keyword
MENU ▼
Read by QxMD icon Read
search

Genome variation

keyword
https://www.readbyqxmd.com/read/29792951/an-analysis-of-variability-in-genome-organisation-of-intracellular-calcium-release-channels-across-insect-orders
#1
Bartlomiej J Troczka, Ewan Richardson, Rafael Homem, T G Emyr Davies
Using publicly available genomic data, combined with RT-PCR validation, we explore structural genomic variation for two major ion channels across insect classes. We have manually curated Ryanodine receptor (RyR) and inositol 1,4,5-trisphosphate receptor (IP3 R) ORFs and their corresponding genomic structures from 26 different insects covering major insect orders. We found that, despite high protein identity for both RyRs (>75%) and IP3 Rs (~67%), the overall complexity of the gene structure varies greatly between different insect orders with the simplest genes (fewest introns) found in Diptera and the most complex in Lepidoptera...
May 21, 2018: Gene
https://www.readbyqxmd.com/read/29792573/inherent-resistance-to-14%C3%AE-demethylation-inhibitor-fungicides-in-colletotrichum-truncatum-is-likely-linked-to-cyp51a-and-or-cyp51b-gene-variants
#2
Shuning Chen, Yunyun Wang, Guido Schnabel, Congyue Annie Peng, Satyanarayana Lagishetty, Kerry Smith, Chao-Xi Luo, Huizhu Yuan
Anthracnose disease, caused by Colletotrichum truncatum, affects marketable yield during preharvest production and postharvest storage of fruits and vegetables worldwide. Demethylation inhibitor fungicides (DMIs) are among the very few chemical classes of single-site mode of action fungicides that are effective in controlling anthracnose disease. However, some species are inherently resistant to DMIs and more information is needed to understand this phenomenon. Isolates of C. truncatum were collected from the USA and China from peach, soybean, citrus, and begonia and sensitivity to six DMIs (difenoconazole, propiconazole, metconazole, tebuconazole, flutriafol and fenbuconazole) was determined...
May 24, 2018: Phytopathology
https://www.readbyqxmd.com/read/29792514/a-flow-procedure-for-linearization-of-genome-sequence-graphs
#3
David Haussler, Maciej Smuga-Otto, Jordan M Eizenga, Benedict Paten, Adam M Novak, Sergei Nikitin, Maria Zueva, Dmitrii Miagkov
Efforts to incorporate human genetic variation into the reference human genome have converged on the idea of a graph representation of genetic variation within a species, a genome sequence graph. A sequence graph represents a set of individual haploid reference genomes as paths in a single graph. When that set of reference genomes is sufficiently diverse, the sequence graph implicitly contains all frequent human genetic variations, including translocations, inversions, deletions, and insertions. In representing a set of genomes as a sequence graph, one encounters certain challenges...
May 24, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29792315/genomic-variation-among-and-within-six-juglans-species
#4
Kristian A Stevens, Keith Woeste, Sandeep Chakraborty, Marc W Crepeau, Charles A Leslie, Pedro J Martínez-García, Daniela Puiu, Jeanne Romero-Severson, Mark Coggeshall, Abhaya M Dandekar, Daniel Kluepfel, David B Neale, Steven L Salzberg, Charles H Langley
Genomic analysis in Juglans (walnuts) is expected to transform the breeding and agricultural production of both nuts and lumber. To that end, we report here the determination of reference sequences for six additional relatives of Juglans regia : Juglans sigillata (also from section Dioscaryon ), Juglans nigra , Juglans microcarpa, Juglans hindsii (from section Rhysocaryon ) , Juglans cathayensis (from section Cardiocaryon ), and the closely related Pterocarya stenoptera. While these are 'draft' genomes, ranging in size between 640Mbp and 990Mbp, their contiguities and accuracies can support powerful annotations of genomic variation that are often the foundation of new avenues of research and breeding...
May 23, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29792231/high-burden-of-birthweight-lowering-genetic-variants-in-africans-and-asians
#5
Fasil Tekola-Ayele, Tsegaselassie Workalemahu, Azmeraw T Amare
BACKGROUND: Birthweight is an important predictor of infant morbidity and mortality, and is associated with cardiovascular diseases, obesity, and diabetes in childhood and adulthood. Birthweight and fetal growth show regional and population variations even under similar maternal conditions, and a large proportion of these differences are not explained by environmental factors. Whether and to what extent population genetic variations at key birthweight-associated loci account for the residual birthweight disparities not explained by environmental determinants is unknown...
May 24, 2018: BMC Medicine
https://www.readbyqxmd.com/read/29792207/metagenomic-analysis-of-viruses-associated-with-maize-lethal-necrosis-in-kenya
#6
Mwathi Jane Wamaitha, Deepti Nigam, Solomon Maina, Francesca Stomeo, Anne Wangai, Joyce Njoki Njuguna, Timothy A Holton, Bramwel W Wanjala, Mark Wamalwa, Tanui Lucas, Appolinaire Djikeng, Hernan Garcia-Ruiz
BACKGROUND: Maize lethal necrosis is caused by a synergistic co-infection of Maize chlorotic mottle virus (MCMV) and a specific member of the Potyviridae, such as Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV) or Johnson grass mosaic virus (JGMV). Typical maize lethal necrosis symptoms include severe yellowing and leaf drying from the edges. In Kenya, we detected plants showing typical and atypical symptoms. Both groups of plants often tested negative for SCMV by ELISA...
May 23, 2018: Virology Journal
https://www.readbyqxmd.com/read/29792158/landraces-of-snake-melon-an-ancient-middle-eastern-crop-reveal-extensive-morphological-and-dna-diversity-for-potential-genetic-improvement
#7
Samer Omari, Yuri Kamenir, Jennifer I C Benichou, Sarah Pariente, Hanan Sela, Rafael Perl-Treves
BACKGROUND: Snake melon (Cucumis melo var. flexuosus, "Faqqous") is a traditional and ancient vegetable in the Mediterranean area. A collection of landraces from 42 grower fields in Israel and Palestinian territories was grown and characterized in a "Common Garden" rain-fed experiment, at the morphological-horticultural and molecular level using seq-DArT markers. RESULTS: The different landraces ("populations") showed extensive variation in morphology and quantitative traits such as yield and femaleness, and clustered into four horticultural varieties...
May 23, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29790900/gscalite-a-web-server-for-gene-set-cancer-analysis
#8
Chun-Jie Liu, Fei-Fei Hu, Mengxuan Xia, Leng Han, Qiong Zhang, An-Yuan Guo
Summary: The availability of cancer genomic data makes it possible to analyze genes related to cancer. Cancer is usually the result of a set of genes and the signal of a single gene could be covered by background noise. Here, we present a web server named Gene Set Cancer Analysis (GSCALite) to analyze a set of genes in cancers with the following functional modules. (i) Differential expression in tumor vs normal, and the survival analysis; (ii) Genomic variations and their survival analysis; (iii) Gene expression associated cancer pathway activity; (iv) miRNA regulatory network for genes; (v) Drug sensitivity for genes; (vi) Normal tissue expression and eQTL for genes...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790872/genomic-sequencing-identifies-secondary-findings-in-a-cohort-of-parent-study-participants
#9
Michelle L Thompson, Candice R Finnila, Kevin M Bowling, Kyle B Brothers, Matthew B Neu, Michelle D Amaral, Susan M Hiatt, Kelly M East, David E Gray, James M J Lawlor, Whitley V Kelley, Edward J Lose, Carla A Rich, Shirley Simmons, Shawn E Levy, Richard M Myers, Gregory S Barsh, E Martina Bebin, Gregory M Cooper
PurposeClinically relevant secondary variants were identified in parents enrolled with a child with developmental delay and intellectual disability.MethodsExome/genome sequencing and analysis of 789 "unaffected" parents was performed.ResultsPathogenic/likely pathogenic variants were identified in 21 genes within 25 individuals (3.2%), with 11 (1.4%) participants harboring variation in a gene defined as clinically actionable by the American College of Medical Genetics and Genomics. These 25 individuals self-reported either relevant clinical diagnoses (5); relevant family history or symptoms (13); or no relevant family history, symptoms, or clinical diagnoses (7)...
April 12, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29790871/phenotypic-expansion-illuminates-multilocus-pathogenic-variation
#10
Ender Karaca, Jennifer E Posey, Zeynep Coban Akdemir, Davut Pehlivan, Tamar Harel, Shalini N Jhangiani, Yavuz Bayram, Xiaofei Song, Vahid Bahrambeigi, Ozge Ozalp Yuregir, Sevcan Bozdogan, Gozde Yesil, Sedat Isikay, Donna Muzny, Richard A Gibbs, James R Lupski
PurposeMultilocus variation-pathogenic variants in two or more disease genes-can potentially explain the underlying genetic basis for apparent phenotypic expansion in cases for which the observed clinical features extend beyond those reported in association with a "known" disease gene.MethodsAnalyses focused on 106 patients, 19 for whom apparent phenotypic expansion was previously attributed to variation at known disease genes. We performed a retrospective computational reanalysis of whole-exome sequencing data using stringent Variant Call File filtering criteria to determine whether molecular diagnoses involving additional disease loci might explain the observed expanded phenotypes...
April 26, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29789885/instability-of-endosperm-development-in-amphiploids-and-their-parental-species-in-the-genus-avena-l
#11
Paulina Tomaszewska, Romuald Kosina
The development of oat endosperm is modified by chromatin and nuclei elimination, intrusive growth of cell walls, and polyploidisation of cell clones. The last event is correlated with somatic crossing-over. Grass endosperm is a variable tissue in terms of its cytogenetics and development. Free-nuclear syncytium and starchy and aleurone endosperm were the main focus of the research. These were studied in oat amphiploids (4x, 6x, and 8x) and parental species (2x, 4x, and 6x). What the levels of cytogenetic disorders and developmental anomalies in species versus hybrids are, and, what the factors are determining phenotypes of both tissue components, are open questions for oats...
May 22, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29789621/taxon-specific-aerosolization-of-bacteria-and-viruses-in-an-experimental-ocean-atmosphere-mesocosm
#12
Jennifer M Michaud, Luke R Thompson, Drishti Kaul, Josh L Espinoza, R Alexander Richter, Zhenjiang Zech Xu, Christopher Lee, Kevin M Pham, Charlotte M Beall, Francesca Malfatti, Farooq Azam, Rob Knight, Michael D Burkart, Christopher L Dupont, Kimberly A Prather
Ocean-derived, airborne microbes play important roles in Earth's climate system and human health, yet little is known about factors controlling their transfer from the ocean to the atmosphere. Here, we study microbiomes of isolated sea spray aerosol (SSA) collected in a unique ocean-atmosphere facility and demonstrate taxon-specific aerosolization of bacteria and viruses. These trends are conserved within taxonomic orders and classes, and temporal variation in aerosolization is similarly shared by related taxa...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789594/in-vitro-dna-scramble
#13
Yi Wu, Rui-Ying Zhu, Leslie A Mitchell, Lu Ma, Rui Liu, Meng Zhao, Bin Jia, Hui Xu, Yun-Xiang Li, Zu-Ming Yang, Yuan Ma, Xia Li, Hong Liu, Duo Liu, Wen-Hai Xiao, Xiao Zhou, Bing-Zhi Li, Ying-Jin Yuan, Jef D Boeke
The power of synthetic biology has enabled the expression of heterologous pathways in cells, as well as genome-scale synthesis projects. The complexity of biological networks makes rational de novo design a grand challenge. Introducing features that confer genetic flexibility is a powerful strategy for downstream engineering. Here we develop an in vitro method of DNA library construction based on structural variation to accomplish this goal. The "in vitro SCRaMbLE system" uses Cre recombinase mixed in a test tube with purified DNA encoding multiple loxPsym sites...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789533/scrambleing-to-understand-and-exploit-structural-variation-in-genomes
#14
Jan Steensels, Anton Gorkovskiy, Kevin J Verstrepen
No abstract text is available yet for this article.
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789446/validation-of-ion-torrent-tm-inherited-disease-panel-with-the-pgm-tm-sequencing-platform-for-rapid-and-comprehensive-mutation-detection
#15
Abeer E Mustafa, Tariq Faquih, Batoul Baz, Rana Kattan, Abdulelah Al-Issa, Asma I Tahir, Faiqa Imtiaz, Khushnooda Ramzan, Moeenaldeen Al-Sayed, Mohammed Alowain, Zuhair Al-Hassnan, Hamad Al-Zaidan, Mohamed Abouelhoda, Bashayer R Al-Mubarak, Nada A Al Tassan
Quick and accurate molecular testing is necessary for the better management of many inherited diseases. Recent technological advances in various next generation sequencing (NGS) platforms, such as target panel-based sequencing, has enabled comprehensive, quick, and precise interrogation of many genetic variations. As a result, these technologies have become a valuable tool for gene discovery and for clinical diagnostics. The AmpliSeq Inherited Disease Panel (IDP) consists of 328 genes underlying more than 700 inherited diseases...
May 22, 2018: Genes
https://www.readbyqxmd.com/read/29789384/mutations-in-eid1-and-lnk2-caused-light-conditional-clock-deceleration-during-tomato-domestication
#16
Niels A Müller, Lei Zhang, Maarten Koornneef, José M Jiménez-Gómez
Circadian period and phase of cultivated tomato ( Solanum lycopersicum ) were changed during domestication, likely adapting the species to its new agricultural environments. Whereas the delayed circadian phase is mainly caused by allelic variation of EID1 , the genetic basis of the long circadian period has remained elusive. Here we show that a partial deletion of the clock gene LNK2 is responsible for the period lengthening in cultivated tomatoes. We use resequencing data to phylogenetically classify hundreds of tomato accessions and investigate the evolution of the eid1 and lnk2 mutations along successive domestication steps...
May 22, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29788921/signatures-of-host-specialization-and-a-recent-transposable-element-burst-in-the-dynamic-one-speed-genome-of-the-fungal-barley-powdery-mildew-pathogen
#17
Lamprinos Frantzeskakis, Barbara Kracher, Stefan Kusch, Makoto Yoshikawa-Maekawa, Saskia Bauer, Carsten Pedersen, Pietro D Spanu, Takaki Maekawa, Paul Schulze-Lefert, Ralph Panstruga
BACKGROUND: Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley (Hordeum vulgare). RESULTS: The near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs)...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29788909/whole-genome-analysis-reveals-the-diversity-and-evolutionary-relationships-between-necrotic-enteritis-causing-strains-of-clostridium-perfringens
#18
Jake A Lacey, Theodore R Allnutt, Ben Vezina, Thi Thu Hao Van, Thomas Stent, Xiaoyan Han, Julian I Rood, Ben Wade, Anthony L Keyburn, Torsten Seemann, Honglei Chen, Volker Haring, Priscilla A Johanesen, Dena Lyras, Robert J Moore
BACKGROUND: Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chicken production due to the cost of the implementation of infection control measures and to productivity losses. This study has focused on the genomic analysis of a range of chicken-derived C. perfringens isolates, from around the world and from different years. The genomes were sequenced and compared with 20 genomes available from public databases, which were from a diverse collection of isolates from chickens, other animals, and humans...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29788473/enhancing-psychosis-spectrum-nosology-through-an-international-data-sharing-initiative
#19
Anna R Docherty, Eduardo Fonseca-Pedrero, Martin Debbané, Raymond C K Chan, Richard J Linscott, Katherine G Jonas, David C Cicero, Melissa J Green, Leonard J Simms, Oliver Mason, David Watson, Ulrich Ettinger, Monika Waszczuk, Alexander Rapp, Phillip Grant, Roman Kotov, Colin G DeYoung, Camilo J Ruggero, Nicolas R Eaton, Robert F Krueger, Christopher Patrick, Christopher Hopwood, F Anthony O'Neill, David H Zald, Christopher C Conway, Daniel E Adkins, Irwin D Waldman, Jim van Os, Patrick F Sullivan, John S Anderson, Andrey A Shabalin, Scott R Sponheim, Stephan F Taylor, Rachel G Grazioplene, Silviu A Bacanu, Tim B Bigdeli, Corinna Haenschel, Dolores Malaspina, Diane C Gooding, Kristin Nicodemus, Frauke Schultze-Lutter, Neus Barrantes-Vidal, Christine Mohr, William T Carpenter, Alex S Cohen
The latent structure of schizotypy and psychosis-spectrum symptoms remains poorly understood. Furthermore, molecular genetic substrates are poorly defined, largely due to the substantial resources required to collect rich phenotypic data across diverse populations. Sample sizes of phenotypic studies are often insufficient for advanced structural equation modeling approaches. In the last 50 years, efforts in both psychiatry and psychological science have moved toward (1) a dimensional model of psychopathology (eg, the current Hierarchical Taxonomy of Psychopathology [HiTOP] initiative), (2) an integration of methods and measures across traits and units of analysis (eg, the RDoC initiative), and (3) powerful, impactful study designs maximizing sample size to detect subtle genomic variation relating to complex traits (the Psychiatric Genomics Consortium [PGC])...
May 16, 2018: Schizophrenia Bulletin
https://www.readbyqxmd.com/read/29788454/variation-in-human-chromosome-21-ribosomal-rna-genes-characterized-by-tar-cloning-and-long-read-sequencing
#20
Jung-Hyun Kim, Alexander T Dilthey, Ramaiah Nagaraja, Hee-Sheung Lee, Sergey Koren, Dawood Dudekula, William H Wood Iii, Yulan Piao, Aleksey Y Ogurtsov, Koichi Utani, Vladimir N Noskov, Svetlana A Shabalina, David Schlessinger, Adam M Phillippy, Vladimir Larionov
Despite the key role of the human ribosome in protein biosynthesis, little is known about the extent of sequence variation in ribosomal DNA (rDNA) or its pre-rRNA and rRNA products. We recovered ribosomal DNA segments from a single human chromosome 21 using transformation-associated recombination (TAR) cloning in yeast. Accurate long-read sequencing of 13 isolates covering ∼0.82 Mb of the chromosome 21 rDNA complement revealed substantial variation among tandem repeat rDNA copies, several palindromic structures and potential errors in the previous reference sequence...
May 21, 2018: Nucleic Acids Research
keyword
keyword
52031
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"