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https://www.readbyqxmd.com/read/28535294/hgva-the-human-genome-variation-archive
#1
Javier Lopez, Jacobo Coll, Matthias Haimel, Swaathi Kandasamy, Joaquin Tarraga, Pedro Furio-Tari, Wasim Bari, Marta Bleda, Antonio Rueda, Stefan Gräf, Augusto Rendon, Joaquin Dopazo, Ignacio Medina
High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion...
May 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28535292/adaptive-radiation-of-p-fluorescens-sbw25-in-experimental-microcosms-provides-an-understanding-of-the-evolutionary-ecology-and-molecular-biology-of-a-l-interface-biofilm-formation
#2
Anna Koza, Anna Kusmierska, Kimberley McLaughlin, Olena Moshynets, Andrew J Spiers
Combined experimental evolutionary and molecular biology approaches have been used to investigate the adaptive radiation of Pseudomonas fluorescens SBW25 in static microcosms leading to the colonisation of the air-liquid interface by biofilm-forming mutants such as the Wrinkly Spreader. In these microcosms, the ecosystem engineering of the early wild-type colonists establish the niche space for subsequent WS evolution and colonisation. Random WS mutations occurring in the developing population that de-regulate diguanylate cyclases and c-di-GMP homeostasis result in cellulose-based biofilms at the air-liquid interface...
May 23, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28535256/epigenetic-and-genetic-contributions-to-adaptation-in-chlamydomonas
#3
Ilkka Kronholm, Andrew Bassett, David Baulcombe, Sinéad Collins
Epigenetic modifications, such as DNA methylation or histone modifications, can be transmitted between cellular or organismal generations. However, there are no experiments measuring their role in adaptation, so here we use experimental evolution to investigate how epigenetic variation can contribute to adaptation. We manipulated DNA methylation and histone acetylation in the unicellular green alga Chlamydomonas reinhardtii both genetically and chemically to change the amount of epigenetic variation generated or transmitted in adapting populations in three different environments (salt stress, phosphate starvation, and high CO2) for two hundred asexual generations...
May 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28535079/the-tomato-kinase-pti1-contributes-to-production-of-reactive-oxygen-species-in-response-to-two-flagellin-derived-peptides-and-promotes-resistance-to-pseudomonas-syringae-infection
#4
Simon Schwizer, Christine M Kraus, Diane M Dunham, Yi Zheng, Noe Fernandez-Pozo, Marina A Pombo, Zhangjun Fei, Suma Chakravarthy, Gregory Martin
The Pti1 kinase was identified from a reverse genetic screen as contributing to pattern-triggered immunity (PTI) against Pseudomonas syringae pv. tomato (Pst). This was unexpected because Pti1 was originally identified as an interactor of the Pto kinase and was implicated in effector-triggered immunity. The tomato genome has two Pti1 genes, referred to as Pti1a and Pti1b. A hairpin-Pti1 (hpPti1) construct was developed and used to generate two independent stable transgenic tomato lines, which had reduced transcript abundance of both genes...
May 23, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28534836/differentiation-and-structure-in-sulfolobus-islandicus-rod-shaped-virus-populations
#5
Maria A Bautista, Jesse A Black, Nicholas D Youngblut, Rachel J Whitaker
In the past decade, molecular surveys of viral diversity have revealed that viruses are the most diverse and abundant biological entities on Earth. In culture, however, most viral isolates that infect microbes are represented by a few variants isolated on type strains, limiting our ability to study how natural variation affects virus-host interactions in the laboratory. We screened a set of 137 hot spring samples for viruses that infect a geographically diverse panel of the hyperthemophilic crenarchaeon Sulfolobus islandicus...
May 19, 2017: Viruses
https://www.readbyqxmd.com/read/28534241/a-genetic-variant-in-fign-gene-reduces-the-risk-of-congenital-heart-disease-in-han-chinese-populations
#6
Dan Wang, Maoping Chu, Feng Wang, Aihua Zhou, Miaohua Ruan, Yiming Chen
Congenital heart disease (CHD) is one of the most common birth anomalies worldwide. Folate deficiency is an independent risk factor for CHD. Genome-wide association studies (GWAS) revealed that human folate level could be significantly influenced by fidgetin (FIGN), methylenetetrahydrofolate reductase (MTHFR), prickle homolog 2 (PRICKLE2), synaptotagmin 9 (SYT9), gamma-aminobutyric acid B receptor 2 (GABBR2), and alkaline phosphatase (ALPL) genes. The association between the above-mentioned six variants and CHD was examined in the two independent case-control studies in a total of 868 CHD patients and 931 healthy controls...
May 22, 2017: Pediatric Cardiology
https://www.readbyqxmd.com/read/28534127/genetics-of-triglycerides-and-the-risk-of-atherosclerosis
#7
REVIEW
Jacqueline S Dron, Robert A Hegele
PURPOSE OF REVIEW: Plasma triglycerides are routinely measured with a lipid profile, and elevated plasma triglycerides are commonly encountered in the clinic. The confounded nature of this trait, which is correlated with numerous other metabolic perturbations, including depressed high-density lipoprotein cholesterol (HDL-C), has thwarted efforts to directly implicate triglycerides as causal in atherogenesis. Human genetic approaches involving large-scale populations and high-throughput genomic assessment under a Mendelian randomization framework have undertaken to sort out questions of causality...
July 2017: Current Atherosclerosis Reports
https://www.readbyqxmd.com/read/28534096/genomic-prediction-ability-for-yield-related-traits-in-german-winter-barley-elite-material
#8
Patrick Thorwarth, Jutta Ahlemeyer, Anne-Marie Bochard, Kerstin Krumnacker, Hubert Blümel, Eberhard Laubach, Nadine Knöchel, László Cselényi, Frank Ordon, Karl J Schmid
Genomic prediction was evaluated in German winter barley breeding lines. In this material, prediction ability is strongly influenced by population structure and main determinant of prediction ability is the close genetic relatedness of the breeding material. To ensure breeding progress under changing environmental conditions the implementation and evaluation of new breeding methods is of crucial importance. Modern breeding approaches like genomic selection may significantly accelerate breeding progress. We assessed the potential of genomic prediction in a training population of 750 genotypes, consisting of multiple six-rowed winter barley (Hordeum vulgare L...
May 22, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28534009/genomic-insight-into-mechanisms-of-reversion-of-antibiotic-resistance-in-multidrug-resistant-mycobacterium-tuberculosis-induced-by-a-nanomolecular-iodine-containing-complex-fs-1
#9
Aleksandr I Ilin, Murat E Kulmanov, Ilya S Korotetskiy, Rinat A Islamov, Gulshara K Akhmetova, Marina V Lankina, Oleg N Reva
Drug induced reversion of antibiotic resistance is a promising way to combat multidrug resistant infections. However, lacking knowledge of mechanisms of drug resistance reversion impedes employing this approach in medicinal therapies. Induction of antibiotic resistance reversion by a new anti-tuberculosis drug FS-1 has been reported. FS-1 was used in this work in combination with standard anti-tuberculosis antibiotics in an experiment on laboratory guinea pigs infected with an extensively drug resistant (XDR) strain Mycobacterium tuberculosis SCAID 187...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28533967/divergent-evolutionary-histories-of-dna-markers-in-a-hawaiian-population-of-the-coral-montipora-capitata
#10
Hollie M Putnam, Diane K Adams, Ehud Zelzion, Nicole E Wagner, Huan Qiu, Tali Mass, Paul G Falkowski, Ruth D Gates, Debashish Bhattacharya
We investigated intra- and inter-colony sequence variation in a population of the dominant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major (M. capitata) and a minor (M. flabellata) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2-3 different mtDNA haplotypes. In contrast, Pax-C and newly identified single-copy nuclear genes showed either no sequence differences or minor variations in SNP frequencies segregating among the colonies...
2017: PeerJ
https://www.readbyqxmd.com/read/28533817/mosaicism-for-structural-non-centromeric-autosomal-rearrangements-in-disease-defined-carriers-sex-differences-in-the-rearrangements-profile-and-maternal-age-distributions
#11
REVIEW
Natalia V Kovaleva, Philip D Cotter
BACKGROUND: Mosaicism for an autosomal structural rearrangement (Rea) associated with clinical manifestation of chromosomal imbalance is rare. Consequently, there is a lack of basic epidemiological characterization of this kind of mosaicism, such as population rate, cytogenetic profile of Reas involved, maternal age distribution, and sex (male to female) ratio among Rea carriers. The objectives of the present study were: (i) determination of the Rea profile in clinically affected individuals, (ii) comparative analysis of the cytogenetic profile and involvement of single chromosomes to rearrangements in affected and previously reported asymptomatic carriers, (iii) analysis of the male/female ratio in carriers of various types of Rea, and, (iv) examination of parental ages distributions according to carriers' sex...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28533786/high-density-linkage-map-construction-and-mapping-of-yield-trait-qtls-in-maize-zea-mays-using-the-genotyping-by-sequencing-gbs-technology
#12
Chengfu Su, Wei Wang, Shunliang Gong, Jinghui Zuo, Shujiang Li, Shizhong Xu
Increasing grain yield is the ultimate goal for maize breeding. High resolution quantitative trait loci (QTL) mapping can help us understand the molecular basis of phenotypic variation of yield and thus facilitate marker assisted breeding. The aim of this study is to use genotyping-by-sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of all F2 individuals from a cross between two varieties of maize that are in clear contrast in yield and related traits. A set of 199 F2 progeny derived from the cross of varieties SG-5 and SG-7 were generated and genotyped by GBS...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28533768/novel-large-sulfur-bacteria-in-the-metagenomes-of-groundwater-fed-chemosynthetic-microbial-mats-in-the-lake-huron-basin
#13
Allison M Sharrar, Beverly E Flood, Jake V Bailey, Daniel S Jones, Bopaiah A Biddanda, Steven A Ruberg, Daniel N Marcus, Gregory J Dick
Little is known about large sulfur bacteria (LSB) that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28533738/genetics-of-tinnitus-still-in-its-infancy
#14
REVIEW
Barbara Vona, Indrajit Nanda, Wafaa Shehata-Dieler, Thomas Haaf
Tinnitus is the perception of a phantom sound that affects between 10 and 15% of the general population. Despite this considerable prevalence, treatments for tinnitus are presently lacking. Tinnitus exhibits a diverse array of recognized risk factors and extreme clinical heterogeneity. Furthermore, it can involve an unknown number of auditory and non-auditory networks and molecular pathways. This complex combination has hampered advancements in the field. The identification of specific genetic factors has been at the forefront of several research investigations in the past decade...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28533454/genomics-of-coloration-in-natural-animal-populations
#15
REVIEW
Luis M San-Jose, Alexandre Roulin
Animal coloration has traditionally been the target of genetic and evolutionary studies. However, until very recently, the study of the genetic basis of animal coloration has been mainly restricted to model species, whereas research on non-model species has been either neglected or mainly based on candidate approaches, and thereby limited by the knowledge obtained in model species. Recent high-throughput sequencing technologies allow us to overcome previous limitations, and open new avenues to study the genetic basis of animal coloration in a broader number of species and colour traits, and to address the general relevance of different genetic structures and their implications for the evolution of colour...
July 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28533441/trends-in-dna-methylation-with-age-replicate-across-diverse-human-populations
#16
Shyamalika Gopalan, Oana Carja, Maud Fagny, Etienne Patin, Justin W Myrick, Lisa M McEwen, Sarah M Mah, Michael S Kobor, Alain Froment, Marcus W Feldman, Lluis Quintana-Murci, Brenna M Henn
Aging is associated with widespread changes in genome-wide patterns of DNA methylation. Thousands of CpG sites whose tissue-specific methylation levels are strongly correlated with chronological age have been previously identified. However, the majority of these studies have focused primarily on cosmopolitan populations living in the developed world; it is not known if age-related patterns of DNA methylation at these loci are similar across a broad range of human genetic and ecological diversity. We investigated genome-wide methylation patterns using saliva- and whole blood-derived DNA from two traditionally hunting and gathering African populations: the Baka of the western Central African rainforest and the ≠Khomani San of the South African Kalahari Desert...
May 22, 2017: Genetics
https://www.readbyqxmd.com/read/28533439/gene-introgression-in-weeds-depends-on-initial-gene-location-in-the-crop-brassica-napus-raphanus-raphanistrum-model
#17
Katarzyna Adamczyk-Chauvat, Sabrina Delaunay, Anne Vannier, Caroline François, Gwenaëlle Thomas, Frédérique Eber, Maryse Lodé, Marie Gilet, Virginie Huteau, Jérôme Morice, Sylvie Nègre, Cyril Falentin, Olivier Coriton, Henri Darmency, Bachar Alrustom, Eric Jenczewski, Mathieu Rousseau-Gueutin, Anne-Marie Chèvre
The effect of gene location within a crop genome on its transfer to a weed genome remains an open question for gene flow assessment. To elucidate this question, we analyzed advanced generations of intergeneric hybrids, derived from an initial pollination of known oilseed rape varieties (Brassica napus, AACC, 2n=38) by a local population of wild radish (Raphanus raphanistrum, RrRr, 2n=18). After five generations of recurrent pollination, 307 G5 plants with a chromosome number similar to wild radish were genotyped using 105 B...
May 22, 2017: Genetics
https://www.readbyqxmd.com/read/28533438/high-resolution-mapping-of-crossover-events-in-the-hexaploid-wheat-genome-suggests-a-universal-recombination-mechanism
#18
Benoit Darrier, Hélène Rimbert, François Balfourier, Lise Pingault, Ambre-Aurore Josselin, Bertrand Servin, Julien Navarro, Frédéric Choulet, Etienne Paux, Pierre Sourdille
During meiosis, crossovers (COs) create new allele associations by reciprocal exchange of DNA. In bread wheat (Triticum aestivum L.), COs are almost limited to subtelomeric regions of chromosomes resulting in a substantial loss of breeding efficiency in the proximal regions though these latter carry ~60-70% of the genes. Identifying sequence and/or chromosome features impacting recombination occurrence is thus relevant to improve and drive recombination. Using the recent release of a reference sequence of chromosome 3B and of the draft assemblies of the 20 other wheat chromosomes, we performed a fine-scale mapping of COs and we revealed that 82% of COs located in the distal ends of chromosome 3B representing 19% of the chromosome length...
May 22, 2017: Genetics
https://www.readbyqxmd.com/read/28533337/development-of-a-medium-density-combined-species-snp-array-for-pacific-and-european-oysters-crassostrea-gigas-and-ostrea-edulis
#19
Alejandro P Gutierrez, Frances Turner, Karim Gharbi, Richard Talbot, Natalie R Lowe, Carolina Peñaloza, Mark McCullough, Paulo A Prodöhl, Tim P Bean, Ross D Houston
SNP arrays are enabling tools for high-resolution studies of the genetic basis of complex traits in farmed and wild animals. Oysters are of critical importance in many regions from both an ecological and economic perspective, and oyster aquaculture forms a key component of global food security. The aim of our study was to design a combined-species medium density SNP array for Pacific oyster (C. gigas) and European flat oyster (O. edulis), and to test the performance of this array on farmed and wild populations from multiple locations, with a focus on European populations...
May 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28533335/rapid-cycling-genomic-selection-in-a-multi-parental-tropical-maize-population
#20
Xuecai Zhang, Paulino Pérez-Rodríguez, Juan Burgueño, Michael Olsen, Edward Buckler, Gary Atlin, Boddupalli M Prasanna, Mateo Vargas, Félix San Vicente, José Crossa
Genomic selection (GS) increases genetic gain by reducing the length of the selection cycle, as has been exemplified in maize using rapid cycling recombination of bi-parental populations. However, no results of GS applied to maize multi-parental populations have been reported so far. This study is the first to show realized genetic gains of rapid cycling genomic selection (RCGS) for four recombination cycles in a multi-parental tropical maize population. Eighteen elite tropical maize lines were intercrossed twice and self-pollinated once to form the cycle 0 (C0) training population...
May 22, 2017: G3: Genes—Genomes—Genetics
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