Immunoinformatics studies and design of a novel multi-epitope peptide vaccine against Toxoplasma gondii based on calcium-dependent protein kinases antigens through an in-silico analysis.

Purpose: Infection by the intracellular apicomplexan parasite Toxoplasma gondii has serious clinical consequences in humans and veterinarians around the world. Although about a third of the world's population is infected with T. gondii, there is still no effective vaccine against this disease. The aim of this study was to develop and evaluate a multimeric vaccine against T. gondii using the proteins calcium-dependent protein kinase (CDPK)1, CDPK2, CDPK3, and CDPK5. Materials and Methods: Top-ranked major histocompatibility complex (MHC)-I and MHC-II binding as well as shared, immunodominant linear B-cell epitopes were predicted and linked using appropriate linkers. Moreover, the 50S ribosomal protein L7/L12 (adjuvant) was mixed with the construct's N-terminal to increase the immunogenicity. Then, the vaccine's physicochemical characteristics, antigenicity, allergenicity, secondary and tertiary structure were predicted. Results: The finally-engineered chimeric vaccine had a length of 680 amino acids with a molecular weight of 74.66 kDa. Analyses of immunogenicity, allergenicity, and multiple physiochemical parameters indicated that the constructed vaccine candidate was soluble, non-allergenic, and immunogenic, making it compatible with humans and hence, a potentially viable and safe vaccine candidate against T. gondii parasite. Conclusion: In silico, the vaccine construct was able to trigger primary immune responses. However, further laboratory studies are needed to confirm its effectiveness and safety.

Application Scopes of Miniaturized MXene-Functionalized Electrospun Nanofibers-Based Electrochemical Energy Devices.

Exploring combinatorial materials, as well as rational device configuration design, are assumed to be the key strategies for deploying versatile electrochemical devices. MXene sheets have revealed a high hydrophilic surface with proper mechanical and electrical characteristics, rendering them supreme additive candidates to integrate in electrospun electrochemical power tools. The synergetic effects of MXene 2D layers with the nanofibrous networks can boost actuator responsive ability, battery capacity retention, fuel cell stability, sensor sensitivity, and supercapacitor areal capacitance. Their superior mechanical features can be endowed to the electrospun layers through the embedding of the MXene additive. In this review, the preparation and inherent features of the MXene configurations are briefly evaluated. The fabrication and overall performance of the MXene-loaded nanofibers applicable in electrochemical actuators, batteries, fuel cells, sensors, and supercapacitors are comprehensively figured out. Eventually, an outlook on the future development of MXene-based electrospun composites is presented. A substantial focus has been devoted to date to engineering conjugated MXene and electrospun fibrous frames. The potential performance of the MXene-decorated nanofibers presents a bright future of nanoengineering toward technological growth. Meanwhile, a balance between the pros and cons of the synthesized MXene composite layers is worthwhile to consider in the future.

SDN-IoT: SDN-based efficient clustering scheme for IoT using improved Sailfish optimization algorithm.

The Internet of Things (IoT) includes billions of different devices and various applications that generate a huge amount of data. Due to inherent resource limitations, reliable and robust data transmission for a huge number of heterogenous devices is one of the most critical issues for IoT. Therefore, cluster-based data transmission is appropriate for IoT applications as it promotes network lifetime and scalability. On the other hand, Software Defined Network (SDN) architecture improves flexibility and makes the IoT respond appropriately to the heterogeneity. This article proposes an SDN-based efficient clustering scheme for IoT using the Improved Sailfish optimization (ISFO) algorithm. In the proposed model, clustering of IoT devices is performed using the ISFO model and the model is installed on the SDN controller to manage the Cluster Head (CH) nodes of IoT devices. The performance evaluation of the proposed model was performed based on two scenarios with 150 and 300 nodes. The results show that for 150 nodes ISFO model in comparison with LEACH, LEACH-E reduced energy consumption by about 21.42% and 17.28%. For 300 ISFO nodes compared to LEACH, LEACH-E reduced energy consumption by about 37.84% and 27.23%.

Investigation of antileishmanial activities of CaO nanoparticles on L. tropica and L. infantum parasites, in vitro.

Stibogluconate sodium and meglumine antimoniate are the main antimonials utilised as the primary treatment option for leishmaniasis. However, have a number of side effects that limit their use. Development of nanoparticles (NPs) use in biological research and remarkable antimicrobial effects and unique optical and structural properties of CaO NPs have motivated this study to evaluated the effect of different times/dilutions of CaO NPs on Leishmania tropica and Leishmania infantum. To evaluate the antileishmanial activity of CaO NPs, the cytotoxic effect of CaO NPs against L. tropica and L. infantum amastigotes, promastigotes, as well as macrophages, was evaluated using counting and MTT assay after adding different concentrations of CaO nanoparticles (800-6.25 µg/ml) to the parasite culture. The possible apoptosis by CaO NPs were evaluated via flow cytometry assay. The XRD-pattern related to CaO nanoparticles indicating the cubic phase structures. According the effects of nanoparticle on promastigotes the IC50 values of CaO nanoparticles within 72 h were 19.81 µg/ml for L. tropica and 22.57 µg/ml for L. infantum. The percentage of the normal, apoptotic, and necrotic cells was estimated to be 82.6%, 14.81%, and 2.69% for L. tropica, and 73.6%, 23.89%, and 2.58% for L. infantum, respectively. Our results showed acceptable in vitro activity level of CaO NPs against L. tropica and L. infantum promastigotes as well as intracellular amastigotes. CaO NPs were more effective against L. infantum compared to L. tropica in vitro study.

In vitro and in vivo study on antiprotozoal activity of calcium oxide (CaO) and magnesium oxide (MgO) nanoparticles on promastigote and amastigote forms of Leishmania major.

BACKGROUND: Currently, anti-leishmanial drugs have been developed. However, the available compounds have several side effects such as drug resistance and toxicity that cause some limitation for use. The development of nanoparticles (NPs) use in biological research and the proven effectiveness of CaONPs and MgONPs on bacteria and fungi, along with the lack of information about its antileishmanial effects, have motivated this study. CaO and MgONPs possess considerable antibacterial effects because of their alkalinity and active oxygen species. This study has taken into account the impacts of these two NPs on the L. major in vitro and in vivo. METHODS: To evaluate the antileishmanial activity of NPs, the cytotoxic effect of CaONPs, MgONPs, and MgOCaONPs against L. major amastigotes, promastigotes, as well as macrophages, was evaluated using counting or MTT assay. The possible apoptosis of L. major by CaONPs, MgONPs, and MgOCaONPs was evaluated via flow cytometry assay. For in vivo study, BALB/c mice were allocated to five groups and the lesions of infected mice with L. major promastigotes were treated with a 200 µg/mL concentration CaONPs, MgONPs, and MgOCaONPs, then the mice underwent a 4-week follow-up to examine the wound diameter and survival rates. RESULTS: The XRD-pattern related to CaONPs and MgONPs indicating the cubic phase and Rocksalt cubic structures. According the effects of nanoparticle on promastigotes the IC50 values of CaONPs, MgONPs, and MgOCaONPs within 72 h were 7.9 ug/mL, 10.3 ug/mL, and 8.0 ug/mL respectively. CaONPs, MgONPs, and MgOCaONPs induced apoptosis in about 7.8%, 53.57%, and 12.8% of promastigotes. All mice presented lesions. MgONPs was the most effective in reducing the size of the lesions. CONCLUSION: According to the results of the present research, MgONPs and CaONPs showed good in vitro and in vivo effects on L. major promastigotes and intracellular amastigotes especially MgONPs, and also it seems that MgONPs are applicable in Leishmania infection treatment due to their potential antileishmanial effects.

Assessing the economic effects of drought using Positive Mathematical Planning model under climate change scenarios.

In recent decades, regions all around the world have experienced severe droughts adversely affecting their agricultural production. Climate change, along with limited access to water will alter future production and agricultural development. The purpose of this study is to provide a perspective for the future cultivation regime in the Divandarre region in the Sepidrood catchment in Iran, using historical climatic, agricultural, and economic information. Future precipitation values are determined for three climate scenarios, then downscaled and converted to pixel-based precipitation maps using the Moving Least Squares method. Future droughts are identified using the Standardized Precipitation Index at 3, 6, and 9-month intervals based on precipitation values and the relationship between different types of droughts (meteorological, agricultural and hydrological). We introduce a new coefficient, the water cost coefficient, derived from drought characteristics that captures the added irrigation cost in drought years because of increased water price. Using the Positive Mathematical Planning method and considering limited land and water, predicted future prices and costs based on a linear regression of supply-demand, and the annual water cost coefficient values, an agroeconomic model is built. After prediction of future price and cost based on historical data from 2005 to 2018, we run future scenarios based on various price and cost values to determine the optimal annual cultivation area for each crop from 2020 to 2040. All scenarios indicate a decline in cultivation area for all crops making agriculture less beneficial in the future. The cultivation regime moves away from more water-consuming products with less economic value (e.g. watermelon) toward less water-consuming, more expensive products (e.g. lentils). The findings of this model along with expert economic judgments help determine the economic effects of climate change on irrigation, farmers' decisions, and water policies, including water markets, and improving irrigation efficiency. Authorities and farmers could adapt to drought shocks and changes in the market while experiencing less revenue loss.

Protective immunity induced with a DNA vaccine encoding B- and T-cells multi-epitope SAG1, ROP16, MIC4, GRA12, M2AP, and multi-epitope ROP8 against acute and chronic toxoplasmosis in BALB/c mice.

BACKGROUND: T. gondii infection is characterized by a high global prevalence. Nearly, 16-40% of people have been infected by T. gondii. Although T. gondii often causes subclinical infection, it may cause severe complications in newborns with congenital infection and immunocompromised individuals. Constant attempts of scientists have made valuable findings in the development of T. gondii candidate vaccines. However, an effective vaccine has not been successfully developed yet. In this study, multi-epitope SAG1, MIC4, ROP16, M2AP, GRA12, and multi-epitope ROP8 were injected into BALB/c mice intramuscularly, as cocktailed plasmids or as single-gene plasmids to assess the immune response against chronic and acute Toxoplasma infection. METHODS: BALB/c mice were immunized on days 0, 21, and 42. The immune responses of both vaccinated and control groups were evaluated using cytokine and antibody measurements, lymphocyte proliferation assay, survival time, and average number of cysts in each brain. RESULTS: The results indicated that DNA vaccination using multi-epitope ROP8 and multi-epitope SAG1, ROP16, MIC4, GRA12, M2AP could elicit both cellular and humoral immune responses, and enhanced the survival time in BALB/c mice. Also, the administration of multi-epitope ROP8 plus multi-epitope SAG1, ROP16, MIC4, GRA12, M2AP could enhance the concentrations of IgG antibody, elicit a mixed IgG1/IgG2a reaction with the predominance of the IgG2a, increase the release of IFN-γ cytokine, prolonge the survival time, and reduce the brain cysts. CONCLUSIONS: Here, we report that vaccination using cocktailed plasmids could induce better protective immunity compared to single plasmid for acute and chronic T. gondii infection.

Microscopic and Molecular Detection of Sarcocystis cruzi (Apicomplexa: Sarcocystidae) in the Heart Muscle of Cattle.

Background: Sarcocystis is a genus of coccidian protozoa that at least seven species of it can parasitize cattle. The global prevalence of Sarcocystis is close to 100% in adult cattle. The main aim of this study was to identify the infection rate of Sarcocystis spp. in heart of cattle in Tehran, Iran by microscopy and PCR-RFLP methods. Methods: Totally, 100 bovine heart samples were collected from the main slaughterhouse of Shahriar, Meysam slaughterhouse, west of Tehran in 2016. At first, heart samples were completely examined for the presence of sarcocystic macrocysts. Then, for microscopic examination, 50 g of each heart was digested in sterile condition using pepsin acid digestion method. Then, the species of the parasite were detected by PCR-RFLP technique and sequencing. Results: Overall, 97 of 100 of the heart muscle samples were infected with Sarcocystis. All the samples were detected as S. cruzi through similar patterns in PCR-RFLP. Conclusion: S. cruzi is the most common species in the heart of cattle slaughtered in Shahriar.

New segmentation and feature extraction algorithm for classification of white blood cells in peripheral smear images.

This article addresses a new method for the classification of white blood cells (WBCs) using image processing techniques and machine learning methods. The proposed method consists of three steps: detecting the nucleus and cytoplasm, extracting features, and classification. At first, a new algorithm is designed to segment the nucleus. For the cytoplasm to be detected, only a part of it located inside the convex hull of the nucleus is involved in the process. This attitude helps us overcome the difficulties of segmenting the cytoplasm. In the second phase, three shapes and four novel color features are devised and extracted. Finally, by using an SVM model, the WBCs are classified. The segmentation algorithm can detect the nucleus with a dice similarity coefficient of 0.9675. The proposed method can categorize WBCs in Raabin-WBC, LISC, and BCCD datasets with accuracies of 94.65%, 92.21%, and 94.20%, respectively. Besides, we show that the proposed method possesses more generalization power than pre-trained CNN models. It is worth mentioning that the hyperparameters of the classifier are fixed only with the Raabin-WBC dataset, and these parameters are not readjusted for LISC and BCCD datasets.

Immunoinformatic Analysis of Calcium-Dependent Protein Kinase 7 (CDPK7) Showed Potential Targets for Toxoplasma gondii Vaccine.

Apicomplexan parasites, including Toxoplasma gondii (T. gondii), express different types of calcium-dependent protein kinases (CDPKs), which perform a variety of functions, including attacking and exiting the host cells. In the current bioinformatics study, we have used several web servers to predict the basic features and specifications of the CDPK7 protein. The findings showed that CDPK7 protein has 2133 amino acid residues with an average molecular weight (MW) of 219085.79 D. The aliphatic index with 68.78 and grand average of hydropathicity (GRAVY) with -0.331 score were estimated. The outcomes of current research showed that the CDPK7 protein included 502 alpha-helix, 1311 random coils, and 320 extended strands with GOR4 method. Considering the Ramachandran plot, the favored region contains more than 92% of the amino acid residues. In addition, evaluation of antigenicity and allergenicity showed that CDPK7 protein has immunogenic and nonallergenic nature. The present research provides key data for more animal-model study on the CDPK7 protein to design an efficient vaccine against toxoplasmosis in the future.

Detection of Anti-Toxoplasma gondii IgG and IgM Antibodies and Associated Risk Factors during Pregnancy in Southwest Iran.

Background: This research was aimed at evaluating the seroprevalence of acute and chronic Toxoplasma gondii (T. gondii) infection in pregnant women and related risk factors in southwest Iran. Methods: In this cross-sectional study, eighty-eight pregnant women were included from October 2019 to December 2019. The presence of anti-T. gondii IgM and IgG antibodies was measured using the enzyme-linked immunosorbent assay (ELISA). In addition, a questionnaire consisting of demographic information was completed for each subject. Results: The overall seroprevalence of T. gondii infection was estimated to be 34.09% (30/88). Of these, 1 (1.13%) and 29 (32.95%) samples were found positive for IgM and IgG, respectively. Regarding the risk factors, the consumption of raw/undercooked meat (P value = 0.007) and history of abortion (P value = 0.017) were significantly associated with IgG seroprevalence in pregnant women. Conclusion: The results showed that the pregnant women of southwest Iran might be moderately exposed to T. gondii. Since the risk of acute T. gondii infection in this susceptible group is very important, regular screening tests to diagnose the infection are recommended before pregnancy.

Fetal QRS Detection in Noninvasive Abdominal Electrocardiograms Using Principal Component Analysis and Discrete Wavelet Transforms with Signal Quality Estimation.

BACKGROUND: Fetal heart rate (FHR) extracted from abdominal electrocardiogram (ECG) is a powerful non-invasive method in appropriately assessing the fetus well-being during pregnancy. Despite significant advances in the field of electrocardiography, the analysis of fetal ECG (FECG) signal is considered a challenging issue which is mainly due to low signal to noise ratio (SNR) of FECG. OBJECTIVE: In this study, we present an approach for accurately locating the fetal QRS complexes in non-invasive FECG. MATERIALS AND METHODS: In this experimental study, the proposed method included 4 steps. In step 1, comb notching filter was employed to pre-process the abdominal ECG (AECG). Furthermore, low frequency noises were omitted using wavelet decomposition. In next step, principal component analysis (PCA) and signal quality assessment (SQA) were used to obtain an optimal AECG reference channel for maternal R-peaks detection. In step 3, maternal ECG (MECG) was removed from mixture signal and FECG was extracted. In final step, the extracted FECG was first decomposed by discrete wavelet transforms at level 10. Then, by employing details of levels 2, 3, 4, the new FECG signal was reconstructed in which various noises and artifacts were removed and FECG components whose frequency were close to the fetal QRS complexes remained which increased the performance of the method. RESULTS: For evaluation, 15 recordings of PhysioNet Noninvasive FECG database were used and the average F1 measure of 98.77% was obtained. CONCLUSION: The results indicate that use of both an efficient analysis of major component of AECG along with a signal quality assessment technique has a promising performance in FECG analysis.

Immunoinformatic analysis of immunogenic B- and T-cell epitopes of MIC4 protein to designing a vaccine candidate against Toxoplasma gondii through an in-silico approach.

PURPOSE: Toxoplasmosis, transmitted by Toxoplasma gondii, is a worldwide parasitic disease that affects approximately one-third of the world's inhabitants. Today, there are no appropriate drugs to deter tissue cysts from developing in infected hosts. So, developing an effective vaccine would be valuable to avoid from toxoplasmosis. Considering the role of microneme antigens such as microneme protein 4 (MIC4) in T. gondii pathogenesis, it can be used as potential candidates for vaccine against T. gondii. MATERIALS AND METHODS: In this study several bioinformatics methods were used to assess the different aspects of MIC4 protein such as secondary and tertiary structure, physicochemical characteristics, the transmembrane domains, subcellular localization, B-cell, helper-T lymphocyte, cytotoxic-T lymphocyte epitopes, and other notable characteristic of this protein design a suitable vaccine against T. gondii. RESULTS: The studies revealed that MIC4 protein includes 59 potential post-translational modification sites without any transmembrane domains. Moreover, several probable epitopes of B- and T-cells were detected for MIC4. The secondary structure comprised 55.69% random coil, 5.86% beta-turn, 19.31% extended strand, and 19.14% alpha helix. According to the Ramachandran plot results, 87.42% of the amino acid residues were located in the favored, 9.44% in allowed, and 3.14% in outlier regions. The protein allergenicity and antigenicity revealed that it was non-allergenic and antigenic. CONCLUSION: This study gives vital basic on MIC4 protein for further research and also established an effective vaccine with different techniques against acute and chronic toxoplasmosis.

Bioinformatics analysis of calcium-dependent protein kinase 4 (CDPK4) as Toxoplasma gondii vaccine target.

OBJECTIVES: Toxoplasma gondii (T. gondii), an obligate intracellular apicomplexan parasite, could affect numerous warm-blooded animals, such as humans. Calcium-dependent protein kinases (CDPKs) are essential Ca2+ signaling mediators and participate in parasite host cell egress, outer membrane motility, invasion, and cell division. RESULTS: Several bioinformatics online servers were employed to analyze and predict the important properties of CDPK4 protein. The findings revealed that CDPK4 peptide has 1158 amino acid residues with average molecular weight (MW) of 126.331 KDa. The aliphatic index and GRAVY for this protein were estimated at 66.82 and - 0.650, respectively. The findings revealed that the CDPK4 protein comprised 30.14% and 34.97% alpha-helix, 59.84% and 53.54% random coils, and 10.02% and 11.49% extended strand with SOPMA and GOR4 tools, respectively. Ramachandran plot output showed 87.87%, 8.40%, and 3.73% of amino acid residues in the favored, allowed, and outlier regions, respectively. Also, several potential B and T-cell epitopes were predicted for CDPK4 protein through different bioinformatics tools. Also, antigenicity and allergenicity evaluation demonstrated that this protein has immunogenic and non-allergenic nature. This paper presents a basis for further studies, thereby provides a fundamental basis for the development of an effective vaccine against T. gondii infection.

Antigenic properties of dense granule antigen 12 protein using bioinformatics tools in order to improve vaccine design against Toxoplasma gondii.

PURPOSE: Toxoplasma gondii is an opportunistic parasite infecting all warm-blooded animals including humans. The dense granule antigens (GRAs) play an important role in parasite survival and virulence and in forming the parasitophorous vacuole. Identification of protein characteristics increases our knowledge about them and leads to develop the vaccine and diagnostic studies. MATERIALS AND METHODS: This paper gave a comprehensive definition of the important aspects of GRA12 protein, including physico-chemical features, a transmembrane domain, subcellular position, secondary and tertiary structure, potential epitopes of B-cells and T-cells, and other important features of this protein using different and reliable bioinformatics methods to determine potential epitopes for designing of a high-efficient vaccine. RESULTS: The findings showed that GRA12 protein had 53 potential post-translational modification sites. Also, only one transmembrane domain was recognized for this protein. The secondary structure of GRA12 protein comprises 35.55% alpha-helix, 19.50% extended strand, and 44.95% random coil. Moreover, several potential B- and T-cell epitopes were identified for GRA12. Based on the results of the Ramachandran plot, 79.26% of amino acid residues were located in favored, 11.85% in allowed and 8.89% in outlier regions. Furthermore, the results of the antigenicity and allergenicity assessment noted that GRA12 is immunogenic and non-allergenic. CONCLUSION: This research provided important basic and conceptual data on GRA12 to develop an effective vaccine against acute and chronic toxoplasmosis for further in vivo investigations. More studies are required on vaccine development using the GRA12 alone or combined with other antigens in the future.

In-depth computational analysis of calcium-dependent protein kinase 3 of Toxoplasma gondii provides promising targets for vaccination.

PURPOSE: The Toxoplasma gondii calcium-dependent protein kinase-3 (CDPK3) is a key enzyme for parasite egress, control of calcium-dependent permeabilization in parasitophorous vacuole membrane and tissue cyst formation. In this study, we comprehensively explored the bioinformatics features of this protein to improve vaccine design against T. gondii. MATERIALS AND METHODS: Various web servers were employed for the analysis of physico-chemical properties, post-translational modifications, localization in the subcellular milieu, secondary and tertiary structures, as well as B-cell, major histocompatibility complex (MHC)-binding and cytotoxic T-lymphocyte (CTL) epitopes. RESULTS: This protein was a 537 amino acid antigenic and non-allergenic molecule with a molecular weight of 60.42 kDa, a grand average of hydropathicity score of -0.508, and aliphatic index of 79.50. There exists 46.74% alpha helix, 12.48% extended strand, and 40.78% random coil in the secondary structure. Ramachandran plot of the refined model demonstrated 99.3%, 0.7%, and 0.0% of residues in the favored, allowed and outlier areas, respectively. Besides, various potential B-cell (continuous and conformational), MHC-binding and CTL epitopes were predicted for Toxoplasma CDPK3 protein. CONCLUSION: This article provides a foundation for further investigations, and laid a theoretical basis for the development of an appropriate vaccine against T. gondii infection.

Toxoplasma gondii ROP38 protein: Bioinformatics analysis for vaccine design improvement against toxoplasmosis.

Rhoptry proteins (ROPs) play a significant role in various stages of Toxoplasma gondii (T. gondii) life cycle, being critical for both invasion and intracellular survival. ROP38 is a key manipulator of host gene expression and has a function in tachyzoite to bradyzoite conversion. In this study, we've employed various bioinformatics online tools for immunogenicity prediction of ROP38 protein, comprising physico-chemical, antigenic and allergenic profiles, transmembrane domain, subcellular localization, post-translational modification (PTM) sites, secondary and 3D structure, B-cell, MHC-binding and cytotoxic T-lymphocyte (CTL) epitopes. The findings showed 54 PTM sites without a transmembrane domain. Also, ROP38 was proved a non-allergenic and antigenic protein. The protein had Sec signal peptide (Sec/SPI) with 0.8762 likelihood. The secondary structure included 52.68% random coil, 29.57% alpha helix and 17.74% extended strand. Based on Ramachandran plot output for refined model, 95.3%, 3.4%, and 1.4% of amino acid residues were incorporated in the favored, allowed, and outlier regions, respectively. B-cell epitopes TFPGDDIQTSS (67-72) and KAKNKWGRTRYTLQG (207-221) as well as T-cell epitope LSPVGFFTAL (6-15) possessed the highest antigenic index in the protein sequence. This paper is a premise for further researches, and provides insights for the development of a suitable vaccine against toxoplasmosis. More empirical studies are required using the ROP38 alone or in combination with other antigens/epitopes in the future.

Computational probing of Toxoplasma gondii major surface antigen 1 (SAG1) for enhanced vaccine design against toxoplasmosis.

The SAG1 is a tachyzoite-specific protein critical for Toxoplasma gondii (T. gondii) adhesion to surface receptors of the host cells. In this study we've comprehensively excavated the sequence of SAG1 using online bioinformatics servers toward better vaccine design against toxoplasmosis. Web-based tools were used to assess the physico-chemical properties, post-translational modifications (PTMs), transmembrane domains, subcellular localization, secondary and 3D structures, as well as B-cell, Cytotoxic T cells (CTL) and major histocompatibility complex (MHC) epitopes. The 336 amino acid sequence possessed a molecular weight of 34829.02 D, aliphatic index of 80.15 and GRAVY score of 0.129. There was 47 PTM sites without any transmembrane domains. Also, the SAG1 protein was appointed to be immunogen and non-allergen. The secondary structure comprised 62.5% random coil, 26.79% extended strand and 10.71% alpha helix. Ramachandran plot of the refined model demonstrated 94.4% residues in the favored region, 4.8% in allowed region and 0.8% in outlier region. Additionally, various potential B-cell (linear and conformational), CTL and HTL epitopes were predicted for T. gondii SAG1. This in silico investigation would be a premise for appropriate immunization strategies against toxoplasmosis. More studies are anticipated to be done empirically using SAG1 immunoprotective epitopes combined with other antigenic compounds.

Structural predication and antigenic analysis of ROP16 protein utilizing immunoinformatics methods in order to identification of a vaccine against Toxoplasma gondii: An in silico approach.

Toxoplasmosis, caused by Toxoplasma gondii, is a common parasitic disease, affecting almost one-third of the world's population. Currently, there are no effective treatments for inhibiting the formation of chronic tissue cysts in infected hosts. Thus, the production of appropriate vaccines against this pathogen is an important goal to avoid toxoplasmosis. considering the role of rhoptry antigens like ROP16 in virulence and satisfactory immunogenicity, they can be used as promising vaccine candidates against T. gondii. In the present study, an in silico approach was used to analyze various aspects of the ROP16 protein, including physicochemical characteristics, the potential epitopes of B and T-cells, the secondary and tertiary structure, the subcellular localization, the transmembrane domain, and other important features of this protein using several bioinformatics tools to design a proper vaccine against T. gondii. The results showed that ROP16 protein includes 93 potential post-translational modification sites. The secondary structure of the ROP16 protein comprises 34.23% alpha-helix, 54.46% random coil, and 11.32% extended strand. Moreover, several potential B- and T-cell epitopes were identified for ROP16. Based on the results of Ramachandran plot, 84.64% of the amino acid residues were located in the favored, 10.34% in allowed, and 5.02% in outlier regions. Furthermore, the results of the antigenicity and allergenicity assessment noted that this protein was immunogenic and non-allergenic. Our findings suggested that structural and functional predictions applied to ROP16 protein using in silico tools can reduce the failure risk of the laboratory studies. This research provided an important basis for further studies and also developed an effective vaccine against acute and chronic toxoplasmosis by various strategies. Further studies are needed on the development of vaccines in vivo using ROP16 alone or in combination with other antigens in the future.