1
|
Zamani K, Mohsenpour M, Malboobi MA. Predicting the allergenic risk of Phosphite-NAD +-Oxidoreductase and purple acid phosphatase 17 proteins in genetically modified canola using bioinformatic approaches. Food Chem Toxicol 2023; 182:114094. [PMID: 37925014 DOI: 10.1016/j.fct.2023.114094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/25/2023] [Accepted: 10/08/2023] [Indexed: 11/06/2023]
Abstract
Recent advancements in the generation of high-throughput multi-omics data have provided a vast array of candidate genes for the genetic engineering of plants. However, as part of their safety assessment, newly expressed proteins in genetically modified crops must be evaluated for potential cross-reactivity with known allergens. In this study, we developed transgenic canola plants expressing the Arabidopsis thaliana PAP17 gene and a novel selectable marker composed of the ptxD gene from Pseudomonas stutzeri. To evaluate the potential allergenic cross-reactivity of the AtPAP17 and PTXD proteins expressed in transgenic canola, we applied a comprehensive approach utilizing sequence-based, motif-based, and 3D structure-based analyses. Our results demonstrate that the risk of conferring cross-reactivity with known allergens is negligible, indicating that the expression of these proteins in transgenic canola poses a low allergenic risk.
Collapse
Affiliation(s)
- Katayoun Zamani
- Department of Genetic Engineering and Biosafety, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 31359-33151, Karaj, Iran.
| | - Motahhareh Mohsenpour
- Department of Genetic Engineering and Biosafety, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 31359-33151, Karaj, Iran
| | - Mohammad Ali Malboobi
- Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology, P.O. Box 14965-161, Tehran, Iran
| |
Collapse
|
2
|
Deciphering transmission dynamics and spillover of avian influenza viruses from avian species to swine populations globally. Virus Genes 2021; 57:541-555. [PMID: 34625868 PMCID: PMC8500266 DOI: 10.1007/s11262-021-01873-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/26/2021] [Indexed: 12/21/2022]
Abstract
Genome sequences of eleven avian influenza virus (AIV) subtypes have been reported in swine populations from seven countries until August 2020. To unravel the transmission dynamics and spillover events of AIVs from avian reservoirs to swine, full-length hemagglutinin (HA) sequences of AIV subtypes (n = 11) reported from various avian species and swine were retrieved from the ‘Influenza Research Database’. Phylogenetic analysis identified closely related avian and swine AIV sequences suggesting potential spillover events from multiple domestic and wild avian species, including chicken, duck, pigeon, goose, quail, and aquatic birds to swine. Furthermore, N-linked glycosylation analysis of these closely related AIV sequences supported the possibility of multiple spillover events of highly pathogenic H5N1 and low pathogenic H9N2 viruses from various avian species to swine. The principal coordinate analysis further validated these findings for H5N1 and H9N2 viruses; however, spillover events of the other nine AIV subtypes were limited. Interestingly, the presence of potential mammalian adaptation markers, particularly in some of the swine H5N1, H7N9, and H9N2 viruses, suggested that these viruses may have already adapted in swine. The occurrence and circulation of these AIVs in swine, especially the H5N1 and H9N2 viruses with numerous spillover events from the avian reservoirs to swine, pose a significant threat in terms of their reassortment with endemic swine viruses or circulating human influenza viruses within the swine which may facilitate the emergence of a novel influenza virus strain with pandemic potential.
Collapse
|
3
|
Foroutan M, Ghaffarifar F, Sharifi Z, Dalimi A. Vaccination with a novel multi-epitope ROP8 DNA vaccine against acute Toxoplasma gondii infection induces strong B and T cell responses in mice. Comp Immunol Microbiol Infect Dis 2020; 69:101413. [DOI: 10.1016/j.cimid.2020.101413] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 12/29/2019] [Accepted: 12/31/2019] [Indexed: 10/25/2022]
|
4
|
Feng Y, Zhang Y, Ding W, Wu P, Cao X, Xue S. Expanding of Phospholipid:Diacylglycerol AcylTransferase (PDAT) from Saccharomyces cerevisiae as Multifunctional Biocatalyst with Broad Acyl Donor/Acceptor Selectivity. Appl Biochem Biotechnol 2019; 188:824-835. [PMID: 30706417 DOI: 10.1007/s12010-019-02954-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/11/2019] [Indexed: 12/27/2022]
Abstract
Triacylglycerols are considered one of the most promising feedstocks for biofuels. Phospholipid:diacylglycerol acyltransferase (PDAT), responsible for the last step of triacylglycerol synthesis in the acyl-CoA-independent pathway, has attracted much attention by catalyzing membrane lipid transformation. However, due to lack of biochemical and enzymatic studies, PDAT has not carried forward in biocatalyst application. Here, the PDAT from Saccharomyces cerevisiae was expressed in Pichia pastoris. The purified enzymes were studied using different acyl donors and acceptors by thin layer chromatography and gas chromatography. In addition of the preferred acyl donor of PE and PC, the results identified that ScPDAT was capable of using broad acyl donors such as PA, PS, PG, MGDG, DGDG, and acyl-CoA, and ScPDAT was more likely to use unsaturated acyl donors comparing 18:0/18:1 to 18:0/18:0 phospholipids. With regard to acyl acceptors, ScPDAT preferred 1,2 to 1,3-diacylglycerol (DAG), while 12:0/12:0 DAG was identified as the optimal acyl acceptor, followed by 18:1/18:1 and 18:1/16:0 DAG. Additionally, ScPDAT reveals esterification activity that can utilize methanol as acyl acceptor to generate fatty acid methyl esters. The results fully expand the enzymatic selectivity of ScPDAT and provide fundamental knowledge for synthesis of triacylglycerol-derived biofuels.
Collapse
Affiliation(s)
- Yanbin Feng
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yunxiu Zhang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Wei Ding
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Peichun Wu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xupeng Cao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Song Xue
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| |
Collapse
|
5
|
Nettleship JE, Rada H, Owens RJ. Overview of a High-Throughput Pipeline for Streamlining the Production of Recombinant Proteins. Methods Mol Biol 2019; 2025:33-49. [PMID: 31267447 DOI: 10.1007/978-1-4939-9624-7_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Production of high quality protein is an essential step for both structural and functional studies. Throughput has increased in the past decade by the use of streamlined workflows with standard operating procedures and automation. In this chapter, we describe the Oxford Protein Production Facility (OPPF) pipeline for protein production, from conception, through vector construction, to expression and purification. Results from projects run in the OPPF demonstrate the value of using parallel expression screening of intracellular proteins in both E. coli and insect cells. Transient expression in Human Embryonic Kidney (HEK) cells is used exclusively for production of secreted glycoproteins. Protein purification and quality assessment are independent of the expression system and enable sample preparation to be simplified and streamlined.
Collapse
Affiliation(s)
- Joanne E Nettleship
- Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Oxford, Oxford, UK
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford, UK
| | - Heather Rada
- Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Oxford, Oxford, UK
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford, UK
| | - Raymond J Owens
- Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Oxford, Oxford, UK.
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
6
|
Mohebbi A, Fotouhi F, Jamali A, Yaghobi R, Farahmand B, Mohebbi R. Molecular epidemiology of the hemagglutinin gene of prevalent influenza virus A/H1N1/pdm09 among patient in Iran. Virus Res 2018; 259:38-45. [PMID: 30336188 DOI: 10.1016/j.virusres.2018.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 11/17/2022]
Abstract
In 2015, the influenza virus A/H1N1/pdm09 strain outbreak became prevalent throughout the different provinces of Iran. There are relatively limited complete genetic sequences available for this virus from Asian countries. Diagnosis and virological surveillance of influenza is essential for detecting novel genetic variants causing epidemic potential. This study describes the genetic properties of HA genome of influenza A/H1N1 pdm09 viruses circulating in Iran during the 2015/2016 season. In order to investigate the genetic pattern of influenza A/H1N1 pdm09, a total of 1758 nasopharyngeal swabs were screened by real-time RT-PCR. Of those, 510 cases were found to be positive for A/H1N1/pdm09 virus. Evolution of the approximately 100 positive specimens with high virus load was conducted via genomic phylogeny. Phylogenetic analysis of the HA genes of the A/H1N1pdm09 viruses revealed the circulation of clade 6B1, characterized by amino acid substitutions S84N, S162N and I216T, where position 162 became glycosylated. The N-glycosylation of HA protein is post or co-translational modification that affect the evolution of influenza viruses. For influenza A(H1N1) pdm09 viruses, we found more mutations in the antigenic sites than in the stem region. The results of this study confirmed the necessity of constant regular antigenic and molecular surveillance of circulating seasonal influenza viruses.
Collapse
Affiliation(s)
- Atefeh Mohebbi
- Department of Microbiology, College of Science Agriculture and Modern Technology, Shiraz Branch, Islamic Azad University, Shiraz, Iran.
| | - Fatemeh Fotouhi
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.
| | - Abbas Jamali
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.
| | - Ramin Yaghobi
- Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Behrokh Farahmand
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.
| | - Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
7
|
Emerging glycobiology tools: A renaissance in accessibility. Cell Immunol 2018; 333:2-8. [PMID: 29759530 DOI: 10.1016/j.cellimm.2018.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 01/01/2023]
Abstract
The glycobiology of the immune response is a topic that has garnered increased attention due to a number of key discoveries surrounding IgG function, the specificity of some broadly neutralizing anti-HIV antibodies, cancer immunoregulation by galectin molecules and others. This review is the opening article in a Special Edition of Cellular Immunology focused on glycoimmunology, and has the goal of setting the context for these articles by providing a mini-review of how glycans impact immunity. We also focus on some of the technological and methodological advances in the field of glycobiology that are being deployed to lower the barrier of entry into the glycosciences, and to more fully interrogate the glycome and its function.
Collapse
|
8
|
Song X, Zhang H, Zhang D, Xie W, Zhao G. Bioinformatics analysis and epitope screening of a potential vaccine antigen TolB from Acinetobacter baumannii outer membrane protein. INFECTION GENETICS AND EVOLUTION 2018; 62:73-79. [PMID: 29673984 DOI: 10.1016/j.meegid.2018.04.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 10/17/2022]
Abstract
The clinical isolation rate of multidrug-resistant or pan-resistant Acinetobacter baumannii (A. baumannii) is increasing, resulting that optional antibiotics are very limited in clinical practice. To deal with such a dilemma in treatment, the development of effective vaccines serves as a good strategy. Outer membrane proteins (Omp) often contain potential excellent vaccine antigens, and NCBI has published >300 Omp sequences of A. baumannii (including the duplicates). To accurately screen out the potential excellent antigen molecules from a large number of sequences, and avoid repetitive experimental processes is of great significance. In this study, we used the bioinformatics software to give extensive predictions of TolB protein. Results suggest it is a potential vaccine antigen. We then cloned the TolB gene fragments and confirmed it was highly conserved among the strains. Finally, we designed a good recombinant epitopes and conducted experimental verification. These findings provided grounds for animal immunology experiments in the future, and showed an orientation for the efficient development of A. baumannii vaccine.
Collapse
Affiliation(s)
- Xiaojie Song
- Department of Respiratory, Qilu Hospital of Shandong University, Qingdao, Shandong Province 255036, People's Republic of China
| | - Hua Zhang
- Department of Geriatric, Qingdao Municipal Hospital, Qingdao, Shandong Province 266011, People's Republic of China
| | - Dongsheng Zhang
- Department of Hepatobiliary Surgery, Qingdao Municipal Hospital, Qingdao, Shandong Province 266011, People's Republic of China
| | - Weifeng Xie
- Department of ICU, Qingdao Municipal Hospital, Qingdao, Shandong Province 266011, People's Republic of China
| | - Guanghui Zhao
- Clinical Laboratory Medicine Center, Qilu Hospital of Shandong University, Jinan, Shandong Province 250012, People's Republic of China.
| |
Collapse
|
9
|
Kim P, Jang YH, Kwon SB, Lee CM, Han G, Seong BL. Glycosylation of Hemagglutinin and Neuraminidase of Influenza A Virus as Signature for Ecological Spillover and Adaptation among Influenza Reservoirs. Viruses 2018; 10:v10040183. [PMID: 29642453 PMCID: PMC5923477 DOI: 10.3390/v10040183] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 03/25/2018] [Accepted: 04/05/2018] [Indexed: 12/12/2022] Open
Abstract
Glycosylation of the hemagglutinin (HA) and neuraminidase (NA) of the influenza provides crucial means for immune evasion and viral fitness in a host population. However, the time-dependent dynamics of each glycosylation sites have not been addressed. We monitored the potential N-linked glycosylation (NLG) sites of over 10,000 HA and NA of H1N1 subtype isolated from human, avian, and swine species over the past century. The results show a shift in glycosylation sites as a hallmark of 1918 and 2009 pandemics, and also for the 1976 “abortive pandemic”. Co-segregation of particular glycosylation sites was identified as a characteristic of zoonotic transmission from animal reservoirs, and interestingly, of “reverse zoonosis” of human viruses into swine populations as well. After the 2009 pandemic, recent isolates accrued glycosylation at canonical sites in HA, reflecting gradual seasonal adaptation, and a novel glycosylation in NA as an independent signature for adaptation among humans. Structural predictions indicated a remarkably pleiotropic influence of glycans on multiple HA epitopes for immune evasion, without sacrificing the receptor binding of HA or the activity of NA. The results provided the rationale for establishing the ecological niche of influenza viruses among the reservoir and could be implemented for influenza surveillance and improving pandemic preparedness.
Collapse
Affiliation(s)
- Paul Kim
- Vaccine Translational Research Center, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.
- Department of Integrated OMICS for Biomedical Science, College of World Class University, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.
| | - Yo Han Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.
| | - Soon Bin Kwon
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.
- Vaccine Translational Research Center, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.
| | - Chung Min Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.
- Biomedicine Pharmaceutical Group, CJ Healthcare R&D Center, CJ HealthCare, 811 Deokpyeong-ro, Majang-myeon, Icheon 17389, Korea.
| | - Gyoonhee Han
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.
- Department of Integrated OMICS for Biomedical Science, College of World Class University, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.
| | - Baik Lin Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.
- Vaccine Translational Research Center, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.
| |
Collapse
|
10
|
Imaizumi C, Tomatsu H, Kitazawa K, Yoshimi Y, Shibano S, Kikuchi K, Yamaguchi M, Kaneko S, Tsumuraya Y, Kotake T. Heterologous expression and characterization of an Arabidopsis β-l-arabinopyranosidase and α-d-galactosidases acting on β-l-arabinopyranosyl residues. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4651-4661. [PMID: 28981776 PMCID: PMC5853685 DOI: 10.1093/jxb/erx279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/11/2017] [Indexed: 05/20/2023]
Abstract
The major plant sugar l-arabinose (l-Ara) has two different ring forms, l-arabinofuranose (l-Araf) and l-arabinopyranose (l-Arap). Although l-Ara mainly appears in the form of α-l-Araf residues in cell wall components, such as pectic α-1,3:1,5-arabinan, arabinoxylan, and arabinogalactan-proteins (AGPs), lesser amounts of it can also be found as β-l-Arap residues of AGPs. Even though AGPs are known to be rapidly metabolized, the enzymes acting on the β-l-Arap residues remain to be identified. In the present study, four enzymes, which we call β-l-ARAPASE (APSE) and α-GALACTOSIDASE 1 (AGAL1), AGAL2, and AGAL3, are identified as those enzymes that are likely to be responsible for the hydrolysis of the β-l-Arap residues in Arabidopsis thaliana. An Arabidopsis apse-1 mutant showed significant reduction in β-l-arabinopyranosidase activity, and an apse-1 agal3-1 double-mutant exhibited even less activity. The apse-1 and the double-mutants both had more β-l-Arap residues in the cell walls than wild-type plants. Recombinant APSE expressed in the yeast Pichia pastoris specifically hydrolyzed β-l-Arap residues and released l-Ara from gum arabic and larch arabinogalactan. The recombinant AGAL3 also showed weak β-l-arabinopyranosidase activity beside its strong α-galactosidase activity. It appears that the β-l-Arap residues of AGPs are hydrolysed mainly by APSE and partially by AGALs in Arabidopsis.
Collapse
Affiliation(s)
- Chiemi Imaizumi
- Graduate School of Science and Engineering, Saitama University, Shimo-okubo, Sakura-ku, Saitama, Japan
| | - Harumi Tomatsu
- Graduate School of Science and Engineering, Saitama University, Shimo-okubo, Sakura-ku, Saitama, Japan
| | - Kiminari Kitazawa
- Graduate School of Science and Engineering, Saitama University, Shimo-okubo, Sakura-ku, Saitama, Japan
| | - Yoshihisa Yoshimi
- Graduate School of Science and Engineering, Saitama University, Shimo-okubo, Sakura-ku, Saitama, Japan
| | - Seiji Shibano
- Graduate School of Science and Engineering, Saitama University, Shimo-okubo, Sakura-ku, Saitama, Japan
| | - Kaoru Kikuchi
- Graduate School of Science and Engineering, Saitama University, Shimo-okubo, Sakura-ku, Saitama, Japan
| | - Masatoshi Yamaguchi
- Graduate School of Science and Engineering, Saitama University, Shimo-okubo, Sakura-ku, Saitama, Japan
| | - Satoshi Kaneko
- Faculty of Agriculture, University of the Ryukyus, Senbaru, Nishihara, Okinawa, Japan
| | - Yoichi Tsumuraya
- Graduate School of Science and Engineering, Saitama University, Shimo-okubo, Sakura-ku, Saitama, Japan
| | - Toshihisa Kotake
- Graduate School of Science and Engineering, Saitama University, Shimo-okubo, Sakura-ku, Saitama, Japan
- Correspondence:
| |
Collapse
|
11
|
Jonsson S, Sveinbjornsson G, de Lapuente Portilla AL, Swaminathan B, Plomp R, Dekkers G, Ajore R, Ali M, Bentlage AEH, Elmér E, Eyjolfsson GI, Gudjonsson SA, Gullberg U, Gylfason A, Halldorsson BV, Hansson M, Holm H, Johansson Å, Johnsson E, Jonasdottir A, Ludviksson BR, Oddsson A, Olafsson I, Olafsson S, Sigurdardottir O, Sigurdsson A, Stefansdottir L, Masson G, Sulem P, Wuhrer M, Wihlborg AK, Thorleifsson G, Gudbjartsson DF, Thorsteinsdottir U, Vidarsson G, Jonsdottir I, Nilsson B, Stefansson K. Identification of sequence variants influencing immunoglobulin levels. Nat Genet 2017. [DOI: 10.1038/ng.3897] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
12
|
circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations. Sci Rep 2016; 6:34985. [PMID: 27725737 PMCID: PMC5057092 DOI: 10.1038/srep34985] [Citation(s) in RCA: 318] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/21/2016] [Indexed: 11/09/2022] Open
Abstract
It has been known that circular RNAs are widely expressed in human tissues and cells, and play important regulatory roles in physiological or pathological processes. However, there is lack of comprehensively annotated human circular RNAs database. In this study we established a circRNA database, named as circRNADb, containing 32,914 human exonic circRNAs carefully selected from diversified sources. The detailed information of the circRNA, including genomic information, exon splicing, genome sequence, internal ribosome entry site (IRES), open reading frame (ORF) and references were provided in circRNADb. In addition, circRNAs were found to be able to encode proteins, which have not been reported in any species. 16328 circRNAs were annotated to have ORF longer than 100 amino acids, of which 7170 have IRES elements. 46 circRNAs from 37 genes were found to have their corresponding proteins expressed according mass spectrometry. The database provides the function of data search, browse, download, submit and feedback for the user to study particular circular RNA of interest and update the database continually. circRNADb will be built to be a biological information platform for circRNA molecules and related biological functions in the future. The database can be freely available through the web server at http://reprod.njmu.edu.cn/circrnadb.
Collapse
|
13
|
Hassan H, Badr A, Abdelhalim MB. Prediction of O-glycosylation Sites Using Random Forest and GA-Tuned PSO Technique. Bioinform Biol Insights 2015; 9:103-9. [PMID: 26244014 PMCID: PMC4494626 DOI: 10.4137/bbi.s26864] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/24/2015] [Accepted: 05/26/2015] [Indexed: 11/22/2022] Open
Abstract
O-glycosylation is one of the main types of the mammalian protein glycosylation; it occurs on the particular site of serine (S) or threonine (T). Several O-glycosylation site predictors have been developed. However, a need to get even better prediction tools remains. One challenge in training the classifiers is that the available datasets are highly imbalanced, which makes the classification accuracy for the minority class to become unsatisfactory. In our previous work, we have proposed a new classification approach, which is based on particle swarm optimization (PSO) and random forest (RF); this approach has considered the imbalanced dataset problem. The PSO parameters setting in the training process impacts the classification accuracy. Thus, in this paper, we perform parameters optimization for the PSO algorithm, based on genetic algorithm, in order to increase the classification accuracy. Our proposed genetic algorithm-based approach has shown better performance in terms of area under the receiver operating characteristic curve against existing predictors. In addition, we implemented a glycosylation predictor tool based on that approach, and we demonstrated that this tool could successfully identify candidate glycosylation sites in case study protein.
Collapse
Affiliation(s)
- Hebatallah Hassan
- Department of Computer Science, College of Computing and Information Technology, Arab Academy for Science and Technology and Maritime Transport (AASTMT), Cairo, Egypt
| | - Amr Badr
- Department of Computer Science, Faculty of Computers and Information, Cairo University, Cairo, Egypt
| | - M B Abdelhalim
- Department of Computer Science, College of Computing and Information Technology, Arab Academy for Science and Technology and Maritime Transport (AASTMT), Cairo, Egypt
| |
Collapse
|