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Genome annotation

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https://www.readbyqxmd.com/read/28647779/transcriptome-profiling-and-digital-gene-expression-analysis-of-the-skin-of-dybowski-s-frog-rana-dybowskii-exposed-to-aeromonas-hydrophila
#1
Yi-Gang Xu, Long-Hui Chai, Wen Shi, Dan-Dan Wang, Jing-Yu Zhang, Xiang-Hong Xiao
Recently, populations of Rana dybowskii, an important amphibian species in Northeast China, have decreased, mainly owing to the disease caused by Aeromonas hydrophila. However, effective control methods have not yet been developed. In order to explore the immune responses of R. dybowskii upon exposure to A. hydrophila infection, Illumina high-throughput transcriptome sequencing and digital gene expression (DGE) technology were employed to investigate transcriptomic changes in the skin of R. dybowskii exposed to A...
June 24, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28647529/-linking-secondary-metabolites-to-biosynthesis-genes-in-the-fungal-endophyte-cyanodermella-asteris-the-anti-cancer-bisanthraquinone-skyrin
#2
Linda Jahn, Thomas Schafhauser, Daniel Wibberg, Christian Rückert, Anika Winkler, Andreas Kulik, Tilmann Weber, Liane Flor, Karl-Heinz van Pée, Jörn Kalinowski, Jutta Ludwig-Müllera, Wolfgang Wohlleben
Fungal aromatic polyketides display a very diverse and widespread group of natural products. Due to their excellent light absorption properties and widely studied biological activities, they offer numerous application for food, textile and pharmaceutical industry. The biosynthetic pathways of fungal aromatic polyketides usually involve a set of successive enzymes, in which a non-reductive polyketide synthases iteratively catalyzes the essential assembly of simple building blocks into (often polycyclic) aromatic compounds...
June 21, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28647306/complete-genome-sequence-of-a-phthalic-acid-esters-degrading-mycobacterium-sp-yc-rl4
#3
Lei Ren, Shuanghu Fan, Junhuan Wang, Nahurira Ruth, Cheng Qiao, Yang Jia, Yanchun Yan
Mycobacterium sp. YC-RL4 is capable of utilizing a broad range of phthalic acid esters (PAEs) as sole source of carbon and energy for growth. The preliminary studies demonstrated its high degrading efficiency and good performance during the bioprocess with environmental samples. Here, we present the complete genome of Mycobacterium sp. YC-RL4, which consists of one circular chromosome (5,801,417bp) and one plasmid (252,568bp). The genomic analysis and gene annotation were performed and many potential genes responsible for the biodegradation of PAEs were identified from the genome...
June 3, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/28646875/genome-analysis-of-diploscapter-coronatus-insights-into-molecular-peculiarities-of-a-nematode-with-parthenogenetic-reproduction
#4
Hideaki Hiraki, Hiroshi Kagoshima, Christopher Kraus, Philipp H Schiffer, Yumiko Ueta, Michael Kroiher, Einhard Schierenberg, Yuji Kohara
BACKGROUND: Sexual reproduction involving the fusion of egg and sperm is prevailing among eukaryotes. In contrast, the nematode Diploscapter coronatus, a close relative of the model Caenorhabditis elegans, reproduces parthenogenetically. Neither males nor sperm have been observed and some steps of meiosis are apparently skipped in this species. To uncover the genomic changes associated with the evolution of parthenogenesis in this nematode, we carried out a genome analysis. RESULTS: We obtained a 170 Mbp draft genome in only 511 scaffolds with a N50 length of 1 Mbp...
June 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28646867/a-high-quality-annotated-transcriptome-of-swine-peripheral-blood
#5
Haibo Liu, Timothy P L Smith, Dan J Nonneman, Jack C M Dekkers, Christopher K Tuggle
BACKGROUND: High throughput gene expression profiling assays of peripheral blood are widely used in biomedicine, as well as in animal genetics and physiology research. Accurate, comprehensive, and precise interpretation of such high throughput assays relies on well-characterized reference genomes and/or transcriptomes. However, neither the reference genome nor the peripheral blood transcriptome of the pig have been sufficiently assembled and annotated to support such profiling assays in this emerging biomedical model organism...
June 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28646617/melanoma-associated-grm3-variants-dysregulate-melanosome-trafficking-and-camp-signaling
#6
Ana Neto, Craig J Ceol
Large-scale sequencing studies have revealed several genes that are recurrently mutated in melanomas. To annotate the melanoma genome we have expressed tumor-associated variants of these genes in zebrafish and characterized their effects on melanocyte development and function. Here, we describe expression of tumor-associated variants of the recurrently-mutated metabotropic glutamate receptor 3 (GRM3) gene. Unlike wild-type GRM3, tumor-associated GRM3 variants disrupted trafficking of melanosomes, causing their aggregation in the cell body...
June 24, 2017: Pigment Cell & Melanoma Research
https://www.readbyqxmd.com/read/28645245/transcriptomic-dynamics-in-soybean-near-isogenic-lines-differing-in-alleles-for-an-aphid-resistance-gene-following-infestation-by-soybean-aphid-biotype-2
#7
Sungwoo Lee, Bryan J Cassone, Asela Wijeratne, Tae-Hwan Jun, Andrew P Michel, M A Rouf Mian
BACKGROUND: Genetic resistance of soybean [Glycine max (L.) Merr] against Aphis glycines provides effective management of this invasive pest, though the underlying molecular mechanisms are largely unknown. This study aimed to investigate genome-wide changes in gene expressions of soybean near-isogenic lines (NILs) either with the Rag5 allele for resistance or the rag5 allele for susceptibility to the aphid following infestation with soybean aphid biotype 2. RESULTS: The resistant (R)-NIL responded more rapidly to aphid infestation than the susceptible (S)-NIL, with differential expressions of 2496 genes during first 12 h of infestation (hai), compared to the aphid-free control...
June 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28645209/genome-wide-mapping-of-in-vivo-er%C3%AE-binding-sites-in-male-mouse-efferent-ductules
#8
Guangxin Yao, Shuanggang Hu, Lu Yu, Yanfei Ru, Charlie Degui Chen, Qiang Liu, Yonglian Zhang
As an important nuclear hormone receptor, estrogen receptor alpha (ERα), which is encoded by Esr1 gene, regulates the expression of hundreds of genes in a stimulus-specific, temporal and tissue-specific fashion, mainly by binding to specific DNA sequences-estrogen response elements (EREs). As an important estrogen target tissue in males, the function of the efferent ductules relies on the presence of the ERα protein, but the underlying regulatory mechanisms are poorly illustrated. In this study, genome-wide ERα-binding sites in mouse efferent ductules were mapped by ChIP-seq...
June 22, 2017: Endocrinology
https://www.readbyqxmd.com/read/28645144/increased-alignment-sensitivity-improves-the-usage-of-genome-alignments-for-comparative-gene-annotation
#9
Virag Sharma, Michael Hiller
Genome alignments provide a powerful basis to transfer gene annotations from a well-annotated reference genome to many other aligned genomes. The completeness of these annotations crucially depends on the sensitivity of the underlying genome alignment. Here, we investigated the impact of the genome alignment parameters and found that parameters with a higher sensitivity allow the detection of thousands of novel alignments between orthologous exons that have been missed before. In particular, comparisons between species separated by an evolutionary distance of >0...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28644415/genome-wide-association-study-of-dietary-pattern-scores
#10
Frédéric Guénard, Annie Bouchard-Mercier, Iwona Rudkowska, Simone Lemieux, Patrick Couture, Marie-Claude Vohl
Dietary patterns, representing global food supplies rather than specific nutrients or food intakes, have been associated with cardiovascular disease (CVD) incidence and mortality. The contribution of genetic factors in the determination of food intakes, preferences and dietary patterns has been previously established. The current study aimed to identify novel genetic factors associated with reported dietary pattern scores. Reported dietary patterns scores were derived from reported dietary intakes for the preceding month and were obtained through a food frequency questionnaire and genome-wide association study (GWAS) conducted in a study sample of 141 individuals...
June 23, 2017: Nutrients
https://www.readbyqxmd.com/read/28643264/genome-editing-of-c-elegans
#11
Takuma Sugi
Caenorhabditis elegans, a 1 mm long free-living nematode, is a traditional model animal for genetic investigations of various biological processes. Characteristic features that make C. elegans a powerful model of choice for eukaryotic genetic studies include its rapid life cycle, well-annotated genome, simple morphology, and transparency. Recently, genome editing technologies have been increasingly used in C. elegans, thereby facilitating their genetic analyses. Here, I introduce a protocol frequently used in C...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28642130/mir-155-expression-is-downregulated-in-kidney-transplant-patients-with-human-cytomegalovirus-infection
#12
Massimiliano Bergallo, Stefano Gambarino, Paola Montanari, Valentina Daprà, Marco Rassu, Ilaria Galliano, Paolo Ravanini
MicroRNAs are small, noncoding RNAs that control expression of target genes through inhibiting protein translation or inducing degradation of mRNA transcripts of target genes. According to the latest update, 2578 unique mature miRNAs are currently annotated in the human genome and participate in the regulation of multiple events, such as cellular proliferation or apoptosis. Herpesvirus family comprehends many viruses able to control and modulate host-cell processes permitting the survival by a latency phase after primary infection...
June 19, 2017: Transplant Immunology
https://www.readbyqxmd.com/read/28641873/targeting-dna-repair-for-precision-radiotherapy-balancing-the-therapeutic-ratio
#13
REVIEW
Osman Mahamud, Jonathan So, Melvin L K Chua, Robert G Bristow
Genomic instability is underpinned by defects in the DNA damage response and DNA repair pathways. Subsequent clonal selection and adaption can lead to a mutator phenotype and tumor aggression. Importantly, tumor cell sensitivity to chemotherapy and radiotherapy can depend highly on the cellular capacity to repair DNA damage within and between tumor types. Annotation of functional defects in DNA damage response and DNA repair function may allow for the development of novel prognostic biomarkers. This information could also be used to predict therapeutic response, including predicting responses following inhibition of DNA repair...
April 25, 2017: Current Problems in Cancer
https://www.readbyqxmd.com/read/28641485/microarray-based-gene-expression-analysis-for-veterinary-pathologists-a-review
#14
Barbara B Raddatz, Ingo Spitzbarth, Katja A Matheis, Arno Kalkuhl, Ulrich Deschl, Wolfgang Baumgärtner, Reiner Ulrich
High-throughput, genome-wide transcriptome analysis is now commonly used in all fields of life science research and is on the cusp of medical and veterinary diagnostic application. Transcriptomic methods such as microarrays and next-generation sequencing generate enormous amounts of data. The pathogenetic expertise acquired from understanding of general pathology provides veterinary pathologists with a profound background, which is essential in translating transcriptomic data into meaningful biological knowledge, thereby leading to a better understanding of underlying disease mechanisms...
January 1, 2017: Veterinary Pathology
https://www.readbyqxmd.com/read/28640246/gwas-signals-revisited-using-human-knockouts
#15
Sateesh Maddirevula, Fatema AlZahrani, Shams Anazi, Mariam Almureikhi, Tawfeg Ben-Omran, Ghada M H Abdel-Salam, Mais Hashem, Niema Ibrahim, Firdous M Abdulwahab, Neama Meriki, Fahad A Bashiri, Meow-Keong Thong, Premala Muthukumarasamy, Rifhan Azwani Mazlan, Ranad Shaheen, Fowzan S Alkuraya
PurposeGenome-wide association studies (GWAS) have been instrumental to our understanding of the genetic risk determinants of complex traits. A common challenge in GWAS is the interpretation of signals, which are usually attributed to the genes closest to the polymorphic markers that display the strongest statistical association. Naturally occurring complete loss of function (knockout) of these genes in humans can inform GWAS interpretation by unmasking their deficiency state in a clinical context.MethodsWe exploited the unique population structure of Saudi Arabia to identify novel knockout events in genes previously highlighted in GWAS using combined autozygome/exome analysis...
June 22, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28639078/a-genome-wide-expression-association-analysis-identifies-genes-and-pathways-associated-with-amyotrophic-lateral-sclerosis
#16
Yanan Du, Yan Wen, Xiong Guo, Jingcan Hao, Wenyu Wang, Awen He, Qianrui Fan, Ping Li, Li Liu, Xiao Liang, Feng Zhang
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease with strong genetic components. To identity novel risk variants for ALS, utilizing the latest genome-wide association studies (GWAS) and eQTL study data, we conducted a genome-wide expression association analysis by summary data-based Mendelian randomization (SMR) method. Summary data were derived from a large-scale GWAS of ALS, involving 12577 cases and 23475 controls. The eQTL annotation dataset included 923,021 cis-eQTL for 14,329 genes and 4732 trans-eQTL for 2612 genes...
June 21, 2017: Cellular and Molecular Neurobiology
https://www.readbyqxmd.com/read/28638141/al-mena-a-comprehensive-resource-of-human-genetic-variants-integrating-genomes-and-exomes-from-arab-middle-eastern-and-north-african-populations
#17
Remya Koshy, Anop Ranawat, Vinod Scaria
Middle East and North Africa (MENA) encompass very unique populations, with a rich history and encompasses characteristic ethnic, linguistic and genetic diversity. The genetic diversity of MENA region has been largely unknown. The recent availability of whole-exome and whole-genome sequences from the region has made it possible to collect population-specific allele frequencies. The integration of data sets from this region would provide insights into the landscape of genetic variants in this region. We integrated genetic variants from multiple data sets systematically, available from this region to create a compendium of over 26 million genetic variations...
June 22, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28637587/comparative-study-on-secretome-and-transmembranome-of-immature-and-mature-metacestodes-of-echinococcus-multilocularis
#18
Fuqiang Huang, Zhisheng Dang, Haoji Zhang, Kinpei Yagi, Kyeongsoon Kim, Magona Joseph, Wenjun Pu, Yuzaburo Oku
Alveolar echinococcosis (AE) is a worldwide zoonosis caused by E. multilocularis. Humans become infected through oral ingestion of the eggs. Host of E. multilocularis produces immune responses that help to either reject and/or limit the growth of this parasite, and in response the parasite produces molecules against this immune attack. This study identifies candidate key molecules in the early infection phase and the chronic stage of the parasite infestation, through comparison of gene expression of 4- and 16-week metacestodes...
May 12, 2017: Veterinary Parasitology
https://www.readbyqxmd.com/read/28636804/new-insights-into-global-biogeography-population-structure-and-natural-selection-from-the-genome-of-the-epipelagic-copepod-oithona
#19
Mohammed-Amin Madoui, Julie Poulain, Kevin Sugier, Marc Wessner, Benjamin Noel, Leo Berline, Karine Labadie, Astrid Cornils, Leocadio Blanco-Bercial, Lars Stemmann, Jean-Louis Jamet, Patrick Wincker
In the epipelagic ocean the genus Oithona is considered as one of the most abundant and widespread copepods and plays an important role in the trophic food web. Despite its ecological importance, little is known about the Oithona and cyclopoid copepods genomics. Therefore, we sequenced, assembled and annotated the genome of Oithona nana. The comparative genomic analysis integrating available copepod genomes highlighted the expansions of genes related to stress response, cell differentiation, and development, including genes coding Lin12-Notch-Repeat (LNR) domain proteins...
June 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28635630/development-of-a-high-density-snp-based-linkage-map-and-detection-of-qtl-for-%C3%AE-glucans-protein-content-grain-yield-per-spike-and-heading-time-in-durum-wheat
#20
Ilaria Marcotuli, Agata Gadaleta, Giacomo Mangini, Antonio Massimo Signorile, Silvana Addolorata Zacheo, Antonio Blanco, Rosanna Simeone, Pasqualina Colasuonno
High-density genetic linkage maps of crop species are particularly useful in detecting qualitative and quantitative trait loci for important agronomic traits and in improving the power of classical approaches to identify candidate genes. The aim of this study was to develop a high-density genetic linkage map in a durum wheat recombinant inbred lines population (RIL) derived from two elite wheat cultivars and to identify, characterize and correlate Quantitative Trait Loci (QTL) for β-glucan, protein content, grain yield per spike and heading time...
June 21, 2017: International Journal of Molecular Sciences
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