Designing an efficient multi-epitope peptide vaccine against Vibrio cholerae via combined immunoinformatics and protein interaction based approaches

Cholera continues to be a major global health concern. Among different Vibrio cholerae strains, only O1 and O139 cause acute diarrheal diseases that are related to epidemic and pandemic outbreaks. The currently available cholera vaccines are mainly lived and attenuated vaccines consisting of V. cholerae virulence factors such as toxin-coregulated pili (TCP), outer membrane proteins (Omps), and nontoxic cholera toxin B subunit (CTB). Nowadays, there is a great interest in designing an efficient epitope vaccine against cholera. Epitope vaccines consisting of immunodominant epitopes and adjuvant molecules enhance the possibility of inciting potent protective immunity. In this study, V. cholerae protective antigens (OmpW, OmpU, TcpA and TcpF) and the CTB, which is broadly used as an immunostimulatory adjuvant, were analyzed using different bioinformatics and immunoinformatics tools. The common regions between promiscuous epitopes, binding to various HLA-II supertype alleles, and B-cell epitopes were defined based upon the aforementioned protective antigens. The ultimately selected epitopes and CTB adjuvant were fused together using proper GPGPG linkers to enhance vaccine immunogenicity. A three-dimensional model of the thus constructed vaccine was generated using I-TASSER. The model was structurally validated using the ProSA-web error-detection software and the Ramachandran plot. The validation results indicated that the initial 3D model needed refinement. Subsequently, a high-quality model obtained after various refinement cycles was used for defining conformational B-cell epitopes. Several linear and conformational B-cell epitopes were determined within the epitope vaccine, suggesting likely antibody triggering features of our designed vaccine. Next, molecular docking was performed between the 3D vaccine model and the tertiary structure of the toll like receptor 2 (TLR2). To gain further insight into the interaction between vaccine and TLR2, molecular dynamics simulation was performed, corroborating stable vaccine-TLR2 binding. In sum, the results suggest that our designed epitope vaccine could incite robust long-term protective immunity against V. cholera.     

In silico epitope identification of unique multidrug resistance proteins from Salmonella Typhi for vaccine development

Typhoid fever is a multisystemic illness caused by Salmonella enterica serovars Typhi and is resistant to most antibiotics and drugs. The resistance is conferred through multidrug resistance (MDR) proteins, which efflux most antibiotics and other drugs. We predicted potential candidate B-cell and T-cell epitopes using bio- and immune-informatics tools in the 11 MDR proteins - EmrA, EmrB, EmrD, MdtA, MdtB, MdtC, MdtG, MdtH, MdtK, MdtL and TolC. The antigenic potential of the MDR proteins was calculated using VaxiJen server. The B-cell and T-cell epitopes of the MDR proteins were predicted using BCPred and ProPredI and ProPred respectively. The binding affinities of the predicted T-cell epitopes were estimated using T-epitope designer and MHCPred tools. 10, 7, 5, 12, 14, 21, 26, 3, 3 and 3 B-cell epitopes were identified in EmrA, EmrB, EmrD, TolC, MdtA, MdtB, MdtC, MdtG, MdtH and MdtL respectively. We predicted 9 T-cell epitopes - YVSRRAVQP (EmrA), FGVANAISI (EmrB), MVNSQVKQA and YQGGMVNSQ (TolC), WDRTNSHKL (MdtA), FLRNIPTAI (MdtB), YVEQLGVTG (MdtG), VKWMYAIEA (MdtH) and LAHTNTVTL (MdtL) capable of eliciting both humoral and adaptive immune responses. These T-cell epitopes specifically bind to HLA alleles - DRB1*0101 and DRB1*0401. This is the first report of epitope prediction in the MDR proteins of S. Typhi. Taken together, these results indicate the MDR proteins – EmrA, MdtA and TolC are the most suitable vaccine candidates for S. Typhi. The findings of our study on the MDR proteins prove to be useful in the development of peptide-based vaccine for the prevention and/or treatment of typhoid fever.     

Fixed-bed study for adsorptive removal of furfural by activated carbon

In our previous study [A.K. Sahu, V.C. Srivastava, I.D. Mall, D.H. Latye, Sep. Sci. Technol. 43 (5) (2008) 1239], commercial grade activated carbon (ACC) was used for adsorptive removal of furfural from aqueous solution using batch studies. In the present study, continuous fixed-bed adsorption was carried out in ACC packed bed for the removal of furfural from aqueous solution. The effects of important factors namely bed height (Z = 15–60 cm), influent concentration of furfural (C_o = 50–200 mg/l), the flow rate (Q = 0.02–0.04 l/min) and column diameter (D = 2–4 cm) were studied. Capacity of the bed to adsorb furfural was found to increase with an increase in the value of Z, C_o and D; and with decrease in the value of Q. Adams–Bohart, Bed-Depth Service-Time, Thomas, Yoon–Nelson, Clark and Wolborska models were applied to the experimental data for the prediction of the breakthrough point, and to determine the characteristic parameters of the column. Error analysis showed that the Yoon–Nelson model best described the experimental breakthrough curve, while Wolborska model showed good prediction of breakthrough curve for the relative concentration region up to 0.5.     

Effect of Steeped Black Tea (Camellia sinensis (L.) var. assamica) on Immunoglobulin Titer and Lymphocyte Proliferation in Responses to Hepatitis B Vaccine in Mice

Effect of steeped black tea (Camellia sinensis (L.) var. assamica) on immunoglobulin titer (IgM and IgG) and lymphocyte proliferation in responses to hepatitis B vaccine inBALB/c mice has been investigated. The study was divided into two stages i.e. the determination of immunoglobulin titer and the test of lymphocytes proliferation. In the first stage mice were divided into 5 groups each consisting of 5 mice. Group I, II and III was given steeped black tea respectively with a dose of 600 mg/kg bw; 1.2 g/kg bw and 2.4 g/kg bw. Group IV was given Stimuno^® with a dose of 6.5 mg/kg bw, and group V was given aquadest as negative control. All groups were induced by hepatitis B vaccine on day-0 (after 7 days of acclimatization). Serum was taken on day-14 and 21 for measurement of IgM titer and IgG, respectively. In the second stage, the mice were grouped as in the first stage, then all groups were induced by hepatitis B vaccine at day-0 and day-7. On day-27 lymphocyte was isolated and then tested for the growth and proliferation of lymphocytes. The results of this study showed that the steeped black tea has an effect in increasingIgM and IgG titer of BALB/cmice induced by hepatitis B vaccine, where the most effective dose was 1.2 g/kg bw. Steeped black tea also could increase lymphocytes proliferation in mice BALB/cinduced by hepatitis B vaccine, where the most effective dose was 1.2 g/kg bw.     

A topographic view of the Pt(1 1 1) surface at the electrochemical interface in the presence of carbon monoxide

In this communication we present topographic images of the Pt(1 1 1) surface in CO saturated 0.1 M HClO₄, obtained by scanning tunneling microscopy.The topography presents two different structures, depending on the CO adsorption potential (E_ad = 0.15 V or E_ad = 0.5 V vs RHE). For adsorption at 0.15 V the system presents a heterogeneous appearance, which totally covers the surface and impedes the observation of steps on the substrate surface. When CO is adsorbed at 0.5 V large clusters forming chains along the steps are observed. These aggregates can be, tentatively, correlated with the H-bonded water structure suggested earlier on the basis of FTIR spectroscopy. The clusters have inhibitory effects on CO oxidation.     

Raman spectra of carriers in ionic-liquid-gated transistors fabricated with poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene)

We observed the Raman spectra of carriers, positive polarons and bipolarons, generated in a poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT-C14) film by FeCl₃ vapor doping. Electrical conductivity and Raman measurements indicate that the dominant carriers in the conducting state were bipolarons. We identified positive polarons and bipolarons generated in an ionic-liquid-gated transistor (ILGT) fabricated with PBTTT-C14 as an active semiconductor and an ionic liquid 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide [BMIM][TFSI] as a gate dielectric using Raman spectroscopy. The relationship between the source−drain current (I_D) at a constant source−drain voltage (V_D) and the gate voltage (V_G) was measured. I_D increased above −V_G = 1.1 V and showed a maximum at −V_G = 2.0 V. Positive polarons were formed at the initial stage of electrochemical doping (−V_G = 0.8 V). As I_D increased, positive bipolarons were formed. Above V_G = −2.0 V, bipolarons were dominant. The charge density (n), the doping level (x), and the mobility of the bipolarons were calculated from the electrochemical measurements. The highest mobility (μ) of bipolarons was 0.72 cm² V⁻¹ s⁻¹ at x = 110 mol%/repeating unit (−V_G = 2.0 V), whereas the highest μ of polarons was 4.6 × 10⁻⁴ cm² V⁻¹ s⁻¹ at x = 10 mol%.     

In situ AFM studies of SEI formation at a Sn electrode

Early stages of the solid electrolyte interphase (SEI) formation at a tin foil electrode in an ethylene carbonate (EC) based electrolyte were investigated by in situ AFM and cyclic voltammetry (CV) at potentials >0.7 V, i.e., above the potential of Sn–Li alloying. We detected and observed initial steps of the surface film formation at ～2.8 V vs. Li/Li⁺ followed by gradual film morphology changes at potentials 0.7 < U < 2.5 V. The SEI layer undergoes continuous reformation during the following CV cycles between 0.7 and 2.5 V. The surface film on Sn does not effectively prevent the electrolyte reduction and a large fraction of the reaction products dissolve in the electrolyte. The unstable SEI layer on Sn in EC-based electrolytes may compromise the use of tin-based anodes in Li-ion battery systems unless the interfacial chemistry of the electrode and/or electrolyte is modified.     

Electrochemical kinetic study of surface layer growth on natural pyrite in acid medium

This paper presents electrochemical experiments on natural pyrite that combine potentiostatic and voltammetric techniques. X-ray microanalysis is used as an auxiliary technique. The layer growth on pyrite surface is conducted in a wide range of pH and potential range: 3.4 ≤ pH ≤ 5.9 with E = 0.80 V (versus SHE), and 0.80 V ≤ E ≤ 1.00 V with pH 4.5 (versus SHE) in acetic acid–acetate buffer. This work is unique for two reasons: (1) phenomenological model about layer growth is applied and mathematical-physic consistence is verified and (2) Meyer's hypotheses of chemical mechanism are used to explain kinetic parameters of the phenomenological model.     

QSAR studies of some side chain modified 7-chloro-4-aminoquinolines as antimalarial agents

The quantitative structure–activity relationship (QSAR) analyses were carried out for a series of new side chain modified 4-amino-7-chloroquinolines to find out the structural requirements of their antimalarial activities against both chloroquine sensitive (HB3) and resistant (Dd2) Plasmodium falciparum strain. The statistically significant best 2D QSAR models for Dd2, having correlation coefficient (r²) = 0.9188 and cross validated squared correlation coefficient (q²) = 0.8349 with external predictive ability (pred_r²) = 0.7258 and for HB3, having r² = 0.9024, q² = 0.8089 and pred_r² = 0.7463 were developed by multiple linear regression coupled with genetic algorithm (GA–MLR) and stepwise (SW–MLR) forward algorithm, respectively. The results of the present study may be useful on the designing of more potent analogues as antimalarial agents.     

Direct determination of arsenate based on its electrocatalytic reduction at the poly(aniline-co-o-aminophenol) electrode

It was found that the copolymer poly(aniline-co-o-aminophenol) (PANOA) can strongly catalyze the reduction of arsenate in a NaCl solution, which was proved by cyclic voltammetry and the determination of activation energy. On the basis of the electrocatalytic reduction of arsenate, the PANOA copolymer was used as a probe to determine directly arsenate. The electrocatalytic activity of the PANOA electrode toward As(V) reduction strongly depended on the pH and the applied potential. Under the optimal conditions, the PANOA electrode can be used to determine directly As(V) concentration in a wide linear range (n = 19) of 0.949 and 495 μM with a correlation coefficient of 0.995 and a limit of detection of 0.495 μM. The sensitivity of the electrode was 0.192 μA μM^?1 cm^?2. The PANOA electrode had the good storage stability and a less negative operation potential of ?0.15 V (vs. SCE).     

A novel in silico minigene vaccine based on CD4+ T-helper and B-cell epitopes of EG95 isolates for vaccination against cystic echinococcosis

EG95 oncospheral antigen plays a crucial role in Echinococcus granulosus pathogenicity. Considering the diversity of antigen among different EG95 isolates, it seems to be an ideal antigen for designing a universal multivalent minigene vaccine, so-called multi-epitope vaccine. This is the first in silico study to design a construct for the development of global EG95-based hydatid vaccine against E. granulosus in intermediate hosts. After antigen sequence selection, the three-dimensional structure of EG95 was modeled and multilaterally validated. The preliminary parameters for B-cell epitope prediction were implemented such as the possible transmembrane helix, signal peptide, post-translational modifications and allergenicity. The high ranked linear and conformational B-cell epitopes derived from several online web-servers (e.g., ElliPro, BepiPred v1.0, BcePred, ABCpred, SVMTrip, IEDB algorithms, SEPPA v2.0 and Discotope v2.0) were utilized for multiple sequence alignment and then for engineering the vaccine construct. T-helper based epitopes were predicted by molecular docking between the high frequent ovar class II allele (Ovar-DRB1*1202) and hexadecamer fragments of the EG95 protein. Having used the immune-informatics tools, we formulated the first EG95-based minigene vaccine based on T-helper epitope with high-binding affinity to the ovar MHC allele. This designed construct was analyzed for different physicochemical properties. It was also codon-optimized for high-level expression in Escherichia coli k12. Taken all, we propose the present in silico vaccine constructs as a promising platform for the generation of broadly protective vaccines for species and genus-specific immunization of the natural hosts of the parasite.     

Assessing Si-based anodes for Ca-ion batteries: Electrochemical decalciation of CaSi2

Density functional theory (DFT) calculations are used to investigate the basic electrochemical characteristics of Si-based anodes in calcium ion batteries (CIBs). The calculated average voltage of Ca alloying with fcc-Si to form the intermetallic Ca_xSi phases (0.5 < x ≤ 2) is of 0.4 V, with a volume variation of 306%. Decalciation of the lower Ca content phase, CaSi₂, is predicted at an average voltage between 0.57 V (formation of Si-fcc, 65% volume variation) and 1.2 V (formation of metastable deinserted-Si phase, 29% volume variation). Experiments carried out in conventional alkyl carbonate electrolytes show evidence that electrochemical “decalciation” of CaSi₂ is possible at moderate temperatures. The decalciation of CaSi₂ is confirmed by different characterization techniques.     

An enzymatic glucose/O2 biofuel cell: Preparation,characterization and performance in serum

This study demonstrates a new kind of single-walled carbon nanotubes (SWNT)-based compartment-less glucose/O₂ biofuel cell (BFC) with glucose dehydrogenase (GDH) and bilirubin oxidase (BOD) as the anodic and cathodic biocatalysts, respectively, and with poly(brilliant creysl blue) (BCB) adsorbed onto SWNT nanocomposite as the electrocatalyst for the oxidation of NADH. The prepared GDH-polyBCB-SWNT bioanode exhibits an excellent electrocatalytic activity toward the oxidation of glucose biofuel; in 0.10 M phosphate buffer containing 20 mM NAD⁺ and 100 mM glucose, the oxidation of glucose commences at −0.25 V and the current reaches its maximum of 310 μA/cm² at −0.05 V vs. Ag/AgCl. At the BOD-SWNT biocathode, a high potential output is achieved for the reduction of O₂ due to the direct electron transfer property of BOD at the SWNTs. In 0.10 M phosphate buffer, the electrocatalytic reduction of O₂ is observed at a high potential of 0.53 V vs. Ag/AgCl with an electrocatalytic current plateau of ca. 28 μA/cm² at 0.45 V under ambient air and ca. 102 μA/cm² under O₂-saturated atmosphere. In 0.10 M phosphate buffer containing 10 mM NAD⁺ and 40 mM glucose under O₂-saturated atmosphere, the power density of the assembled SWNT-based glucose/O₂ BFC reaches 53.9 μW/cm² at 0.50 V. The performance and the stability of the glucose/O₂ BFC are also evaluated in serum. This study could offer a new route to the development of new kinds of enzymatic BFCs with a high performance and provide useful information on future studies on the enzymatic BFCs as in vivo power sources.     

Novel inorganic ionic liquids possessing low melting temperatures and wide electrochemical windows: Binary mixtures of alkali bis(fluorosulfonyl)amides

Thermal properties of alkali bis(fluorosulfonyl)amides, MFSI (M = Li, Na, K, Rb, Cs), have been investigated. Binary phase diagrams of LiFSI–KFSI and NaFSI–KFSI systems have been constructed. Eutectic point for LiFSI–KFSI is 338 K at (x_Li, x_K) = (0.45, 0.55) and, that for NaFSI–KFSI is 330 K at (x_Na, x_K) = (0.45, 0.55). The electrochemical window of the eutectic LiFSI–KFSI is as wide as 6.0 V at 348 K with the cathode limit being lithium metal deposition. The electrochemical window of the eutectic NaFSI–KFSI is 5.0 V at 340 K with sodium metal deposition at the cathode limit. These new inorganic ionic liquids are highly promising for various electrochemical applications.     

Structural effects on the oxidation of formic acid on the high index planes of palladium

Electrochemical oxidation of formic acid has been studied on the stepped and kinked-stepped surfaces of Pd in 0.1 M HClO₄ containing 0.1 M formic acid with the use of voltammetry. The surfaces examined are Pd(S)-[n(1 0 0) × (1 1 0)], Pd(S)-[n(1 1 1) × (1 0 0)] and Pd(S)-[n(1 1 1) × (1 1 1)] series (n = 2–9). The results are compared with those of Pd(S)-[n(1 0 0) × (1 1 1)] series reported previously. All the electrodes give maximum currents of formic acid oxidation j_P between 0.5 and 0.8 V (RHE). The values of j_P plotted against the density of step (kink) atoms d_S depend on the surface structure remarkably. Pd(S)-[n(1 1 1) × (1 0 0)] surfaces provide maximum of j_P at n = 5, whereas Pd(S)-[n(1 0 0) × (1 1 0)] and Pd(S)-[n(1 1 1) × (1 1 1)] do not give maximum of j_P. The values of j_P have the following order: Pd(S)-[n(1 1 1) × (1 1 1)] < Pd(S)-[n(1 1 1) × (1 0 0)] < Pd(S)-[n(1 0 0) × (1 1 0)] < Pd(S)-[n(1 0 0) × (1 1 1)]. The anodic current at more negative potential 0.20 V (RHE) shows different activity series: Pd(1 1 1) and Pd(1 1 0) have the highest rate for formic acid oxidation at 0.20 V (RHE).     

Dual-signal anodic stripping voltammetric determination of trace arsenic(III) at a glassy carbon electrode modified with internal-electrolysis deposited gold nanoparticles

A glassy carbon electrode (GCE) modified with internal-electrolysis deposited gold nanoparticles (AuNPs_ied) was applied to sensitively and selectively detect As(III) by anodic stripping linear sweep voltammetry (ASLSV). The AuNPs_ied/GCE was prepared based on the redox replacement reaction between a supporting-electrolyte-free aqueous HAuCl₄ and a copper sheet in saturated KCl separated by a salt bridge. Under optimum conditions (0.5 M aqueous H₂SO₄, 300-s preconcentration at − 0.4 V), the ASLSV peak current for the As(0)–As(III) oxidation responded linearly to As(III) concentration from 0.02 to 3 μM with a limit of detection (LOD) of 0.9 nM (0.07 μg L^− 1) (S/N = 3), while that for the As(III)–As(V) oxidation was linear with As(III) concentration from 0.02 to 1 μM with a LOD of 4 nM (0.3 μg L^− 1) (S/N = 3). An appropriate high-scan-rate for ASLSV can enhance both the sensitivity and signal-to-noise ratio. This method was applied for analyses of As(III) in real water samples.     

A rebuttal to the comments on the genome order index

Recently, Elhaik et al. [Elhaik, E., Graur, D., Josic, K., 2008. ‘Genome order index’ should not be used for defining compositional constraints in nucleotide sequences. Comp. Biol. Chem. 32, 147] commented on the genome order index, which is defined as S = a² + c² + g² + t² where a, c, g and t denote corresponding base frequencies. They claimed that (1) “S < 1/3 is in fact a mathematical property that is always true”, and (2) “S is strictly equivalent to and derivable from the Shannon H function”. The first claim is apparently wrong: for instance, when a = c =0.5, g = t =0, S = 0.5 > 1/3. The second claim is also incorrect because S and H are different special cases of the α-order entropy, having different functional forms that are neither strictly derivable from nor equivalent to each other. Therefore, the conclusions made in their comments are wrong.     

Bioelectrocatalytic formate oxidation and carbon dioxide reduction at high current density and low overpotential with tungsten-containing formate dehydrogenase and mediators

We show a great possibility of mediated enzymatic bioelectrocatalysis in the formate oxidation and the carbon dioxide (CO₂) reduction at high current densities and low overpotentials. Tungsten-containing formate dehydrogenase (FoDH1) from Methylobacterium extorquens AM1 was used as a catalyst and immobilized on a Ketjen Black-modified electrode. For the formate oxidation, a high limiting current density (j_lim) of ca. 24 mA cm^− 2 was realized with a half wave potential (E_1/2) of only 0.12 V more positive than the formal potential of the formate/CO₂ couple (E°′_CO2) at 30 °C in the presence of methyl viologen (MV^2 +) as a mediator, and j_lim reached ca. 145 mA cm^− 2 at 60 °C. Even when a viologen-functionalized polymer was co-immobilized with FoDH1 on the porous electrode, j_lim of ca. 30 mA cm^− 2 was attained at 60 °C with E_1/2 = E°′_CO2 + 0.13 V. On the other hand, the CO₂ reduction was also realized with j_lim ≈ 15 mA cm^− 2 and E_1/2 = E°′_CO2 − 0.04 V at pH 6.6 and 60 °C in the presence of MV^2 +.     

Electron excitation coefficients of neutral and ionic levels of krypton in Townsend discharges

In this paper, we present experimental results for excitation coefficients of krypton atoms to several Kr and Kr⁺ excited levels for E/N (electric field to gas particle number density ratio usually in units of Townsend, 1 Td = 10^− 21 V m²) values from 7 × 10^− 20 V m² to above 1 × 10^− 17 V m². The data have been obtained in two different parallel plate self-sustained Townsend discharge drift tubes. The spatial distribution of the emission intensities were recorded and then normalized to give excitation coefficients at the anode, by using the electron flux at this point. The values of these coefficients are placed on an absolute scale by using a standard tungsten ribbon lamp calibrated against a primary blackbody radiation standard. The ionization rates at different E/N are obtained from the spatial emission profiles.The data for atomic krypton levels 2p₂, 2p₃, 2p₅, 2p₆, 2p₇, 2p₈, 3p₅ and 3p₆ (in Paschen notation) were converted to excitation coefficients by using quenching coefficients from the literature. The emission coefficients of eight 4s²4p⁴ (³P)5p levels of Kr⁺ have also been measured for E/N values from about 1 × 10^− 18 V m² up to nearly 8 × 10^− 18 V m².     

Impact of cell-voltage on energy and power performance of supercapacitors with single-walled carbon nanotube electrodes

We report the energy and power voltage-dependencies of supercapacitors using single-walled carbon nanotube electrodes. The energy density was dependent on the cell-voltage cubed (up to 4 V: E = 1.43 × V³). The cubic relationship was attributed to the linear increase of the capacitance as a function of voltage, enabled by electrochemical doping. Furthermore, while up to 3.5 V, the maximum power rating of the nanotube electrodes increased as a function of the cell-voltage squared, beyond 3.5 V, a decline in power was observed as a result of depletion of the electrolyte's ions.