genetic-analysis-links-field-and-controlled-environment-phenotypes-in-the-model-c4-grass-setaria
#4
Max J Feldman, Rachel E Paul, Darshi Banan, Jennifer F Barrett, Jose Sebastian, Muh-Ching Yee, Hui Jiang, Alexander E Lipka, Thomas P Brutnell, José R Dinneny, Andrew D B Leakey, Ivan Baxter
Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed six controlled growth trials of an interspecific Setaria italica x Setaria viridis recombinant inbred line population to assess how the genetic architecture of plant height is influenced by developmental queues, water availability and planting density. The non-destructive nature of plant height measurements has enabled us to monitor height throughout the plant life cycle in both field and controlled environments...
June 23, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28644843/a-high-density-genetic-map-and-qtl-analysis-of-agronomic-traits-in-foxtail-millet-setaria-italica-l-p-beauv-using-rad-seq
#5
Jun Wang, Zhilan Wang, Xiaofen Du, Huiqing Yang, Fang Han, Yuanhuai Han, Feng Yuan, Linyi Zhang, Shuzhong Peng, Erhu Guo
Foxtail millet (Setaria italica), a very important grain crop in China, has become a new model plant for cereal crops and biofuel grasses. Although its reference genome sequence was released recently, quantitative trait loci (QTLs) controlling complex agronomic traits remains limited. The development of massively parallel genotyping methods and next-generation sequencing technologies provides an excellent opportunity for developing single-nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of complex quantitative traits...
2017: PloS One
https://www.readbyqxmd.com/read/28644137/analyses-of-germline-variants-associated-with-ovarian-cancer-survival-identify-functional-candidates-at-the-1q22-and-19p12-outcome-loci
#6
Dylan M Glubb, Sharon E Johnatty, Michael C J Quinn, Tracy A O'Mara, Jonathan P Tyrer, Bo Gao, Peter A Fasching, Matthias W Beckmann, Diether Lambrechts, Ignace Vergote, Digna R Velez Edwards, Alicia Beeghly-Fadiel, Javier Benitez, Maria J Garcia, Marc T Goodman, Pamela J Thompson, Thilo Dörk, Matthias Dürst, Francesmary Modungo, Kirsten Moysich, Florian Heitz, Andreas du Bois, Jacobus Pfisterer, Peter Hillemanns, Beth Y Karlan, Jenny Lester, Ellen L Goode, Julie M Cunningham, Stacey J Winham, Melissa C Larson, Bryan M McCauley, Susanne Krüger Kjær, Allan Jensen, Joellen M Schildkraut, Andrew Berchuck, Daniel W Cramer, Kathryn L Terry, Helga B Salvesen, Line Bjorge, Penny M Webb, Peter Grant, Tanja Pejovic, Melissa Moffitt, Claus K Hogdall, Estrid Hogdall, James Paul, Rosalind Glasspool, Marcus Bernardini, Alicia Tone, David Huntsman, Michelle Woo, Aocs Group, Anna deFazio, Catherine J Kennedy, Paul D P Pharoah, Stuart MacGregor, Georgia Chenevix-Trench
We previously identified associations with ovarian cancer outcome at five genetic loci. To identify putatively causal genetic variants and target genes, we prioritized two ovarian outcome loci (1q22 and 19p12) for further study. Bioinformatic and functional genetic analyses indicated that MEF2D and ZNF100 are targets of candidate outcome variants at 1q22 and 19p12, respectively. At 19p12, the chromatin interaction of a putative regulatory element with the ZNF100 promoter region correlated with candidate outcome variants...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28643872/circulating-microrna-as-candidates-for-early-embryonic-viability-in-cattle
#7
K G Pohler, J A Green, L A Moley, S Gunewardena, W T Hung, R R Payton, X Hong, L K Christenson, T W Geary, M F Smith
Blood-borne extracellular vesicles (i.e. exosomes and microvesicles) carrying microRNAs (miRNAs) could make excellent biomarkers of disease and different physiologic states, including pregnancy status. We tested the hypothesis that circulating extracellular vesicle-derived miRNAs might differentiate the pregnancy status of cows that had maintained pregnancy to Day 30 from non-pregnant cows or from those that exhibited embryonic mortality between Days 17-30 of gestation. Cows were randomly assigned for artificial insemination with fertile semen (n= 36) or dead semen (n = 8; control group) on Day 0 (day of estrus)...
June 23, 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/28643332/integrative-eqtl-analysis-of-tumor-and-host-omics-data-in-individuals-with-bladder-cancer
#8
Silvia Pineda, Kristel Van Steen, Núria Malats
Integrative analyses of several omics data are emerging. The data are usually generated from the same source material (i.e., tumor sample) representing one level of regulation. However, integrating different regulatory levels (i.e., blood) with those from tumor may also reveal important knowledge about the human genetic architecture. To model this multilevel structure, an integrative-expression quantitative trait loci (eQTL) analysis applying two-stage regression (2SR) was proposed. This approach first regressed tumor gene expression levels with tumor markers and the adjusted residuals from the previous model were then regressed with the germline genotypes measured in blood...
June 23, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28642868/an-exploration-of-gene-gene-interactions-and-their-effects-on-hypertension
#9
Ying Meng, Susan Groth, Jill R Quinn, John Bisognano, Tong Tong Wu
Hypertension tends to perpetuate in families and the heritability of hypertension is estimated to be around 20-60%. So far, the main proportion of this heritability has not been found by single-locus genome-wide association studies. Therefore, the current study explored gene-gene interactions that have the potential to partially fill in the missing heritability. A two-stage discovery-confirmatory analysis was carried out in the Framingham Heart Study cohorts. The first stage was an exhaustive pairwise search performed in 2320 early-onset hypertensive cases with matched normotensive controls from the offspring cohort...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28642863/friends-enemies-endogenous-retroviruses-are-major-transcriptional-regulators-of-human-dna
#10
REVIEW
Anton A Buzdin, Vladimir Prassolov, Andrew V Garazha
Endogenous retroviruses are mobile genetic elements hardly distinguishable from infectious, or "exogenous," retroviruses at the time of insertion in the host DNA. Human endogenous retroviruses (HERVs) are not rare. They gave rise to multiple families of closely related mobile elements that occupy ~8% of the human genome. Together, they shape genomic regulatory landscape by providing at least ~320,000 human transcription factor binding sites (TFBS) located on ~110,000 individual HERV elements. The HERVs host as many as 155,000 mapped DNaseI hypersensitivity sites, which denote loci active in the regulation of gene expression or chromatin structure...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28642824/identification-of-quantitative-trait-loci-that-determine-plasma-total-cholesterol-and-triglyceride-concentrations-in-ddd-sgn-and-c57bl-6j-inbred-mice
#11
Jun-Ichi Suto, Misaki Kojima
DDD/Sgn mice have significantly higher plasma lipid concentrations than C57BL/6J mice. In the present study, we performed quantitative trait loci (QTL) mapping for plasma total-cholesterol (CHO) and triglyceride (TG) concentrations in reciprocal F2 male intercross populations between the two strains. By single-QTL scans, we identified four significant QTL on chromosomes (Chrs) 1, 5, 17, and 19 for CHO and two significant QTL on Chrs 1 and 12 for TG. By including cross direction as an interactive covariate, we identified separate significant QTL on Chr 17 for CHO but none for TG...
2017: Cholesterol
https://www.readbyqxmd.com/read/28642778/characterization-of-salt-induced-epigenetic-segregation-by-genome-wide-loss-of-heterozygosity-and-its-association-with-salt-tolerance-in-rice-oryza-sativa-l
#12
Min Li, Wen-Sheng Wang, Yun-Long Pang, Jessica R Domingo, Jauhar Ali, Jian-Long Xu, Bin-Ying Fu, Elec B Venus, Zhi-Kang Li
In a breeding effort to develop salt tolerant (ST) rice varieties by designed QTL pyramiding, large numbers of progenies derived from four crosses between salt- or drought- tolerant BC2F5 IR64 introgression lines, were subjected to severe salt stress, resulting in 422 ST plants. The progeny testing of the selected F3 lines under more severe salt stress resulted in identification of 16 promising homozygous lines with high levels of ST. Genetic characterization of the 422 ST F3 progeny and 318 random F2 plants from the same four crosses using 105 segregating SSR markers lead to three interesting discoveries: (1) salt stress can induce genome-wide epigenetic segregation (ES) characterized by complete loss of heterozygosity (LOH) and nearly complete loss of an allele (LOA) in the F3 progenies of four rice populations in a single generation; (2) ∼25% of the stress-induced ES loci were transgenerational and inherited from their salt- and drought- selected parents; and (3) the salt-induced LOH and LOA loci (regions) appeared to contain genes/alleles associated with ST and/or drought tolerance...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642772/assessment-of-five-chilling-tolerance-traits-and-gwas-mapping-in-rice-using-the-usda-mini-core-collection
#13
Michael R Schläppi, Aaron K Jackson, Georgia C Eizenga, Aiju Wang, Chengcai Chu, Yao Shi, Naoki Shimoyama, Debbie L Boykin
Rice (Oryza sativa L.) is often exposed to cool temperatures during spring planting in temperate climates. A better understanding of genetic pathways regulating chilling tolerance will enable breeders to develop varieties with improved tolerance during germination and young seedling stages. To dissect chilling tolerance, five assays were developed; one assay for the germination stage, one assay for the germination and seedling stage, and three for the seedling stage. Based on these assays, five chilling tolerance indices were calculated and assessed using 202 O...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642597/a-single-amino-acid-polymorphism-in-the-glycosyltransferase-cpsk-defines-four-streptococcus-suis-serotypes
#14
David Roy, Taryn B T Athey, Jean-Philippe Auger, Guillaume Goyette-Desjardins, Marie-Rose Van Calsteren, Daisuke Takamatsu, Masatoshi Okura, Sarah Teatero, Martín Alcorlo, Juan A Hermoso, Mariela Segura, Marcelo Gottschalk, Nahuel Fittipaldi
The capsular polysaccharide (CPS) is the major virulence factor of the emerging zoonotic pathogen Streptococcus suis. CPS differences are also the basis for serological differentiation of the species into 29 serotypes. Serotypes 2 and 1/2, which possess identical gene content in their cps loci, express CPSs that differ only by substitution of galactose (Gal) by N-acetylgalactosamine (GalNAc) in the CPS side chain. The same sugar substitution differentiates the CPS of serotypes 14 and 1, whose cps loci are also identical in gene content...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642589/multiple-origins-and-a-narrow-genepool-characterise-the-african-tea-germplasm-concordant-patterns-revealed-by-nuclear-and-plastid-dna-markers
#15
Moses Cheloti Wambulwa, Muditha Kasun Meegahakumbura, Samson Kamunya, Alice Muchugi, Michael Möller, Jie Liu, Jian-Chu Xu, De-Zhu Li, Lian-Ming Gao
Despite the highly economic value of tea in Africa, its genetic and geographic origins remain largely unexplored. Here we address this by collecting 439 samples across 11 countries in Africa and Asia to investigate the origin and genepool composition of African tea based on 23 nuclear microsatellites loci (nSSRs) and three cpDNA intergenic spacer regions. Our results indicated that the African tea represents a potpourri originating from multiple introductions over time. The nSSR analysis revealed that the majority (79%) of tea accessions collected in Africa belong to Indian Assam tea which have likely originated from India and/or Sri Lanka...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642574/replication-of-gout-urate-concentrations-gwas-susceptibility-loci-associated-with-gout-in-a-han-chinese-population
#16
Zhiqiang Li, Zhaowei Zhou, Xu Hou, Dajiang Lu, Xuan Yuan, Jie Lu, Can Wang, Lin Han, Lingling Cui, Zhen Liu, Jianhua Chen, Xiaoyu Cheng, Keke Zhang, Jue Ji, Zhaotong Jia, Lidan Ma, Ying Xin, Tian Liu, Qing Yu, Wei Ren, Xuefeng Wang, Xinde Li, Qing-Sheng Mi, Yongyong Shi, Changgui Li
Gout is a chronic disease resulting from elevated serum urate (SU). Previous genome-wide association studies (GWAS) have identified dozens of susceptibility loci for SU/gout, but few have been conducted for Chinese descent. Here, we try to extensively investigate whether these loci contribute to gout risk in Han Chinese. A total of 2255 variants in linkage disequilibrium (LD) with GWAS identified SU/gout associated variants were analyzed in a Han Chinese cohort of 1255 gout patients and 1848 controls. Cumulative genetic risk score analysis was performed to assess the cumulative effect of multiple "risk" variants on gout incidence...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642272/networks-underpinning-symbiosis-revealed-through-cross-species-eqtl-mapping
#17
Yuelong Guo, Sylwia Fudali, Jacinta Gimeno, Peter DiGennaro, Stella Chang, Valerie M Williamson, David McK Bird, Dahlia M Nielsen
Organisms engage in extensive cross-species molecular dialogue, yet the underlying molecular actors are known for only a few interactions. Many techniques have been designed to uncover genes involved in signaling between organisms. Typically, these focus on only one of the partners. We developed an expression quantitative trait locus (eQTL) mapping-based approach to identify cause-and-effect relationships between genes from two partners engaged in an interspecific interaction. We demonstrated the approach by assaying expression of ninety-eight isogenic plants (Medicago truncatula), each inoculated with a genetically distinct line of the diploid parasitic nematode Meloidogyne hapla With this design, systematic differences in gene expression across host plants could be mapped to genetic polymorphisms of their infecting parasites...
June 22, 2017: Genetics
https://www.readbyqxmd.com/read/28641886/genome-wide-expression-in-veterans-with-schizophrenia-further-validates-the-immune-hypothesis-for-schizophrenia
#18
Gabriel R Fries, Dimitre H Dimitrov, Shuko Lee, Nicole Braida, Jesse Yantis, Craig Honaker, Joe Cuellar, Consuelo Walss-Bass
This study aimed to test whether a dysregulation of gene expression may be the underlying cause of previously reported elevated levels of inflammatory cytokines in veterans with schizophrenia. We performed a genome-wide expression analysis in peripheral blood mononuclear cells from veterans with schizophrenia and controls, and our results show that 167 genes and putative loci were differently expressed between groups. These genes were enriched primarily for pathways related to inflammatory mechanisms and formed networks related to cell death and survival, immune cell trafficking, among others, which is in line with previous reports and further validates the inflammatory hypothesis of schizophrenia...
June 19, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28641109/rare-copy-number-variants-in-nrxn1-and-cntn6-increase-risk-for-tourette-syndrome
#19
Alden Y Huang, Dongmei Yu, Lea K Davis, Jae Hoon Sul, Fotis Tsetsos, Vasily Ramensky, Ivette Zelaya, Eliana Marisa Ramos, Lisa Osiecki, Jason A Chen, Lauren M McGrath, Cornelia Illmann, Paul Sandor, Cathy L Barr, Marco Grados, Harvey S Singer, Markus M Nöthen, Johannes Hebebrand, Robert A King, Yves Dion, Guy Rouleau, Cathy L Budman, Christel Depienne, Yulia Worbe, Andreas Hartmann, Kirsten R Müller-Vahl, Manfred Stuhrmann, Harald Aschauer, Mara Stamenkovic, Monika Schloegelhofer, Anastasios Konstantinidis, Gholson J Lyon, William M McMahon, Csaba Barta, Zsanett Tarnok, Peter Nagy, James R Batterson, Renata Rizzo, Danielle C Cath, Tomasz Wolanczyk, Cheston Berlin, Irene A Malaty, Michael S Okun, Douglas W Woods, Elliott Rees, Carlos N Pato, Michele T Pato, James A Knowles, Danielle Posthuma, David L Pauls, Nancy J Cox, Benjamin M Neale, Nelson B Freimer, Peristera Paschou, Carol A Mathews, Jeremiah M Scharf, Giovanni Coppola
Tourette syndrome (TS) is a model neuropsychiatric disorder thought to arise from abnormal development and/or maintenance of cortico-striato-thalamo-cortical circuits. TS is highly heritable, but its underlying genetic causes are still elusive, and no genome-wide significant loci have been discovered to date. We analyzed a European ancestry sample of 2,434 TS cases and 4,093 ancestry-matched controls for rare (< 1% frequency) copy-number variants (CNVs) using SNP microarray data. We observed an enrichment of global CNV burden that was prominent for large (> 1 Mb), singleton events (OR = 2...
June 21, 2017: Neuron
https://www.readbyqxmd.com/read/28640939/global-transcriptome-and-co-expression-network-analyses-reveal-cultivar-specific-molecular-signatures-associated-with-seed-development-and-seed-size-weight-determination-in-chickpea
#20
Rohini Garg, Vikash K Singh, Mohan Singh Rajkumar, Vinay Kumar, Mukesh Jain
Seed development is an intricate process regulated via a complex transcriptional regulatory network. To understand the molecular mechanisms governing seed development and seed size/weight in chickpea, we performed a comprehensive analysis of transcriptome dynamics during seed development in two cultivars with contrasting seed size/weight (small seeded, Himchana 1 and large-seeded, JGK 3). Our analysis identified stage-specific expression for a significant proportion (>13%) of the genes. About one-fourth of total genes exhibited significant differential expression in JGK 3 as compared to Himchana 1...
June 22, 2017: Plant Journal: for Cell and Molecular Biology
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