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https://www.readbyqxmd.com/read/29150909/genetic-analysis-of-osteogenesis-imperfecta-in-the-palestinian-population-molecular-screening-of-49-affected-families
#1
Osama Essawi, Sofie Symoens, Maha Fannana, Mohammad Darwish, Mohammad Farraj, Andy Willaert, Tamer Essawi, Bert Callewaert, Anne De Paepe, Fransiska Malfait, Paul J Coucke
BACKGROUND: Osteogenesis imperfecta (OI) is a heterogeneous hereditary connective tissue disorder clinically hallmarked by increased susceptibility to bone fractures. METHODS: We analyzed a cohort of 77 diagnosed OI patients from 49 unrelated Palestinian families. Next-generation sequencing technology was used to screen a panel of known OI genes. RESULTS: In 41 probands, we identified 28 different disease-causing variants of 9 different known OI genes...
November 18, 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/29150721/adaptive-snp-set-association-testing-in-generalized-linear-mixed-models-with-application-to-family-studies
#2
Jun Young Park, Chong Wu, Saonli Basu, Matt McGue, Wei Pan
In genome-wide association studies (GWAS), it has been increasingly recognized that, as a complementary approach to standard single SNP analyses, it may be beneficial to analyze a group of functionally related SNPs together. Among the existent population-based SNP-set association tests, two adaptive tests, the aSPU test and the aSPUpath test, offer a powerful and general approach at the gene- and pathway-levels by data-adaptively combining the results across multiple SNPs (and genes) such that high statistical power can be maintained across a wide range of scenarios...
November 17, 2017: Behavior Genetics
https://www.readbyqxmd.com/read/29150689/distinct-genetic-architectures-for-phenotype-means-and-plasticities-in-zea-mays
#3
Aaron Kusmec, Srikant Srinivasan, Dan Nettleton, Patrick S Schnable
Phenotypic plasticity describes the phenotypic variation of a trait when a genotype is exposed to different environments. Understanding the genetic control of phenotypic plasticity in crops such as maize is of paramount importance for maintaining and increasing yields in a world experiencing climate change. Here, we report the results of genome-wide association analyses of multiple phenotypes and two measures of phenotypic plasticity in a maize nested association mapping (US-NAM) population grown in multiple environments and genotyped with ~2...
September 2017: Nature Plants
https://www.readbyqxmd.com/read/29150626/constructing-genetic-networks-using-biomedical-literature-and-rare-event-classification
#4
Amira Al-Aamri, Kamal Taha, Yousof Al-Hammadi, Maher Maalouf, Dirar Homouz
Text mining has become an important tool in bioinformatics research with the massive growth in the biomedical literature over the past decade. Mining the biomedical literature has resulted in an incredible number of computational algorithms that assist many bioinformatics researchers. In this paper, we present a text mining system called Gene Interaction Rare Event Miner (GIREM) that constructs gene-gene-interaction networks for human genome using information extracted from biomedical literature. GIREM identifies functionally related genes based on their co-occurrences in the abstracts of biomedical literature...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150608/rapid-neo-sex-chromosome-evolution-and-incipient-speciation-in-a-major-forest-pest
#5
Ryan R Bracewell, Barbara J Bentz, Brian T Sullivan, Jeffrey M Good
Genome evolution is predicted to be rapid following the establishment of new (neo) sex chromosomes, but it is not known if neo-sex chromosome evolution plays an important role in speciation. Here we combine extensive crossing experiments with population and functional genomic data to examine neo-XY chromosome evolution and incipient speciation in the mountain pine beetle. We find a broad continuum of intrinsic incompatibilities in hybrid males that increase in strength with geographic distance between reproductively isolated populations...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29150594/mating-design-and-genetic-structure-of-a-multi-parent-advanced-generation-inter-cross-magic-population-of-sorghum-sorghum-bicolor-l-moench
#6
Patrick O Ongom, Gebisa Ejeta
MAGIC populations are powerful next generation mapping resources. We describe here the mating design and structure of the first MAGIC population in sorghum and test its utility for mapping. The population was developed by intercrossing 19 diverse founder lines, through a series of paired crosses with a genetic male sterile source, followed by 10 generations of random mating. At the final stage of random mating, one thousand random fertile plants in the population were identified and subjected to six generations of selfing to produce 1000 immortal MAGIC inbred lines...
November 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29150007/crispr-in-animals-and-animal-models
#7
Ellen Shrock, Marc Güell
CRISPR-Cas9 has revolutionized the generation of transgenic animals. This system has demonstrated an unprecedented efficiency, multiplexability, and ease of use, thereby reducing the time and cost required for genome editing and enabling the production of animals with more extensive genetic modifications. It has also been shown to be applicable to a wide variety of animals, from early-branching metazoans to primates. Genome-wide screens in model organisms have been performed, accurate models of human diseases have been constructed, and potential therapies have been tested and validated in animal models...
2017: Progress in Molecular Biology and Translational Science
https://www.readbyqxmd.com/read/29149916/whole-exome-sequencing-in-amyotrophic-lateral-sclerosis-suggests-nek1-is-a-risk-gene-in-chinese
#8
Jacob Gratten, Qiongyi Zhao, Beben Benyamin, Fleur Garton, Ji He, Paul J Leo, Marie Mangelsdorf, Lisa Anderson, Zong-Hong Zhang, Lu Chen, Xiang-Ding Chen, Katie Cremin, Hong-Weng Deng, Janette Edson, Ying-Ying Han, Jessica Harris, Anjali K Henders, Zi-Bing Jin, Zhongshan Li, Yong Lin, Xiaolu Liu, Mhairi Marshall, Bryan J Mowry, Shu Ran, David C Reutens, Sharon Song, Li-Jun Tan, Lu Tang, Robyn H Wallace, Lawrie Wheeler, Jinyu Wu, Jian Yang, Huji Xu, Peter M Visscher, Perry F Bartlett, Matthew A Brown, Naomi R Wray, Dongsheng Fan
BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a progressive neurological disease characterised by the degeneration of motor neurons, which are responsible for voluntary movement. There remains limited understanding of disease aetiology, with median survival of ALS of three years and no effective treatment. Identifying genes that contribute to ALS susceptibility is an important step towards understanding aetiology. The vast majority of published human genetic studies, including for ALS, have used samples of European ancestry...
November 17, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29149838/genetic-variation-in-populations-of-the-earthworm-lumbricus-rubellus-across-contaminated-mine-sites
#9
Craig Anderson, Luis Cunha, Pierfrancesco Sechi, Peter Kille, David Spurgeon
BACKGROUND: Populations of the earthworm, Lumbricus rubellus, are commonly found across highly contaminated former mine sites and are considered to have under-gone selection for mitigating metal toxicity. Comparison of adapted populations with those found on less contaminated soils can provide insights into ecological processes that demonstrate the long-term effects of soil contamination. Contemporary sequencing methods allow for portrayal of demographic inferences and highlight genetic variation indicative of selection at specific genes...
November 17, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29149730/divergence-of-insulin-superfamily-ligands-receptors-and-igf-binding-proteins-in-marine-versus-freshwater-stickleback-evidence-of-selection-in-known-and-novel-genes
#10
Tim Pellissier, Hend Al Nafea, Sara V Good
Three-spine stickleback (Gasterosteus aculeatus) is a teleost model for understanding genetic, physiological and morphological changes accompanying freshwater (FW) adaptation. There is growing evidence that the insulin superfamily plays important roles in traits involved in marine and FW adaptation. We performed a candidate gene analysis to look for evidence of selection on 33 insulin superfamily ligand-receptor genes and insulin-like growth factor binding proteins (Igfbp's) in stickleback. Using genotype data from 11 marine and 10 FW populations, we calculated the number of SNPs per site in regulatory and intronic regions, the number of synonymous and nonsynonymous mutations in coding regions, Wright's fixation index (Fst), and performed t-tests to identify SNPs with divergent genotype frequencies between marine/FW versus Atlantic/Pacific populations...
November 10, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29149410/tctp-in-neuronal-circuitry-assembly
#11
Cláudio Gouveia Roque, Christine E Holt
Although tctp expression in many areas of the human brain was reported more than 15 years ago, little was known about how it functions in neurons. The early notion that Tctp is primarily expressed in mitotic cells, together with reports suggesting a relative low abundance in the brain, has perhaps potentiated this almost complete disregard for the study of Tctp in the context of neuron biology. However, recent evidence has challenged this view, as a number of independent genome-wide profiling studies identified tctp mRNA among the most enriched in the axonal compartment across diverse neuronal populations, including embryonic retinal ganglion cells...
2017: Results and Problems in Cell Differentiation
https://www.readbyqxmd.com/read/29149250/modeling-the-causal-role-of-dna-methylation-in-the-association-between-cigarette-smoking-and-inflammation-in-african-americans-a-2-step-epigenetic-mendelian-randomization-study
#12
Min A Jhun, Jennifer A Smith, Erin B Ware, Sharon L R Kardia, Thomas H Mosley, Stephen T Turner, Patricia A Peyser, Sung Kyun Park
The association between cigarette smoking and inflammation is well known. However, the biological mechanisms behind the association are not fully understood, particularly the role of DNA methylation, which is known to be affected by smoking. Using 2-step epigenetic Mendelian randomization, we investigated the role of DNA methylation in the association between cigarette smoking and inflammation. In 822 African Americans from the Genetic Epidemiology Network of Arteriopathy, phase 2 (Jackson, Mississippi; 2000-2005), study population, we examined the association of cigarette smoking with DNA methylation using single nucleotide polymorphisms identified in previous genome-wide association studies of cigarette smoking...
November 15, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/29149222/personalized-medicine-and-hispanic-health-improving-health-outcomes-and-reducing-health-disparities-a-national-heart-lung-and-blood-institute-workshop-report
#13
M Larissa Avilés-Santa, John Heintzman, Nangel M Lindberg, Rafael Guerrero-Preston, Kenneth Ramos, Ana L Abraído-Lanza, Jonca Bull, Adolph Falcón, Mary Ann McBurnie, Ernest Moy, George Papanicolaou, Ileana L Piña, Jennifer Popovic, Shakira F Suglia, Miguel A Vázquez
Persons of Hispanic/Latino descent may represent different ancestries, ethnic and cultural groups and countries of birth. In the U.S., the Hispanic/Latino population is projected to constitute 29% of the population by 2060. A personalized approach focusing on individual variability in genetics, environment, lifestyle and socioeconomic determinants of health may advance the understanding of some of the major factors contributing to the health disparities experienced by Hispanics/Latinos and other groups in the U...
2017: BMC Proceedings
https://www.readbyqxmd.com/read/29149077/rna-virus-evolution-via-a-quasispecies-based-model-reveals-a-drug-target-with-a-high-barrier-to-resistance
#14
Richard J Bingham, Eric C Dykeman, Reidun Twarock
The rapid occurrence of therapy-resistant mutant strains provides a challenge for anti-viral therapy. An ideal drug target would be a highly conserved molecular feature in the viral life cycle, such as the packaging signals in the genomes of RNA viruses that encode an instruction manual for their efficient assembly. The ubiquity of this assembly code in RNA viruses, including major human pathogens, suggests that it confers selective advantages. However, their impact on viral evolution cannot be assessed in current models of viral infection that lack molecular details of virus assembly...
November 17, 2017: Viruses
https://www.readbyqxmd.com/read/29148600/new-evidence-for-the-recent-divergence-of-devil-s-hole-pupfish-and-the-plausibility-of-elevated-mutation-rates-in-endangered-taxa
#15
Christopher H Martin, Sebastian Höhna
Saglam et al. (2016) recently argued that the Devil's Hole Pupfish (Cyprinodon diabolis), a conservation icon with the smallest known species range, was isolated 60 kya based on a new genomic dataset. If true, this would be a radically long timescale for any species to persist at population sizes less than 500 individuals, in contrast to conservation genetics theory. However, here we argue that their analyses and interpretation are inappropriate. They placed highly restrictive prior distributions on divergence times, which do not appropriately model the large uncertainty and result in removing nearly all uncertainty from their analyses, and chose among models by assuming that pupfishes exhibit human mutation rates...
November 17, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29147991/the-role-of-the-gut-microbiome-in-multiple-sclerosis-risk-and-progression-towards-characterization-of-the-ms-microbiome
#16
REVIEW
Anne-Katrin Pröbstel, Sergio E Baranzini
Multiple sclerosis (MS) is the prototypic complex disease, in which both genes and the environment contribute to its pathogenesis. To date, > 200 independent loci across the genome have been associated with MS risk. However, these only explain a fraction of the total phenotypic variance, suggesting the possible presence of additional genetic factors, and, most likely, also environmental factors. New DNA sequencing technologies have enabled the sequencing of all kinds of microorganisms, including those living in and around humans (i...
November 16, 2017: Neurotherapeutics: the Journal of the American Society for Experimental NeuroTherapeutics
https://www.readbyqxmd.com/read/29146914/cat-d-a-targeted-sequencing-method-for-the-simultaneous-detection-of-small-dna-mutations-and-large-dna-deletions-with-flexible-boundaries
#17
Ru Hong, Udita Chandola, Li-Feng Zhang
We developed a targeted DNA sequencing method that is capable of detecting a comprehensive panel of DNA mutations including small DNA mutations and large DNA deletions with unknown/flexible boundaries. The method directly identifies the large DNA deletions (Cat-D) without relying on sequencing coverage to make the genotype calls. We performed the method to simultaneously detect 10 small DNA mutations in β-thalassemia and 2 large genomic deletions in α-thalassemia from 10 genomic DNA samples. Cat-D was performed on 8 genomic DNA samples in duplicate...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29146814/natural-selection-shaped-the-rise-and-fall-of-passenger-pigeon-genomic-diversity
#18
Gemma G R Murray, André E R Soares, Ben J Novak, Nathan K Schaefer, James A Cahill, Allan J Baker, John R Demboski, Andrew Doll, Rute R Da Fonseca, Tara L Fulton, M Thomas P Gilbert, Peter D Heintzman, Brandon Letts, George McIntosh, Brendan L O'Connell, Mark Peck, Marie-Lorraine Pipes, Edward S Rice, Kathryn M Santos, A Gregory Sohrweide, Samuel H Vohr, Russell B Corbett-Detig, Richard E Green, Beth Shapiro
The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. Although theory predicts that large populations will be more genetically diverse, passenger pigeon genetic diversity was surprisingly low. To investigate this disconnect, we analyzed 41 mitochondrial and 4 nuclear genomes from passenger pigeons and 2 genomes from band-tailed pigeons, which are passenger pigeons' closest living relatives. Passenger pigeons' large population size appears to have allowed for faster adaptive evolution and removal of harmful mutations, driving a huge loss in their neutral genetic diversity...
November 17, 2017: Science
https://www.readbyqxmd.com/read/29146770/environmental-population-and-life-stage-plasticity-in-the-visual-system-of-atlantic-cod
#19
Ragnhild Valen, Rita Karlsen, Jon Vidar Helvik
The visual system is for many fishes essential in guiding behaviors such as foraging, predator avoidance and mate choice. The marine environment is characterized by large spatiotemporal fluctuations in light intensity and spectral composition. However, visual capabilities are restricted by both space limitations set by eye size, and by the genomic content of light absorbing opsin genes. The rich array of visual opsins in teleosts may be used differentially to tune vision towards specific needs during ontogeny, and to changing light...
November 16, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29145855/generation-of-a-platform-strain-for-ionic-liquid-tolerance-using-adaptive-laboratory-evolution
#20
Elsayed T Mohamed, Shizeng Wang, Rebecca M Lennen, Markus J Herrgård, Blake A Simmons, Steven W Singer, Adam M Feist
BACKGROUND: There is a need to replace petroleum-derived with sustainable feedstocks for chemical production. Certain biomass feedstocks can meet this need as abundant, diverse, and renewable resources. Specific ionic liquids (ILs) can play a role in this process as promising candidates for chemical pretreatment and deconstruction of plant-based biomass feedstocks as they efficiently release carbohydrates which can be fermented. However, the most efficient pretreatment ILs are highly toxic to biological systems, such as microbial fermentations, and hinder subsequent bioprocessing of fermentative sugars obtained from IL-treated biomass...
November 16, 2017: Microbial Cell Factories
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