scholarly journals ArVirInd - a database of arboviral antigenic proteins from the Indian subcontinent

Author(s):  
Nitin Atre ◽  
Kalichamy Alagarasu ◽  
Pratip Shil

Studies on antigenic proteins for arboviruses are important for providing diagnostics and vaccine development. India and its neighbouring countries have huge burden of arboviral diseases. Data mining for country-specific sequences from existing databases is cumbersome and time-consuming. This necessitated the development of a database of antigenic proteins from arbo-viruses isolated from the countries of the Indian subcontinent. Arboviral antigenic protein sequences were obtained from the NCBI and other databases. In silico antigenic characterization was performed (Epitope predictions) and data incorporated in the database. The front end is designed and developed using HTML, CSS and PHP. For the backend of the database, we have used MySQL. A database, named ArVirInd, is created as a repository of information on antigenic proteins. This enlists sequences by country and year of outbreak or origin of the viral strain. For each entry antigenic information is provided along with functional sites, etc. Researchers can search this database by virus/protein name, country and year of collection (or in combination). It is available publicly via Internet at http://www.arvirind.co.in. ArVirInd will be useful in the study of immuno-informatics, diagnostics and vaccinology for arboviruses.

Pathogens ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1078 ◽  
Author(s):  
Albert Ros-Lucas ◽  
Florencia Correa-Fiz ◽  
Laia Bosch-Camós ◽  
Fernando Rodriguez ◽  
Julio Alonso-Padilla

African swine fever virus is the etiological agent of African swine fever, a transmissible severe hemorrhagic disease that affects pigs, causing massive economic losses. There is neither a treatment nor a vaccine available, and the only method to control its spread is by extensive culling of pigs. So far, classical vaccine development approaches have not yielded sufficiently good results in terms of concomitant safety and efficacy. Nowadays, thanks to advances in genomic and proteomic techniques, a reverse vaccinology strategy can be explored to design alternative vaccine formulations. In this study, ASFV protein sequences were analyzed using an in-house pipeline based on publicly available immunoinformatic tools to identify epitopes of interest for a prospective vaccine ensemble. These included experimentally validated sequences from the Immune Epitope Database, as well as de novo predicted sequences. Experimentally validated and predicted epitopes were prioritized following a series of criteria that included evolutionary conservation, presence in the virulent and currently circulating variant Georgia 2007/1, and lack of identity to either the pig proteome or putative proteins from pig gut microbiota. Following this strategy, 29 B-cell, 14 CD4+ T-cell and 6 CD8+ T-cell epitopes were selected, which represent a starting point to investigating the protective capacity of ASFV epitope-based vaccines.


1998 ◽  
Vol 188 (7) ◽  
pp. 1223-1229 ◽  
Author(s):  
Hisashi Fujioka ◽  
Steven N. Emancipator ◽  
Masamichi Aikawa ◽  
Dennis S. Huang ◽  
Frank Blatnik ◽  
...  

Immunoglobulin (Ig)A provides the initial immune barrier to viruses at mucosal surfaces. Specific IgA interrupts viral replication in polarized epithelium during receptor-mediated transport, probably by binding to newly synthesized viral proteins. Here, we demonstrate by immunoelectron microscopy that specific IgA monoclonal antibodies (mAbs) accumulate within Sendai virus–infected polarized cell monolayers and colocalize with the hemagglutinin– neuraminidase (HN) viral protein in a novel intracellular structure. Neither IgG specific for HN nor irrelevant IgA mAbs colocalize with viral protein. Treatment of cultures with viral-specific IgA but not with viral-specific IgG or irrelevant IgA decreases viral titers. These observations provide definitive ultrastructural evidence of a subcellular compartment in which specific IgA and viral envelope proteins interact, further strengthening our hypothesis of intracellular neutralization of virus by specific IgA antibodies. Our results have important implications for intracellular protein trafficking, viral replication, and viral vaccine development.


2016 ◽  
Vol 80 (2) ◽  
Author(s):  
. Siswanto

AbstrakLateks karet alam banyak digunakan untuk produksi peralatan medis, industri dan rumah tangga. Reaksi alergi yang disebabkan oleh protein asal lateks telah banyak dilaporkan terutama berkaitan dengan penggunaan sarung tangan asal karet alam. Namun tidak semua jenis protein dari karet alam bisamenyebabkan alergi. Penelitian ini dilakukan untuk mendeteksi jenis protein antigenik yang berasal dari karet alam menggunakan teknik imunobloting. Protein diekstrak dari tiga fraksi sentrifugasi lateks (serum B sebagai fraksi dasar, serum C atau serum sitosolik sebagai fase tengah dan partikel karet sebagai fase atas) dan tujuh jenis sarung tangan komersial, kemudian dipisahkan berdasarkan berat molekulnya melalui Gel elektroforesis 1-D (SDS PAGE) dan 2-D. Selanjutnya untuk deteksi protein antigenik secara immuno-chemiluminescense dilakukan imunobloting menggunakan IgG antibodi poliklonal anti protein lateks dari kelinci putih New Zealand dan diwarnai dengan Sypro Ruby protein blot fluorescence. Hasil imunobloting menunjukkan bahwa tidak semua protein serum C dan serum B bersifat antigenik. Terdapat lebih dari 14 spot protein antigenik yang terdeteksi dari serum C pada posisi pI antara pH 4,2 s/d pH 6,8, serta lebih dari 16 spot protein antigenik yang terdeteksi pada serum B dengan pI antara pH 5,5 s/d pH 7,0. Protein yang bersifat antigenik dalam serum C a.l: dengan BM 43 kDa diduga Hev b 7,01, BM 22 kDa adalah Hev b 3 dan BM 15 kDa adalah Hev b 8. Sedangkan protein antigenik dalam serum B dengan BM 42 kDa diduga adalah Hev b 10, dan BM 39 kDa adalah Hev b 2. Protein yang bersifat antigenik pada sarung tangan yang terdeteksi dengan IgG kelinci anti serum-C antara lain Hev b 5 dengan BM 14 kDa, Hev b 1 (BM 10 kDa), Hev b 6.03 (BM 18 dan 19 kDa), dan Hev b9 (BM 55 kDa). Sedangkan yang terdeteksi dengan antibodi IgG anti serum B antara lain Hev b 6.02 dengan BM 7 kDa, serta Hev b 10 (BM 46 kDa) dan Hev b9 (BM 55 kDa). AbstractNatural rubber latex is widely used for the production of medical, industrial and household devices. Allergic reactions caused by latex proteins have been reported primarily related with the use of natural rubber gloves. However, not all types of proteins from natural rubber can cause allergies. This study was conducted to detect the type of antigenic proteins derived from natural rubber with immunobloting techniques. Proteins were extracted from three fractions of latex centrifugation (Bserum as bottom fractions, C-serum or cytosolic serum asmiddle phase and rubber particles as upper phase) and seven types of commercial gloves, then separated by molecular weight through 1-D gel electrophoresis (SDS PAGE) and 2-D. Detection of antigenic protein byimmuno-chemiluminescense, was performed by immunoblotting using polyclonal antibody IgG anti-protein latex from New Zealand white rabbits and stained withSypro Ruby protein blot fluorescence. Immunobloting results indicate that not all proteins from C-serum and Bserum were antigenic. More than 14 antigenic protein spots were detected in the samples of C-serum at pI between pH 4.2 to pH 6.8, and more than 16 antigenic protein spots were detected in the samples of B-serum at pI between pH 5.5 to pH 7.0. Antigenic proteins detected in C-serum were MW 43 kDa suspected as Hev b 7:01, MW 22 kDa was Hev b 3 and MW 15 kDa was Hev b 8. While the antigenic protein detected in B-serumwith MW 42 kDa was suspected as Hev b 10, and protein with MW 39 kDa was Hev b 2. Antigenic proteins detected on the rubber gloves with rabbit IgG anti-Cserum were Hev b 5 with MW 14 kDa, Hev b 1 (MW 10 kDa), Hev b 6:03 (MW 18 and 19 kDa), and Hev b9 (MW 55 kDa). Whereas antigenic protein of rubbergloves detected with IgG anti-B serum were Hev b 6:02 with MW 7 kDa, and Hev b 10 (46 kDa) and Hev b9 (MW 55 kDa).


2020 ◽  
Vol 15 (8) ◽  
pp. 497-505
Author(s):  
Rakshanda Sajeed ◽  
Kishore Sarma ◽  
Kimmi Sarmah ◽  
Dipankar Biswas ◽  
Biswajyoti Borkakoty

Aim: Arboviral diseases are a health hazard and Flavivirus and Alphavirus infections are the most common in humans. This study focuses on immunoinformatic approaches to identify potential MHC class I restricted epitopes common for some selected arboviral diseases. Materials & methods: T-cell epitope prediction tool of Immune Epitope Database was employed to identify putative epitopes from the polyproteins of the selected viruses. Further, population coverage, conservancy, antigenic properties and docking analyses were performed to identify potential common epitopes for the selected viruses. Results: Eight common epitopes were screened for the selected viruses based on their population coverage, conservancy, antigenic properties and binding affinity. Conclusion: Considering the in silico potency, identified epitopes may further be subjected for candidate vaccine development against these arboviruses.


2014 ◽  
Vol 9 (8) ◽  
pp. 753-767 ◽  
Author(s):  
Michael McCarthy ◽  
Tonya Villafana ◽  
Elizabeth Stillman ◽  
Mark T Esser

2005 ◽  
Vol 73 (12) ◽  
pp. 8109-8118 ◽  
Author(s):  
Job E. Lopez ◽  
William F. Siems ◽  
Guy H. Palmer ◽  
Kelly A. Brayton ◽  
Travis C. McGuire ◽  
...  

ABSTRACT Immunization with purified Anaplasma marginale outer membranes induces complete protection against infection that is associated with CD4+ T-lymphocyte-mediated gamma interferon secretion and immunoglobulin G2 (IgG2) antibody titers. However, knowledge of the composition of the outer membrane immunogen is limited. Recent sequencing and annotation of the A. marginale genome predicts at least 62 outer membrane proteins (OMP), enabling a proteomic and genomic approach for identification of novel OMP by use of IgG serum antibody from outer membrane vaccinates. Outer membrane proteins were separated by two-dimensional electrophoresis, and proteins recognized by total IgG and IgG2 in immune sera of outer membrane-vaccinated cattle were detected by immunoblotting. Immunoreactive protein spots were excised and subjected to liquid chromatography-tandem mass spectrometry. A database search of the A. marginale genome identified 24 antigenic proteins that were predicted to be outer membrane, inner membrane, or membrane-associated proteins. These included the previously characterized surface-exposed outer membrane proteins MSP2, operon associated gene 2 (OpAG2), MSP3, and MSP5 as well as recently identified appendage-associated proteins. Among the 21 newly described antigenic proteins, 14 are annotated in the A. marginale genome and include type IV secretion system proteins, elongation factor Tu, and members of the MSP2 superfamily. The identification of these novel antigenic proteins markedly expands current understanding of the composition of the protective immunogen and provides new candidates for vaccine development.


2016 ◽  
Vol 91 (5) ◽  
pp. 642-646
Author(s):  
M.-R. Lee ◽  
J.-W. Ju ◽  
H.-W. Yang ◽  
T.-S. Kim ◽  
M.-Y. Park ◽  
...  

AbstractSparganosis is one of the top three tissue-dwelling heterologous helminthic diseases, along with cysticercosis and paragonimiasis, in Korea. Due to a lack of effective early diagnosis and treatment methods, this parasitic disease is regarded as a public health threat. This study evaluated reactivity, against sparganum extracts, of sera from inhabitants of Cheorwon-gun, Goseong-gun and Ongjin-gun in Korea. The sera from 836 subjects were subjected to enzyme-linked immunosorbent assay and immunoblot analysis. The sera from 18 (5.8%) and 15 (5.1%) inhabitants in Cheorwon-gun (n = 312) and Goseong-gun (n = 294), respectively, exhibited highly positive reactions to the sparganum antigen, whereas only two (0.9%) inhabitants in Ongjin-gun (n = 230) showed positivity. We sought antigenic proteins for serodiagnosis of positive sera by immunoproteomic approaches. Total sparganum lysates were separated by two-dimensional electrophoresis and then subjected to immunoblot analysis with mixed sparganosis-positive sera. We found seven antigenic spots and identified paramyosin as an antigenic protein by liquid chromatography–mass spectrometry. By two-dimensional (2D)-based mass analysis and immunoblotting against sparganosis-positive sera, paramyosin was identified as a candidate antigen for serodiagnosis of sparganosis.


2016 ◽  
Vol 80 (2) ◽  
Author(s):  
. Siswanto

AbstrakLateks karet alam banyak digunakan untuk produksi peralatan medis, industri dan rumah tangga. Reaksi alergi yang disebabkan oleh protein asal lateks telah banyak dilaporkan terutama berkaitan dengan penggunaan sarung tangan asal karet alam. Namun tidak semua jenis protein dari karet alam bisamenyebabkan alergi. Penelitian ini dilakukan untuk mendeteksi jenis protein antigenik yang berasal dari karet alam menggunakan teknik imunobloting. Protein diekstrak dari tiga fraksi sentrifugasi lateks (serum B sebagai fraksi dasar, serum C atau serum sitosolik sebagai fase tengah dan partikel karet sebagai fase atas) dan tujuh jenis sarung tangan komersial, kemudian dipisahkan berdasarkan berat molekulnya melalui Gel elektroforesis 1-D (SDS PAGE) dan 2-D. Selanjutnya untuk deteksi protein antigenik secara immuno-chemiluminescense dilakukan imunobloting menggunakan IgG antibodi poliklonal anti protein lateks dari kelinci putih New Zealand dan diwarnai dengan Sypro Ruby protein blot fluorescence. Hasil imunobloting menunjukkan bahwa tidak semua protein serum C dan serum B bersifat antigenik. Terdapat lebih dari 14 spot protein antigenik yang terdeteksi dari serum C pada posisi pI antara pH 4,2 s/d pH 6,8, serta lebih dari 16 spot protein antigenik yang terdeteksi pada serum B dengan pI antara pH 5,5 s/d pH 7,0. Protein yang bersifat antigenik dalam serum C a.l: dengan BM 43 kDa diduga Hev b 7,01, BM 22 kDa adalah Hev b 3 dan BM 15 kDa adalah Hev b 8. Sedangkan protein antigenik dalam serum B dengan BM 42 kDa diduga adalah Hev b 10, dan BM 39 kDa adalah Hev b 2. Protein yang bersifat antigenik pada sarung tangan yang terdeteksi dengan IgG kelinci anti serum-C antara lain Hev b 5 dengan BM 14 kDa, Hev b 1 (BM 10 kDa), Hev b 6.03 (BM 18 dan 19 kDa), dan Hev b9 (BM 55 kDa). Sedangkan yang terdeteksi dengan antibodi IgG anti serum B antara lain Hev b 6.02 dengan BM 7 kDa, serta Hev b 10 (BM 46 kDa) dan Hev b9 (BM 55 kDa). AbstractNatural rubber latex is widely used for the production of medical, industrial and household devices. Allergic reactions caused by latex proteins have been reported primarily related with the use of natural rubber gloves. However, not all types of proteins from natural rubber can cause allergies. This study was conducted to detect the type of antigenic proteins derived from natural rubber with immunobloting techniques. Proteins were extracted from three fractions of latex centrifugation (Bserum as bottom fractions, C-serum or cytosolic serum asmiddle phase and rubber particles as upper phase) and seven types of commercial gloves, then separated by molecular weight through 1-D gel electrophoresis (SDS PAGE) and 2-D. Detection of antigenic protein byimmuno-chemiluminescense, was performed by immunoblotting using polyclonal antibody IgG anti-protein latex from New Zealand white rabbits and stained withSypro Ruby protein blot fluorescence. Immunobloting results indicate that not all proteins from C-serum and Bserum were antigenic. More than 14 antigenic protein spots were detected in the samples of C-serum at pI between pH 4.2 to pH 6.8, and more than 16 antigenic protein spots were detected in the samples of B-serum at pI between pH 5.5 to pH 7.0. Antigenic proteins detected in C-serum were MW 43 kDa suspected as Hev b 7:01, MW 22 kDa was Hev b 3 and MW 15 kDa was Hev b 8. While the antigenic protein detected in B-serumwith MW 42 kDa was suspected as Hev b 10, and protein with MW 39 kDa was Hev b 2. Antigenic proteins detected on the rubber gloves with rabbit IgG anti-Cserum were Hev b 5 with MW 14 kDa, Hev b 1 (MW 10 kDa), Hev b 6:03 (MW 18 and 19 kDa), and Hev b9 (MW 55 kDa). Whereas antigenic protein of rubbergloves detected with IgG anti-B serum were Hev b 6:02 with MW 7 kDa, and Hev b 10 (46 kDa) and Hev b9 (MW 55 kDa).


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