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https://www.readbyqxmd.com/read/28732180/the-role-of-noncoding-genetic-variation-in-isolated-orofacial-clefts
#1
F Thieme, K U Ludwig
In the past decade, medical genetic research has generated multiple discoveries, many of which were obtained via genome-wide association studies (GWASs). A major GWAS finding is that the majority of risk variants for complex traits map to noncoding regions. This has resulted in a paradigm shift in terms of the interpretation of human genomic sequence variation, with more attention now being paid to what was previously termed "junk DNA." Translation of genetic findings into biologically meaningful results requires 1) large-scale and cell-specific efforts to annotate non-protein-coding regions and 2) the integration of comprehensive genomic data sets...
July 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28732084/increased-parb-level-affects-expression-of-stress-response-adaptation-and-virulence-operons-and-potentiates-repression-of-promoters-adjacent-to-the-high-affinity-binding-sites-pars3-and-pars4-in-pseudomonas-aeruginosa
#2
Adam Kawalek, Krzysztof Glabski, Aneta Agnieszka Bartosik, Anna Fogtman, Grazyna Jagura-Burdzy
Similarly to its homologs in other bacteria, Pseudomonas aeruginosa partitioning protein ParB facilitates segregation of newly replicated chromosomes. Lack of ParB is not lethal but results in increased frequency of anucleate cells production, longer division time, cell elongation, altered colony morphology and defective swarming and swimming motility. Unlike in other bacteria, inactivation of parB leads to major changes of the transcriptome, suggesting that, directly or indirectly, ParB plays a role in regulation of gene expression in this organism...
2017: PloS One
https://www.readbyqxmd.com/read/28731861/genetic-control-of-apoprotein-a-i-and-atheroprotection-some-insights-from-inbred-strains-of-mice
#3
Godfrey S Getz, Catherine A Reardon
PURPOSE OF REVIEW: Previous epidemiological studies and studies in experimental animals have provided strong evidence for the atheroprotective effect of HDL and its major apoprotein, apolipoprotein A-I (apoA-I). Identification of genetic loci associating apoA-I/HDL with cardiovascular disease is needed to establish a causal relationship. RECENT FINDINGS: Pharmacological interventions to increase apoA-I or HDL cholesterol levels in humans are not associated with reduction in atherosclerosis...
July 20, 2017: Current Opinion in Lipidology
https://www.readbyqxmd.com/read/28731541/demography-and-genome-divergence-of-lake-and-stream-populations-of-an-east-african-cichlid-fish
#4
Bernd Egger, Marius Rösti, Astrid Böhne, Olivia Roth, Walter Salzburger
Disentangling the processes and mechanisms underlying divergent selection in diversification is facilitated by the comparative study of replicate population pairs that have diverged along a similar environmental gradient. Such a setting is realized in a cichlid fish from southern Lake Tanganyika, Astatotilapia burtoni, which occurs both within the lake proper as well as in various affluent rivers. Previous studies demonstrated that independent lake and stream populations show respectively similar adaptations to the two habitat regimes...
July 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28731473/ninety-nine-de-novo-assembled-genomes-from-the-moose-alces-alces-rumen-microbiome-provide-new-insights-into-microbial-plant-biomass-degradation
#5
Olov Svartström, Johannes Alneberg, Nicolas Terrapon, Vincent Lombard, Ino de Bruijn, Jonas Malmsten, Ann-Marie Dalin, Emilie El Muller, Pranjul Shah, Paul Wilmes, Bernard Henrissat, Henrik Aspeborg, Anders F Andersson
The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28730642/myc-expression-and-translocation-analyses-in-low-grade-and-transformed-follicular-lymphoma
#6
S M Aukema, R van Pel, I Nagel, S Bens, R Siebert, S Rosati, E van den Berg, A G Bosga-Bouwer, R E Kibbelaar, M Hoogendoorn, G W van Imhoff, J C Kluin-Nelemans, P M Kluin, M Nijland
Low grade follicular lymphoma (FL1/2) has an annual risk of transformation of approximately 3% which is associated with aberrations in CDKN2A/B, TP53 and MYC. Like in DLBCL high MYC expression in transformed FL (tFL) might predict a MYC breakpoint. We quantified MYC expression by immunohistochemistry and digital analysis in 41 paired biopsies from 20 patients with FL1/2 with subsequent transformation and in 4 isolated biopsies of tFL. As controls 28 biopsies of FL1/2 without transformation (median follow up 105 months) and 9 FL3A/B were analyzed...
July 21, 2017: Histopathology
https://www.readbyqxmd.com/read/28730502/establishment-of-11-linked-x-str-loci-within-1-1-mb-to-assist-with-kinship-testing
#7
James Chun-I Lee, Chun-Yen Lin, Li-Chin Tsai, Yu-Jen Yu, Keng-Hsien Liao, Adrian Linacre, Hsing-Mei Hsieh
This report identifies and characterizes 10 novel short tandem repeat (STR) loci on the human X chromosome, all of which are within a range of 1.1 Mb. These newly characterized loci were developed to aid in kinship assignment when the X chromosome is specifically required. The repeat DNA sequences were identified initially using data in GenBank and are located immediately upstream and downstream from the previously described locus DXS6807. Only those loci with seven or more observed alleles were used for further study resulting in the identification of 10 new loci...
July 20, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28730464/genome-wide-association-mapping-of-canopy-wilting-in-diverse-soybean-genotypes
#8
Avjinder S Kaler, Jeffery D Ray, William T Schapaugh, C Andy King, Larry C Purcell
Genome-wide association analysis identified 61 SNP markers for canopy wilting, which likely tagged 51 different loci. Based on the allelic effects of the significant SNPs, the slowest and fastest wilting genotypes were identified. Drought stress is a major global constraint for crop production, and slow canopy wilting is a promising trait for improving drought tolerance. The objective of this study was to identify genetic loci associated with canopy wilting and to confirm those loci with previously reported canopy wilting QTLs...
July 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28730463/exploring-new-alleles-for-frost-tolerance-in-winter-rye
#9
Wiltrud Erath, Eva Bauer, D Brian Fowler, Andres Gordillo, Viktor Korzun, Mira Ponomareva, Malthe Schmidt, Brigitta Schmiedchen, Peer Wilde, Chris-Carolin Schön
Rye genetic resources provide a valuable source of new alleles for the improvement of frost tolerance in rye breeding programs. Frost tolerance is a must-have trait for winter cereal production in northern and continental cropping areas. Genetic resources should harbor promising alleles for the improvement of frost tolerance of winter rye elite lines. For frost tolerance breeding, the identification of quantitative trait loci (QTL) and the choice of optimum genome-based selection methods are essential. We identified genomic regions involved in frost tolerance of winter rye by QTL mapping in a biparental population derived from a highly frost tolerant selection from the Canadian cultivar Puma and the European elite line Lo157...
July 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28729957/decline-of-heterozygosity-in-a-large-but-isolated-population-a-45-year-examination-of-moose-genetic-diversity-on-isle-royale
#10
Renae L Sattler, Janna R Willoughby, Bradley J Swanson
Wildlife conservation and management approaches typically focus on demographic measurements to assess population viability over both short and long periods. However, genetic diversity is an important predictor of long term population vitality. We investigated the pattern of change in genetic diversity in a large and likely isolated moose (Alces alces) population on Isle Royale (Lake Superior) from 1960-2005. We characterized samples, partitioned into five different 5-year periods, using nine microsatellite loci and a portion of the mtDNA control region...
2017: PeerJ
https://www.readbyqxmd.com/read/28729954/clinical-streptococcal-isolates-distinct-from-streptococcus-pneumoniae-but-containing-the-%C3%AE-glucosyltransferase-tts-gene-and-expressing-serotype-37-capsular-polysaccharide
#11
Carmen L Sheppard, Georgia Kapatai, Karen Broughton, Ulf Schaefer, Matthew Hannah, David J Litt, Norman K Fry
The major virulence factor of the pneumococcus, and target for conjugate vaccines, is the polysaccharide capsule, which is usually encoded by the highly variable cps locus. Serotype 37 is an unusual pneumococcal type in which the single β-glucosyltransferase gene responsible for serotype capsule production (tts) is located outside of the capsular operon region. Using a previously described automated whole genome sequence (WGS)-based serotyping bioinformatics tool, PneumoCaT, we identified and investigated seven clinical isolates (three from blood cultures) of non-pneumococcal streptococci containing a highly homologous tts and included them in a study panel of 20 isolates which included a 11 further clinical isolates of S...
2017: PeerJ
https://www.readbyqxmd.com/read/28729884/genome-wide-landscape-of-position-effects-on-heterogeneous-gene-expression-in-saccharomyces-cerevisiae
#12
Xiao-Le Wu, Bing-Zhi Li, Wen-Zheng Zhang, Kai Song, Hao Qi, Jun-Biao Dai, Ying-Jin Yuan
BACKGROUND: Integration of heterogeneous genes is widely applied in synthetic biology and metabolic engineering. However, knowledge about the effect of integrative position on gene expression remains limited. RESULTS: We established a genome-wide landscape of position effect on gene expression in Saccharomyces cerevisiae. The expression cassette of red fluorescence protein (RFP) gene was constructed and inserted at 1044 loci, which were scattered uniformly in the yeast genome...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28729876/genetic-architecture-of-flooding-tolerance-in-the-dry-bean-middle-american-diversity-panel
#13
Ali Soltani, Samira MafiMoghaddam, Katelynn Walter, Daniel Restrepo-Montoya, Sujan Mamidi, Stephan Schroder, Rian Lee, Phillip E McClean, Juan M Osorno
Flooding is a devastating abiotic stress that endangers crop production in the twenty-first century. Because of the severe susceptibility of common bean (Phaseolus vulgaris L.) to flooding, an understanding of the genetic architecture and physiological responses of this crop will set the stage for further improvement. However, challenging phenotyping methods hinder a large-scale genetic study of flooding tolerance in common bean and other economically important crops. A greenhouse phenotyping protocol was developed to evaluate the flooding conditions at early stages...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28729871/molecular-mapping-of-flowering-time-major-genes-and-qtls-in-chickpea-cicer-arietinum-l
#14
Bingi P Mallikarjuna, Srinivasan Samineni, Mahendar Thudi, Sobhan B Sajja, Aamir W Khan, Ayyanagowda Patil, Kannalli P Viswanatha, Rajeev K Varshney, Pooran M Gaur
Flowering time is an important trait for adaptation and productivity of chickpea in the arid and the semi-arid environments. This study was conducted for molecular mapping of genes/quantitative trait loci (QTLs) controlling flowering time in chickpea using F2 populations derived from four crosses (ICCV 96029 × CDC Frontier, ICC 5810 × CDC Frontier, BGD 132 × CDC Frontier and ICC 16641 × CDC Frontier). Genetic studies revealed monogenic control of flowering time in the crosses ICCV 96029 × CDC Frontier, BGD 132 × CDC Frontier and ICC 16641 × CDC Frontier, while digenic control with complementary gene action in ICC 5810 × CDC Frontier...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28729817/ssr-marker-variations-in-brassica-species-provide-insight-into-the-origin-and-evolution-of-brassica-amphidiploids
#15
Ajay Kumar Thakur, Kunwar Harendra Singh, Lal Singh, Joghee Nanjundan, Yasin Jeshima Khan, Dhiraj Singh
BACKGROUND: Oilseed Brassica represents an important group of oilseed crops with a long history of evolution and cultivation. To understand the origin and evolution of Brassica amphidiploids, simple sequence repeat (SSR) markers were used to unravel genetic variations in three diploids and three amphidiploid Brassica species of U's triangle along with Eruca sativa as an outlier. RESULTS: Of 124 Brassica-derived SSR loci assayed, 100% cross-transferability was obtained for B...
2018: Hereditas
https://www.readbyqxmd.com/read/28729732/evidence-of-selection-on-splicing-associated-loci-in-human-populations-and-relevance-to-disease-loci-mapping
#16
Eric R Gamazon, Anuar Konkashbaev, Eske M Derks, Nancy J Cox, Younghee Lee
We performed a whole-genome scan of genetic variants in splicing regulatory elements (SREs) and evaluated the extent to which natural selection has shaped extant patterns of variation in SREs. We investigated the degree of differentiation of single nucleotide polymorphisms (SNPs) in SREs among human populations and applied long-range haplotype- and multilocus allelic differentiation-based methods to detect selection signatures. We describe an approach, sampling a large number of loci across the genome from functional classes and using the consensus from multiple tests, for identifying candidates for selection signals...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729714/maize-zea-mays-l-genome-size-indicated-by-180-bp-knob-abundance-is-associated-with-flowering-time
#17
Yinqiao Jian, Cheng Xu, Zifeng Guo, Shanhong Wang, Yunbi Xu, Cheng Zou
Flowering time is considered one of the most important agronomic traits in maize (Zea mays L.), and previous studies have indicated that this trait is correlated with genome size. We observed a significant difference in genome size between tropical and temperate inbred lines and a moderate positive correlation between genome size and 180-bp knob abundance determined by high-throughput sequencing in maize inbred lines in this study. We assembled the reads that were mapped to 180-bp knob sequences and found that the top ten abundant 180-bp knob sequences are highly variable...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729708/new-mycobacterium-tuberculosis-beijing-clonal-complexes-in-china-revealed-by-phylogenetic-and-bayesian-population-structure-analyses-of-24-loci-miru-vntrs
#18
Chao Zheng, Yann Reynaud, Changsong Zhao, Thierry Zozio, Song Li, Dongxia Luo, Qun Sun, Nalin Rastogi
Beijing lineage of Mycobacterium tuberculosis constitutes the most predominant lineage in East Asia. Beijing epidemiology, evolutionary history, genetics are studied in details for years revealing probable origin from China followed by worldwide expansion, partially linked to higher mutation rate, hypervirulence, drug-resistance, and association with cases of mixed infections. Considering huge amount of data available for 24-loci Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats, we performed detailed phylogenetic and Bayesian population structure analyses of Beijing lineage strains in mainland China and Taiwan using available 24-loci MIRU-VNTR data extracted from publications or the SITVIT2 database (n = 1490)...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729637/genetic-variants-including-markers-from-the-exome-chip-and-metabolite-traits-of-type-2-diabetes
#19
Susanne Jäger, Simone Wahl, Janine Kröger, Sapna Sharma, Per Hoffmann, Anna Floegel, Tobias Pischon, Cornelia Prehn, Jerzy Adamski, Martina Müller-Nurasyid, Melanie Waldenberger, Konstantin Strauch, Annette Peters, Christian Gieger, Karsten Suhre, Harald Grallert, Heiner Boeing, Matthias B Schulze, Karina Meidtner
Diabetes-associated metabolites may aid the identification of new risk variants for type 2 diabetes. Using targeted metabolomics within a subsample of the German EPIC-Potsdam study (n = 2500), we tested previously published SNPs for their association with diabetes-associated metabolites and conducted an additional exploratory analysis using data from the exome chip including replication within 2,692 individuals from the German KORA F4 study. We identified a total of 16 loci associated with diabetes-related metabolite traits, including one novel association between rs499974 (MOGAT2) and a diacyl-phosphatidylcholine ratio (PC aa C40:5/PC aa C38:5)...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729434/cohesins-and-condensins-orchestrate-the-4d-dynamics-of-yeast-chromosomes-during-the-cell%C3%A2-cycle
#20
Luciana Lazar-Stefanita, Vittore F Scolari, Guillaume Mercy, Héloise Muller, Thomas M Guérin, Agnès Thierry, Julien Mozziconacci, Romain Koszul
Duplication and segregation of chromosomes involves dynamic reorganization of their internal structure by conserved architectural proteins, including the structural maintenance of chromosomes (SMC) complexes cohesin and condensin. Despite active investigation of the roles of these factors, a genome-wide view of dynamic chromosome architecture at both small and large scale during cell division is still missing. Here, we report the first comprehensive 4D analysis of the higher-order organization of the Saccharomyces cerevisiae genome throughout the cell cycle and investigate the roles of SMC complexes in controlling structural transitions...
July 20, 2017: EMBO Journal
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