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Gene annotation

Ye Liu, Jen-Chien Chang, Chung-Chau Hon, Naoshi Fukui, Nobuho Tanaka, Zhenya Zhang, Ming Ta Michael Lee, Aki Minoda
Osteoarthritis (OA) is a common joint disorder with increasing impact in an aging society. While genetic and transcriptomic analyses have revealed some genes and non-coding loci associated to OA, the pathogenesis remains incompletely understood. Chromatin profiling, which provides insight into gene regulation, has not been reported in OA mainly due to technical difficulties. Here, we employed Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) to map the accessible chromatin landscape in articular knee cartilage of OA patients...
October 19, 2018: Scientific Reports
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
Wen-Tong Liu, Yu-Jin Lv, Rui-Cheng Yang, Ji-Yang Fu, Lu Liu, Huan Wang, Qi Cao, Chen Tan, Huan-Chun Chen, Xiang-Ru Wang
BACKGROUND: Bacterial meningitis remains a big threat to the integrity of the central nervous system (CNS), despite the advancements in antimicrobial reagents. Escherichia coli is a bacterial pathogen that can disrupt the CNS function, especially in neonates. E. coli meningitis occurs after bacteria invade the brain microvascular endothelial cells (BMECs) that form a direct and essential barrier restricting the entry of circulating microbes and toxins to the brain. Previous studies have reported on several cellular proteins that function during meningitic E...
October 19, 2018: Journal of Neuroinflammation
Tianquan Yang, Qian Yu, Wei Xu, De-Zhu Li, Fu Chen, Aizhong Liu
BACKGROUND: Malania oleifera Chun et Lee (Olacaceae), an evergreen broad-leaved woody tree native to southwest China, is an important oilseed tree. Its seed oil has a high level of nervonic acid (cis-tetracos-15-enoic acid, over 60%), which is essential for human health. M. oleifera seed oil is a promising source of nervonic acid, but little is known about the physiological and molecular mechanisms underlying its biosynthesis. RESULTS: In this study, we recorded oil accumulation at four stages of seed development...
October 19, 2018: BMC Plant Biology
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
Jatziri Mota-Gutierrez, Ilario Ferrocino, Kalliopi Rantsiou, Luca Cocolin
Next-generation sequencing has been used to strengthen knowledge about taxonomic diversity and ecology of fungi within food ecosystems. However, primer amplification and identification bias could edge our understanding into the fungal ecology. The aim of this study is to compare the performance of two primer pairs over two nuclear ribosomal RNA (rRNA) regions of the fungal kingdom, namely the ITS2 and 26S regions. Fermented cocoa beans were employed as biological material and the fungal ecology during fermentation was studied using amplicon-based sequencing tools, making use of a manually curated 26S database constructed in this study, and validated with SILVA's database...
October 10, 2018: International Journal of Food Microbiology
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
Laura L Baxter, Dawn E Watkins-Chow, William J Pavan, Stacie K Loftus
Over the past century, studies of human pigmentary disorders along with mouse and zebrafish models have shed light on the many cellular functions associated with visible pigment phenotypes. This has led to numerous genes annotated with the ontology term "pigmentation" in independent human, mouse and zebrafish databases. Comparisons among these datasets revealed that each is individually incomplete in documenting all genes involved in integument-based pigmentation phenotypes. Additionally, each database contained inherent species-specific biases in data annotation, and the term "pigmentation" did not solely reflect integument pigmentation phenotypes...
October 19, 2018: Pigment Cell & Melanoma Research
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
Changhong Yang, Jiarui Li, Qixi Wu, Xiaoxu Yang, August Yue Huang, Jie Zhang, Adam Yongxin Ye, Yanmei Dou, Linlin Yan, Wei-Zhen Zhou, Lei Kong, Meng Wang, Chen Ai, Dechang Yang, Liping Wei
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with strong genetic contributions. To provide a comprehensive resource for the genetic evidence of ASD, we have updated the Autism KnowledgeBase (AutismKB) to version 2.0. AutismKB 2.0 integrates multiscale genetic data on 1379 genes, 5420 copy number variations and structural variations, 11 669 single-nucleotide variations or small insertions/deletions (SNVs/indels) and 172 linkage regions. In particular, AutismKB 2.0 highlights 5669 de novo SNVs/indels due to their significant contribution to ASD genetics and includes 789 mosaic variants due to their recently discovered contributions to ASD pathogenesis...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Lu Yu, Xindi Liu, Daniel J O'Sullivan
Bifidobacterium longum DJO10A was previously demonstrated to be able to produce a broad-spectrum lantibiotic, but production in media was very limited and only periodically on solid media. Given the difficulty of obtaining these lantibiotic peptides using B. longum DJO10A due to its tightly controlled production, genes predicted to be required for its production and immunity were designed and codon optimized according to the preferred codon used by Lactococcus lactis. Since the lanR1 gene within this lantibiotic gene cluster was the only one without a characterized analogue from other lantibiotic gene clusters, its annotation was re-examined as it was previously suggested to be a regulatory protein...
October 19, 2018: Microbiology
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
Xiaofeng Su, Guoqing Lu, Huiming Guo, Kaixuan Zhang, Xiaokang Li, Hongmei Cheng
Verticillium wilt caused by the soil-borne fungus Verticillium dahliae is a common, devastating plant vascular disease notorious for causing economic losses. Despite considerable research on plant resistance genes, there has been little progress in modeling the effects of this fungus owing to its complicated pathogenesis. Here, we analyzed the transcriptional and metabolic responses of Arabidopsis thaliana to V. dahliae inoculation by Illumina-based RNA sequencing (RNA-seq) and nuclear magnetic resonance (NMR) spectroscopy...
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
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