In silico design of an epitope-based vaccine against PspC in Streptococcus pneumoniae using reverse vaccinology.

BACKGROUND: Streptococcus pneumoniae is a major pathogen that poses a significant hazard to global health, causing a variety of infections including pneumonia, meningitis, and sepsis. The emergence of antibiotic-resistant strains has increased the difficulty of conventional antibiotic treatment, highlighting the need for alternative therapies such as multi-epitope vaccines. In this study, immunoinformatics algorithms were used to identify potential vaccine candidates based on the extracellular immunogenic protein Pneumococcal surface protein C (PspC). METHOD: The protein sequence of PspC was retrieved from NCBI for the development of the multi-epitope vaccine (MEV), and potential B cell and T cell epitopes were identified. Linkers including EAAAK, AAY, and CPGPG were used to connect the epitopes. Through molecular docking, molecular dynamics, and immunological simulation, the affinity between MEV and Toll-like receptors was determined. After cloning the MEV construct into the PET28a ( +) vector, SnapGene was used to achieve expression in Escherichia coli. RESULT: The constructed MEV was discovered to be stable, non-allergenic, and antigenic. Microscopic interactions between ligand and receptor are confirmed by molecular docking and molecular dynamics simulation. The use of an in-silico cloning approach guarantees the optimal expression and translation efficiency of the vaccine within an expression vector. CONCLUSION: Our study demonstrates the potential of in silico approaches for designing effective multi-epitope vaccines against S. pneumoniae. The designated vaccine exhibits the required physicochemical, structural, and immunological characteristics of a successful vaccine against SPN. However, laboratory validation is required to confirm the safety and immunogenicity of the proposed vaccine design.

An immunoinformatics approach to epitope-based vaccine design against PspA in Streptococcus pneumoniae.

BACKGROUND: Streptococcus pneumoniae (SPN) is the agent responsible for causing respiratory diseases, including pneumonia, which causes severe health hazards and child deaths globally. Antibiotics are used to treat SPN as a first-line treatment, but nowadays, SPN is showing resistance to several antibiotics. A vaccine can overcome this global problem by preventing this deadly pathogen. The conventional methods of wet-laboratory vaccine design and development are an intense, lengthy, and costly procedure. In contrast, epitope-based in silico vaccine designing can save time, money, and energy. In this study, pneumococcal surface protein A (PspA), one of the major virulence factors of SPN, is used to design a multi-epitope vaccine. METHODS: For designing the vaccine, the sequence of PspA was retrieved, and then, phylogenetic analysis was performed. Several CTL epitopes, HTL epitopes, and LBL epitopes of PspA were all predicted by using several bioinformatics tools. After checking the antigenicity, allergenicity, and toxicity scores, the best epitopes were selected for the vaccine construction, and then, physicochemical and immunological properties were analyzed. Subsequently, vaccine 3D structure prediction, refinement, and validation were performed. Molecular docking, molecular dynamic simulation, and immune simulation were performed to ensure the binding between HLA and TLR4. Finally, codon adaptation and in silico cloning were performed to transfer into a suitable vector. RESULTS: The constructed multi-epitope vaccine showed a strong binding affinity with the receptor molecule TLR4. Analysis of molecular dynamic simulation, C-immune simulation, codon adaptation, and in silico cloning validated that our designed vaccine is a suitable candidate against SPN. CONCLUSION: The in silico analysis has proven the vaccine as an alternative medication to combat against S. pneumoniae. The designated vaccine can be further tested in the wet lab, and a novel vaccine can be developed.

Identification of B and T Cell Epitopes to Design an Epitope-Based Peptide Vaccine against the Cell Surface Binding Protein of Monkeypox Virus: An Immunoinformatics Study.

Background: Although the monkeypox virus-associated illness was previously confined to Africa, recently, it has started to spread across the globe and become a significant threat to human lives. Hence, this study was designed to identify the B and T cell epitopes and develop an epitope-based peptide vaccine against this virus's cell surface binding protein through an in silico approach to combat monkeypox-associated diseases. Results: The analysis revealed that the cell surface binding protein of the monkeypox virus contains 30 B cell and 19 T cell epitopes within the given parameter. Among the T cell epitopes, epitope "ILFLMSQRY" was found to be one of the most potential peptide vaccine candidates. The docking analysis revealed an excellent binding affinity of this epitope with the human receptor HLA-B∗15:01 with a very low binding energy (-7.5 kcal/mol). Conclusion: The outcome of this research will aid the development of a T cell epitope-based peptide vaccine, and the discovered B and T cell epitopes will facilitate the creation of other epitope and multi-epitope-based vaccines in the future. This research will also serve as a basis for further in vitro and in vivo analysis to develop a vaccine that is effective against the monkeypox virus.

Fabrication of ZnO-SnO2 nanocomposite and its photocatalytic activity for enhanced degradation of Biebrich scarlet.

The n-n-type ZnO-SnO2 nanocomposite was fabricated using malic acid following a simple one-pot co-precipitation method. The fabricated ZnO-SnO2 nanocomposite was employed as a photocatalyst in the degradation of Biebrich scarlet dye under UV254 light. TEM, SAED, XRD, XPS, EDX, FTIR, and UV spectra have been recorded to characterize the synthesized ZnO-SnO2 nanostructures. TEM studies found that the average particle size was 10-12 nm, and the SAED confirmed the polycrystalline nature of the synthesized nanocomposite. It was found that 97% of 10 mg/L Biebrich scarlet dye was degraded by 25 mg/L of photocatalyst within 40-min irradiation of UV254 light at an optimum pH of 6. Further studies showed that the degradation followed pseudo-first-order kinetics with a rate constant of 5.48 × 10-2 min-1. The fabricated ZnO-SnO2 nanocomposite was reusable up to 8 times; hence, it proved to be an efficient catalyst for the photodegradation of Biebrich scarlet dye.

The degradation of textile industry dyes using the effective bacterial consortium.

The effluents from textile industries without proper treatment contains a remarkable amount of synthetic dyes which are harmful to the environment and a big challenge globally to degrade it with a eco-friendly way. Conventional methods are extremely energy-consuming, non-effective and generate a toxic sludge impacting the environment. Several microorganisms can be utilized to treat these effluents. The research deals with five bacteria isolated from textile effluent and their consortium for the biodegradation ability of Novacron dyes. The isolates were identified through the Biolog™ identification system and molecular technique. Biodegradation was confirmed by measuring optical density (OD) optimizing conditions (pH 7.0, temperature 37 °C, 10 % inoculums and 100 mg/L dye) under static condition. The isolates started decolourization at 24 h whereas, the consortium started decolourization at 18 h and exhibited a maximum after 72 h. The presence of low molecular weight protein as metabolite supported the biodegradation and non hazardous to environment. This study revealed that these bacteria might have degradation potentials, and research results will help to set up dye removal eco-friendly methods to expose the dye effulents to environment in future.

The Prospects of Lactobacillus oris as a Potential Probiotic With Cholesterol-Reducing Property From Mother's Milk.

This experiment was conducted to characterize potential Lactobacillus spp. isolated from mother's milk and infant feces to obtain new and specific probiotic strains. In this study, seven ascendant strains were identified as Lactobacillus spp. based on their morphological characteristics and biochemical properties. Among them, only one (C-1) isolate was identified as Lactobacillus oris through BioLogTM identification. The study further investigated the isolate through probiotic potentiality tests such as pH and bile tolerance, NaCl tolerance test, gastric juice tolerance, antioxidant activity, resistance to hydrogen, reduction of sodium nitrate, antimicrobial activity, and antibiotic susceptibility test. The result showed that the strain is a potential probiotic based on probiotic capability. The identified strain was most acid-tolerant and retained around 80% viability for up to 4 h at pH 1.0 and 2.0. The isolate showed tolerance against up to 1.50% bile concentration and gastric juice and was able to grow 1-6% NaCl concentrations. Lactobacillus oris showed resistance to most antibiotics as well as antagonistic activity against the tested pathogen, good antioxidant properties, reduction of sodium nitrate and H2O2. The isolate exhibited good intestinal epithelial adhesion properties, and SDS page was performed for secreted protein analysis. Moreover, the strain showed promising cholesterol-lowering properties based on the cholesterol level. This present result indicates that L. oris has superior probiotic properties and can be regarded as a potential probiotic candidate.

Green synthesis of SnO2 quantum dots using Parkia speciosa Hassk pods extract for the evaluation of anti-oxidant and photocatalytic properties.

In the present study, microwave heating method was established for the biosynthesis of SnO2 Quantum dots (QDs) using Parkia speciosa Hassk pods extract. The as-synthesized quantum dots have been characterized by various techniques such as UV, XRD, EDX, TEM, HRTEM, SAED and FTIR spectroscopy. The biosynthesized SnO2 QDs was employed for the first time as an efficient photocatalyst for the degradation of a food dye, acid yellow 23 dye from aqueous phase under the UV254 light. Various parameters, such as the effect of catalyst dose, the initial concentration of acid yellow 23 dye (AY23), pH of the solution and irradiation time on the photodegradation process are also studied for efficient and better use of the synthesized SnO2 QDs as a catalyst. The biosynthesized SnO2 QDs exhibited excellent photocatalytic performances with degradation efficiency 98% on the degradation of an aqueous solution of AY23 of concentration 5 mg/L with a catalyst dose of 20 mg under UV254 light within 24 min. The synthesized SnO2 QDs can be reused up to 5 cycles of photodegradation experiment without losing its stability and efficiency. The biosynthesized SnO2 QDs also shows a fair activity in the scavenging of 2,2-diphenyl-1-picrylhydrazyl free radical with the IC50 value of 312.6 ±â€¯0.025 µg/mL.

CTAB and SDS assisted facile fabrication of SnO2 nanoparticles for effective degradation of carbamazepine from aqueous phase: A systematic and comparative study of their degradation performance.

In the present study, SnO2 nanoparticles were successfully synthesized by chemical precipitation method using anhydrous aspartic acid and surfactant at two annealing temperatures, 300 °C and 600 °C. The effect of surfactants cationic CTAB and anionic SDS on the synthesized SnO2 nanoparticles (NPs) were studied elaborately. In this article, for the first time, SnO2 NPs were employed as an excellent photocatalyst in the degradation of carbamazepine (CBZ), a popular antiepileptic drug which is most commonly detected pharmaceutically active compounds (PhACs) in municipal wastewater under UV-C light irradiation. Comparative studies between the photocatalytic activity of SnO2 NPs synthesized with CTAB (SC1) and SDS (SS1) on the degradation of the CBZ drug were investigated. Parameters like the effect of catalytic loading, initial concentration, pH and contact time were also studied for optimization. The results indicate that SC1 is a better photocatalyst with rate constant 6.66 × 10-2 min-1 than SS1 with rate 5.7 × 10-2 min-1. To determine the transformation product formed on the photodegradation LCMS (ESI) analysis was done. The synthesized SnO2 NPs can be recycled up to 8th cycles without any notable alteration in its photocatalytic activity.

Photo-catalytic activity of Plasmonic Ag@AgCl nanoparticles (synthesized via a green route) for the effective degradation of Victoria Blue B from aqueous phase.

This study reports a green process for the fabrication of Ag@AgCl (silver@silver chloride) nanoparticles by using Aquilaria agallocha (AA) leaves juice without using any external reagents. The effect of various reaction parameters, such as reaction temperature, reaction time and concentration of Aquilaria agallocha leaves juice in the formation of nanoparticles have also been investigated. From the FTIR spectra of leaves juice and phytochemicals test, it was found that flavonoids present in the leaves are responsible for the reduction of Ag(+) ions to Ag(0) species and leads to the formation of Ag@AgCl NPs. The synthesized Ag@AgCl NPs were utilized for the removal of toxic and hazardous dyes, such as Victoria Blue B from aqueous phase. Approximately, 99.46% degradation of Victoria Blue B dye were observed with Ag@AgCl NPs. Furthermore, the photocatalytic activity of the Ag@AgCl nanoparticles was unchanged after 5cycles of operation.

Facile synthesis of 2D CuO nanoleaves for the catalytic elimination of hazardous and toxic dyes from aqueous phase: a sustainable approach.

This article reports for the first time a facile, green synthesis of 2D CuO nanoleaves (NLs) using the amino acid, namely aspartic acid, and NaOH by a microwave heating method. The amino acid acts as a complexing/capping agent in the synthesis of CuO NLs. This method resulted in the formation of self-assembled 2D CuO NLs with an average length and width of ~300-400 and ~50-82 nm, respectively. The as-synthesized 2D CuO NLs were built up from the primary CuO nanoparticles by oriented attachment growth mechanism. The CuO NLs were characterized by an X-ray diffraction (XRD) method, transmission electron microscopy (TEM), selected-area electron diffraction (SAED) pattern, and Fourier transform infrared spectroscopy (FT-IR). The optical properties were investigated using UV-visible spectroscopy. For the first time, rose bengal and eosin Y dyes were degraded photochemically by solar irradiation using CuO NLs as a photocatalyst. The synthesized CuO NLs act as an efficient photocatalyst in the degradation of rose bengal and eosin Y dye under direct sunlight. The degradation of both the dyes, namely rose bengal and eosin Y, took place within 120 and 45 min, respectively, using CuO NLs as a photocatalyst, whereas commercial CuO, SnO2 quantum dots (QDs), and commercial SnO2 took more than 120 and 45 min for the degradation of rose bengal and eosin Y, respectively. The synthesized CuO NLs showed a superior photocatalytic activity as compared to that of commercial CuO, SnO2 QDs, and commercial SnO2. The reusability of the CuO NLs as a photocatalyst in the degradation of dyes was investigated, and it was evident that the catalytic efficiency decreases to a small extent (5-6 %) after the fifth cycle of operation.

On the origin and variation of colors in lobster carapace.

The chemical basis of the blue-black to pink-orange color change on cooking of lobster, due to thermal denaturation of an astaxanthin-protein complex, α-crustacyanin, in the lobster carapace, has so far been elusive. Here, we investigate the relaxation of the astaxanthin pigment from its bound enolate form to its neutral hydroxyketone form, as origin of the spectral shift, by analyzing the response of UV-vis spectra of a water-soluble 3-hydroxy-4-oxo-ß-ionone model of astaxanthin to increases in pH, and by performing extensive quantum chemical calculations over a wide range of chemical conditions. The enolization of astaxanthin is consistent with the X-ray diffraction data of ß-crustacyanin (PDB code: ) whose crystals possess the distinct blue color. We find that enolate formation is possible within the protein environment and associated with a large bathochromic shift, thus offering a cogent explanation for the blue-black color and the response to thermal denaturation and revealing the chemistry of astaxanthin upon complex formation.

Expression and characterization of chicken ovoinhibitor in Pichia pastoris.

Chicken ovoinhibitor cDNA was prepared by reverse transcriptase-polymerase chain reaction (RT-PCR) using chicken oviduct mRNA. The ovoinhibitor cDNA was successfully cloned downstream from the AOXI promoter of pPICZalphaA plasmid vector to facilitate its expression in the methylotrophic yeast Pichia pastoris. The pPICZalphaA carrying the ovoinhibitor cDNA was integrated into the Pichia genome. The secreted recombinant ovoinhibitor was purified by ion-exchange chromatography on a DEAE sepharose column. The recombinant ovoinhibitor had a molecular mass of 49 kDa, as determined from sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and time of flight-mass spectrometry (TOF-MS) analyses. The recombinant ovoinhibitor, just as the native ovoinhibitor, showed inhibitory activity against trypsin, chymotrypsin and elastase.

Improved functional properties of the ovoinhibitor by conjugating with galactomannan.

The chicken egg white ovoinhibitor, a multi-type proteinase inhibitor, was conjugated with galactomannan through the Maillard reaction in a controlled dry heating state at 60 degrees C and 65% relative humidity. The formation of an ovoinhibitor-galactomannan conjugate during dry heating was confirmed by SDS-PAGE. The resulting ovoinhibitor-galactomannan conjugate showed almost the same inhibitory activity toward trypsin, chymotrypsin and elastase as that of the untreated ovoinhibitor, while the conjugate showed stronger heat stability and better emulsifying properties than the untreated ovoinhibitor. These results suggest that the ovoinhibitor-galactomannan conjugate can be used as a protease inhibitor having heat stability and outstanding emulsifying properties for industrial application.