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https://www.readbyqxmd.com/read/29145629/the-reactome-pathway-knowledgebase
#1
Antonio Fabregat, Steven Jupe, Lisa Matthews, Konstantinos Sidiropoulos, Marc Gillespie, Phani Garapati, Robin Haw, Bijay Jassal, Florian Korninger, Bruce May, Marija Milacic, Corina Duenas Roca, Karen Rothfels, Cristoffer Sevilla, Veronica Shamovsky, Solomon Shorser, Thawfeek Varusai, Guilherme Viteri, Joel Weiser, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio
The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism, and other cellular processes as an ordered network of molecular transformations-an extended version of a classic metabolic map, in a single consistent data model. Reactome functions both as an archive of biological processes and as a tool for discovering unexpected functional relationships in data such as gene expression profiles or somatic mutation catalogues from tumor cells...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29145497/rare-genetic-variants-in-the-endocannabinoid-system-genes-cnr1-and-dagla-are-associated-with-neurological-phenotypes-in-humans
#2
Douglas R Smith, Christine M Stanley, Theodore Foss, Richard G Boles, Kevin McKernan
Rare genetic variants in the core endocannabinoid system genes CNR1, CNR2, DAGLA, MGLL and FAAH were identified in molecular testing data from 6,032 patients with a broad spectrum of neurological disorders. The variants were evaluated for association with phenotypes similar to those observed in the orthologous gene knockouts in mice. Heterozygous rare coding variants in CNR1, which encodes the type 1 cannabinoid receptor (CB1), were found to be significantly associated with pain sensitivity (especially migraine), sleep and memory disorders-alone or in combination with anxiety-compared to a set of controls without such CNR1 variants...
2017: PloS One
https://www.readbyqxmd.com/read/29145476/an-immunohistochemical-identification-key-for-cell-types-in-adult-mouse-prostatic-and-urethral-tissue-sections
#3
Kyle A Wegner, Mark T Cadena, Ryan Trevena, Anne E Turco, Adam Gottschalk, Richard B Halberg, Jinjin Guo, Jill A McMahon, Andrew P McMahon, Chad M Vezina
Though many methods can be used to identify cell types contained in complex tissues, most require cell disaggregation and destroy information about where cells reside in relation to their microenvironment. Here, we describe a polytomous key for cell type identification in intact sections of adult mouse prostate and prostatic urethra. The key is organized as a decision tree and initiates with one round of immunostaining for nerve, epithelial, fibromuscular/hematolymphoid, or vascular associated cells. Cell identities are recursively eliminated by subsequent staining events until the remaining pool of potential cell types can be distinguished by direct comparison to other cells...
2017: PloS One
https://www.readbyqxmd.com/read/29145401/anatomically-specific-intratubular-and-interstitial-biominerals-in-the-human-renal-medullo-papillary-complex
#4
Ling Chen, Ryan S Hsi, Feifei Yang, Benjamin A Sherer, Marshall L Stoller, Sunita P Ho
Limited information exists on the anatomically-specific early stage events leading to clinically detectable mineral aggregates in the renal papilla. In this study, quantitative multiscale correlative maps of structural, elemental and biochemical properties of whole medullo-papillary complexes from human kidneys were developed. Correlative maps of properties specific to the uriniferous and vascular tubules using high-resolution X-ray computed tomography, scanning and transmission electron microscopy, energy dispersive X-ray spectroscopy, and immunolocalization of noncollagenous proteins (NCPs) along with their association with anatomy specific biominerals were obtained...
2017: PloS One
https://www.readbyqxmd.com/read/29144012/uterine-cervical-adenocarcinoma-associated-with-lobular-endocervical-glandular-hyperplasia-radiologic-pathologic-correlation
#5
Ayumi Ohya, Shiho Asaka, Yasunari Fujinaga, Masumi Kadoya
AIM: We aimed to identify the radiologic features of uterine cervical adenocarcinoma associated with lobular endocervical glandular hyperplasia (LEGH). METHODS: We retrospectively analyzed magnetic resonance (MR) images and pathologic findings of eight patients who underwent preoperative MR imaging followed by surgical resection and who were pathologically diagnosed with adenocarcinoma (except for adenocarcinoma in situ) associated with LEGH. We assessed the following MR findings: multicystic component (MC), solid component (SC), signal intensity of SC on diffusion-weighted imaging (DWI) and the apparent diffusion coefficient (ADC) map, and radiological stage (r-stage) based on the FIGO classification...
November 16, 2017: Journal of Obstetrics and Gynaecology Research
https://www.readbyqxmd.com/read/29143610/development-of-f1-hybrid-population-and-the-high-density-linkage-map-for-european-aspen-populus-tremula-l-using-radseq-technology
#6
Anatoly V Zhigunov, Pavel S Ulianich, Marina V Lebedeva, Peter L Chang, Sergey V Nuzhdin, Elena K Potokina
BACKGROUND: Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe. RESULTS: We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143603/evolution-of-vrn-1-homoeologous-loci-in-allopolyploids-of-triticum-and-their-diploid-precursors
#7
REVIEW
Andrey B Shcherban, Elena A Salina
BACKGROUND: The key gene in genetic system controlling the duration of the vegetative period in cereals is the VRN1 gene, whose product under the influence of low temperature (vernalization) promotes the transition of the apical meristem cells into a competent state for the development of generative tissues of spike. As early genetic studies shown, the dominant alleles of this gene underlie the spring forms of plants that do not require vernalization for this transition. In wheat allopolyploids various combinations of alleles of the VRN1 homoeologous loci (VRN1 homoeoalleles) provide diversity in such important traits as the time to heading, height of plants and yield...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143298/a-single-nucleotide-mutation-of-ispf-gene-involved-in-the-mep-pathway-for-isoprenoid-biosynthesis-causes-yellow-green-leaf-phenotype-in-rice
#8
Rui Huang, Yang Wang, Pingrong Wang, Chunmei Li, Fuliang Xiao, Nenggang Chen, Na Li, Caixia Li, Changhui Sun, Lihua Li, Rongjun Chen, Zhengjun Xu, Jianqing Zhu, Xiaojian Deng
We identified IspF gene through yellow-green leaf mutant 505ys in rice. OsIspF was expressed in all tissues detected, and its encoded protein was targeted to the chloroplast. On expression levels of genes in this mutant, OsIspF itself and the genes encoding other enzymes of the MEP pathway and chlorophyll synthase were all up-regulated, however, among eight genes associated with photosynthesis, only psaA, psaN and psbA genes for three reaction center subunits of photosystem obviously changed. Isoprenoids are the most abundant natural compounds in all organisms, which originate from the basic five-carbon units isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP)...
November 15, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29143067/characterization-and-fine-mapping-of-qkc7-03-a-major-locus-for-kernel-cracking-in-maize
#9
Mingtao Yang, Lin Chen, Xun Wu, Xing Gao, Chunhui Li, Yanchun Song, Dengfeng Zhang, Yunsu Shi, Yu Li, Yong-Xiang Li, Tianyu Wang
A major locus conferring kernel cracking in maize was characterized and fine mapped to an interval of 416.27 kb. Meanwhile, combining the results of transcriptomic analysis, the candidate gene was inferred. Seed development requires a proper structural and physiological balance between the maternal tissues and the internal structures of the seeds. In maize, kernel cracking is a disorder in this balance that seriously limits quality and yield and is characterized by a cracked pericarp at the kernel top and endosperm everting...
November 15, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29142306/an-exome-sequencing-based-approach-for-genome-wide-association-studies-in-the-dog
#10
Bart J G Broeckx, Thomas Derrien, Stéphanie Mottier, Valentin Wucher, Edouard Cadieu, Benoît Hédan, Céline Le Béguec, Nadine Botherel, Kerstin Lindblad-Toh, Jimmy H Saunders, Dieter Deforce, Catherine André, Luc Peelman, Christophe Hitte
Genome-wide association studies (GWAS) are widely used to identify loci associated with phenotypic traits in the domestic dog that has emerged as a model for Mendelian and complex traits. However, a disadvantage of GWAS is that it always requires subsequent fine-mapping or sequencing to pinpoint causal mutations. Here, we performed whole exome sequencing (WES) and canine high-density (cHD) SNP genotyping of 28 dogs from 3 breeds to compare the SNP and linkage disequilibrium characteristics together with the power and mapping precision of exome-guided GWAS (EG-GWAS) versus cHD-based GWAS...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142228/genome-wide-mapping-of-genetic-determinants-influencing-dna-methylation-and-gene-expression-in-human-hippocampus
#11
Herbert Schulz, Ann-Kathrin Ruppert, Stefan Herms, Christiane Wolf, Nazanin Mirza-Schreiber, Oliver Stegle, Darina Czamara, Andreas J Forstner, Sugirthan Sivalingam, Susanne Schoch, Susanne Moebus, Benno Pütz, Axel Hillmer, Nadine Fricker, Hartmut Vatter, Bertram Müller-Myhsok, Markus M Nöthen, Albert J Becker, Per Hoffmann, Thomas Sander, Sven Cichon
Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142224/health-and-disease-phenotyping-in-old-age-using-a-cluster-network-analysis
#12
Jesus Felix Valenzuela, Christopher Monterola, Victor Joo Chuan Tong, Tze Pin Ng, Anis Larbi
Human ageing is a complex trait that involves the synergistic action of numerous biological processes that interact to form a complex network. Here we performed a network analysis to examine the interrelationships between physiological and psychological functions, disease, disability, quality of life, lifestyle and behavioural risk factors for ageing in a cohort of 3,270 subjects aged ≥55 years. We considered associations between numerical and categorical descriptors using effect-size measures for each variable pair and identified clusters of variables from the resulting pairwise effect-size network and minimum spanning tree...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29141802/examining-the-contributions-of-environmental-quality-to-pediatric-multiple-sclerosis
#13
Amy M Lavery, Amy T Waldman, T Charles Casper, Shelly Roalstad, Meghan Candee, John Rose, Anita Belman, Bianca Weinstock-Guttman, Greg Aaen, Jan-Mendelt Tillema, Moses Rodriguez, Jayne Ness, Yolanda Harris, Jennifer Graves, Lauren Krupp, Leslie Benson, Mark Gorman, Manikum Moodley, Mary Rensel, Manu Goyal, Soe Mar, Tanuja Chitnis, Teri Schreiner, Tim Lotze, Benjamin Greenberg, Ilana Kahn, Jennifer Rubin, Emmanuelle Waubant
BACKGROUND: Multiple sclerosis (MS) is a presumed autoimmune disease caused by genetic and environmental factors. It is hypothesized that environmental exposures (such as air and water quality) trigger the innate immune response thereby activating a pro-inflammatory cascade. OBJECTIVE: To examine potential environmental factors in pediatric MS using geographic information systems (GIS). METHODS: Pediatric MS cases and healthy controls were identified as part of an ongoing multicenter case-control study...
November 2017: Multiple Sclerosis and related Disorders
https://www.readbyqxmd.com/read/29141579/a-missense-variant-in-the-coil1a-domain-of-the-keratin-25-gene-is-associated-with-the-dominant-curly-hair-coat-trait-crd-in-horse
#14
Caroline Morgenthaler, Mathieu Diribarne, Aurélien Capitan, Rachel Legendre, Romain Saintilan, Maïlys Gilles, Diane Esquerré, Rytis Juras, Anas Khanshour, Laurent Schibler, Gus Cothran
BACKGROUND: Curly horses present a variety of curl phenotypes that are associated with various degrees of curliness of coat, mane, tail and ear hairs. Their origin is still a matter of debate and several genetic hypotheses have been formulated to explain the diversity in phenotype, including the combination of autosomal dominant and recessive alleles. Our purpose was to map the autosomal dominant curly hair locus and identify the causal variant using genome-wide association study (GWAS) and whole-genome sequencing approaches...
November 15, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29141028/developing-methods-for-assessing-abundance-and-distribution-of-european-oysters-ostrea-edulis-using-towed-video
#15
Linnea Thorngren, Thomas Dunér Holthuis, Susanne Lindegarth, Mats Lindegarth
Due to large-scale habitat losses and increasing pressures, benthic habitats in general, and perhaps oyster beds in particular, are commonly in decline and severely threatened on regional and global scales. Appropriate and cost-efficient methods for mapping and monitoring of the distribution, abundance and quality of remaining oyster populations are fundamental for sustainable management and conservation of these habitats and their associated values. Towed video has emerged as a promising method for surveying benthic communities in a both non-destructive and cost-efficient way...
2017: PloS One
https://www.readbyqxmd.com/read/29141011/nucleotide-patterns-aiding-in-prediction-of-eukaryotic-promoters
#16
Martin Triska, Victor Solovyev, Ancha Baranova, Alexander Kel, Tatiana V Tatarinova
Computational analysis of promoters is hindered by the complexity of their architecture. In less studied genomes with complex organization, false positive promoter predictions are common. Accurate identification of transcription start sites and core promoter regions remains an unsolved problem. In this paper, we present a comprehensive analysis of genomic features associated with promoters and show that probabilistic integrative algorithms-driven models allow accurate classification of DNA sequence into "promoters" and "non-promoters" even in absence of the full-length cDNA sequences...
2017: PloS One
https://www.readbyqxmd.com/read/29140792/a-bayesian-hierarchical-model-for-identifying-significant-polygenic-effects-while-controlling-for-confounding-and-repeated-measures
#17
Christopher McMahan, James Baurley, William Bridges, Chase Joyner, Muhamad Fitra Kacamarga, Robert Lund, Carissa Pardamean, Bens Pardamean
Genomic studies of plants often seek to identify genetic factors associated with desirable traits. The process of evaluating genetic markers one by one (i.e. a marginal analysis) may not identify important polygenic and environmental effects. Further, confounding due to growing conditions/factors and genetic similarities among plant varieties may influence conclusions. When developing new plant varieties to optimize yield or thrive in future adverse conditions (e.g. flood, drought), scientists seek a complete understanding of how the factors influence desirable traits...
November 15, 2017: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29140754/comparing-diversity-of-fungi-from-living-leaves-using-culturing-and-high-throughput-environmental-sequencing
#18
Peter R Johnston, Duckchul Park, Rob D Smissen
High-throughput sequencing technologies using amplicon approaches have changed the way that studies investigating fungal distribution are undertaken. These powerful and time-efficient technologies have the potential for the first time to accurately map fungal distributions across landscapes or changes in diversity across ecological or biological gradients of interest. There is no requirement for a fungus to form a fruiting body to be detected, and both culturable and nonculturable organisms can be detected...
October 6, 2017: Mycologia
https://www.readbyqxmd.com/read/29139172/association-between-structural-brain-network-efficiency-and-intelligence-increases-during-adolescence
#19
Marinka M G Koenis, Rachel M Brouwer, Suzanne C Swagerman, Inge L C van Soelen, Dorret I Boomsma, Hilleke E Hulshoff Pol
Adolescence represents an important period during which considerable changes in the brain take place, including increases in integrity of white matter bundles, and increasing efficiency of the structural brain network. A more efficient structural brain network has been associated with higher intelligence. Whether development of structural network efficiency is related to intelligence, and if so to which extent genetic and environmental influences are implicated in their association, is not known. In a longitudinal study, we mapped FA-weighted efficiency of the structural brain network in 310 twins and their older siblings at an average age of 10, 13, and 18 years...
November 14, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/29139076/extended%C3%A2-spectrum%C3%A2-beta-lactamase-esbl-producing-bacteria-isolated-from-hospital-wastewaters-rivers-and-aquaculture-sources-in-nigeria
#20
Olawale Olufemi Adelowo, Serena Caucci, Omowunmi Abosede Banjo, Ozioma Chinyere Nnanna, Eunice Olubunmi Awotipe, Florence Bosede Peters, Obasola Ezekiel Fagade, Thomas U Berendonk
Untreated wastewater is a risk factor for the spread of antibiotic resistance in the environment. However, little is known about the contribution of untreated wastewater to the burden of antibiotic resistance in the Nigerian environment. In this study, a total of 143 ceftazidime-/cefpodoxime-resistant bacteria isolated from untreated wastewater and untreated wastewater-contaminated surface and groundwater in Nigeria were screened for extended-spectrum β-lactamase (ESBL) genes, integrons and integron gene cassettes by PCR...
November 14, 2017: Environmental Science and Pollution Research International
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