Bioinformatic prediction of epitopes in the Emy162 antigen of Echinococcus multilocularis

Designing a conjugate vaccine targeting Klebsiella pneumoniae ST258 and ST11

Klebsiella pneumoniae (K. pneumoniae) is a common bacterium that can cause iatrogenic infection. Recently, the rise of antibiotic resistance among K. pneumoniae strains is one key factor associated with antibiotic treatment failure. Hencefore, there is an urgent need for effective K. pneumoniae vaccines. This study aimed to design a multi-epitope vaccine (MEV) candidate against K. pneumonia by utilizing an immunoinformatics method. In this study, we obtained 15 cytotoxic T lymphocyte epitopes, 10 helper T lymphocyte epitopes, 6 linear B-cell epitopes, and 2 conformational B-cell epitopes for further research. Then, we designed a multi-epitope vaccine composed of a total of 743 amino acids, containing the epitopes linked by GPGPG flexible links and an EAAAK linker to the Cholera Toxin Subunit B coadjuvant. The observed properties of the MEV, including non-allergenicity, high antigenicity, and hydrophilicity, are noteworthy. The improvements in the tertiary structure through structural refinement and disulfide bonding, coupled with promising molecular interactions revealed by molecular dynamics simulations with TLR4, position the MEV as a strong candidate for further investigation against K. pneumoniae.

Designing a multi-epitope vaccine to control porcine epidemic diarrhea virus infection using immunoinformatics approaches

Porcine epidemic diarrhea virus (PEDV), a continuously evolving pathogen, causes severe diarrhea in piglets with high mortality rates. However, current vaccines cannot provide complete protection against PEDV, so vaccine development is still necessary and urgent. Here, with the help of immunoinformatics approaches, we attempted to design a multi-epitope vaccine named rPMEV to prevent and control PEDV infection. The epitopes of rPMEV were constructed by 9 cytotoxic T lymphocyte epitopes (CTLs), 11 helper T lymphocyte epitopes (HTLs), 6 linear B cell epitopes (LBEs), and 4 conformational B cell epitopes (CBEs) based on the S proteins from the four representative PEDV G2 strains. To enhance immunogenicity, porcine β-defensin-2 (PBD-2) was adjoined to the N-terminal of the vaccine as an adjuvant. All of the epitopes and PBD-2 were joined by corresponding linkers and recombined into the multivalent vaccine, which is stable, antigenic, and non-allergenic. Furthermore, we adopted molecular docking and molecular dynamics simulation methods to analyze the interaction of rPMEV with the Toll-like receptor 4 (TLR4): a stable interaction between them created by 13 hydrogen bonds. In addition, the results of the immune simulation showed that rPMEV could stimulate both cellular and humoral immune responses. Finally, to raise the expression efficiency, the sequence of the vaccine protein was cloned into the pET28a (+) vector after the codon optimization. These studies indicate that the designed multi-epitope vaccine has a potential protective effect, providing a theoretical basis for further confirmation of its protective effect against PEDV infection in vitro and in vivo studies.

A novel fusion protein candidate for the serodiagnosis of Mycoplasma agalactiae infection

BACKGROUND

The aim of current study was to construct, express, purify and immunogenicity evaluate of a novel recombinant fusion protein including Pyruvate dehydrogenase beta subunit (PDHB) and high antigenic region of lipoprotein P80 of Mycoplasma agalactiae. Using bioinformatics tools, antigenicity and physiochemical properties of fused protein were assessed.

MATERIAL AND METHODS

The recombinant fusion protein of GST-PDHB-P80 were expressed in pGEX4T-1 and purified then verified by Western blot assay. The purified protein was successfully used for immunization of mice. 30 female BALB/c mice were divided into three groups (10 mice per each group) injected with GST-PDHB-P80, inactivated bacteria vaccine and PBS as negative control, separately.

RESULTS

Western blot analysis confirmed the interaction between the immunized mice serum and the blotted recombinant protein GST-PDHB-P80, demonstrating the immunogenicity of this protein. Moreover, the sera of vaccinated mice with inactivated bacteria vaccine, containing whole cell proteins, detected the recombinant protein GST-PDHB-P80 confirming the antigenicity of PDHB-P80. Negative control displayed no reactivity with GST-PDHB-P80.

CONCLUSION

We proposed a novel designed chimeric protein of Mycoplasma agalactiae as a potential marker for serodiagnostic assays but still further field research is required.

Tim-3/Galectin-9 signaling pathway is involved in the cytokine changes in mice with alveolar echinococcosis

BACKGROUND

Tim-3/Galectin-9 is involved in the immune escape of many pathogens. However, the role of Tim-3/Galectin-9 in persistent infection of Echinococcus multilocularis (Em), which is related to immune escape, is still unclear.

OBJECTIVE

To investigate the role of Tim-3/Galectin-9 and related cytokines in mice with persistent infection of Em.

METHODS

Em infection model was established by injecting the protoscoleces. Serum was collected at days 2, 8, 30, 60, 90, 180 and 270 after infection. Lymphocytes were isolated from liver tissue samples with Ficoll. Tim-3 + CD4 + T percentage was analyzed by flow cytometry. CD4 + T cells were isolated from liver tissues of Em infected mice and cultured in vitro. The mRNA levels of Tim-3, Galectin-9, IFN-γ and IL-4 were detected by qRT-PCR. Cytokine levels in serum and culture supernatant (IFN-γ and IL-4) were analyzed by cytometric bead array.

RESULTS

The expression of Tim-3 and Galectin-9 mRNA significantly increased after 30 days of infection, reached peak on day 90, and then decreased slightly on days 180-270. The expression of IFN-γ mRNA, increased on day 2 and 8 after infection, slightly decreased on days 30-60, and obvious decreased on days 90-270, but were still higher than those of the control group. The expression of IL-4 mRNA gradually increased along with the time of infection. In serum of Em infected mice, level of IFN-γ peaked at day 30 and then gradually decreased; whereas IL-4 level peaked at day 90 and then gradually decreased. In vitro experiment found that Tim-3/Galectin-9 directly caused the changes in the levels of IFN-γ and IL-4.

CONCLUSIONS

Tim-3/Galectin-9 signaling pathway may be involved in the development of persistent infection of Em by regulating the production of Th1 and Th2 cytokines.

Exploring Klebsiella pneumoniae capsule polysaccharide proteins to design multiepitope subunit vaccine to fight against pneumonia

BACKGROUND

Klebsiella pneumoniae is an emerging human pathogen causing neonatal lung disease, catheter-associated infections, and nosocomial outbreaks with high fatality rates. Capsular polysaccharide (CPS) protein plays a major determinant in virulence and is considered as a promising target for vaccine development.

RESEARCH DESIGN AND METHODS

In this study, we used immunoinformatic approaches to design a multi-peptide vaccine against K. pneumonia. The epitopes were selected through several immune filters, such as antigenicity, conservancy, nontoxicity, non-allergenicity, binding affinity to HLA alleles, overlapping epitopes, and peptides having common epitopes.

RESULTS

Finally, a construct comprising 2 B-Cell, 8 CTL, 2 HTL epitopes, along with adjuvant, linkers was designed. Peptide-HLA interaction analysis showed strong binding of these epitopes with several common HLA molecules. The in silico immune simulation and population coverage analysis of the vaccine showed its potential to evoke strong immune responses.. Further, the interaction between vaccine and immune was evaluated by docking and simulation, revealing high affinity and complex stability. Codon adaptation and in silico cloning revealed higher expression of vaccine in E. coli K12 expression system.

CONCLUSIONS

Conclusively, the findings of the present study suggest that the designed novel multi-epitopic vaccine holds potential for further experimental validation against the pathogen.

Discovering the Ultimate Limits of Protein Secondary Structure Prediction

Secondary structure prediction (SSP) of proteins is an important structural biology technique with many applications. There have been ~300 algorithms published in the past seven decades with fierce competition in accuracy. In the first 60 years, the accuracy of three-state SSP rose from ~56% to 81%; after that, it has long stayed at 81-86%. In the 1990s, the theoretical limit of three-state SSP accuracy had been estimated to be 88%. Thus, SSP is now generally considered not challenging or too challenging to improve. However, we found that the limit of three-state SSP might be underestimated. Besides, there is still much room for improving segment-based and eight-state SSPs, but the limits of these emerging topics have not been determined. This work performs large-scale sequence and structural analyses to estimate SSP accuracy limits and assess state-of-the-art SSP methods. The limit of three-state SSP is re-estimated to be ~92%, 4-5% higher than previously expected, indicating that SSP is still challenging. The estimated limit of eight-state SSP is 84-87%. Several proposals for improving future SSP algorithms are made based on our results. We hope that these findings will help move forward the development of SSP and all its applications.

The influence of dataset homology and a rigorous evaluation strategy on protein secondary structure prediction

The secondary structure prediction (SSP) of proteins has long been an essential structural biology technique with various applications. Despite its vital role in many research and industrial fields, in recent years, as the accuracy of state-of-the-art secondary structure predictors approaches the theoretical upper limit, SSP has been considered no longer challenging or too challenging to make advances. With the belief that the substantial improvement of SSP will move forward many fields depending on it, we conducted this study, which focused on three issues that have not been noticed or thoroughly examined yet but may have affected the reliability of the evaluation of previous SSP algorithms. These issues are all about the sequence homology between or within the developmental and evaluation datasets. We thus designed many different homology layouts of datasets to train and evaluate SSP prediction models. Multiple repeats were performed in each experiment by random sampling. The conclusions obtained with small experimental datasets were verified with large-scale datasets using state-of-the-art SSP algorithms. Very different from the long-established assumption, we discover that the sequence homology between query datasets for training, testing, and independent tests exerts little influence on SSP accuracy. Besides, the sequence homology redundancy between or within most datasets would make the accuracy of an SSP algorithm overestimated, while the redundancy within the reference dataset for extracting predictive features would make the accuracy underestimated. Since the overestimating effects are more significant than the underestimating effect, the accuracy of some SSP methods might have been overestimated. Based on the discoveries, we propose a rigorous procedure for developing SSP algorithms and making reliable evaluations, hoping to bring substantial improvements to future SSP methods and benefit all research and application fields relying on accurate prediction of protein secondary structures.

Design of a new multi-epitope vaccine against Brucella based on T and B cell epitopes using bioinformatics methods

Brucellosis is one of the most serious and widespread zoonotic diseases, which seriously threatens human health and the national economy. This study was based on the T/B dominant epitopes of Brucella outer membrane protein 22 (Omp22), outer membrane protein 19 (Omp19) and outer membrane protein 28 (Omp28), with bioinformatics methods to design a safe and effective multi-epitope vaccine. The amino acid sequences of the proteins were found in the National Center for Biotechnology Information (NCBI) database, and the signal peptides were predicted by the SignaIP-5.0 server. The surface accessibility and hydrophilic regions of proteins were analysed with the ProtScale software and the tertiary structure model of the proteins predicted by I-TASSER software and labelled with the UCSF Chimera software. The software COBEpro, SVMTriP and BepiPred were used to predict B cell epitopes of the proteins. SYFPEITHI, RANKpep and IEDB were employed to predict T cell epitopes of the proteins. The T/B dominant epitopes of three proteins were combined with HEYGAALEREAG and GGGS linkers, and carriers sequences linked to the N- and C-terminus of the vaccine construct with the help of EAAAK linkers. Finally, the tertiary structure and physical and chemical properties of the multi-epitope vaccine construct were analysed. The allergenicity, antigenicity and solubility of the multi-epitope vaccine construct were 7.37–11.30, 0.788 and 0.866, respectively. The Ramachandran diagram of the mock vaccine construct showed 96.0% residues within the favoured and allowed range. Collectively, our results showed that this multi-epitope vaccine construct has a high-quality structure and suitable characteristics, which may provide a theoretical basis for future laboratory experiments.

Structural and immunogenicity analysis of reconstructed ancestral and consensus P48/45 for cross-species anti malaria transmission-blocking vaccine

The development of the anti-malaria vaccine holds a promising future in malaria control. One of the anti-malaria vaccine strategies known as the transmission-blocking vaccine (TBV) is to inhibit the parasite transmission between humans and mosquitoes by targeting the parasite gametocyte. Previously, we found that P48/45 included in the 6-Cysteine protein family shared by Plasmodium sp. We also detected vaccine properties possessed by all human-infecting Plasmodium and could be used as a cross-species anti-malaria vaccine. In this study, we investigated the efficacy of P48/45 through the ancestral and consensus reconstruction approach. P48/45 phylogenetic and time tree analysis was done by RAXML and BEAST2. GRASP server and Ugene software were used to reconstruct ancestral and consensus sequences, respectively. The protein structural prediction was made by using a psipred and Rosetta program. Each protein characteristic of P48/45 was analyzed by assessing hydrophobicity and Post-Translational Modification sites. Meanwhile, the Epitope sequence for B-cell, T-cell, and HLA was determined using an immunoinformatics approach. Lastly, molecular docking simulation was done to determine native binding interactions of P48/45-P230. The result showed a distinct protein characteristic of ancestral and consensus sequences. The immunogenicity analysis revealed the number of epitopes in the ancestral sequence is greater than the consensus sequence. The study also found a conserved epitope located in the binding site and consists of specific Post-Translational Modification sites. Hence, our research provides detailed insight into ancestral and consensus P48/45 efficacy for the cross-species anti-malaria vaccine.

Immunogenicity and structural efficacy of P41 of Plasmodium sp. as potential cross-species blood-stage malaria vaccine

Vaccine based strategies offer a promising future in malaria control by generating protective immunity against natural infection. However, vaccine development is hindered by the Plasmodium sp. genetic diversity. Previously, we have shown P41 protein from 6-Cysteine shared by Plasmodium sp. and could be used for cross-species anti-malaria vaccines. Two different approaches, ancestral, and consensus sequence, could produce a single target for all human-infecting Plasmodium. In this study, we investigated the efficacy of ancestral and consensus of P41 protein. Phylogenetic and time tree reconstruction was conducted by RAXML and BEAST2 package to determine the relationship of known P41 sequences. Ancestral and consensus sequences were reconstructed by the GRASP server and Unipro Ugene software, respectively. The structural prediction was made using the Psipred and Rosetta program. The protein characteristic was analyzed by assessing hydrophobicity and Post-Translational Modification sites. Meanwhile, the immunogenicity score for B-cell, T-cell, and MHC was determined using an immunoinformatic approach. The result suggests that ancestral and consensus have a distinct protein characteristic with high immunogenicity scores for all immune cells. We found one shared conserved epitope with phosphorylation modification from the ancestral sequence to target the cross-species vaccine. Thus, this study provides detailed insight into P41 efficacy for the cross-species anti-malaria blood-stage vaccine.

Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies

Antibody therapeutics and vaccines are among our last resort to end the raging COVID-19 pandemic. They, however, are prone to over 5000 mutations on the spike (S) protein uncovered by a Mutation Tracker based on over 200 000 genome isolates. It is imperative to understand how mutations will impact vaccines and antibodies in development. In this work, we first study the mechanism, frequency, and ratio of mutations on the S protein which is the common target of most COVID-19 vaccines and antibody therapies. Additionally, we build a library of 56 antibody structures and analyze their 2D and 3D characteristics. Moreover, we predict the mutation-induced binding free energy (BFE) changes for the complexes of S protein and antibodies or ACE2. By integrating genetics, biophysics, deep learning, and algebraic topology, we reveal that most of the 462 mutations on the receptor-binding domain (RBD) will weaken the binding of S protein and antibodies and disrupt the efficacy and reliability of antibody therapies and vaccines. A list of 31 antibody disrupting mutants is identified, while many other disruptive mutations are detailed as well. We also unveil that about 65% of the existing RBD mutations, including those variants recently found in the United Kingdom (UK) and South Africa, will strengthen the binding between the S protein and human angiotensin-converting enzyme 2 (ACE2), resulting in more infectious COVID-19 variants. We discover the disparity between the extreme values of RBD mutation-induced BFE strengthening and weakening of the bindings with antibodies and angiotensin-converting enzyme 2 (ACE2), suggesting that SARS-CoV-2 is at an advanced stage of evolution for human infection, while the human immune system is able to produce optimized antibodies. This discovery, unfortunately, implies the vulnerability of current vaccines and antibody drugs to new mutations. Our predictions were validated by comparison with more than 1400 deep mutations on the S protein RBD. Our results show the urgent need to develop new mutation-resistant vaccines and antibodies and to prepare for seasonal vaccinations.

Prediction and Identification of Epitopes in the Emy162 Antigen of Echinococcus multilocularis

INTRODUCTION

Alveolar echinococcosis (AE) is a zoonotic disease caused by the parasitism of Echinococcus multilocularis larvae in the intermediate host or the final host. This study aims to identify and analyze the B-cell and T-cell (Th1, Th2 and Th17) epitopes of E. multilocularis antigen Emy162.

METHODS

(1) The secondary structural characteristics of the Emy162 protein were predicted by bioinformatics software to further predict the potential T- and B-cell epitopes. (2) The dominant antigen epitopes were detected by ELISA through the reaction of patient serum with small B-cell antigen peptide and assessing the proliferation of splenic lymphocytes of mice immunized with Emy162. (3) The expression of cytokines in splenic lymphocytes of mice stimulated by small T-cell antigen peptides was detected by ELISA, ELISpot and flow cytometry to enable the identification of the T-cell epitopes.

RESULTS

(1) The high-scored T-cell epitopes were located at positions E7-13, E36-41, E80-89, E87-96, E97-106 and E129-139, while B-cell epitopes were located at positions E7-13, E19-27, E28-36, E37-48, E78-83, E101-109, E112-121 and E129-139. (2) The three advanced antigen epitopes of Emy162 were E19-27, E112-121 and E129-139. (3) The four Th1 advanced antigen epitopes of Emy162 were E7-13, E36-41, E80-89 and E129-139. The three Th2 advanced antigen epitopes were E36-41, E87-96 and E97-106. The three Th17 advanced antigen epitopes were E36-41, E87-96 and E97-106.

CONCLUSION

(1) The Emy162 protein has advanced antigenicity and numerous potential epitopes. Six T-cell and eight B-cell dominant epitopes were revealed using bioinformatics methods. (2) There are three dominant B-cell epitopes, four dominant Th1 epitopes, three dominant Th2 epitopes, and three dominant Th17 epitopes in the Emy162 antigen.

Engineering an efficient poly-epitope vaccine against Toxoplasma gondii infection: A computational vaccinology study

Toxoplasmosis is a zoonotic disease caused by Toxoplasma gondii. Despite the importance of toxoplasmosis, there is no comprehensive strategy to control this disease. Hence, applying the new methods such as the poly-epitope vaccine can be successful. In the current project, to engineer a potent poly-epitope vaccine, 10 antigenic proteins including BiP, GRA1, GRA2, GRA5, MIC8, MIC13, P30, PI1, SOD and Rop2 were selected based on the database. Then, B cell, MHCI and MHCII epitopes of the selected antigenic proteins were isolated by the most accurate servers. The best predicted epitopes along with a molecular adjuvant were employed to engineer a poly-epitope vaccine. After engineering, different physicochemical features, secondary and tertiary structures, molecular docking of the designed vaccine were assessed. The results of this project revealed that the designed vaccine with 730 amino acids in length and molecular weight of 77.67 kDa was a soluble protein which could bind to its receptor with an energy of 6223.43. According to the achievements of this study, it seems the designed vaccine can be an appropriate candidate to apply.

Molecular and immunochemical characterization of Pop n 2: A new allergen of Populus nigra pollen

BACKGROUND

Pollen is one of the most common allergens that cause respiratory allergies worldwide. Pollen grains from poplars have been reported as important sources of pollinosis in many countries.

OBJECTIVE

The aim of the present study was to determine the molecular and immunochemical characterization of Pop n 2, a novel allergen of Populus nigra (P nigra) pollen extract.

METHODS

In this study, the pollen extract of P nigra was analysed by SDS-PAGE, and the allergenic profile was determined by IgE immunoblotting and specific ELISA using the sera of twenty allergic patients. The coding sequence of Pop n 2 was cloned and expressed in the Escherichia coli BL21 (DE3) using plasmid the pET-21b (+). Finally, the expressed recombinant Pop n 2 was purified by affinity chromatography.

RESULTS

Pop n 2 belongs to the profilin family with a molecular weight of approximately 14 kDa. Pop n 2 is the most IgE-reactive protein (about 65%) in the P nigra pollen extract. The cDNA sequencing results indicated an open reading frame 396 bp that encodes 131 amino acid residues. The results of ELISA and Immunoblotting assays showed that recombinant Pop n 2 could react with the IgE antibody in patients' sera, like its natural counterpart.

CONCLUSION

Our data revealed that Pop n 2 is a significant allergen in the P nigra pollen extract. Moreover, we observed that the recombinant Pop n 2 produced by the pET-21b (+) vector in the E colisystem acts as its natural counterpart.

A bio-safe multiple antigenic peptide (MAP) enzyme-linked immunoassay for the detection of antibodies to infectious bronchitis virus in chickens

The objective of the study was to develop a bio-safe synthetic peptide ELISA for the detection of antibodies against the infectious bronchitis virus (IBV) using a novel multiple antigenic peptide approach (MAP). After initial ELISA optimization, diagnostic sensitivity (DSn) and specificity (DSp) for the linear peptides were determined using receiver operator curve (ROC) analysis. The peptide IBVP1 showed 90.44% DSn and 88.64% DSp at ROC cut off 22.8% while IBVP2 showed 88.24% DSn and 85.23% DSp at ROC cut off 23.05%. The multimerization of linear peptides to MAP design resulted in the improvement of the diagnostic efficiency up to 94.85% DSn and 92.05% DSp for IBVM1 with 19.95% cut off. A similar improvement in the performance was also observed with 92.65% DSn and 90.91% DSp for IBVM2 at 20.72% cut off. All the peptides were tested for diagnostic specificity and did not show the cross-reactivity with Newcastle disease virus and infectious bursal disease virus positive serum samples. In addition, repeatability testing for all linear and multimeric peptide showed that the coefficient of variation for intra-assay was within the expected limits, ranging from 2.4 to 10.4% and inter-assay coefficient of variation was ranging from 5.56 to 14.3%. In a nutshell, the present study used predicted B cell epitope, the synthetic peptide in linear and multimeric design for IBV antibody detection. The study also highlights peptide antigen with modified scaffold design could be a safe alternative to whole virion-based ELISA for IBV antibody detection.

A Comparative Analysis of Allergen Proteins between Plants and Animals Using Several Computational Tools and Chou's PseAAC Concept

BACKGROUND

A large number of allergens are derived from plant and animal proteins. A major challenge for researchers is to study the possible allergenic properties of proteins. The aim of this study was in silico analysis and comparison of several physiochemical and structural features of plant- and animal-derived allergen proteins, as well as classifying these proteins based on Chou's pseudo-amino acid composition (PseAAC) concept combined with bioinformatics algorithms.

METHODS

The physiochemical properties and secondary structure of plant and animal allergens were studied. The classification of the sequences was done using the PseAAC concept incorporated with the deep learning algorithm. Conserved motifs of plant and animal proteins were discovered using the MEME tool. B-cell and T-cell epitopes of the proteins were predicted in conserved motifs. Allergenicity and amino acid composition of epitopes were also analyzed via bioinformatics servers.

RESULTS

In comparison of physiochemical features of animal and plant allergens, extinction coefficient was different significantly. Secondary structure prediction showed more random coiled structure in plant allergen proteins compared with animal proteins. Classification of proteins based on PseAAC achieved 88.24% accuracy. The amino acid composition study of predicted B- and T-cell epitopes revealed more aliphatic index in plant-derived epitopes.

CONCLUSIONS

The results indicated that bioinformatics-based studies could be useful in comparing plant and animal allergens.

A simple strategy to enhance the speed of protein secondary structure prediction without sacrificing accuracy

The secondary structure prediction of proteins is a classic topic of computational structural biology with a variety of applications. During the past decade, the accuracy of prediction achieved by state-of-the-art algorithms has been >80%; meanwhile, the time cost of prediction increased rapidly because of the exponential growth of fundamental protein sequence data. Based on literature studies and preliminary observations on the relationships between the size/homology of the fundamental protein dataset and the speed/accuracy of predictions, we raised two hypotheses that might be helpful to determine the main influence factors of the efficiency of secondary structure prediction. Experimental results of size and homology reductions of the fundamental protein dataset supported those hypotheses. They revealed that shrinking the size of the dataset could substantially cut down the time cost of prediction with a slight decrease of accuracy, which could be increased on the contrary by homology reduction of the dataset. Moreover, the Shannon information entropy could be applied to explain how accuracy was influenced by the size and homology of the dataset. Based on these findings, we proposed that a proper combination of size and homology reductions of the protein dataset could speed up the secondary structure prediction while preserving the high accuracy of state-of-the-art algorithms. Testing the proposed strategy with the fundamental protein dataset of the year 2018 provided by the Universal Protein Resource, the speed of prediction was enhanced over 20 folds while all accuracy measures remained equivalently high. These findings are supposed helpful for improving the efficiency of researches and applications depending on the secondary structure prediction of proteins. To make future implementations of the proposed strategy easy, we have established a database of size and homology reduced protein datasets at http://10.life.nctu.edu.tw/UniRefNR.

Variability of the EG95 antigen-coding gene of Echinococcus granulosus in animal and human origin: implications for vaccine development

In the present study, the genetic variability of the EG95 protein-coding gene in several animal and human isolates of Echinococcus granulosus was investigated. A total of 24 isolates collected from cattle, buffalo, sheep, goat, dog and man were amplified by Eg95-coding gene-specific primers. From the generated sequence information, a conceptual amino acid sequence was deduced. Phylogenetically, the Eg95 coding gene belongs to the Eg95-1/Eg95-2/Eg95-3/Eg95-4 cluster. Further confirmation on the maximum composite likelihood analysis revealed that the overall transition/transversion bias was 2.913. This finding indicated thatthere is bias towards transitional and transversional substitution. Using artificial neural networks, a B-cell epitope was predicted on primary sequence information. Stretches of amino acid residues varied between animal and human isolates when hydrophobicity was considered. Flexibility also varied between larval and adult stages of the organism. This observation is important to develop vaccines. However, cytotoxic T-lymphocyte epitopes on primary sequence data remained constant in all isolates. In this study, agretope identification started with hydrophobic amino acids. Amino acids with the same physico-chemical properties were present in the middle. The conformational propensity of the Eg95-coding gene of 156 amino acid residues had α-turns and β-turns, and α-amphipathic regions up to 129, 138-156 and 151-155 residues, respectively. The results indicated potential T-cell antigenic sites. The overall Tajima's D value was negative (-2.404165), indicative of negative selection pressure.

Determination of immunodominant scaffolds of Com1 and OmpH antigens of Coxiella burnetii

Today, there is an increasing emphasis on recombinant vaccines to eliminate the side effects of conventional vaccines such as whole-cell bacteria. Query fever is an emerging disease that causes irreparable complications for both humans and domestic animals. The cause of this disease is Coxiella burnetii, a gram-negative intracellular bacteria. In order to determine the most immunodominant epitopes of Com1 and OmpH antigens of C. burnetii, the most reliable bioinformatics tools with high rates of citation in predicting B cell and T cell epitopes were used. Finally, by comparing the results of all servers, the best overlapped epitopes with the highest antigenicity among different servers were selected. In this regard, epitopes in 18-27and 67-82 amino acids residues were introduced for MHCI and MHCII of T cell, respectively, whereas epitope in 16-25 amino acids residues was introduced for B cell of OmpH antigen. The epitopes in the range of 193-202, 100-108 and 215-223 amino acid residues were preferred for MHCI class of T cell, MHCII class of T cell and B cell of Com1 antigen, respectively. For each antigen, some empirical common epitopic regions were introduced, which included both T and B cells epitopes, 53-65 and 102-111 amino acid residues of OmpH antigen as well as 38-54 range of the amino acid of Com1 antigen. All the predicted epitopes were selected based on their high antigenicity scores and number of non-digestive enzymes. To optimize the application of reported epitopes, various orders of epitopes were arranged in three categories of B cell, T cell and common T and B cells epitopes for each antigen. Then, the best immunodominant scaffolds for each antigen were proposed in these categories. The results demonstrated that the scaffold arranged based on B cell epitopes had the highest antigenicity in both antigens.

Prediction and analysis of promiscuous T cell-epitopes derived from the vaccine candidate antigens of Leishmania donovani binding to MHC class-II alleles using in silico approach

Visceral leishmaniasis is a dreadful infectious disease and caused by the intracellular protozoan parasites, Leishmania donovani and Leishmania infantum. Despite extensive efforts for developing effective prophylactic vaccine, still no vaccine is available against leishmaniasis. However, advancement in immunoinformatics methods generated new dimension in peptide based vaccine development. The present study was aimed to identify T-cell epitopes from the vaccine candidate antigens like Lipophosphogylcan-3(LPG-3) and Nucleoside hydrolase (NH) from the L. donovani using in silico methods. Available best tools were used for the identification of promiscuous peptides for MHC class-II alleles. A total of 34 promiscuous peptides from LPG-3, 3 from NH were identified on the basis of their 100% binding affinity towards all six HLA alleles, taken in this study. These peptides were further checked computationally to know their IFN-γ and IL4 inducing potential and nine peptides were identified. Peptide binding interactions with predominant HLA alleles were done by docking. Out of nine docked promiscuous peptides, only two peptides (QESRILRVIKKKLVR, RILRVIKKKLVRKTL), from LPG-3 and one peptide (FDKFWCLVIDALKRI) from NH showed lowest binding energy with all six alleles. These promiscuous T-cell epitopes were predicted on the basis of their antigenicity, hydrophobicity, potential immune response and docking scores. The immunogenicity of predicted promiscuous peptides might be used for subunit vaccine development with immune-modulating adjuvants.

Immunology of Alveolar and Cystic Echinococcosis (AE and CE)

Cystic and alveolar echinococcosis are severe chronic helminthic diseases caused by the cystic growth or the intrahepatic tumour-like growth of the metacestode of Echinococcus granulosus or Echinococcus multilocularis, respectively. Both parasites have evolved sophisticated strategies to escape host immune responses, mainly by manipulating and directing this immune response towards anergy and/or tolerance. Recent research studies have revealed a number of respective immunoregulatory mechanisms related to macrophages and dendritic cell as well as T cell activities (regulatory T cells, Tregs). A better understanding of this complex parasite-host relationship, and the elucidation of specific crucial events that lead to disease, represents targets towards the development of novel treatment strategies and options.

Cloning, molecular analysis and epitopics prediction of a new chaperone GroEL Brucella melitensis antigen

OBJECTIVES

Brucellosis is a well-known domestic animal infectious disease, which is caused by Brucella bacterium. GroEL antigen increases Brucella survival and is one of the major antigens that stimulates the immune system. Hence, the objective of the present study was cloning and bioinformatics analysis of GroEL gene.

MATERIALS AND METHODS

The full-length open reading frame of this gene was amplified by specific primers and cloned into pTZ57R/T vector. Also, the sequence of this gene in the Brucella melitensis strain Rev 1 was submitted to the NCBI gene bank for the first time. Several prediction software applications were also used to predict B and T-cell epitopes, secondary and tertiary structures, antigenicity ability and enzymatic degradation sites. The used software applications validated experimental results.

RESULTS

The results of phylogenetic analysis showed that the GroEL sequence had near homology with other species instead of other Brucella spp. The bioinformatics tools used in the current study were validated by the results of four different experimental epitope predictions. Bioinformatics analysis identified eight B and seven T-cell epitopes.

CONCLUSION

According to the antigenic ability and proteasomal cleavage sites, four (150-160, 270-285,351-361 and 385-395) common epitopes were predicted for GroEL gene. Bioinformatics analysis showed that these regions had proper epitope characterization and so may be useful for stimulation of cell-mediated and humoral immunity system.

Upregulation of PD-1 on CD4⁺CD25⁺ T cells is associated with immunosuppression in liver of mice infected with Echinococcus multilocularis

Alveolar echinococcosis is a zoonotic disease caused by Echinococcus multilocularis (E. multilocularis) infection. The relationship between PD-1/PD-L1 pathway and Tregs at different stages of E. multilocularis infection has rarely been reported. This study aims to investigate the role of PD-1/PD-L1 in immunosuppression of Tregs in E. multilocularis infection. Hematoxylin-eosin staining, flow cytometry, immunohistochemistry, quantitative RT-PCR analysis, cytometric bead array and MTT assay were used to analyze liver pathological changes, percentages of PD-1(+) Tregs and PD-L1(+) dendritic cells (DCs), expression levels of PD-1, PD-L1 and Foxp3, levels of interleukin-10 (IL-10) and transforming growth factor beta (TGF-β) and proliferation of lymphocytes. During middle-late stage (day 30 to day 330) the percentages of PD-1(+) Tregs and PD-L1(+) DCs together with levels of Foxp3, IL-10 and TGF-β increased significantly and maintained at high level. The expression of PD-1 and PD-L1 was increased with the enlarging erosion of E. multilocularis, and was mainly distributed in hepatic sinus, fibrous wall of alveolar hydatid and germinal layer around foci of infection. PD-1/PD-L1 promoted the secretion of IL-10 and TGF-β. Our results indicate that engagement of the PD-1 and PD-L1 correlates with inhibition of T-cell effector function, cytokine secretion and proliferation. High expression of PD-1/PD-L1 may play an important role in stimulating CD4(+)CD25(+) T cells, and maintaining peripheral tolerance and immune evasion during chronic infection of E. multilocularis.

Identification, expression and phylogenetic analysis of EgG1Y162 from Echinococcus granulosus

OBJECTIVE

This study was to clone, identify and analyze the characteristics of egG1Y162 gene from Echinococcus granulosus.

METHODS

Genomic DNA and total RNAs were extracted from four different developmental stages of protoscolex, germinal layer, adult and egg of Echinococcus granulosus, respectively. Fluorescent quantitative PCR was used for analyzing the expression of egG1Y162 gene. Prokaryotic expression plasmid of pET41a-EgG1Y162 was constructed to express recombinant His-EgG1Y162 antigen. Western blot analysis was performed to detect antigenicity of EgG1Y162 antigen. Gene sequence, amino acid alignment and phylogenetic tree of EgG1Y162 were analyzed by BLAST, online Spidey and MEGA4 software, respectively.

RESULTS

EgG1Y162 gene was expressed in four developmental stages of Echinococcus granulosus. And, egG1Y162 gene expression was the highest in the adult stage, with the relative value of 19.526, significantly higher than other three stages. Additionally, Western blot analysis revealed that EgG1Y162 recombinant protein had good reaction with serum samples from Echinococcus granulosus infected human and dog. Moreover, EgG1Y162 antigen was phylogenetically closest to EmY162 antigen, with the similarity over 90%.

CONCLUSION

Our study identified EgG1Y162 antigen in Echinococcus granulosus for the first time. EgG1Y162 antigen had a high similarity with EmY162 antigen, with the genetic differences mainly existing in the intron region. And, EgG1Y162 recombinant protein showed good antigenicity.

Prokaryotic expression and identification of B- and T-cell combined epitopes of Em95 antigen of Echinococcus multilocularis

OBJECTIVE

This study is to clone and identify B- and T-cell combined epitopes from Em95 antigen.

METHODS

The B- and T-cell combined epitopes were predicted using bioinformatic software. Two DNA sequences of Em95-1 (which contained the coding region of one B- and T-cell combined epitope) and Em95-2 (which contained the coding regions of two B- and T-cell combined epitopes) were amplified by PCR. Em95-1 and Em95-2 were cloned into pET32a vector for protein expression. Rabbit was immunized with the expressed proteins of rEm95-1 and rEm95-2 to produce polyclonal antibodies. The immunogenicity and antigenicity of rEm95-1 and rEm95-2 were examined by Western blot analysis.

RESULTS

The three B- and T-cell combined epitopes were successfully cloned and expressed in PET32a vector. The recombinant antigens of rEm95-1 and rEm95-2 could specifically bind the human serum from patients with alveolar echinococcosis and specifically bind the prepared polyclonal antibodies.

CONCLUSION

Three B- and T-cell combined epitopes were successfully cloned with good immunogenicity and antigenicity. Our data suggest that B- and T-cell combined epitopes predicted from the Em95 antigen may be used for the construction of high-valence vaccines and as targets for prevention of echinococcosis.