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Salinity severely affects crop yield by hindering nitrogen uptake and reducing plant growth. Plant growth-promoting bacteria (PGPB) are capable of providing cross-protection against biotic/abiotic stresses and facilitating plant growth. Genome-level knowledge of PGPB is necessary to translate the knowledge into a product as efficient biofertilizers and biocontrol agents. The current study aimed to isolate and characterize indigenous plant growth-promoting strains with the potential to promote plant growth under various stress conditions. In this regard, 72 bacterial strains were isolated from various saline-sodic soil/lakes; 19 exhibited multiple in vitro plant growth-promoting traits, including indole 3 acetic acid production, phosphate solubilization, siderophore synthesis, lytic enzymes production, biofilm formation, and antibacterial activities. To get an in-depth insight into genome composition and diversity, whole-genome sequence and genome mining of one promising Bacillus paralicheniformis strain ES-1 were performed. The strain ES-1 genome carries 12 biosynthetic gene clusters, at least six genomic islands, and four prophage regions. Genome mining identified plant growth-promoting conferring genes such as phosphate solubilization, nitrogen fixation, tryptophan production, siderophore, acetoin, butanediol, chitinase, hydrogen sulfate synthesis, chemotaxis, and motility. Comparative genome analysis indicates the region of genome plasticity which shapes the structure and function of B. paralicheniformis and plays a crucial role in habitat adaptation. The strain ES-1 has a relatively large accessory genome of 649 genes (~ 19%) and 180 unique genes. Overall, these results provide valuable insight into the bioactivity and genomic insight into B. paralicheniformis strain ES-1 with its potential use in sustainable agriculture.

The current study is focused on the lipid extract of microalgae; Pectinodesmus strain HM3 (PHM3) and its general analysis in terms of chemical contents. Combinations of both chemical and mechanistic approaches were applied to obtain the maximum yield of lipids which was recorded to be 23% per gram through continuous agitation using Folch solution. The extraction methods used in this study included: Bligh and Dyers method, Continuous agitation method, Extraction using Soxhlet and Acid base extraction method. Lipid quantification of ethanol and Folch solution lipid extract was performed through gravimetric methods and qualification was done through Fourier Transmission Infrared Spectroscopy (FTIR) and Gas Chromatography-mass spectrometry (GC-MS). Phytochemical analysis identified other compounds in ethanol extract and the results confirmed the presence of steroids, coumarins, tannins, phenols and carbohydrates. Transesterification of lipids showed 7% per gram dry weight yield of Pectinodesmus PHM3. GC-MS studies of extracted biodiesel suggested that 72% of biofuels was in the form of dipropyl ether, ethyl butyl ethers, methyl butyl ether and propyl butyl ether. Lipid processing of acid-base extract showed that oily nature of lipid shifted to a more precipitated form which is a common observation when mixture of lipids is converted to phosphatides.

Proteases that can remain active under extreme conditions such as high temperature, pH, and salt concentration are widely applicable in the commercial sector. The majority of the proteases are rendered useless under harsh conditions in industries. Therefore, there is a need to search for new proteases that can tolerate and function in harsh conditions, thus improving their commercial value. In this study, 142 bacterial isolates were isolated from diverse alkaline soil habitats. The two highest protease-producing bacterial isolates were identified as Bacillus subtilis S1 and Bacillus amyloliquefaciens KSM12, respectively, based on 16S rRNA sequencing. Optimal protease production was detected at pH 8, 37 °C, 48 h, 5% (w/v) NaCl for Bacillus subtilis S1 (99.8 U/mL) and pH 9, 37 °C, 72 h, 10% (w/v) NaCl for Bacillus amyloliquefaciens KSM12 (94.6 U/mL). The molecular weight of these partially purified proteases was then assessed on SDS-PAGE (17 kDa for Bacillus subtilis S1 and 65 kDa for Bacillus amyloliquefaciens KSM12), respectively. The maximum protease activity for Bacillus subtilis S1 was detected at pH 8, 40 °C, and for Bacillus amyloliquefaciens KSM12 at pH 9, 60 °C. These results suggest that the proteases secreted by Bacillus subtilis S1 and Bacillus amyloliquefaciens KSM12 are suitable for industries working in a highly alkaline environment.

Circular RNAs (circRNAs) are ubiquitously expressed, covalently closed rings, produced by pre-mRNA splicing in a reversed order during post-transcriptional processing. Circularity endows 3'-5'-linked circRNAs with stability and resistance to exonucleolytic degradation which raises the question whether circRNAs may be relevant as potential therapeutic targets or agents. High stability in biological systems is the most remarkable property and a major criterion for why circRNAs could be exploited for a range of RNA-centred medical applications. Even though various biological roles and regulatory functions of circRNAs have been reported, their in-depth study is challenging because of their circular structure and sequence-overlap with linear mRNA counterparts. Moreover, little is known about their role in viral infections and in antiviral immune responses. We believe that an in-depth and detailed understanding of circRNA mediated viral protein regulations will increase our knowledge of the biology of these novel molecules. In this review, we aimed to provide a comprehensive basis and overview on the biogenesis, significance and regulatory roles of circRNAs in the context of antiviral immune responses and viral infections including hepatitis C virus infection, hepatitis B virus infection, hepatitis delta virus infection, influenza A virus infection, Epstein-Barr virus infection, kaposi's sarcoma herpesvirus infection, human cytomegalovirus infection, herpes simplex virus infection, human immunodeficiency virus infection, porcine epidemic diarrhoea virus infection, ORF virus infection, avian leukosis virus infection, simian vacuolating virus 40 infection, transmissible gastroenteritis coronavirus infection, and bovine viral diarrhoea virus infection. We have also discussed the critical regulatory role of circRNAs in provoking antiviral immunity, providing evidence for implications as therapeutic agents and as diagnostic markers.

Heliotropium crispum-mediated assembly of silver nanoparticles exhibit profound antibacterial and anti-biofilm effects against multiple drug-resistant bacteria, but its stability and biocompatibility remain a hurdle in commercialization. Herein, we adopted a surface chemistry-based steric repulsion approach to investigate the colloidal stability of H. crispum silver nanoparticles (HC-AgNPs) and determine its application as a commercial antibacterial formulation. Two primary silver nanoparticles (AgNPs) were synthesized, i.e., HC-AgNPs and citrate-HC-AgNPs initially, which were then modulated to assemble various derivatives of AgNPs using polyethylene glycol (PEG) and polyvinylpyrrolidone (PVP) as stabilizing agents. Various parameters were assessed to investigate the morphology, colloidal physio-chemistry, and surface capping using various analytical techniques, such as UV–Vis spectrophotometer, zeta–dynamic light scattering (DLS), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM, and transmission electron microscopy (TEM). Selective AgNPs were then screened on the basis of stability for up to 8 months, heat resistance at 100 °C, and bioactivity via MTT assay using HEP-2, MCF-7, and HCEC cell lines. The UV–Vis and electron microscope results revealed that HC-AgNPs confer near-spherical and slight triangular-shaped morphology and the size of all synthesized AgNPs is in the range of 400–450 nm. All AgNPs synthesized from HC-source have characteristic FTIR peaks recorded near 2931 cm−1, 1996 cm−1, and 825 cm−1. This study highlights promising evidence for the commercial application of HC-AgNPs as an antimicrobial agent. Additionally, it provides a methodology for modulating the surface capping of biological nanoparticles and assesses its corresponding effect on the stability.

An extensive screening survey was conducted on Pakistani filamentous fungal isolates for the identification of viral infections. A total of 396 fungal samples were screened, of which 36 isolates were found double-stranded (ds) RNA positive with an overall frequency of 9% when analysed by a classical dsRNA isolation method. One of 36 dsRNA-positive strains, strain SP1 of a plant pathogenic fungus

An extensive screening survey was conducted on Pakistani filamentous fungal isolates for the identification of viral infections. A total of 396 fungal samples were screened, of which 36 isolates were found double-stranded (ds) RNA positive with an overall frequency of 9% when analysed by a classical dsRNA isolation method. One of 36 dsRNA-positive strains, strain SP1 of a plant pathogenic fungus Fusarium mangiferae, was subjected to virome analysis. Next-generation sequencing and subsequent completion of the entire genome sequencing by a classical Sanger sequencing method showed the SP1 strain to be co-infected by 11 distinct viruses, at least seven of which should be described as new taxa at the species level according to the ICTV (International Committee on Taxonomy of Viruses) species demarcation criteria. The newly identified F. mangiferae viruses (FmVs) include two partitivirids, one betapartitivirus (FmPV1) and one gammapartitivirus (FmPV2); six mitovirids, three unuamitovirus (FmMV2, FmMV4, FmMV6), one duamitovirus (FmMV5), and two unclassified mitovirids (FmMV1, FmMV3); and three botourmiavirids, two magoulivirus (FmBOV1, FmBOV3) and one scleroulivirus (FmBOV2). The number of coinfecting viruses is among the largest ones of fungal coinfections. Their molecular features are thoroughly described here. This represents the first large virus survey in the Indian sub-continent.

In the current study, Chryseobacterium cucumeris strain MW-6 isolated from Arabian seawater exhibited broad-spectrum antibacterial activity against indicator bacterial pathogens. The partially extracted antibacterial metabolites with ethyl acetate revealed promising activity against Escherichia coli, Pseudomonas aeruginosa, Salmonella typhimurium, Listeria monocytogenes, and Staphylococcus aureus. The minimum inhibitory concentrations (MICs) were determined against indicator strains that ranged from 65–90 µg/ml. The genome size of C. cucumeris MW-6 is 4.81 Mbs containing 4227 coding DNA sequences, 74 tRNAs, 3 rRNAs, and 3 ncRNAs genes with 36.90% GC contents. The genome harbors nine putative biosynthetic gene clusters (BGCs) involved in the biosynthesis of lanthipeptide, NRPS-like, RiPPs-like, terpene, microviridin, T1PKS (hg1E-KS), resorcinol, and siderophore. Additionally, the strain encodes genes for sodium/proton antiporter, glutathione, superoxide dismutase, and cold shock protein to survive under stress conditions such as osmotic, oxidative, and cold shock. These putative BGCs and stress-related genes can be associated with in-vitro antibacterial activities and adaptation of this strain to the marine environment. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-03039-5.

Many PTMs dysregulation is known to be the major cause of many cancers including HCV induced HCC. PTMs of hepatitis C virus (HCV) regions NS3/4A, NS5A and NS5B are crucial for proper protein functions and replication that directly affect the generation of infectious virus particles and completion of its life cycle. In this study, we have performed comprehensive analysis of PTMs within HCV non-structural proteins (NS3/4A, NS5A and NS5B) through bioinformatics analysis to examine post-translational crosstalk between phosphorylation, palmitoylation, methylation, acetylation and ubiquitination sites in selected viral proteins. Our analysis has revealed many highly putative PTMs sites that are also conserved among major genotypes conferring the importance of these sites. We have also analysed viral 3D structures in their modified and unmodified forms to address extent and signatures of structural changes upon PTM. This study provides evidence that PTMs induce significant conformational changes and make viral proteins more stable. To find the potential role of PTMs in HCV induced HCC, docking analysis between selected viral proteins and p38-MAPK has been performed which also confirms their strong association with HCV induced HCC. The major findings proposed that PTMs at specific sites of HCV viral proteins could dysregulate specific pathways that cause the development of HCC.

Marmatite and bornite are commonly associated together in nature, and their interactions in an acidic environment are vital for both (bio)hydrometallurgy and acid mine drainage (AMD) production. In this work, dissolution experiments (marmatite : bornite = 2 : 0, 3 : 1, 1 : 1, 1 : 3 and 0 : 2) accompanied by analytic techniques such as electrochemical methods, Raman spectroscopy and synchrotron radiation-XRD (SR-XRD) were utilized to interpret the interactions between marmatite and bornite in acidic abiotic and biotic systems. The dissolution experiments showed that marmatite can significantly accelerate the oxidative dissolution of bornite, especially in the abiotic system. On the contrary, bornite inhibited the oxidative dissolution of marmatite when the percentage of bornite was high. Electrochemical measurements proved that the galvanic interactions between marmatite and bornite were slight and should not be the main cause for the interactions. Combined with the dissolution experiments, analytic techniques and previous references, it could be speculated that marmatite accelerated bornite dissolution mainly by providing an iron source, which acted as the energy source for microorganisms and oxidants. Bornite affected the dissolution of marmatite mainly by Cu2+ ions dissolving from bornite. Bornite inhibited the oxidative dissolution of marmatite mainly because a high Cu2+ concentration could significantly hinder marmatite dissolution. In addition, the formation of elemental sulfur or jarosite was also one important cause. Bornite intensified marmatite dissolution when the percentage of bornite or the Cu2+ concentration was extremely low and then, a synergic dissolution process occurred.

Anaerobic digestion (AD) can be used to recover nutrients from waste streams by isolating its phases. Here, we present a phase-restricted AD system (phase I only) for Phosphorus (P) release, production of Volatile Fatty Acids (VFA), ammonia (as NH4+) and biogas by digesting Chlorella vulgaris grown on agricultural waste-water using sewage sludge as inoculum. In our phase I AD system, we observed that changing the digester hydraulic retention time (HRT) altered the P, NH4+ and VFA concentrations in the effluent and biogas production. The reactor operated at 10 days HRT released maximum inorganic P (orthophosphate) in the effluent with a value of 199 ± 1 mg/L, the highest amongst considered HRTs. Maximum N in the phase-restricted AD system was observed at 14 days HRT with a final concentration of 118 ± 1 mg NH4+/L. However, the value was exceeded by a single-stage two-phase positive control batch reactor with a value of 350 ± 0.2 mg NH4+/L. The Gas Chromatography (GC) analysis indicated that VFA were present in all phase I AD reactors, with the 10 days HRT digester featuring the highest concentration at 233 mg/L. Furthermore, the phase-restricted AD approach had a positive impact on biogas generation. The 14 days HRT digester exhibited the greatest biogas production at 522 ± 1 mL in the digester’s headspace, followed by the 10 days HRT. The results of the study have established that anaerobic digesters operated at phase I with microalgae could be a promising approach for harvesting nutrients and generating biofuels in a green bioremediation system.

Here, we report the coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolate obtained from a nasopharyngeal swab from the first patient with COVID-19 in Gilgit, Pakistan.

Polystyrene (PS) was blended with polyethylene glycol (PEG) and silver sulfadiazine (SS) with different weight proportions to form polymeric blends. These synthesized blends were preliminary characterized in terms of functional groups through the FTIR technique. All compositions were subjected to thermogravimetric analysis for studying thermal transition and were founded thermally stable even at 280°C. The zeta potential and average diameter of algal strains of Dictyosphaerium sp. (DHM1), Dictyosphaerium sp. (DHM2), and Pectinodesmus sp. (PHM3) were measured to be -32.7 mV, -33.0 mV, and -25.7 mV and 179.6 nm, 102.6 nm, and 70.4 nm, respectively. Upon incorporation of PEG and SS into PS blends, contact angles were decreased while hydrophilicity and surface energy were increased. However, increase of surface energy did not led to decrease of antialgal activities. This has indicated that biofilm adhesion is not a major antialgal factor in these blended materials. The synergetic effect of PEG and SS in PS blends has exhibited significant antialgal activity via the agar disk diffusion method. The PSPS10 composition with 10 w / w % PEG and 10 w / w % SS has exhibited highest inhibition zones 10.8 mm, 10.8 mm, and 11.3 mm against algal strains DHM1, DHM2, and DHM3, respectively. This thermally stable polystyrene blends with improved antialgal properties have potential for a wide range of applications including marine coatings.

Multidrug resistance (MDR) has been a potentiator for the exploration of antibiotics. Nano drug delivery systems have opened new avenues to overcome this challenge. Although antibacterial nanocarriers are extensively realized, their effect on the bacteria residing inside the tissues and their toxicity is rarely explored. This study investigated the effects of flavonoid coated gold nanoparticles (FAuNPs) on the colonization of Enterococcus faecalis in the mouse liver and kidneys. Flavonoids were extracted from the leaves of Berberis lycium Royle and used to stabilize gold following a green synthesis approach. FAuNPs were characterized by ultraviolet-visible (UV-Vis) spectroscopy, Fourier-transform infrared spectroscopy (FTIR), scanning transmission electron microscopy (STEM), X-ray powder diffraction (XRD), and energy-dispersive X-ray spectroscopy (EDS). FAuNPs showed significantly higher reduction in bacterial counts in in-vitro and in-vivo in mice organs as compared to the free flavonoids owing to their biocompatibility and effectiveness.

The scope of optical sensors and scanners in aquatic media, fluids, and medical diagnostics has been limited by paucity of transparent shielding materials with antifouling potential. In this research endeavor, facile synthesis, characterization, and bioassay of antifouling transparent functional copolymers are reported. Copolymers of 3-sulfopropyl methacrylate (SPMA) and methyl methacrylate (MMA) were synthesized by free radical polymerization in various proportions. Samples PSM20, PSM30, PSM40, PSM50, and PSM60 contain 20%, 30%, 40%, 50%, and 60% SPMA by weight, respectively. Resultant products were characterized by FTIR and 1H-NMR spectroscopy. The synthesized copolymers have exhibited excellent transparency, i.e., 75% to 88%, as determined by the UV-Vis spectroscopic analysis. Transmittance was decreased from 6% to 2% in these copolymers upon changing the concentration of 3-sulfopropyl methacrylate from 20% to 50% owing to bacterial and algal biofilm formation. Water contact angle values were ranged from 18° to 63° and decreased with the increase in the polarity of copolymers. The surface energy lowest value 58 mJ/m2 and highest value 72 mJ/m2 were calculated for PSM20 and PSM50, respectively, by the Chibowski approach and Young equation. Sample PSM50 has exhibited the highest antibacterial activities, i.e., 18 mm and 19 mm, against Escherichia coli and Staphylococcus aureus, respectively, by the disk diffusion method. Copolymer PSM50 has shown minimum algal adhesion for Dictyosphaerium algae as observed by optical microscopy. This lower bacterial and algal adhesion is attributed to higher concentrations of anionic SPMA monomer that cause electrostatic repulsion between functional groups of the polymer and microorganisms. Thus, the resultant PSM50 product has exhibited good potential for optronics shielding application in aquatic medium and medical diagnostics.

The present study reports the isolation of antibacterial exhibiting Bacillus pumilus (B. pumilus) SF-4 from soil field. The genome of this strain SF-4 was sequenced and analyzed to acquire in-depth genomic level insight related to functional diversity, evolutionary history, and biosynthetic potential. The genome of the strain SF-4 harbor 12 Biosynthetic Gene Clusters (BGCs) including four Non-ribosomal peptide synthetases (NRPSs), two terpenes, and one each of Type III polyketide synthases (PKSs), hybrid (NRPS/PKS), lipopeptide, β-lactone, and bacteriocin clusters. Plant growth-promoting genes associated with de-nitrification, iron acquisition, phosphate solubilization, and nitrogen metabolism were also observed in the genome. Furthermore, all the available complete genomes of B. pumilus strains were used to highlight species boundaries and diverse niche adaptation strategies. Phylogenetic analyses revealed local diversification and indicate that strain SF-4 is a sister group to SAFR-032 and 150a. Pan-genome analyses of 12 targeted strains showed regions of genome plasticity which regulate function of these strains and proposed direct strain adaptations to specific habitats. The unique genome pool carries genes mostly associated with “biosynthesis of secondary metabolites, transport, and catabolism” (Q), “replication, recombination and repair” (L), and “unknown function” (S) clusters of orthologous groups (COG) categories. Moreover, a total of 952 unique genes and 168 exclusively absent genes were prioritized across the 12 genomes. While newly sequenced B. pumilus SF-4 genome consists of 520 accessory, 59 unique, and seven exclusively absent genes. The current study demonstrates genomic differences among 12 B. pumilus strains and offers comprehensive knowledge of the respective genome architecture which may assist in the agronomic application of this strain in future.

In this study, gold nanoparticles (AuNPs) and novel gold nanoformulations loaded with diosgenin (Dio-AuNPs) were synthesized through green approach using algal extract from Dictyosphaerium sp. strain DHM2 (LC159306) as a reducing agent. AuNPs and Dio-AuNPs synthesized were characterized through UV–vis spectroscopy, zeta potential analysis, FT-IR spectroscopy, X-ray diffraction (XRD) analysis and scanning transmission electron miroscopy. An average zeta potential value of -32.4 mV indicated that AuNPs were highly stable. Fourier transmission infrared spectroscopy (FT-IR) of AuNPs showed the presence of hydroxyl groups and carbonyl groups alongwith various other capping and stabilizing functional groups. Also, in FT-IR spectrum of Dio-AuNPs characteristic peaks of both AuNPs and diosgenin were observed. XRD analysis of AuNPs and Dio-AuNPs showed that both nanostuctures exist in the crystalline form. Scanning transmission electron microscopy (STEM) studies revealed that AuNPs and Dio-AuNPs had spherical morphology with average size range of 7.9 ± 2.4 nm and 10.3 ± 2.4 nm, respectively. Moreover, in-vitro antiproliferative activities of AuNPs and Dio-AuNPs were determined on colorectal cancer cell line HCT116 and breast cancer cell line HCC1954 using sulforhodamine B (SRB) proliferation assay. Dio-AuNPs were extremely potent with GI50 values of 1.03 ± 0.27 μg/mL and 1.69 ± 0.18 μg/mL in HCT116 and HCC1954 cell lines, respectively. AuNPs however, were almost 18 fold less potent as compared to Dio-AuNPs in both the cell lines. The current study has demonstrated biological synthesis, characterization and antiproliferative activities of gold nanoparticles and novel diosgenin loaded gold nanoformulations in colorectal and breast cancer cell lines and provided evidence that anticancer activities of both diosgenin and AuNPs can be enhanced many folds when used in conjugation.

Methicillin resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa (PA) infections in thermally injured patients have led to intrusive disease causing mortality. Silver nanoparticles (AgNPs) employed in treatment have limitations owing to their oxidative damage and toxicity in tissues. Present study focuses on the synthesis of biocompatible AgNPs from antioxidant-rich aqueous extract of Aerva javanica. Capping of phenols on AgNPs surface was confirmed through FTIR analysis and hence spherically assembled particles of low polydispersity index exhibited Surface Plasmon Resonance at 430 nm. These assembled antibacterial AgNPs were assessed for their radical scavenging properties and cytotoxic potential on both primary (HCEC) and cancerous cell lines (Huh-7, HeLa). Potential agglomeration of intraperitoneally administered AgNPs (3–24 mg kg−1) in liver, spleen and kidney of balb/c mice was assessed through histological analysis and corresponding mortality and weight loss studies were evaluated. These AgNPs after incorporation in chitosan hydrogels were topically applied on partial thickness burn wound infections (2 × 108 CFUs of MRSA and PA) created in Balb/c mice. A significant reduction in the infection was observed with application of AgNPs incorporated hydrogels that improved the healing time.

The therapeutic efficacy of universal drug-delivery systems depends on their capability to escape the immune system by overcoming the biological barriers of the body and concentrate at target tissues to eradicate only diseased cells. Biologically synthesized nanoparticle systems possess almost all of these qualities and utilize their targeting ability through cellular membrane interactions and making the targeting system biocompatible. In the present study, microalgae-mediated silver nanoparticles (AgNPs) targeted bacterial, fungal, cancerous and viral infected cells without harming normal cells. These AgNPs provide a comparative study on broader range of size and shape, synthesized by ethanolic extract of three different freshwater microalgae species, Dictyosphaerium sp. strain HM1 (DHM1), Dictyosphaerium sp. strain HM2 (DHM2) and Pectinodesmus sp. strain HM3 (PHM3). Characterization of AgNPs was done by XRD, SEM, TEM, EDS, FTIR and UV-Vis spectrophotometry. Significant activity against 14 bacterial strains, the fungal strain Candida albicans, hepatocellular carcinoma (HepG2) and breast cancer (MCF7) cell lines, and Newcastle Disease Virus (NDV) on Huh7-infected cells suggest the potential use of microalgae extract prepared nanoparticles in biomedicine, pharmaceutics and drug delivery.

Violacein is a bacterial quorum-sensing chromophore, also referred to as ‘purple treasure’ for its versatile utility in the pharmaceutical, food, cosmetic and textile industries. Moreover, it provides broad spectrum biological activity that is the subject of expansive scientific research. The major limitation in the drug delivery of violacein is its hydrophobic nature that results in poor bioavailability. Nanoparticles (NPs) coupled with these drugs tend to enhance their delivery, efficacy and safety profiles. In this study, we established that violacein capped silver NPs (vAgNPs) have shown enhanced stability with 3 to 10 times higher therapeutic effect against multidrug resistant bacteria, fungi and algae compared to starch capped silver NPs (cAgNPs). The surface plasmon resonance, size, shape, crystalline nature and capping agent of these NPs were studied with UV-Vis spectroscopy, Scanning Transmission Electron Microscopy, Atomic Force Microscopy, X-ray Diffraction and Fourier Transform Infrared Spectroscopy, respectively. This comparative study examines the efficacy of vAgNPs against cAgNPs and establishes that surface capping of AgNPs with violacein yields conjugative benefits, i.e., strengthening each other's therapeutic effect, increased bioavailability of violacein, higher stability and maneuvering the therapeutic effect of vAgNPs towards Gram positive bacteria.

The study describes the optimized method for silver nanoparticle (AgNPs) synthesis using Heliotropium crispum (HC) plant extract. Optimization of physicochemical parameters resulted in stable and rapidly assembled AgNPs. FTIR results suggest presence of plant phytochemicals that helped in the reduction, stabilization and capping of AgNPs. The assembled Ag nano-composites displayed the peak surface plasmon resonance (SPR) around 428 nm. The presence of uniquely assembled Ag-biomolecule composites, cap and stabilize nanoparticles in aqueous plant suspension. Spherical, uniform-shaped AgNPs with low poly-dispersion and average particle size of 42 nm and was determined through dynamic light scattering (DLS) and scanning election microscopy (SEM) which present robust interaction with microbes. The study also evaluates the antimicrobial and anti-biofilm properties of biologically synthesized AgNPs on clinical isolates of MRSA, Pseudomonas aeruginosa and Acinetobacter baumannii. Minimum inhibitory concentration (0.5 mg mL−1) of nanoparticles that presented bactericidal effect was made through inhibition assays on bacterial strains. The concentration which presented potent bactericidal response was then evaluated through growth inhibition in liquid medium for anti-biofilm studies at 2.0 mg mL−1. HC-Ag nanoparticles mediated anti-biofilm effects on Pseudomonas aeruginosa was revealed through SEM. Complete breakdown of biofilm’s extracellular polymeric substances resulted after incubation with AgNPs. Peptidoglycan cell wall destruction was also revealed on planktonic bacterial images after 24 h of incubation.

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.

This study reports on a simple approach for the fabrication of an electrode modified with biocompatible C-dot wrapped ZnO nanoparticles for selective photoelectrochemical monitoring of H2O2 released from living cells. The biocompatibility of the ZnO nanoparticles was confirmed through in-vitro cellular testing using the MTT assay on Huh7 cell lines. The ZnO nanoparticles wrapped with dopamine-derived C-dots possess numerous catalytically active sites, excessive surface defects, good electrical conductivity, and efficient separation ability of photo-induced electrons and holes. These properties offer highly sensitive and selective non-enzymatic photo-electrochemical monitoring of H2O2 released from HeLa cells after stimulation with N-formylmethionyl-leucyl-phenylalanine. The sensor has a wide linear range (20–800 nM), low detection limit (2.4 nM), and reliable reproducibility, this implying its suitability for biological and biomedical applications.

Poliovirus 2A protease (PV2Apro) plays a vital role in viral replication and down-regulation of host cell protein synthesis. In order to understand more concerning PV2Apro, the protein was over-expressed in bacteria following amplification using sense and antisense primers and cloning in pET15b. Several expression hosts were tested and BL21 (DE3) pLysS cells gave the best expression of PV2Apro with minimal unwanted protein expression following IPTG induction. The 2Apro protein was purified to homogeneity using column chromatography, its solubility determined and its molecular weight and composition determined by MALDI-TOF mass spectrometry. The protease was found in the insoluble fraction and the purified protein had a slightly lower molecular weight than predicted. Moreover, three dimensional structure was modelled using template 1z8r with 58% identity and validated using ramachandran plot. Results revealed that most of the residues lie in favoured and allowed regions. These findings could help in a better understanding of PV2Apro structure and inhibition thus, highlighting potential targets for antiviral drug development.

The present study was focused on the fabrication and characterization of polymeric wound dressings, composed of PVA and Starch. Graphitic carbon nitride (g-C3N4) was incorporated as a filler and Silver deposited-Titania nanoparticles (Ag@TiO2 NPs) as an antibacterial agent. The hydrogel membranes were fabricated by solution casting under ambient conditions. The prepared hydrogels were subjected to various characterizations techniques and obtained data demonstrated good compatibility among the constituents of the membranes. The antibacterial activity was investigated against Escherichia coli and Staphylococcus aureus. The maximum zone of inhibition achieved was 37.33 and 33.25 mm, respectively at the composition PVA/Starch/0.14GCN/0.7Ag@TiO2 NPs. Furthermore, swelling, moisture retention and water vapor transmission results demonstrated that hydrogels were capable of absorbing large volume of wound exudates. Porosity and oxygen permeability results have demonstrated that hydrogels membranes were breathable. Lastly, kinetics of drug release was performed by using various mathematical models where Higuchian model was found to be the best fit. Non-Fickian diffusion mechanism prevailed and a sustained and slow release of nanoparticles was observed. The complete healing was accomplished in seven days. The fabricated hydrogel membranes depicted better healing than conventional cotton gauze wound dressings. The prepared hydrogel membranes have demonstrated all the potential to be used as wound dressing for partial and full thickness excision wounds after complete biological characterization.

An improved active packaging system was developed for fresh fruits using silver nanoparticles (AgNPs) coupled with calcium alginate (Ca-ALG). For the synthesis of AgNPs aqueous, ethanol and methanol extracts of Artemisia scoparia (AS) were used. These AgNP's were characterized using UV–Vis, SEM, EDS, AFM, FTIR and gel electrophoresis. Ethanol extract of AS (ASE) produced AgNPs with smallest size in comparison to aqueous AS (ASA) and methanol extract of AS (ASM). AgNPs synthesized from ASE had a size range of 12.0–23.3 nm and were tested on Human Corneal Epithelial Cells to evaluate their cytotoxicity. At 0.05 ng/mL of AgNP's concentration, no toxic effects were observed on the evaluated cell line. Therefore, 0.05 ng/mL of AgNPs mixed with edible coating of Ca-ALG were applied on strawberries and loquats as active coating to increase their shelf life. Significant improvement was observed in the quality parameters of strawberries and loquats such as microbial analysis, acidity loss, soluble solid content loss, weight loss and quality decay. Ca-ALG coating incorporated with AgNPs enhanced the shelf life of strawberries and loquats in comparison to no treatment and simple Ca-ALG coatings. This study provides an insight to food industry to extend the shelf life of fresh fruits using AgNP's formulated coatings.

This study reports on a simple approach for the fabrication of an electrode modified with biocompatible C-dot wrapped ZnO nanoparticles for selective photoelectrochemical monitoring of H

Extensive utilization of silver nanoparticles (AgNP) has raised concerns of their safety profile upon interaction with biological system. In past decade, various nanoparticles (NPs) with excellent antimicrobial potential have been synthesized, a majority of which have struggled with the established toxicity in biological systems. The NPs safety is still a hot debate and various strategies are being adopted to overcome this giant limitation. This paper successfully reports comparative toxicity profiles of previously synthesized antimicrobial NPs in our lab and concludes the effectiveness of biologically synthesized NPs for its safe usage in biological systems. In this study, five of our previously synthesized NPs that showed excellent antimicrobial potential were compared for their in vivo toxicity and corresponding radical scavenging activities. Based on lowest morbidity, mortality, weight loss, toxicity and agglomeration profile, best NPs with highest antimicrobial potentials were screened out and used for further biomedical applications. The previously reported NPs used in this study included Aerva javanica synthesized nanoparticles (AjNPs), Heliotropium crispium synthesized nanoparticles (HcNPs), and violacein capped nanoparticles (VNPs), these showed least toxicity upon in vivo histological analysis. AjNPs among them showed maximum safety and efficacy profile and consistently showed least production of reactive oxygen species, least mortality and morbidity rate as compared to other groups. Present study establishes that all these biologically synthesized NPs and specifically AjNPs can be efficiently employed as antimicrobial agents as they have not exhibited toxic profile and have shown least accumulation into the organs such as liver spleen and kidney.

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.

Polio viral proteinase 2A performs several essential functions in genome replication. Its inhibition prevents viral replication, thus making it an excellent substrate for drug development. In this study, the three-dimensional structure of 2A protease was determined and optimized by homology modelling. To predict the molecular basis of the interaction of small molecular agonists, docking simulations were performed on a structurally diverse dataset of poliovirus 2A protease (PV2Apr°) inhibitors. Docking results were employed to identify high risk missense mutations that are highly damaging to the structure, as well as the function, of the protease. Intrinsic disorder regions (IDRs), drug binding sites (DBS), and protein stability changes upon mutations were also identified among them. Our results demonstrated dominant roles for Lys 15, His 20, Cys 55, Cys 57, Cys 64, Asp 108, Cys 109 and Gly 110, indicating the presence of various important drug binding sites of the protein. Upon subjecting these sites to single-nucleotide polymorphism (SNP) analysis, we observed that out of 155 high risk SNPs, 139 residues decrease the protein stability. We conclude that these missense mutations can affect the functionality of the 2A protease, and that identified protein binding sites can be directed for the attachment and inhibition of the target proteins.

The present work is focused on preparation, characterization, and antibacterial activity evaluation of graphene oxide/polyethersulfone mixed matrix filtration membranes. Graphene oxide (GO) was synthesized via improved Hummer’s method and characterized by XRD, FTIR, and SEM. FT-IR spectra showed the presence of carboxylic acid and hydroxyl groups on GO nanosheets. Different concentrations of the synthesized GO at 0.25, 0.5, and 1.0 wt. % were incorporated in polyethersulfone (PES) matrix via phase inversion method to fabricate GO-PES membranes. Increasing porosity and formation of wider, finger-like channels were observed with increased GO concentrations relative to pristine membranes as evident from scanning electron microscopy (SEM) micrographs of the fabricated membranes. However, membranes prepared with 1 wt. % GO appear to contain aggregation and narrowing of pore morphology. GO-incorporated membranes demonstrated enhanced flux, water-retaining capacities, and wettability as compared to pristine PES membranes. Shake flask and colony counting methods were employed to carry out antibacterial testing of synthesized GO and fabricated GO-PES membranes against Salmonella typhi (S. typhi)—a gram-negative bacteria present in water that is known as causative agent of typhoid. Synthesized GO showed significant reduction up to 70.8% in S. typhi cell count. In the case of fabricated membranes, variable concentrations of GO are observed to significantly influence the percentage viability of S. typhi, with reduction percentages observed at 41, 60, and 69% for 0.25, 0.5, and 1.0 wt. % GO-incorporated membranes relative to 17% in the case of pristine PES membranes. The results indicate a good potential for applying GO/PES composite membranes for water filtration application.

Among solid tumors, hepatocellular carcinoma (HCC) emerges as a prototypical therapy-resistant tumor. Considering the emerging sorafenib resistance crisis in HCC, future studies are urgently required to overcome resistance. Recently noncoding RNAs (ncRNAs) have emerged as significant regulators in signalling pathways involved in cancer drug resistance and pharmacologically targeting these ncRNAs might be a novel stratagem to reverse drug resistance. In the current study, using a hybrid Petri net based computational model, we have investigated the harmonious effect of miR-17-92 cluster inhibitors/mimics and circular RNAs on sorafenib resistant HCC cells in order to explore potential resistance mechanisms and to identify putative targets for sorafenib-resistant HCC cells. An integrated model was developed that incorporates seven miRNAs belonging to miR-17-92 cluster (hsa-miR-17-5p, hsa-miR-17-3p, hsa-miR-19a, hsa-miR-19b, hsa-miR-18a, hsa-miR-20a and hsa-miR-92) and crosstalk of two signaling pathways (EGFR and IL-6) that are differentially regulated by these miRNAs. The mechanistic connection was proposed by the correlation between members belonging to miR-17-92 cluster and corresponding changes in the protein levels of their targets in HCC, specifically those targets that have verified importance in sorafenib resistance. Current findings uncovered potential pathway features, underlining the significance of developing modulators of this cluster to combat drug resistance in HCC.

Cellular homeostasis is a continuous phenomenon that if compromised can lead to several disorders including cancer. There is a need to understand the dynamics of cellular proliferation to get deeper insights into the prevalence of cancer. Mechanistic Target of Rapamycin (mTOR) is implicated as the central regulator of the metabolic pathway involved in growth whereas its two distinct complexes mTORC1 and mTORC2 perform particular functions in cellular propagation. To date, mTORC1 is a well defined therapeutic target to inhibit uncontrolled cell division, while the role of mTORC2 is not well characterized. Therefore, the current study is designed to understand the signaling dynamics of mTOR and its partner proteins such as PI3K, PTEN, mTORC2, PKB (Akt), mTORC1, and FOXO. For this purpose, a qualitative model of mTOR-associated Biological Regulatory Network (BRN) is constructed to predict its regulatory behaviors which may not be predictable otherwise. The depleted expression of PTEN and FOXO along with the overexpression of PI3K, mTORC2, mTORC1 and Akt is predicted as a stable steady state which is in accordance with their observed expression levels in the progression of various cancers. The qualitative model also predicts the homeostasis of all the entities in the form of qualitative cycles. The significant qualitative (discrete) cycle is identified by analyzing betweenness centralities of the qualitative (discrete) states. This cycle is further refined as a linear hybrid automaton model with the production (activation) and degradation (inhibition) time delays in order to analyze the real-time constraints for its existence. The analysis of the hybrid model provides a formal proof that during homeostasis the inhibition time delay of Akt is less than the inhibition time delay of mTORC2. In conclusion, our observations characterize that in homeostasis Akt is degraded with a faster rate than mTORC2 which suggests that the inhibition of Akt along with the activation of mTORC2 may be a better therapeutic strategy for the treatment of cancer.

The blood-brain barrier (BBB) poses a huge challenge and is a serious issue in deciphering the pathophysiology of central nervous system disorders. Endothelial tight junctions play an essential role in maintaining the integrity of the BBB. Post-translational modifications (PTMs) in endothelial tight junction proteins are known to cause deleterious functional impairment and possible disruptions in BBB integrity. PTMs in tight junction proteins play an important role in human immunodeficiency virus type 1 (HIV-1) entry through the BBB. Human claudin-5 is one of the highly expressed brain endothelial tight junction protein and various PTMs in claudin-5 are expected to aid HIV-1 in crossing the BBB. A precise characterization of PTMs in claudin-5 is important for understanding its role in HIV-1 brain infiltration. In this study, we have examined post-translational crosstalk between phosphorylation, O-glycosylation, palmitoylation and methylation sites in claudin-5, which could alter claudin-5's ability to maintain BBB integrity. To the best of our knowledge, this is the first report on claudin-5 protein that suggests a novel interplay between potential PTM sites. PTMs of predicted residues in claudin-5, suggested in this study, can serve as compelling targets for potential therapeutic agents against HIV-1 induced neuropathogenesis. Further site-specific experimental studies in this aspect are highly recommended.

Background 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. Results 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. Conclusion 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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2951-4) contains supplementary material, which is available to authorized users.

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.

Cellular immune responses (T cell responses) during hepatitis C virus (HCV) infection are significant factors for determining the outcome of infection. HCV adapts to host immune responses by inducing mutations in its genome at specific sites that are important for HLA processing/presentation. Moreover, HCV also adapts to resist potential drugs that are used to restrict its replication, such as direct-acting antivirals (DAAs). Although DAAs have significantly reduced disease burden, resistance to these drugs is still a challenge for the treatment of HCV infection. Recently, drug resistance mutations (DRMs) observed in HCV proteins (NS3/4A, NS5A and NS5B) have heightened concern that the emergence of drug resistance may compromise the effectiveness of DAAs. Therefore, the NS3/4A, NS5A and NS5B drug resistance variations were investigated in this study, and their prevalence was examined in a large number of protein sequences from all HCV genotypes. Furthermore, potential CD4+ and CD8+ T cell epitopes were predicted and their overlap with genetic variations was explored. The findings revealed that many reported DRMs within NS3/4A, NS5A and NS5B are not drug-induced; rather, they are already present in HCV strains, as they were also detected in HCV-naive patients. This study highlights several hot spots in which HLA and drug selective pressure overlap. Interestingly, these overlapping mutations were frequently observed among many HCV genotypes. This study implicates that knowledge of the host HLA type and HCV subtype/genotype can provide important information in defining personalized therapy.

Purpose The complex interactions between genetic machinery of HIV-1 and host immune cells mediate dynamic adaptive responses leading to Autoimmune Deficiency Syndrome. These interactions are captured as Biological Regulatory Network (BRN) which acts to maintain the viability of host cell machinery through feedback control mechanism which is a characteristic of complex adaptive systems. In this study, the BRN of immune response against HIV-1 infection is modeled to investigate the role of NF-κB and TNF-α in disease transmission using qualitative (discrete) and hybrid modeling formalisms. Methods Qualitative and Hybrid modeling approaches are used to model the BRN for the dynamic analysis. The qualitative model is based on the logical parameters while the hybrid model is based on the time delay parameters. Results The qualitative model gives useful insights about the physiological condition observed as the homeostasis of all the entities of the BRN as well as pathophysiological behaviors representing high expression levels of NF-κB, TNF-α and HIV. Since the qualitative model is time abstracted, so a hybrid model is developed to analyze the behavior of the BRN by associating activation and inhibition time delays with each entity. HyTech tool synthesizes time delay constraints for the existence of homeostasis. Conclusion Hybrid model reveals various viability constraints that characterize the conditional existence of cyclic states (homeostasis). The resultant relations suggest larger cycle period of HIV-1 than the cycle periods of the other two entities (NF-κB and TNF-α) to maintain a homeostatic expressions of these entities.