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genomics,genome annotation,

Jonathan Dorival, Sophie Ruppert, Melissa Gunnoo, Adam Orłowski, Maylis Chapelais-Baron, Jérôme Dabin, Aurore Labourel, Damien Thompson, Gurvan Michel, Mirjam Czjzek, Sabine Genicot
Cell walls of marine macroalgae are composed of diverse polysaccharides that provide abundant carbon sources for marine heterotrophic bacteria. Among them, Zobellia galactanivorans is considered as a model for studying algae-bacteria interactions. The degradation of typical algal polysaccharides, such as agars or alginate, has been intensively studied in this bacterium, but the catabolism of plant-like polysaccharides is essentially uncharacterized. Here we identify a polysaccharide utilization locus in the genome of Z...
October 19, 2018: Biochemical Journal
Anand Mayakonda, De-Chen Lin, Yassen Assenov, Christoph Plass, H Phillip Koeffler
Numerous large-scale genomic studies of matched tumor-normal samples have established the somatic landscapes of most cancer types. However, the downstream analysis of data from somatic mutations entails a number of computational and statistical approaches, requiring usage of independent software and numerous tools. Here, we describe an R Bioconductor package, Maftools, which offers a multitude of analysis and visualization modules that are commonly used in cancer genomic studies, including driver gene identification, pathway, signature, enrichment, and association analyses...
October 19, 2018: Genome Research
Yueh-Chiang Han, Chun-Mean Lin, Thomas T Chen
BACKGROUND: In the past years, our laboratory successfully generated transgenic rainbow trout bearing cecropin P1 transgene. These fish exhibited resistant characteristic to infection by Aeromonas salmonicida, Infectious Hematopoietic Necrosis Virus (IHNV) and Ceratomyxa shasta (a parasitic pathogen). Previously, treating rainbow trout macrophage cells (RTS-11) with cecropin B, pleurocidin and CF17, respectively, resulted in elevated expression of two pro-inflammatory genes, e.g. cyclooxygenase-2 (cox-2) and interleukin-1β (il-1β)...
October 19, 2018: BMC Genomics
Elham Khodayari Moez, Saumyadipta Pyne, Irina Dinu
BACKGROUND: AKT and MYC are two of the most prevalent oncogenes associated with prostate cancer. The precise effects of overexpression of these two key oncogenes on the regulation of metabolic pathways in prostate cancer are under active investigation; however, few studies have investigated their bivariate oncogene-pair expressions in metabolic prostate cancer phenotypes. This is primarily due to the lack of a suitable statistical method to analyze the data in the presence of oncogene interactions and within-metabolite-set correlations...
October 4, 2018: Computers in Biology and Medicine
Ajaraporn Sriboonlert, Passorn Wonnapinij
The first mitochondrial genome of the firefly genus Inflata Boontop, Inflata indica (Lampyridae, Luciolinae) is reported here. Thirteen protein coding genes, 22 tRNA, 2 rRNA genes and a 1570 bp non-coding region were annotated. The comparative analysis showed that the size, GC content, gene content and gene arrangement of this mitochondrial genome are similar to those of other Lampyridae. The mitochondrial phylogenomic analysis showed that I. indica is clustered with other fireflies belonging to the subfamily Luciolinae and most closely related to Pteroptyx maipo...
October 16, 2018: International Journal of Biological Macromolecules
Angelo Pavesi, Alberto Vianelli, Nicola Chirico, Yiming Bao, Olga Blinkova, Robert Belshaw, Andrew Firth, David Karlin
Overlapping genes represent a fascinating evolutionary puzzle, since they encode two functionally unrelated proteins from the same DNA sequence. They originate by a mechanism of overprinting, in which point mutations in an existing frame allow the expression (the "birth") of a completely new protein from a second frame. In viruses, in which overlapping genes are abundant, these new proteins often play a critical role in infection, yet they are frequently overlooked during genome annotation. This results in erroneous interpretation of mutational studies and in a significant waste of resources...
2018: PloS One
Marek Harhala, Jakub Barylski, Kinga Humińska-Lisowska, Dorota Lecion, Jacek Wojciechowicz, Karolina Lahutta, Marta Kuś, Andrew M Kropinski, Sylwia Nowak, Grzegorz Nowicki, Katarzyna Hodyra-Stefaniak, Krystyna Dąbrowska
Only 3% of phage genomes in NCBI nucleotide database represent phages that are active against Streptococcus sp. With the aim to increase general awareness of phage diversity, we isolated two bacteriophages, Str01 and Str03, active against health-threatening Group A Streptococcus (GAS). Both phages are members of the Siphoviridae, but their analysis revealed that Str01 and Str03 do not belong to any known genus. We identified their structural proteins based on LC-ESI29 MS/MS and list their basic thermal stability and physico-chemical features including optimum pH...
2018: PloS One
Hao Wang, Hanwei Yan, Huanlong Liu, Rui Liu, Jun Chen, Yan Xiang
A gene family is formed by duplication of a single original gene. Poplar trees (genus Populus) are important, principally because of their ecological and economic benefits, and are one of the most widely distributed and adaptable trees in the world. Systematic identification and annotation of gene family members are primary steps in studying the function and evolution of poplar genomes. Here, we describe the construction of the Gene Family Database in Poplar (GFDP), which contains information that systematically describes 6551 genes distributed in 145 gene families...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Junhao Chen, Jiawei Zhang, Meigui Lin, Wei Dong, Xinyue Guo, Yang Dong, Zhengjia Wang, Liangsheng Zhang, Fei Chen
Maca (Lepidium meyenii), a Brassicaceae herb plant originated from Andean mountains, has attracted wide interests due to its unique health benefits in reproduction and fertility. Because of its adaptation to the 4000 m high-altitude harsh environment, maca is attracting more and more attention from both crop breeders and basic biologists. After our previous release of the maca genome sequence, there's a growing need to store, query, analyze and integrate various maca resources efficiently. Here, we created Maca Genome Hub (MGH), a genomics and genetics database of maca...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Hyun-Sook Kim, Ke Dong, Jinsoo Kim, Sang-Seob Lee
Crude oil is a major pollutant of marine and coastal ecosystems, and it causes environmental problems more seriously. It is believed ultimate and complete degradation is accomplished mainly by microorganisms. In this study, we aim to search out for bacterial strains with high ability in degrading crude oil. From sediments contaminated by the petroleum spilled in 2007, an accident in Taean, South Korea, we isolated thirty-one bacterial strains in total with potential application in crude oil contamination remediation...
October 19, 2018: MicrobiologyOpen
Zachary D Wallen, Honglei Chen, Erin M Hill-Burns, Stewart A Factor, Cyrus P Zabetian, Haydeh Payami
Objective: To identify modifiers of age at diagnosis of Parkinson disease (PD). Methods: Genome-wide association study (GWAS) included 1,950 individuals with PD from the NeuroGenetics Research Consortium (NGRC) study. Replication was conducted in the Parkinson's, Genes and Environment study, including 209 prevalent (PAGEP ) and 517 incident (PAGEI ) PD cases. Cox regression was used to test association with age at diagnosis. Individuals without neurologic disease were used to rule out confounding...
October 2018: Neurology. Genetics
Ruiqi Yang, Guangxiu Liu, Tuo Chen, Wei Zhang, Gaosen Zhang, Sijing Chang
Planococcus maritimus Y42, isolated from the petroleum-contaminated soil of the Qaidam Basin, can use crude oil as its sole source of carbon and energy at 20 °C. The genome of P. maritimus strain Y42 has been sequenced to provide information on its properties. Genomic analysis shows that the genome of strain Y42 contains one circular DNA chromosome with a size of 3,718,896 bp and a GC content of 48.8%, and three plasmids (329,482; 89,073; and 12,282 bp). Although the strain Y42 did not show a remarkably higher ability in degrading crude oil than other oil-degrading bacteria, the existence of strain Y42 played a significant role to reducing the overall environmental impact as an indigenous oil-degrading bacterium...
2018: Standards in Genomic Sciences
Doglas Parise, Mariana T D Parise, Marcus V C Viana, Adrian V Muñoz-Bucio, Yazmin A Cortés-Pérez, Beatriz Arellano-Reynoso, Efrén Díaz-Aparicio, Fernanda A Dorella, Felipe L Pereira, Alex F Carvalho, Henrique C P Figueiredo, Preetam Ghosh, Debmalya Barh, Anne C P Gomide, Vasco A C Azevedo
Corynebacterium pseudotuberculosis is a pathogenic bacterium which has been rapidly spreading all over the world, causing economic losses in the agricultural sector and sporadically infecting humans. Six C. pseudotuberculosis strains were isolated from goats, sheep, and horses with distinct abscess locations. For the first time, Mexican genomes of this bacterium were sequenced and studied in silico. All strains were sequenced using Ion Personal Genome Machine sequencer, assembled using Newbler and SPAdes software...
2018: Standards in Genomic Sciences
Eva Bauwens, Myrthe Joosten, Joemar Taganna, Mirko Rossi, Ayla Debraekeleer, Alfred Tay, Fanny Peters, Steffen Backert, James Fox, Richard Ducatelle, Han Remaut, Freddy Haesebrouck, Annemieke Smet
Helicobacter (H.) pylori is an important risk factor for gastric malignancies worldwide. Its outer membrane proteome takes an important role in colonization of the human gastric mucosa. However, in zoonotic non-H. pylori helicobacters (NHPHs) also associated with human gastric disease, the composition of the outer membrane (OM) proteome and its relative contribution to disease remain largely unknown. By means of a comprehensive survey of the diversity and distribution of predicted outer membrane proteins (OMPs) identified in all known gastric Helicobacter species with fully annotated genome sequences, we found genus- and species-specific families known or thought to be implicated in virulence...
October 18, 2018: Scientific Reports
Adil Lateef, Sudheesh K Prabhudas, Purushothaman Natarajan
Solanum trilobatum L. is an important medicinal plant in traditional Indian system of medicine belonging to Solanaceae family. However, non-availability of genomic resources hinders its research at the molecular level. We have analyzed the S. trilobatum leaf transcriptome using high throughput RNA sequencing. The de novo assembly of 136,220,612 reads produced 128,934 non-redundant unigenes with N50 value of 1347 bp. Annotation of unigenes was performed against databases such as NCBI nr database, Gene Ontology, KEGG, Uniprot, Pfam, and plnTFDB...
October 18, 2018: Scientific Reports
Bijurica Chakraborty, Payel Mondal, Pragya Gajendra, Mitashree Mitra, Chandrima Das, Sanghamitra Sengupta
BACKGROUND: Plasmodium falciparum and Plasmodium vivax are two major parasites responsible for malaria which remains a threat to almost 50% of world's population despite decade-long eradication program. One possible reason behind this conundrum is that the bases of clinical variability in malaria caused by either species are complex and poorly understood. METHODS: Whole-genome transcriptome was analyzed to identify the active and predominant pathways in the PBMC of P...
October 15, 2018: EBioMedicine
James W E Lowe
DNA sequencing has been characterised by scholars and life scientists as an example of 'big', 'fast' and 'automated' science in biology. This paper argues, however, that these characterisations are a product of a particular interpretation of what sequencing is, what I call 'thin sequencing'. The 'thin sequencing' perspective focuses on the determination of the order of bases in a particular stretch of DNA. Based upon my research on the pig genome mapping and sequencing projects, I provide an alternative 'thick sequencing' perspective, which also includes a number of practices that enable the sequence to travel across and be used in wider communities...
October 15, 2018: Studies in History and Philosophy of Biological and Biomedical Sciences
Chaoran Yu, Hiju Hong, Jiaoyang Lu, Xuan Zhao, Wenjun Hu, Sen Zhang, Yaping Zong, Zhihai Mao, Jianwen Li, Mingliang Wang, Bo Feng, Jing Sun, Minhua Zheng
BACKGROUND: Cetuximab has been regularly added to the treatments for metastatic colorectal cancer worldwide. However, due to its therapeutic insensitivity and underlying mechanisms being largely unknown, the clinical implementation of cetuximab in colorectal cancer remains limited. METHODS: The gene expression profile GSE56386 was retrieved from the Gene Expression Omnibus database. Differentially expressed genes were identified between cetuximab-responsive patients and nonresponders, annotated by gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway analysis, and further analyzed by protein-protein interaction networks...
January 1, 2018: Technology in Cancer Research & Treatment
James Amor Smith, Maor Bar-Peled
The rare branched-chain sugar apiose, once thought to only be present in the plant kingdom, was found in two bacterial species: Geminicoccus roseus and Xanthomonas pisi. Glycans with apiose residues were detected in aqueous methanol-soluble fractions as well as in the insoluble pellet fraction of X. pisi. Genes encoding bacterial uridine diphosphate apiose (UDP-apiose) synthases (bUASs) were characterized in these bacterial species, but the enzyme(s) involved in the incorporation of the apiose into glycans remained unknown...
2018: PloS One
Jesús Murga-Moreno, Marta Coronado-Zamora, Alejandra Bodelón, Antonio Barbadilla, Sònia Casillas
Since the migrations that led humans to colonize Earth, our species has faced frequent adaptive challenges that have left signatures in the landscape of genetic variation and that we can identify in our today's genomes. Here, we (i) perform an outlier approach on eight different population genetic statistics for 22 non-admixed human populations of the Phase III of the 1000 Genomes Project to detect selective sweeps at different historical ages, as well as events of recurrent positive selection in the human lineage; and (ii) create PopHumanScan, an online catalog that compiles and annotates all candidate regions under selection to facilitate their validation and thoroughly analysis...
October 18, 2018: Nucleic Acids Research
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