Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets. The pan-genome of all available A. baumannii strains (30 complete genomes) is estimated to contain 7,606 gene families and the core genome consists of 2,445 gene families (~32 % of the pan-genome). Phylogenetic tree, comparative genomic and proteomic analysis revealed both intra- and inter genomic similarities and evolutionary relationships. Among the conserved core genome, thirteen proteins, including P pilus assembly protein, pili assembly chaperone, AdeK, PonA, OmpA, general secretion pathway protein D, FhuE receptor, Type VI secretion system OmpA/MotB, TonB dependent siderophore receptor, general secretion pathway protein D, outer membrane protein, peptidoglycan associated lipoprotein and peptidyl-prolyl cis-trans isomerase are identified as highly antigenic. Epitope mapping of the target proteins revealed the presence of antigenic surface exposed 9-mer T-cell epitopes. Protein-protein interaction and functional annotation have shown their involvement in significant biological and molecular processes. The pipeline is validated by predicting already known immunogenic targets against Gram negative pathogen Helicobacter pylori as a positive control. The study, based upon combinatorial approach of pan-genomics, core genomics, proteomics and reverse vaccinology led us to find out potential vaccine candidates against A. baumannii. The comprehensive analysis of all the completely sequenced genomes revealed thirteen putative antigens which could elicit substantial immune response. The integration of computational vaccinology strategies would facilitate in tackling the rapid dissemination of resistant A.baumannii strains. The scarcity of effective antibiotics and the global expansion of sequencing data making this approach desirable in the development of effective vaccines against A. baumannii and other bacterial pathogens.

Hepatitis C virus (HCV) vaccines, designed to augment specific T-cell responses, have been designated as an important aspect of effective antiviral treatment. However, despite the current satisfactory progress of these vaccines, extensive past efforts largely remained unsuccessful in mediating clinically relevant anti-HCV activity in humans. In this study, we used a series of immunoinformatics approaches to propose a multiepitope vaccine against HCV by prioritizing 16 conserved epitopes from three viral proteins (i.e., NS34A, NS5A, and NS5B). The prioritised epitopes were tested for their possible antigenic combinations with each other along with linker AAY using structural modelling and epitope–epitope interactions analysis. An adjuvant (β-defensin) at the N-terminal of the construct was added to enhance the immunogenicity of the vaccine construct. Molecular dynamics (MD) simulation revealed the most stable structure of the proposed vaccine. The designed vaccine is potentially antigenic in nature and can form stable and significant interactions with Toll-like receptor 3 and Toll-like receptor 8. The proposed vaccine was also subjected to an in silico cloning approach, which confirmed its expression efficiency. These analyses suggest that the proposed vaccine can elicit specific immune responses against HCV; however, experimental validation is required to confirm the safety and immunogenicity profile of the proposed vaccine construct.

Semi-conductor quantum dots (QDs) are favorite candidates for many applications especially for potential use as optical bioimaging agents. But the major issue of QDs is toxicity. In the present study, carbon nanodots were synthesized using a green hydrothermal approach from gelatin protein using a previously established protocol. However, the PL properties and applications of the as-synthesized CG (bovine gelatin) nanodots were remarkably different from those of previously reported gelatin carbon dots. CG (bovine gelatin) nanodots had sizes greater than the Bohr exciton radius but still had QD like fluorescence characteristics. Furthermore, the results from fluorescence spectroscopy demonstrated a tunable PL emission profile at various excitation wavelengths. Second, carbon nanodots were also synthesized from algal biomass of Pectinodesmus sp. via a green hydrothermal approach, denoted as CA (PHM3 algae) nanodots. A study of the PL properties and surface chemical composition of CG (bovine gelatin) and CA (PHM3 algae) nanodots suggested that the surface chemical composition significantly alters the surface states which directly influence their PL properties. CG (bovine gelatin) nanodots were used for imaging of plant and bacterial cells with good imaging sensitivity comparable to toxic semiconductor quantum dots. Moreover, the results from in vitro studies suggested good anticancer properties of CA (PHM3 algae) and CG (bovine gelatin) nanodots with minimum GI50 values of 0.316 ± 0.447 ng ml⁻¹ (n = 2) and 8.156 ± 6.596 ng ml⁻¹ (n = 2) for HCC 1954 (breast cancer) and 0.542 ± 0.715 ng ml⁻¹ (n = 2) and 23.860 ± 14.524 ng ml⁻¹ (n = 2) for HCT 116 (colorectal cancer) cell lines, respectively.

Autophagy, an evolutionary conserved multifaceted lysosome-mediated bulk degradation system, plays a vital role in liver pathologies including hepatocellular carcinoma (HCC). Post-translational modifications (PTMs) and genetic variations in autophagy components have emerged as significant determinants of autophagy related proteins. Identification of a comprehensive spectrum of genetic variations and PTMs of autophagy related proteins and their impact at molecular level will greatly expand our understanding of autophagy based regulation. In this study, we attempted to identify high risk missense mutations that are highly damaging to the structure as well as function of autophagy related proteins including LC3A, LC3B, BECN1 and SCD1. Number of putative structural and functional residues, including several sites that undergo PTMs were also identified. In total, 16 high-risk SNPs in LC3A, 18 in LC3B, 40 in BECN1 and 43 in SCD1 were prioritized. Out of these, 2 in LC3A (K49A, K51A), 1 in LC3B (S92C), 6 in BECN1 (S113R, R292C, R292H, Y338C, S346Y, Y352H) and 6 in SCD1 (Y41C, Y55D, R131W, R135Q, R135W, Y151C) coincide with potential PTM sites. Our integrated analysis found LC3B Y113C, BECN1 I403T, SCD1 R126S and SCD1 Y218C as highly deleterious HCC-associated mutations. This study is the first extensive in silico mutational analysis of the LC3A, LC3B, BECN1 and SCD1 proteins. We hope that the observed results will be a valuable resource for in-depth mechanistic insight into future investigations of pathological missense SNPs using an integrated computational platform.

Recently, crop management has involved excessive use of chemical fertilizers and pesticides, compromising public health and environmental integrity. Rhizobacteria, which can enhance plant growth and protect plants from phytopathogen, are eco-friendly and have been attracting increasing attention. In the current study, Bacillus subtilis RS10 isolated from the rhizosphere region of Cynodon dactylon, inhibited the growth of indicator strains and exhibited in vitro plant growth-promoting traits. A whole-genome analysis identified numerous biosynthetic gene clusters encoding antibacterial and antifungal metabolites including bacillibactin, bogorol A, fengycin, bacteriocin, type III polyketides (PKs), and bacilysin. The plant growth-promoting conferring genes involved in nitrogen metabolism, phosphate solubilization, hydrogen sulfide, phytohormones, siderophore biosynthesis, chemotaxis and motility, plant root colonization, lytic enzymes, and biofilm formation were determined. Furthermore, genes associated with abiotic stresses such as high salinity and osmotic stress were identified. A comparative genome analysis indicated open pan-genome and the strain was identified as a novel sequence type (ST-176). In addition, several horizontal gene transfer events were found which putatively play a vital role in the evolution and new functionalities of a strain. In conclusion, the current study demonstrates the potential of RS10 antagonism against important pathogens and plant growth promotion, highlighting its application in sustainable agriculture.