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Xiao R, Zhou H, Chen CM, Cheng H, Li H, Xie J, Zhao H, Han Q, Diao X. Transcriptional responses of Acropora hyacinthus embryo under the benzo(a)pyrene stress by deep sequencing. CHEMOSPHERE 2018; 206:387-397. [PMID: 29754063 DOI: 10.1016/j.chemosphere.2018.04.149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
Coral embryos are a critical and sensitive period for the early growth and development of coral. Benzo(a)pyrene (BaP) is widely distributed in the ocean and has strong toxicity, but there is little information on the toxic effects to coral embryos exposed to this widespread environmental contaminant. Thus, in this study, we utilized the Illumina Hiseq™ 4000 platform to explore the gene response of Acropora hyacinthus embryos under the BaP stress. A total of 130,042 Unigenes were obtained and analyzed, and approximately 37.67% of those matched with sequences from four different species. In total, 2606 Unigenes were up-regulated, and 3872 Unigenes were down-regulated. After Gene Ontology (GO) annotation, the results show that the "cellular process" and "metabolic process" were leading in the category of biological processes, which the "binding" and "catalytic activity" were the most abundant subcategories in molecular function. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the most differentially expressed genes (DEGs) were enriched, as well as down-regulated in the pathways of oxidative phosphorylation, metabolism of xenobiotics, immune-related genes, apoptosis and human disease genes. At the same time, 388,197 of Single-nucleotide Polymorphisms (SNPs) and 6164 of Simple Sequence Repeats (SSRs) were obtained, which can be served as the richer and more valuable SSRs molecular markers in the future. The results of this study can help to better understand the toxicological mechanism of coral embryo exposed to BaP, and it is also essential for the protection and restoration of coral reef ecosystem in the future.
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Affiliation(s)
- Rong Xiao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Hailong Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Chien-Min Chen
- Department of Environmental Resources Management, Chia Nan University of Pharmacy & Science, Tainan, Taiwan, China
| | - Huamin Cheng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Hongwu Li
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; College of Ocean, Hainan University, Haikou 570228, China
| | - Jia Xie
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; College of Ocean, Hainan University, Haikou 570228, China
| | - Hongwei Zhao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Qian Han
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Xiaoping Diao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; Ministry of Education Key Laboratory of Tropical Island Ecology, Hainan Normal University, Haikou, 571158, China.
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Sharma AS, Gupta HO, Prasad R. PPDB: A Tool for Investigation of Plants Physiology Based on Gene Ontology. Interdiscip Sci 2015; 7:295-308. [DOI: 10.1007/s12539-015-0017-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/10/2014] [Accepted: 02/07/2014] [Indexed: 01/23/2023]
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Foulger RE, Osumi-Sutherland D, McIntosh BK, Hulo C, Masson P, Poux S, Le Mercier P, Lomax J. Representing virus-host interactions and other multi-organism processes in the Gene Ontology. BMC Microbiol 2015; 15:146. [PMID: 26215368 PMCID: PMC4517558 DOI: 10.1186/s12866-015-0481-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 07/10/2015] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The Gene Ontology project is a collaborative effort to provide descriptions of gene products in a consistent and computable language, and in a species-independent manner. The Gene Ontology is designed to be applicable to all organisms but up to now has been largely under-utilized for prokaryotes and viruses, in part because of a lack of appropriate ontology terms. METHODS To address this issue, we have developed a set of Gene Ontology classes that are applicable to microbes and their hosts, improving both coverage and quality in this area of the Gene Ontology. Describing microbial and viral gene products brings with it the additional challenge of capturing both the host and the microbe. Recognising this, we have worked closely with annotation groups to test and optimize the GO classes, and we describe here a set of annotation guidelines that allow the controlled description of two interacting organisms. CONCLUSIONS Building on the microbial resources already in existence such as ViralZone, UniProtKB keywords and MeGO, this project provides an integrated ontology to describe interactions between microbial species and their hosts, with mappings to the external resources above. Housing this information within the freely-accessible Gene Ontology project allows the classes and annotation structure to be utilized by a large community of biologists and users.
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Affiliation(s)
- R E Foulger
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - D Osumi-Sutherland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - B K McIntosh
- Department of Biochemistry and Biophysics, Texas Agrilife Research, Texas A&M University, College Station, TX, 77843, USA.
| | - C Hulo
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland.
| | - P Masson
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland.
| | - S Poux
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland.
| | - P Le Mercier
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland.
| | - J Lomax
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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Sharma AS, Gupta HO, Prasad R. PPDB - A tool for investigation of plants physiology based on gene ontology. Interdiscip Sci 2014. [PMID: 25183354 DOI: 10.1007/s12539-013-0065-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/10/2014] [Accepted: 02/07/2014] [Indexed: 09/29/2022]
Abstract
Representing the way forward, from functional genomics and its ontology to functional understanding and physiological model, in a computationally tractable fashion is one of the ongoing challenges faced by computational biology. To tackle the standpoint, we herein feature the applications of contemporary database management to the development of PPDB, a searching and browsing tool for the Plants Physiology Database that is based upon the mining of a large amount of gene ontology data currently available. The working principles and search options associated with the PPDB are publicly available and freely accessible on-line ( http://www.iitr.ernet.in/ajayshiv/ ) through a user friendly environment generated by means of Drupal-6.24. By knowing that genes are expressed in temporally and spatially characteristic patterns and that their functionally distinct products often reside in specific cellular compartments and may be part of one or more multi-component complexes, this sort of work is intended to be relevant for investigating the functional relationships of gene products at a system level and, thus, helps us approach to the full physiology.
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Affiliation(s)
- Ajay Shiv Sharma
- Department of Electrical Engineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India,
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Abstract
BACKGROUND The Gene Ontology (GO) is an ontology representing molecular biology concepts related to genes and their products. Current annotations from the GO Consortium tend to be highly specific, and contemporary genome-scale studies often return a long list of genes of potential interest, such as genes in a cancer tumor that are differentially expressed than those found in normal tissue. It is therefore a challenging task to reveal, at a conceptual level, the major functional themes in which genes are involved. Presently, there is a need for tools capable of revealing such themes through mining and representing semantic information in an objective and quantitative manner. METHODS In this study, we utilized the hierarchical organization of the GO to derive a more abstract representation of the major biological processes of a list of genes based on their annotations. We cast the task as follows: given a list of genes, identify non-disjoint, functionally coherent subsets, such that the functions of the genes in a subset are summarized by an informative GO term that accurately captures the semantic information of the original annotations. RESULTS We evaluated different metrics for assessing information loss when merging GO terms, and different statistical schemes to assess the functional coherence of a set of genes. We found that the best discriminative power was achieved by using a combination of the information-content-based measure as the information-loss metric, and the graph-based statistics derived from a Steiner tree connecting genes in an augmented GO graph. CONCLUSIONS Our methods provide an objective and quantitative approach to capturing the major directions of gene functions in a context-specific fashion.
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Kumar S, Kunec D, Buza JJ, Chiang HI, Zhou H, Subramaniam S, Pendarvis K, Cheng HH, Burgess SC. Nuclear Factor kappa B is central to Marek's disease herpesvirus induced neoplastic transformation of CD30 expressing lymphocytes in-vivo. BMC SYSTEMS BIOLOGY 2012; 6:123. [PMID: 22979947 PMCID: PMC3472249 DOI: 10.1186/1752-0509-6-123] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 09/04/2012] [Indexed: 12/15/2022]
Abstract
Background Marek’s Disease (MD) is a hyperproliferative, lymphomatous, neoplastic disease of chickens caused by the oncogenic Gallid herpesvirus type 2 (GaHV-2; MDV). Like several human lymphomas the neoplastic MD lymphoma cells overexpress the CD30 antigen (CD30hi) and are in minority, while the non-neoplastic cells (CD30lo) form the majority of population. MD is a unique natural in-vivo model of human CD30hi lymphomas with both natural CD30hi lymphomagenesis and spontaneous regression. The exact mechanism of neoplastic transformation from CD30lo expressing phenotype to CD30hi expressing neoplastic phenotype is unknown. Here, using microarray, proteomics and Systems Biology modeling; we compare the global gene expression of CD30lo and CD30hi cells to identify key pathways of neoplastic transformation. We propose and test a specific mechanism of neoplastic transformation, and genetic resistance, involving the MDV oncogene Meq, host gene products of the Nuclear Factor Kappa B (NF-κB) family and CD30; we also identify a novel Meq protein interactome. Results Our results show that a) CD30lo lymphocytes are pre-neoplastic precursors and not merely reactive lymphocytes; b) multiple transformation mechanisms exist and are potentially controlled by Meq; c) Meq can drive a feed-forward cycle that induces CD30 transcription, increases CD30 signaling which activates NF-κB, and, in turn, increases Meq transcription; d) Meq transcriptional repression or activation of the CD30 promoter generally correlates with polymorphisms in the CD30 promoter distinguishing MD-lymphoma resistant and susceptible chicken genotypes e) MDV oncoprotein Meq interacts with proteins involved in physiological processes central to lymphomagenesis. Conclusions In the context of the MD lymphoma microenvironment (and potentially in other CD30hi lymphomas as well), our results show that the neoplastic transformation is a continuum and the non-neoplastic cells are actually pre-neoplastic precursor cells and not merely immune bystanders. We also show that NF-κB is a central player in MDV induced neoplastic transformation of CD30-expressing lymphocytes in vivo. Our results provide insights into molecular mechanisms of neoplastic transformation in MD specifically and also herpesvirus induced lymphoma in general.
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Affiliation(s)
- Shyamesh Kumar
- Department of Pathobiology and Population Medicine, Mississippi State University, MS 39762, USA.
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du Plessis L, Skunca N, Dessimoz C. The what, where, how and why of gene ontology--a primer for bioinformaticians. Brief Bioinform 2011; 12:723-35. [PMID: 21330331 PMCID: PMC3220872 DOI: 10.1093/bib/bbr002] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
With high-throughput technologies providing vast amounts of data, it has become more important to provide systematic, quality annotations. The Gene Ontology (GO) project is the largest resource for cataloguing gene function. Nonetheless, its use is not yet ubiquitous and is still fraught with pitfalls. In this review, we provide a short primer to the GO for bioinformaticians. We summarize important aspects of the structure of the ontology, describe sources and types of functional annotations, survey measures of GO annotation similarity, review typical uses of GO and discuss other important considerations pertaining to the use of GO in bioinformatics applications.
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Affiliation(s)
- Louis du Plessis
- ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland
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Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop. Viruses 2010; 2:2258-2268. [PMID: 21994619 PMCID: PMC3185566 DOI: 10.3390/v2102258] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 09/18/2010] [Accepted: 09/20/2010] [Indexed: 11/29/2022] Open
Abstract
Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world’s biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop.
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A genotype and phenotype database of genetically modified malaria-parasites. Trends Parasitol 2010; 27:31-9. [PMID: 20663715 DOI: 10.1016/j.pt.2010.06.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 06/15/2010] [Accepted: 06/16/2010] [Indexed: 11/20/2022]
Abstract
The RMgm database, www.pberghei.eu, is a web-based, manually curated, repository containing information on genetically modified rodent-malaria parasites. It provides easy and rapid access to information on the genotype and phenotype of mutant and reporter parasites. The database also contains information on unpublished mutants without a clear phenotype and negative trials to disrupt genes. Information can be searched using pre-defined key features, such as phenotype, life-cycle stage, gene model, gene-tags and mutations. The information relating to the mutants is reciprocally linked to PlasmoDB and GeneDB. Access to mutant-parasite information, and gene function/ontology inferred from mutant phenotypes provides a timely resource aimed at enhancing research into Plasmodium gene function and (systems) biology.
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