In Silico Designing a Candidate Vaccine Against Breast Cancer

International Journal of Peptide Research and Therapeutics - Breast cancer (BC) is the most common type of women’s cancer with a prevalence of about 25%, although it is rare in men...     

In Silico Design of a New Multi-Epitope Peptide-Based Vaccine Candidate Against Q Fever

Molecular Biology - Novel types of the vaccines with high immunogenicity and low risks, including epitope-based vaccines, are sought. Among zoonotic disease, Q fever caused by Coxiella burnetii is...     

Functional Exposed Amino Acids of CarO Analysis as a Potential Vaccine Candidate in Acinetobacter Baumannii

Acinetobacter baumannii is a well-recognized cause of nosocomial infections. This organism is recognized to be among the most difficult antimicrobial-resis     

Design of a Multi-epitope Vaccine Against Acinetobacter baumannii Using Immunoinformatics Approach

International Journal of Peptide Research and Therapeutics - Acinetobacter baumannii is one of the most successful pathogens causing nosocomial infections and has significantly multidrug-resistant....     

In Silico Analyses of Staphylococcal Enterotoxin B as a DNA Vaccine for Cancer Therapy

Immunotherapy has been suggested as a compelling alternative approach for conventional breast cancer treatment methods. Despite the paramount rolesof T cells in this approach, insufficient numbers of them in the combat against progressive tumor growth still remain to be dealt with. Super antigens are a class of antigens, capable of eliciting T cell proliferation response against desired antigens. Staphylococcal enterotoxin B (SEB) is categorized as a super antigen, its anti-tumor properties has been previously reported. However, to the best our knowledge, SEB has not been ever administered as a DNA construct. In the present study, we exploited bioinformatics tools to assess the immunoreactivity of a SEB-coding DNA construct that serves as a DNA vaccine for breast cancer therapy. Potential B and T (MHC class I and II binders) cell epitopes of the hypothetically expressed protein, along with its sub cellular localization were predicted. Moreover, probable glycosylation and phosphorylation sites within the protein sequence were determined. The gene sequence was optimized according to murine model codon bias and its mRNA stability was analyzed. Employing an integrative in silico approach, we revealed that apparently the construct could be efficiently expressed in mouse model. Moreover, the hypothetically expressed protein could act as an amenable adjuvant in cancer immunotherapy.     

Production of a Subunit Vaccine Candidate against Porcine Post-Weaning Diarrhea in High-Biomass Transplastomic Tobacco

Post-weaning diarrhea (PWD) in piglets is a major problem in piggeries worldwide and results in severe economic losses. Infection with Enterotoxigenic Escherichia coli (ETEC) is the key culprit for the PWD disease. F4 fimbriae of ETEC are highly stable proteinaceous polymers, mainly composed of the major structural subunit FaeG, with a capacity to evoke mucosal immune responses, thus demonstrating a potential to act as an oral vaccine against ETEC-induced porcine PWD. In this study we used a transplastomic approach in tobacco to produce a recombinant variant of the FaeG protein, rFaeG(ntd/dsc), engineered for expression as a stable monomer by N-terminal deletion and donor strand-complementation (ntd/dsc). The generated transplastomic tobacco plants accumulated up to 2.0 g rFaeG(ntd/dsc) per 1 kg fresh leaf tissue (more than 1% of dry leaf tissue) and showed normal phenotype indistinguishable from wild type untransformed plants. We determined that chloroplast-produced rFaeG(ntd/dsc) protein retained the key properties of an oral vaccine, i.e. binding to porcine intestinal F4 receptors (F4R), and inhibition of the F4-possessing (F4+) ETEC attachment to F4R. Additionally, the plant biomass matrix was shown to delay degradation of the chloroplast-produced rFaeG(ntd/dsc) in gastrointestinal conditions, demonstrating a potential to function as a shelter-vehicle for vaccine delivery. These results suggest that transplastomic plants expressing the rFaeG(ntd/dsc) protein could be used for production and, possibly, delivery of an oral vaccine against porcine F4+ ETEC infections. Our findings therefore present a feasible approach for developing an oral vaccination strategy against porcine PWD.     

In Silico Design of Multimeric HN-F Antigen as a Highly Immunogenic Peptide Vaccine Against Newcastle Disease Virus

Application of molecular biology techniques to the production of new vaccines against different strains of the Newcastle disease virus (NDV) has been the subject of recent research reports. Development of improved techniques for genome sequencing has led to the recognition of protective mechanisms and the identification of possible candidate antigens. Such procedures could generate meaningful results regarding the virulence determinants of NDV. This study proposed an in silico approach by assembling potential and conserved epitopic regions of hemagglutinin–neuraminidase (HN) and fusion (F) glycoproteins of NDV to induce multiepitopic responses against the virus. Epitope predictions showed that the hypothetical synthetic construct could induce immature B and T cell epitopes that expect a high immune response because of their location in four distinct parts of the construct, namely the head, stalk and the heptad repeated regions known as the HRA and HRB domains. Most regions of the chimeric construct were found to have high antigenic propensity and surface accessibility, which further confirmed the strategy for selection of precise continuous and discontinuous epitopes of HN and F antigens. Thermodynamic folding of mRNA structures revealed correct folding of the RNA construct, indicating good stability of the mRNA to increase the efficiency of translation in the target host. The three-dimensional structure of the native HN-F chimeric protein was successfully generated and validated as a proper model which may define reliability, structural quality and conformation.     

Designing a Fusion Protein Vaccine Against HCV: An In Silico Approach

Hepatitis C virus (HCV) infection is a major global issue that leads to serious liver disease such as chronic liver inflammation and hepatocellular carcinoma. At present, no approved vaccine is available for control or treatment of HCV infection. Therefore, the development of an efficient vaccine against HCV is an urgent need. Today, designing an effective vaccine against hepatitis C is one of the outmost propriety for researchers. Fusion protein vaccines containing the immunogen proteins and adjuvant molecules are able to stimulate both humoral and cellular responses that are crucial for eradicating HCV infection. Herein, in silico design of fusion forms of vaccine candidates against HCV, including flagellin (fliC) from Pseudomonas aeruginosa and NS5B antigen (NT300) from HCV was performed. First, two forms of fusion protein (NT300-fliC and fliC-NT300) were designed and analyzed using different bioinformatics tools. For this aim, the Iterative threading assembly refinement (I-TASSER) server was used for modeling the fusion forms of protein; namely, NT300-fliC and fliC-NT300, then the high-rank 3D model of fusion protein was selected, subsequently various physico-chemical, and structural parameters were examined bioinformatically. After the selection of the best construct (fliC-NT300), the interaction of flagellin part of vaccine with toll-like receptor 5 (TLR5) was evaluated via docking studies. Our results represented that based on data obtained from various servers, and the docking analyses of two constructs, fliC-NT300 fusion form showed better results than NT300-fliC. For this reason, the fliC-NT300 form was selected for further evaluations. In sum, structural and immunological computational studies showed that the fliC-NT300 can be introduced as a prophylactic or therapeutic candidate vaccine against the HCV, after the efficacy of that was confirmed via in vitro and in vivo assays.

     

In Silico Identification of Epitope-Based Peptide Vaccine for Nipah Virus

International Journal of Peptide Research and Therapeutics - Nipah virus was first appeared in Malaysian 1998, which further found be outburst in neighbor countries i.e. Bangladesh, Singapore, and...     

Evaluation of Salmonella Porins as a Broad Spectrum Vaccine Candidate

Porins were prepared from smooth strain of Salmonella typhi 0–901 and chemotype of rough mutant of S. typhimurium Ra-30. Mice were immunized with both the porin preparations in different groups and challenged with S. typhimurium LT2–71 and S. enteritidis SH-1269. Porin immunized mice showed significant protection (P <0.01) against challenge with homologous as well as heterologous strains. Hence, the use of porins may be attempted in future to protect against salmonellosis.     

IRS-PCR在鲍曼不动杆菌基因分型研究中的应用

探讨低频限制性位点聚合酶链反应(infrequent-restriction-site polym erase chain site,IRS-PCR)在鲍曼不动杆菌基因分型中的应用。用IRS-PCR分别扩增上海、哈尔滨两地各20株鲍曼不动杆菌DNA稀有限制区旁序列并分型。与RAPD法比较两种基因分型方法的分型率、分辨力、重复性。IRS-PCR可将上海株分13个型别,RAPD分为19个型别,两种方法分型的一致率为60%(12/20);IRS-PCR将哈尔滨株分成19个型别,RAPD分为20个型别,两种方法分型的一致率为90%(18/20)。与RAPD相比,IRS-PCR的条带数多,分辨力强,重复性好。故IRS-PCR可用于鲍曼不动杆菌的分型研究,也是一种有价值的分子流行病学研究工具。     

Evaluation of the C-Terminal Fragment of Entamoeba histolytica Gal/GalNAc Lectin Intermediate Subunit as a Vaccine Candidate against Amebic Liver Abscess

Background

Entamoeba histolytica is an intestinal protozoan parasite that causes amoebiasis, including amebic dysentery and liver abscesses. E. histolytica invades host tissues by adhering onto cells and phagocytosing them depending on the adaptation and expression of pathogenic factors, including Gal/GalNAc lectin. We have previously reported that E. histolytica possesses multiple CXXC sequence motifs, with the intermediate subunit of Gal/GalNAc lectin (i.e., Igl) as a key factor affecting the amoeba''s pathogenicity. The present work showed the effect of immunization with recombinant Igl on amebic liver abscess formation and the corresponding immunological properties.

Methodology/Principal Findings

A prokaryotic expression system was used to prepare the full-length Igl and the N-terminal, middle, and C-terminal fragments (C-Igl) of Igl. Vaccine efficacy was assessed by challenging hamsters with an intrahepatic injection of E. histolytica trophozoites. Hamsters intramuscularly immunized with full-length Igl and C-Igl were found to be 92% and 96% immune to liver abscess formation, respectively. Immune-response evaluation revealed that C-Igl can generate significant humoral immune responses, with high levels of antibodies in sera from immunized hamsters inhibiting 80% of trophozoites adherence to mammalian cells and inducing 80% more complement-mediated lysis of trophozoites compared with the control. C-Igl was further assessed for its cellular response by cytokine-gene qPCR analysis. The productions of IL-4 (8.4-fold) and IL-10 (2-fold) in the spleen cells of immunized hamsters were enhanced after in vitro stimulation. IL-4 expression was also supported by increased programmed cell death 1 ligand 1 gene.

Conclusions/Significance

Immunobiochemical characterization strongly suggests the potential of recombinant Igl, especially the C-terminal fragment, as a vaccine candidate against amoebiasis. Moreover, protection through Th2-cell participation enabled effective humoral immunity against amebic liver abscesses.     

Molecular Analysis of the Acinetobacter baumannii Biofilm-Associated Protein

Acinetobacter baumannii is a multidrug-resistant pathogen associated with hospital outbreaks of infection across the globe, particularly in the intensive care unit. The ability of A. baumannii to survive in the hospital environment for long periods is linked to antibiotic resistance and its capacity to form biofilms. Here we studied the prevalence, expression, and function of the A. baumannii biofilm-associated protein (Bap) in 24 carbapenem-resistant A. baumannii ST92 strains isolated from a single institution over a 10-year period. The bap gene was highly prevalent, with 22/24 strains being positive for bap by PCR. Partial sequencing of bap was performed on the index case strain MS1968 and revealed it to be a large and highly repetitive gene approximately 16 kb in size. Phylogenetic analysis employing a 1,948-amino-acid region corresponding to the C terminus of Bap showed that Bap_MS1968 clusters with Bap sequences from clonal complex 2 (CC2) strains ACICU, TCDC-AB0715, and 1656-2 and is distinct from Bap in CC1 strains. By using overlapping PCR, the bap_MS1968 gene was cloned, and its expression in a recombinant Escherichia coli strain resulted in increased biofilm formation. A Bap-specific antibody was generated, and Western blot analysis showed that the majority of A. baumannii strains expressed an ∼200-kDa Bap protein. Further analysis of three Bap-positive A. baumannii strains demonstrated that Bap is expressed at the cell surface and is associated with biofilm formation. Finally, biofilm formation by these Bap-positive strains could be inhibited by affinity-purified Bap antibodies, demonstrating the direct contribution of Bap to biofilm growth by A. baumannii clinical isolates.     

In Silico Designing of Peptidomimetics Enhancing Endoribonucleolytic Activities of Acinetobacter MazF Toxin as the Novel Anti-bacterial Candidates

International Journal of Peptide Research and Therapeutics - Acinetobacter infection is one of the main causes of mortality in the patients admitted to the intensive care units (ICUs). Activation...     

Histopathological Analysis of Acinetobacter baumannii Lung Infection in a Mouse Model

Acinetobacter baumannii is the main causative pathogen of nosocomial infections that causes severe infections in the lungs. In this study, we analyzed the histopathological characteristics of lung infection with two strains of A. baumannii (ATCC 19606 and the clinical isolate TK1090) and Pseudomonas aeruginosa PAO-1 in C3H/HeN mice to evaluate the virulence of A. baumannii. Survival was evaluated over 14 days. At 1, 2, 5, or 14 days postinfection, mice of C3H/HeN were sacrificed, and histopathological analysis of lung specimens was also performed. Histopathological changes and accumulation of neutrophils and macrophages in the lungs after infection with A. baumannii and P. aeruginosa were analyzed. Following intratracheal inoculation, the lethality of ATCC 19606- and TK1090-infected mice was lower than that of PAO-1-infected mice. However, when mice were inoculated with a sub-lethal dose of A. baumannii, the lung bacterial burden remained in the mice until 14 days post-infection. Additionally, histopathological analysis revealed that macrophages infiltrated the lung foci of ATCC 19606-, TK1090-, and PAO-1-infected mice. Although neutrophils infiltrated the lung foci of ATCC 19606- and TK1090-infected mice, they poorly infiltrated the lung foci of PAO-1-infected mice. Accumulation of these cells in the lung foci of ATCC 19606- and TK1090-infected mice, but not PAO-1-infected mice, was observed for 14 days post-infection. These results suggest that A. baumannii is not completely eliminated despite the infiltration of immune cells in the lungs and that inflammation lasts for prolonged periods in the lungs. Further studies are required to understand the mechanism of A. baumannii infection, and novel drugs and vaccines should be developed to prevent A. baumannii infection.     

Multidrug-resistant Acinetobacter baumannii as an emerging concern in hospitals

Molecular Biology Reports - Acinetobacter baumannii has become a major concern for scientific attention due to extensive antimicrobial resistance. This resistance causes an increase in mortality...     

Genetic Variation In Vitro and In Vivo of an Attenuated Lassa Vaccine Candidate

The attenuated Lassa vaccine candidate ML29 is a laboratory-produced reassortant between Lassa and Mopeia viruses, two Old World arenaviruses that differ by 40% in nucleic acid sequence. In our previous studies, ML29 elicited sterilizing immunity against Lassa virus challenge in guinea pigs and marmosets and virus-specific cell-mediated immunity in both simian immunodeficiency virus (SIV)-infected and uninfected rhesus macaques. Here, we show that ML29 is stable after 12 passages in vitro without losing its plaque morphology or its attenuated phenotype in suckling mice. Additionally, we used deep sequencing to characterize the viral population comprising the original stock of ML29, the stock of ML29 after 12 passages in Vero cells, and the ML29 isolates obtained from vaccinated animals. Twenty-seven isolates bore approximately 77 mutations that exceeded 20% of the single-nucleotide polymorphism (SNP) changes at any single locus. Of these 77 mutations, 5 appeared to be host specific, for example, appearing in mice but not in primates. None of these mutations were reversions of ML29 to the sequences of the parental Lassa and Mopeia viruses. The host-specific mutations indicate viral adaptations to virus-host interactions, and such interactions make reasonable targets for antiviral approaches. Variants capable of chronic infection did not emerge from any of the primate infections, even in immune-deficient animals, indicating that the ML29 reassortant is reasonably stable in vivo. In conclusion, the preclinical studies of ML29 as a Lassa virus vaccine candidate have been advanced, showing high levels of protection in nonhuman primates and acceptable stability both in vitro and in vivo.     

Phospholipase D as a key modulator of cancer progression

The phospholipase D (PLD) family has a ubiquitous expression in cells. PLD isoforms (PLDs) and their hydrolysate phosphatidic acid (PA) have been demonstrated to engage in multiple stages of cancer progression. Aberrant expression of PLDs, especially PLD1 and PLD2, has been detected in various cancers. Inhibition or elimination of PLDs activity has been shown to reduce tumour growth and metastasis. PLDs and PA also serve as downstream effectors of various cell‐surface receptors, to trigger and regulate propagation of intracellular signals in the process of tumourigenesis and metastasis. Here, we discuss recent advances in understanding the functions of PLDs and PA in discrete stages of cancer progression, including cancer cell growth, invasion and migration, and angiogenesis, with special emphasis on the tumour‐associated signalling pathways mediated by PLDs and PA and the functional importance of PLDs and PA in cancer therapy.