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Gu X, Ding Y, Xiao P. MLapRVFL: Protein sequence prediction based on Multi-Laplacian Regularized Random Vector Functional Link. Comput Biol Med 2023; 167:107618. [PMID: 37925912 DOI: 10.1016/j.compbiomed.2023.107618] [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: 07/31/2023] [Revised: 10/14/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
Protein sequence classification is a crucial research field in bioinformatics, playing a vital role in facilitating functional annotation, structure prediction, and gaining a deeper understanding of protein function and interactions. With the rapid development of high-throughput sequencing technologies, a vast amount of unknown protein sequence data is being generated and accumulated, leading to an increasing demand for protein classification and annotation. Existing machine learning methods still have limitations in protein sequence classification, such as low accuracy and precision of classification models, rendering them less valuable in practical applications. Additionally, these models often lack strong generalization capabilities and cannot be widely applied to various types of proteins. Therefore, accurately classifying and predicting proteins remains a challenging task. In this study, we propose a protein sequence classifier called Multi-Laplacian Regularized Random Vector Functional Link (MLapRVFL). By incorporating Multi-Laplacian and L2,1-norm regularization terms into the basic Random Vector Functional Link (RVFL) method, we effectively improve the model's generalization performance, enhance the robustness and accuracy of the classification model. The experimental results on two commonly used datasets demonstrate that MLapRVFL outperforms popular machine learning methods and achieves superior predictive performance compared to previous studies. In conclusion, the proposed MLapRVFL method makes significant contributions to protein sequence prediction.
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Affiliation(s)
- Xingyue Gu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yijie Ding
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang, 324003, China; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 611730, China.
| | - Pengfeng Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
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Liu F, Song YY, Zhang R, Liu RD, Jiang P, Cui *J, Wang ZQ. Cloning and Expression of a New Trichinella spiralis Serine Protease and Its Role in Invading Host Intestinal Epithelium. IRANIAN JOURNAL OF PARASITOLOGY 2022; 17:375-384. [PMID: 36466014 PMCID: PMC9682372 DOI: 10.18502/ijpa.v17i3.10628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/22/2021] [Indexed: 06/17/2023]
Abstract
BACKGROUND In previous studies, a new Trichinella spiralis serine protease 1.1 (TsSP1.1) was identified in surface proteins of T. spiralis muscle larvae (ML) by proteomics analysis, but its functions in T. spiralis infection are unknown. The aim of this study was to investigate the roles of TsSP1.1 during larval intrusion of gut epithelium. METHODS From January 2019 to March 2021, complete TsSP1.1 cDNA sequence was cloned and expressed in Escherichia coli BL21 at the Department of Parasitology, Medical College of Zhengzhou University, Zhengzhou, China. Expression and location of TsSP1.1 in the parasite were investigated using indirect immunofluorescence assay (IIFA) and Western blotting. The in vitro intestinal epithelium cells (IECs) intrusion assay was used to ascertain the roles of TsSP1.1 during larval intrusion of IECs and gut epithelium. RESULTS TsSP1.1 was a surface and secretory protein, which was expressed at various T. spiralis stages, and principally localized at cuticle, stichosome and embryos of the nematode. rTsSP1.1 accelerated larval intrusion of IECs, whereas anti-rTsSP1.1 antibodies impeded larval intrusion. The acceleration and inhibtion was dose-dependently related to rTsSP1.1 and anti-TsSP1.1 antibodies. Block of the IIL with anti-rTsSP1.1 serum also impeded larval intrusion of gut mucosa. CONCLUSION TsSP1.1 participates in T. spiralis intrusion of gut epithelium.
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Liu W, Gong T, Chen S, Liu Q, Zhou H, He J, Wu Y, Li F, Liu Y. Epidemiology, Diagnosis, and Prevention of Sparganosis in Asia. Animals (Basel) 2022; 12:1578. [PMID: 35739914 PMCID: PMC9219546 DOI: 10.3390/ani12121578] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 11/17/2022] Open
Abstract
Sparganosis is a zoonotic parasitic disease caused by the larvae (spargana) of the genus Spirometra, which is widely distributed globally and threatens human health. More than 60 species of Spirometra have already been identified, and over 2000 cases have been reported. This review summarizes the prevalence of humans, frogs, snakes, and other animals with spargana. Furthermore, the infection mode, distribution, and site are summarized and analyzed. We also describe the epidemiology, molecular diagnosis, and other aspects which are of considerable significance to preventing sparganum.
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Affiliation(s)
- Wei Liu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (W.L.); (T.G.); (S.C.); (H.Z.); (J.H.)
- Hunan Provincial the Key Laboratory of Protein Engineering in Animal Vaccine, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China;
| | - Tengfang Gong
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (W.L.); (T.G.); (S.C.); (H.Z.); (J.H.)
| | - Shuyu Chen
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (W.L.); (T.G.); (S.C.); (H.Z.); (J.H.)
| | - Quan Liu
- School of Life Sciences and Engineering, Foshan University, Foshan 528225, China;
| | - Haoying Zhou
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (W.L.); (T.G.); (S.C.); (H.Z.); (J.H.)
| | - Junlin He
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (W.L.); (T.G.); (S.C.); (H.Z.); (J.H.)
| | - Yong Wu
- Hunan Provincial the Key Laboratory of Protein Engineering in Animal Vaccine, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China;
| | - Fen Li
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (W.L.); (T.G.); (S.C.); (H.Z.); (J.H.)
- Hunan Provincial the Key Laboratory of Protein Engineering in Animal Vaccine, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China;
| | - Yisong Liu
- Hunan Provincial the Key Laboratory of Protein Engineering in Animal Vaccine, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China;
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Kisworo D, Depamede SN. Bioinformatics analysis of structures and ligand-bindings of predicted zymogen granule protein observed on Bali cattle ( Bos javanicus) saliva. J Adv Vet Anim Res 2021; 8:224-229. [PMID: 34395592 PMCID: PMC8280989 DOI: 10.5455/javar.2021.h506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 11/03/2022] Open
Abstract
Objective Previously, we have shown that predicted zymogen granule protein 16 homolog B (P-G3MZ19) existed in Bali cattle (Bos javanicus) saliva. It was suggested that P-G3MZ19 is a member of the mannose-binding lectin family that plays an essential role in innate immunity. In the present study, we aimed to analyze the structure and ligand-binding of P-3MZ19 in Bali cattle saliva. Materials and Methods Saliva of four adult healthy Bali cattle was collected, lyophilized, and subjected to two-dimensional (2-D) gel electrophoresis. The target spot of around 17 kDa related to P-G3MZ19 was excised for matrix-assisted laser desorption ionization time-of-flight mass spectrometer/time-of-flight mass spectrometer mass spectrometry analysis and sequencing. The structure and the ligand-binding of P-3MZ19 were analyzed using bioinformatics software programs published elsewhere. Results Based on Iterative Threading ASSEmbly Refinement the 3D model of P-G3MZ19 was suggested to have similarities to exo-alpha-sialidase (EC 3.2.1.18); while its ligand-binding sites consisted of seven residues, i.e., 25aa-26aa (Gly-Gly), 95aa (Phe), 138aa (Tyr), 140aa (Leu), 141aa (Gly), and 143aa (Thr). Conclusion The structure of P-G3MZ19 of Bali cattle saliva and its ligand-binding sites have been successfully determined by using bioinformatics techniques. The biological and immunological roles of the peptide are currently under investigation based on P-G3MZ19 synthetic peptides.
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Affiliation(s)
- Djoko Kisworo
- Faculty of Animal Science, University of Mataram, Mataram, Indonesia
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Yuan S, Ke D, Li R, Li X, Wang L, Chen H, Zhang C, Huang Y, Chen L, Hao Q, Yang H, Cao D, Chen S, Guo W, Shan Z, Yang Z, Zhang X, Qiu D, Guan Y, Zhou X. Genome-wide survey of soybean papain-like cysteine proteases and their expression analysis in root nodule symbiosis. BMC PLANT BIOLOGY 2020; 20:517. [PMID: 33183238 PMCID: PMC7659060 DOI: 10.1186/s12870-020-02725-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/26/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plant papain-like cysteine proteases (PLCPs) are a large class of proteolytic enzymes and play important roles in root nodule symbiosis (RNS), while the whole-genome studies of PLCP family genes in legume are quite limited, and the roles of Glycine max PLCPs (GmPLCPs) in nodulation, nodule development and senescence are not fully understood. RESULTS In the present study, we identified 97 GmPLCPs and performed a genome-wide survey to explore the expansion of soybean PLCP family genes and their relationships to RNS. Nineteen paralogous pairs of genomic segments, consisting of 77 GmPLCPs, formed by whole-genome duplication (WGD) events were identified, showing a high degree of complexity in duplication. Phylogenetic analysis among different species showed that the lineage differentiation of GmPLCPs occurred after family expansion, and large tandem repeat segment were specifically in soybean. The expression patterns of GmPLCPs in symbiosis-related tissues and nodules identified RNS-related GmPLCPs and provided insights into their putative symbiotic functions in soybean. The symbiotic function analyses showed that a RNS-related GmPLCP gene (Glyma.04G190700) really participate in nodulation and nodule development. CONCLUSIONS Our findings improved our understanding of the functional diversity of legume PLCP family genes, and provided insights into the putative roles of the legume PLCPs in nodulation, nodule development and senescence.
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Affiliation(s)
- Songli Yuan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Danxia Ke
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Sciences & Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
| | - Rong Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiangyong Li
- College of Life Sciences & Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
| | - Lei Wang
- College of Life Sciences & Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
| | - Haifeng Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chanjuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Limiao Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Qingnan Hao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hongli Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dong Cao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shuilian Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Wei Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zhihui Shan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zhonglu Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaojuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dezhen Qiu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuefeng Guan
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Xinan Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China.
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Qi X, Yue X, Han Y, Jiang P, Yang F, Lei JJ, Liu RD, Zhang X, Wang ZQ, Cui J. Characterization of Two Trichinella spiralis Adult-Specific DNase II and Their Capacity to Induce Protective Immunity. Front Microbiol 2018; 9:2504. [PMID: 30455671 PMCID: PMC6230719 DOI: 10.3389/fmicb.2018.02504] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 10/02/2018] [Indexed: 12/13/2022] Open
Abstract
Deoxyribonuclease II (DNase II) is a widespread endonuclease, which can degrade the DNA. Trichinella spiralis adult-specific DNase II-1 (TsDNase II-1) and DNase II-7 (TsDNase II-7) were identified in excretory-secretory (ES) or surface proteins of adult worm (AW) and intestinal infective larvae (IIL) using immunoproteomics with early infection sera. The aim of this study was to characterize the two T. spiralis DNase II enzymes and to investigate their role as potential vaccine candidate target molecules. The cDNA sequences of the two DNase II enzymes from 3 days old AWs of T. spiralis were cloned and expressed. The sequencing results showed that the complete cDNA sequences of the two DNase II enzymes were 1221 and 1161 bp long, and the predicted open reading frames encoded 347 and 348 amino acids, respectively. On Western blot analysis, natural TsDNase II-1 and TsDNase II-7 in the crude extracts of IIL, AWs, and newborn larvae (NBL) and AW ES proteins were recognized by both anti-rTsDNase II-1 and anti-rTsDNase II-7 sera. Indirect immunofluorescence test and qPCR showed that the two DNase II enzymes were highly expressed at AW and NBL stages and were mainly located at the cuticle and stichosome of the nematode. Vaccination with the two recombinant DNase II enzymes triggered prominent humoral responses that exhibited significant immune protection against T. spiralis larval infection, as demonstrated by the notable reduction in intestinal AW and muscle larva burdens. Specific antibodies to the two molecules evidently inhibited the in vitro parasite invasion of enterocytes and participated in the killing of NBL by an antibody-dependent cell-mediated cytotoxicity (ADCC) mode. The enzymes DNase II-1 and DNase II-7 are the potential target molecules for anti-Trichinella vaccine for blocking both larval invasion and development.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhong Q. Wang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
| | - Jing Cui
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, China
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Tsubokawa D, Hatta T, Maeda H, Mikami F, Goso Y, Nakamura T, Alim MA, Tsuji N. A cysteine protease from Spirometra erinaceieuropaei plerocercoid is a critical factor for host tissue invasion and migration. Acta Trop 2017; 167:99-107. [PMID: 28012905 DOI: 10.1016/j.actatropica.2016.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 12/14/2016] [Accepted: 12/18/2016] [Indexed: 01/13/2023]
Abstract
Sparganosis in humans caused by the plerocercoid larvae of Spirometra erinaceieuropaei is found worldwide, especially in Eastern Asia and the Far East. Previous studies have suggested that dissolution of plerocercoid body, plerocercoid invasion of host tissue, and migration are important processes for sparganosis progression. However, the mechanisms underlying these processes have yet to be determined. Here, we demonstrated the enzymatic property and involvement of a native 23kDa cysteine protease (Se23kCP), purified from plerocercoids, in sparganosis pathogenesis. Se23kCP is mature protease consisting of 216 amino acids and has a high sequence similarity with cathepsin L in various organisms. Se23kCP conjugated with N-glycans, which have a core fucose residue. Both cysteine and serine protease-specific activities were determined in Se23kCP and their optimal pHs were found to be different, indicating that Se23kCP has a wide range of substrate specificity. Se23kCP was secreted from tegumental vacuoles of the plerocercoid to host subcutaneous tissues and degraded human structural proteins, such as collagen and fibronectin. In addition, the plerocercoid body was lysed by Se23kCP, which facilitated larval invasion of host tissue. Our findings suggest that Se23kCP induces host tissue invasion and migration, and might be an essential molecule for sparganosis onset and progression.
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Affiliation(s)
- Daigo Tsubokawa
- Department of Molecular and Cellular Parasitology, Kitasato University Graduate School of Medical Sciences, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa 252-0373, Japan; Department of Parasitology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa 252-0374, Japan
| | - Takeshi Hatta
- Department of Molecular and Cellular Parasitology, Kitasato University Graduate School of Medical Sciences, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa 252-0373, Japan; Department of Parasitology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa 252-0374, Japan
| | - Hiroki Maeda
- Department of Parasitology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa 252-0374, Japan; Department of Pathological and Preventive Veterinary Science, The United Graduate School of Veterinary Science, Yamaguchi University, Yoshida, Yamaguchi 753-8515, Japan
| | - Fusako Mikami
- Department of Parasitology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa 252-0374, Japan
| | - Yukinobu Goso
- Department of Biochemistry, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa 252-0374, Japan
| | - Takeshi Nakamura
- Department of Parasitology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa 252-0374, Japan
| | - M Abdul Alim
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Naotoshi Tsuji
- Department of Molecular and Cellular Parasitology, Kitasato University Graduate School of Medical Sciences, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa 252-0373, Japan; Department of Parasitology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa 252-0374, Japan.
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Bennett HM, Mok HP, Gkrania-Klotsas E, Tsai IJ, Stanley EJ, Antoun NM, Coghlan A, Harsha B, Traini A, Ribeiro DM, Steinbiss S, Lucas SB, Allinson KSJ, Price SJ, Santarius TS, Carmichael AJ, Chiodini PL, Holroyd N, Dean AF, Berriman M. The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion. Genome Biol 2015. [PMID: 25413302 PMCID: PMC4265353 DOI: 10.1186/s13059-014-0510-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sparganosis is an infection with a larval Diphyllobothriidea tapeworm. From a rare cerebral case presented at a clinic in the UK, DNA was recovered from a biopsy sample and used to determine the causative species as Spirometra erinaceieuropaei through sequencing of the cox1 gene. From the same DNA, we have produced a draft genome, the first of its kind for this species, and used it to perform a comparative genomics analysis and to investigate known and potential tapeworm drug targets in this tapeworm. RESULTS The 1.26 Gb draft genome of S. erinaceieuropaei is currently the largest reported for any flatworm. Through investigation of β-tubulin genes, we predict that S. erinaceieuropaei larvae are insensitive to the tapeworm drug albendazole. We find that many putative tapeworm drug targets are also present in S. erinaceieuropaei, allowing possible cross application of new drugs. In comparison to other sequenced tapeworm species we observe expansion of protease classes, and of Kuntiz-type protease inhibitors. Expanded gene families in this tapeworm also include those that are involved in processes that add post-translational diversity to the protein landscape, intracellular transport, transcriptional regulation and detoxification. CONCLUSIONS The S. erinaceieuropaei genome begins to give us insight into an order of tapeworms previously uncharacterized at the genome-wide level. From a single clinical case we have begun to sketch a picture of the characteristics of these organisms. Finally, our work represents a significant technological achievement as we present a draft genome sequence of a rare tapeworm, and from a small amount of starting material.
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Liu LN, Wang ZQ, Zhang X, Jiang P, Qi X, Liu RD, Zhang ZF, Cui J. Characterization of Spirometra erinaceieuropaei Plerocercoid Cysteine Protease and Potential Application for Serodiagnosis of Sparganosis. PLoS Negl Trop Dis 2015; 9:e0003807. [PMID: 26046773 PMCID: PMC4457932 DOI: 10.1371/journal.pntd.0003807] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 05/01/2015] [Indexed: 11/22/2022] Open
Abstract
Background Sparganosis is a neglected but important food-borne parasitic zoonosis. Clinical diagnosis of sparganosis is difficult because there are no specific manifestations. ELISA using plerocercoid crude or excretory–secretory (ES) antigens has high sensitivity but has cross-reactions with other helminthiases. The aim of this study was to characterize Spirometra erinaceieuropaei cysteine protease (SeCP) and to evaluate its potential application for serodiagnosis of sparganosis. Methodology/Principal Findings The full length SeCP gene was cloned, and recombinant SeCP (rSeCP) was expressed and purified. Western blotting showed that rSeCP was recognized by the serum of sparganum-infected mice, and anti-rSeCP serum recognized the native SeCP protein of plerocercoid crude or ES antigens. Expression of SeCP was observed at plerocercoid stages but not at the adult and egg stages. Immunolocalization identified SeCP in plerocercoid tegument and parenchymal tissue. The rSeCP had CP activity, and the optimum pH and temperature were 5.5 and 37°C, respectively. Enzymatic activity was significantly inhibited by E-64. rSeCP functions to degrade different proteins and the function was inhibited by anti-rSeCP serum and E-64. Immunization of mice with rSeCP induced Th2-predominant immune responses and anti-rSeCP antibodies had the potential capabilities to kill plerocercoids in an ADCC assay. The sensitivity of rSeCP-ELISA and ES antigen ELISA was 100% when performed on sera of patients with sparganosis. The specificity of rSeCP-ELISA and ES antigen ELISA was 98.22% (166/169) and 87.57% (148/169), respectively (P<0.05). Conclusions The rSeCP had the CP enzymatic activity and SeCP seems to be important for the survival of plerocercoids in host. The rSeCP is a potential diagnostic antigen for sparganosis. Sparganosis is a neglected tropical disease; its diagnosis is difficult and it is often misdiagnosed. ELISA using the crude or ES antigens of plerocercoids cross reacts with other helminthiases. Cysteine protease is a type of hydrolase and plays important roles in the development and survival of parasites; it has been used for diagnostic markers and vaccine targets for some parasitic diseases. In this study, a 36 kDa Spirometra erinaceieuropaei cysteine protease (SeCP) was expressed and purified. The results showed that SeCP was a plerocercoid stage-specific protein located in the teguments and parenchymal tissue. The rSeCP had cysteine protease activity and functioned to degrade host proteins. Vaccination of mice with rSeCP induced high levels of IgG1 and anti-rSeCP antibodies with the ability to kill plerocercoids in an ADCC assay. The rSeCP had a high sensitivity and specificity for detecting anti-plerocercoid antibodies, and could be used as a potential antigen for serodiagnosis of sparganosis.
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Affiliation(s)
- Li Na Liu
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Zhong Quan Wang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
- * E-mail: (ZQW); (JC)
| | - Xi Zhang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Peng Jiang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Xin Qi
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Ruo Dan Liu
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Zi Fang Zhang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Jing Cui
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
- * E-mail: (ZQW); (JC)
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Protein sequence classification with improved extreme learning machine algorithms. BIOMED RESEARCH INTERNATIONAL 2014; 2014:103054. [PMID: 24795876 PMCID: PMC3985160 DOI: 10.1155/2014/103054] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/15/2014] [Accepted: 02/16/2014] [Indexed: 11/30/2022]
Abstract
Precisely classifying a protein sequence from a large biological protein sequences database plays an important role for developing competitive pharmacological products. Comparing the unseen sequence with all the identified protein sequences and returning the category index with the highest similarity scored protein, conventional methods are usually time-consuming. Therefore, it is urgent and necessary to build an efficient protein sequence classification system. In this paper, we study the performance of protein sequence classification using SLFNs. The recent efficient extreme learning machine (ELM) and its invariants are utilized as the training algorithms. The optimal pruned ELM is first employed for protein sequence classification in this paper. To further enhance the performance, the ensemble based SLFNs structure is constructed where multiple SLFNs with the same number of hidden nodes and the same activation function are used as ensembles. For each ensemble, the same training algorithm is adopted. The final category index is derived using the majority voting method. Two approaches, namely, the basic ELM and the OP-ELM, are adopted for the ensemble based SLFNs. The performance is analyzed and compared with several existing methods using datasets obtained from the Protein Information Resource center. The experimental results show the priority of the proposed algorithms.
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Bennett HM, Mok HP, Gkrania-Klotsas E, Tsai IJ, Stanley EJ, Antoun NM, Coghlan A, Harsha B, Traini A, Ribeiro DM, Steinbiss S, Lucas SB, Allinson KSJ, Price SJ, Santarius TS, Carmichael AJ, Chiodini PL, Holroyd N, Dean AF, Berriman M. The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion. Genome Biol 2014; 15:510. [PMID: 25413302 PMCID: PMC4265353 DOI: 10.1186/preaccept-2413673241432389] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 10/28/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sparganosis is an infection with a larval Diphyllobothriidea tapeworm. From a rare cerebral case presented at a clinic in the UK, DNA was recovered from a biopsy sample and used to determine the causative species as Spirometra erinaceieuropaei through sequencing of the cox1 gene. From the same DNA, we have produced a draft genome, the first of its kind for this species, and used it to perform a comparative genomics analysis and to investigate known and potential tapeworm drug targets in this tapeworm. RESULTS The 1.26 Gb draft genome of S. erinaceieuropaei is currently the largest reported for any flatworm. Through investigation of β-tubulin genes, we predict that S. erinaceieuropaei larvae are insensitive to the tapeworm drug albendazole. We find that many putative tapeworm drug targets are also present in S. erinaceieuropaei, allowing possible cross application of new drugs. In comparison to other sequenced tapeworm species we observe expansion of protease classes, and of Kuntiz-type protease inhibitors. Expanded gene families in this tapeworm also include those that are involved in processes that add post-translational diversity to the protein landscape, intracellular transport, transcriptional regulation and detoxification. CONCLUSIONS The S. erinaceieuropaei genome begins to give us insight into an order of tapeworms previously uncharacterized at the genome-wide level. From a single clinical case we have begun to sketch a picture of the characteristics of these organisms. Finally, our work represents a significant technological achievement as we present a draft genome sequence of a rare tapeworm, and from a small amount of starting material.
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Affiliation(s)
- Hayley M Bennett
- />Wellcome Trust Sanger Institute, Parasite Genomics, Cambridge, CB10 1SA UK
| | - Hoi Ping Mok
- />Department of Infectious Diseases, Addenbrooke’s NHS Trust, Cambridge, CB2 0QQ UK
| | | | - Isheng J Tsai
- />Wellcome Trust Sanger Institute, Parasite Genomics, Cambridge, CB10 1SA UK
- />Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Eleanor J Stanley
- />Wellcome Trust Sanger Institute, Parasite Genomics, Cambridge, CB10 1SA UK
- />Eagle Genomics, Babraham Research Campus, Babraham, Cambridge, CB22 3AT UK
| | - Nagui M Antoun
- />Department of Radiology, Addenbrookes’s NHS Trust, Cambridge, CB2 0QQ UK
| | - Avril Coghlan
- />Wellcome Trust Sanger Institute, Parasite Genomics, Cambridge, CB10 1SA UK
| | - Bhavana Harsha
- />Wellcome Trust Sanger Institute, Parasite Genomics, Cambridge, CB10 1SA UK
| | - Alessandra Traini
- />Wellcome Trust Sanger Institute, Parasite Genomics, Cambridge, CB10 1SA UK
| | - Diogo M Ribeiro
- />Wellcome Trust Sanger Institute, Parasite Genomics, Cambridge, CB10 1SA UK
| | - Sascha Steinbiss
- />Wellcome Trust Sanger Institute, Parasite Genomics, Cambridge, CB10 1SA UK
| | - Sebastian B Lucas
- />Department of Histopathology, St Thomas’s Hospital, London, SE1 UK
| | - Kieren SJ Allinson
- />Department of Histopathology Section, Addenbrookes’s NHS Trust, Cambridge, CB2 0QQ UK
| | - Stephen J Price
- />Department of Neurosurgery, Addenbrookes’s NHS Trust, Cambridge, CB2 0QQ UK
| | - Thomas S Santarius
- />Department of Neurosurgery, Addenbrookes’s NHS Trust, Cambridge, CB2 0QQ UK
| | - Andrew J Carmichael
- />Department of Infectious Diseases, Addenbrooke’s NHS Trust, Cambridge, CB2 0QQ UK
| | - Peter L Chiodini
- />Hospital for Tropical Diseases and London School of Hygiene and Tropical Medicine, London, WC1E 6JD UK
| | - Nancy Holroyd
- />Wellcome Trust Sanger Institute, Parasite Genomics, Cambridge, CB10 1SA UK
| | - Andrew F Dean
- />Department of Histopathology Section, Addenbrookes’s NHS Trust, Cambridge, CB2 0QQ UK
| | - Matthew Berriman
- />Wellcome Trust Sanger Institute, Parasite Genomics, Cambridge, CB10 1SA UK
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