In silico studies on the interaction of phage displayed biorecognition element (TFQAFDLSPFPS) with the structural protein VP28 of white spot syndrome virus.

White spot disease caused by the white spot syndrome virus (WSSV) incurs a huge loss to the shrimp farming industry. Since no effective therapeutic measures are available, early detection and prevention of the disease are indispensable. Towards this goal, we previously identified a 12-mer phage displayed peptide (designated as pep28) with high affinity for VP28, the structural protein of the white spot syndrome virus (WSSV). The peptide pep28 was successfully used as a biorecognition probe in the lateral flow assay developed for rapid, on-site detection of WSSV. To unravel the structural determinants for the selective binding between VP28 and pep28, we used bioinformatics, structural modeling, protein-protein docking, and binding-free energy studies. We performed atomistic molecular dynamics simulations of pep28-pIII model totaling 300 ns timescale. The most representative pep28-pIII structure from the simulation was used for docking with the crystal structure of VP28. Our results reveal that pep28 binds in a surface groove of the monomeric VP28 ß-barrel and makes several hydrogen bonds and non-polar interactions. Ensemble-based binding-free energy studies reveal that the binding is dominated by non-polar interactions. Our studies provide molecular level insights into the binding mechanism of pep28 with VP28, which explain why the peptide is selective and can assist in modifying pep28 for its practical use, both as a biorecognition probe and a therapeutic.

Nanomaterials: new weapons in a crusade against phytopathogens.

Bacteria, fungi, viruses, and nematodes are the major causal agents of plant diseases. These phytopathogens are responsible for about 10-40% losses in productivity and quality of food crops and horticultural produce. Although eradication of pathogens is not possible, control of plant diseases has been an area of continuous improvement/research. Use of antimicrobials, bacteriophages, and biocontrol agents, natural and synthetic agrochemicals along with best farm management practices constitute integrated measures for disease control. However, the quest for new materials continues due to pesticide resistance in the pathogens, emergence of new serotypes, and accumulation of high quantities of agrochemical contaminants in the ecosystem and associated environmental hazards, specificity of biocontrol agents, succession of pathogens during the plant growth phase, etc. The emergence of "nanotechnology," a multidisciplinary field of research, has provided a plethora of nanomaterials for potential applications in the agricultural sector. Control of plant diseases requires agents that reduce the pathogen to manageable levels, tools for early-stage detection of pathogen, and compounds that elicit immune response in the host plants. Nanomaterials have in fact been assessed for their utility in all these approaches for disease control. The present review discusses nanomaterials for controlling phytopathogens, nanomaterials in plant disease diagnostics, and nanomaterials as elicitors of the plant immune system. These nanomaterials thus represent new weapons in the fight against the phytopathogens. Recent studies indicate that nanomaterials will be a crucial component in the agroecosystem.

Nanomaterials for the control of bacterial blight disease in pomegranate: quo vadis?

Bacterial blight, caused by Xanthomonas axonopodis pv. punicae, Xap is a serious threat to commercially successful pomegranate (Punica granatum L) crop. Owing to the non-availability of disease-resistant varieties of pomegranate, integrated disease management involving change of season, adequate nutrition, and preventive sprays of bactericides is used to control Xap. We undertook a systematic study to assess the efficacy of metal-based nanomaterials (Cu, CuO, ZnO, CaO, MgO) for the control of Xap. The antimicrobial effectiveness was in the order Cu > ZnO > MgO > CuO with MIC (minimum inhibitory concentration) 2.5, 20, 190, 200, and 1600 µg/ml. A time-to-kill curve indicated that Cu nanoparticles (CuNPs) killed Xap cells within 30 min at 2.5 µg/ml. Under controlled conditions (polyhouse), foliar application of CuNPs (400 µg/ml) resulted in ~ 90 and ~ 15% disease reduction in 6-month-old infected plants at early (disease severity 10%) and established (disease severity 40%) stages of infection, respectively. In a subsequent field study on severely infected 7-year-old plants, applications of nanoparticles reduced the disease incidence by ~ 20% as compared to untreated control. Microscopic observations revealed that CuNPs reduced the bacterial colonization of the leaf surface. Anti-Xap activity of foliar applied CuNPs was on par with conventionally used copper oxychloride (3000 µg/ml) albeit at 8-fold reduced copper concentration. Thus, early disease detection and application of effective dosage of copper nanoparticles can indeed help the farmer in achieving rapid infection control. Further studies on use of combinations of nanoparticles for management of bacterial blight are warranted.

Transcriptome analysis of silver nanoparticles treated Staphylococcus aureus reveals potential targets for biofilm inhibition.

The biofilms of Staphylococcus aureus on the implanted materials and chronic wounds are life-threatening and are a substantial financial burden on the healthcare system. Silver nanoparticles (SNP), known for their multi-level physiological effects in planktonic cells could be a promising agent in the treatment of biofilm-related infections also. To gain insight into the effects of SNP on various physiological processes in biofilms we studied the transcriptome of Staphylococcus aureus ATCC 29213. To distinguish between 'nanoparticles-specific' and 'ion-specific' effect of silver, we performed a comparative analysis of the functional genes in response to Ag+. As compared to untreated biofilms, 21% (i.e. 629 genes) and 28.5% (i. e. 830 genes) of the total functional coding genes were differentially regulated upon exposure to SNP and Ag+. Genes encoding capsular polysaccharides, intercellular adhesion, virulence were downregulated in SNP and Ag+ treated biofilms. Genes involved in carbohydrate, protein metabolism including DNA and RNA synthesis, oxidative stress etc. were differentially expressed. Further, activation of efflux pumps and multidrug export proteins was observed, which clearly indicates the presence of metal stress resistance determinants in S. aureus. Silver blocked the integration of mobile genetic elements in S. aureus genome. Our study points out quorum sensing and virulence determinants as possible targets for inhibition of biofilms possibly with/without existing antibiotics. However, further studies on these aspects are warranted. Scanning electron microscopy (SEM) and confocal microscopy revealed changes in biofilm morphology, architecture and thickness in presence of silver nanoparticles and ionic silver, substantiating the transcriptome data.

Applications of bacterial cellulose and its composites in biomedicine.

Bacterial cellulose produced by few but specific microbial genera is an extremely pure natural exopolysaccharide. Besides providing adhesive properties and a competitive advantage to the cellulose over-producer, bacterial cellulose confers UV protection, ensures maintenance of an aerobic environment, retains moisture, protects against heavy metal stress, etc. This unique nanostructured matrix is being widely explored for various medical and nonmedical applications. It can be produced in various shapes and forms because of which it finds varied uses in biomedicine. The attributes of bacterial cellulose such as biocompatibility, haemocompatibility, mechanical strength, microporosity and biodegradability with its unique surface chemistry make it ideally suited for a plethora of biomedical applications. This review highlights these qualities of bacterial cellulose in detail with emphasis on reports that prove its utility in biomedicine. It also gives an in-depth account of various biomedical applications ranging from implants and scaffolds for tissue engineering, carriers for drug delivery, wound-dressing materials, etc. that are reported until date. Besides, perspectives on limitations of commercialisation of bacterial cellulose have been presented. This review is also an update on the variety of low-cost substrates used for production of bacterial cellulose and its nonmedical applications and includes patents and commercial products based on bacterial cellulose.

Radio frequency induced hyperthermia mediated by dextran stabilized LSMO nanoparticles: in vitro evaluation of heat shock protein response.

Dextran stabilized La(0.7)Sr(0.3)MnO(3) (Dex-LSMO) is an alternative cancer hyperthermia agent holding considerable promise. Here, we have carried out a comparative study on radio frequency (~264 kHz) induced Dex-LSMO mediated heating and extraneous heating (mimicking generalized hyperthermia) in terms of changes in the morphology, proliferation pattern and induction of heat shock proteins in a human melanoma cell line (A375). Our results clearly show that the cellular effects seen with extraneous heating (60 min at 43 °C) could be reproduced by just six minutes of radio frequency induced Dex-LSMO mediated heating. More importantly, the observed enhanced levels of HSP 70 and 90 (molecular markers of heat shock that trigger favorable immunological reactions) seen with Dex-LSMO mediated heating were comparable to extraneous heating. These results suggest the possible utility of Dex-LSMO as a cancer hyperthermia agent.

Multiplexed detection of waterborne pathogens in circular microfluidics.

Microfluidic lab-on-a-chip presents an ideal solution for bacterial sensing and identification due to its advantages like large surface-to-volume ratio, requirement of low sample volume and multiplexing possibility. The present work deals with the development of an immunosensor chip using circular microchannels fabricated directly with microdimensional copper wire and permanent magnet for capture of Fe(3)O(4) magnetic nanoparticle (MNP) conjugate. The MNP facilitate capture of the antigen in a confined space and hence, enhanced fluorescence signal for detection. The multiplexed microfluidic chip permits visual detection and quantification of waterborne pathogens viz. Escherichia coli and Salmonella typhimurium simultaneously. CdTe quantum dots (QDs) with different emission wavelengths were conjugated with anti-E. coli and anti-S. typhimurium antibodies for concurrent fluorescence detection. The present technique provides an inexpensive yet powerful tool to image and quantify pathogens at low numbers with passage of large sample volumes.

Flocculation of dimorphic yeast Benjaminiella poitrasii is altered by modulation of NAD-glutamate dehydrogenase.

A strategy to control flocculation is investigated using dimorphic yeast, Benjaminiella poitrasii as a model. Parent form of this yeast (Y) exhibited faster flocculation (11.1 min) than the monomorphic yeast form mutant Y-5 (12.6 min). Atomic force microscopy revealed higher surface roughness of Y (439.34 rms) than Y-5 (52 rms). Also, the former had a zeta potential of -65.97+/-3.45 as against -50.21+/-2.49 for the latter. Flocculation of both Y and Y-5 could be altered by supplementing either substrates or inhibitor of NAD-glutamate dehydrogenase (NAD-GDH) in the growth media. The rate of flocculation was promoted by alpha-ketoglutarate or isophthalic acid and decelerated by glutamate with a statistically significant inverse correlation to corresponding NAD-GDH levels. These interesting findings open up new possibilities of using NAD-GDH modulating agents to control flocculation in fermentations for easier downstream processing.

Interactions of silver nanoparticles with primary mouse fibroblasts and liver cells.

Primary cells are ideal for in vitro toxicity studies since they closely resemble tissue environment. Here, we report a detailed study on the in vitro interactions of 7-20 nm spherical silver nanoparticles (SNP) with primary fibroblasts and primary liver cells isolated from Swiss albino mice. The intended use of silver nanoparticles is in the form of a topical antimicrobial gel formulation for the treatment of burns and wounds. Upon exposure to SNP for 24 h, morphology of primary fibroblasts and primary liver cells remained unaltered up to 25 microg/mL and 100 microg/mL SNP, respectively, although with minor decrease in confluence. IC(50) values for primary fibroblasts and primary liver cells as revealed by XTT assay were 61 microg/mL and 449 microg/mL, respectively. Ultra-thin sections of primary cells exposed to 1/2 IC(50) SNP for 24 h, visualized under Transmission electron microscope showed the presence of dark, electron dense, spherical aggregates inside the mitochondria, and cytoplasm, probably representing the intracellular SNP. When the cells were challenged with approximately 1/2 IC(50) concentration of SNP (i.e. 30 microg/mL and 225 microg/mL for primary fibroblasts and primary liver cells, respectively), enhancement of GSH (approximately 1.2 fold) and depletion of lipid peroxidation (approximately 1.4 fold) were seen in primary fibroblasts which probably protect the cells from functional damage. In case of primary liver cells; increased levels of SOD ( approximately 1.4 fold) and GSH ( approximately 1.1 fold) as compared to unexposed cells were observed. Caspase-3 activity assay indicated that the SNP concentrations required for the onset of apoptosis were found to be much lower (3.12 microg/mL in primary fibroblasts, 12.5 microg/mL in primary liver cells) than the necrotic concentration (100 microg/mL in primary fibroblasts, 500 microg/mL in primary liver cells). These observations were confirmed by CLSM studies by exposure of cells to 1/2 IC(50) SNP (resulting in apoptosis) and 2 x IC(50)) cells (resulting in necrosis). These results clearly suggest that although silver nanoparticles seem to enter the eukaryotic cells, cellular antioxidant mechanisms protect the cells from possible oxidative damage. This property, in conjunction with the finding that primary cells possess much higher SNP tolerance than the concentration in the gel (approximately 20 microg/g), indicates preliminary safety of the formulation and warrants further study for possible human application.

Hydrazine based facile synthesis and ordered assembly of metal nanoparticles (Au, Ag) on a bacterial surface layer protein template.

An efficient and facile procedure is developed for concurrent in situ synthesis and ordered assembly of metal nanoparticles on a periodic two dimensional protein array. The S-layer protein of Bacillus subtilis exhibiting uniform pore size is used as template. Synthesis of gold and silver nanoparticles anchoring on the pores of S-layer is achieved by chemical reduction of respective metal salt laden protein template. Transmission electron microscopy reveals formation of well ordered and separated gold and silver nanoparticles with an average diameter of 6 +/- 1 nm and 4 +/- 1 nm, respectively. The periodic arrangement of nanoparticles is dictated by the native structure of S-layer protein array as the nanoparticle locations are found to be correlated to the nanosized pores of the crystalline S-layer array.

Cellular responses induced by silver nanoparticles: In vitro studies.

A systematic study on the in vitro interactions of 7-20 nm spherical silver nanoparticles (SNP) with HT-1080 and A431 cells was undertaken as a part of an on-going program in our laboratory to develop a topical antimicrobial agent for the treatment of burn wound infections. Upon exposure to SNP (up to 6.25 microg/mL), morphology of both the cell types remained unaltered. However, at higher concentrations (6.25-50 microg/mL) cells became less polyhedral, more fusiform, shrunken and rounded. IC(50) values for HT-1080 and A431 as revealed by XTT assay were 10.6 and 11.6 microg/mL, respectively. When the cells were challenged with approximately 1/2 IC(50) concentration of SNP (6.25 microg/mL), clear signs of oxidative stress, i.e. decreased GSH ( approximately 2.5-folds in HT-1080, approximately 2-folds in A431) and SOD ( approximately 1.6-folds in HT-1080, 3-folds in A431) as well as increased lipid peroxidation ( approximately 2.5-folds in HT-1080, approximately 2-folds in A431) were seen. Changes in the levels of catalase and GPx in A431 cells were statistically insignificant in both cell types. DNA fragmentation in SNP-exposed cells suggested apoptosis. When the apoptotic thresholds of SNP were monitored with caspase-3 assay the concentrations required for the onset of apoptosis were found to be much lower (0.78 microg/mL in HT-1080, 1.56 microg/mL in A431) than the necrotic concentration (12.5 microg/mL in both cell types). These results can be used to define a safe range of SNP for the intended application as a topical antimicrobial agent after appropriate in vivo studies.

Biodegradation of γ-hexachlorocyclohexane (Lindane) by a non-white rot fungus conidiobolus 03-1-56 isolated from litter.

Biodegradation of chlorinated pesticide γ-hexachlorocyclohexane (lindane) by a nonwhite rot fungus Conidiobolus 03-1-56 is reported for the first time. Conidiobolus 03-1-56, a phycomyceteous fungus isolated from litter, completely degraded lindane on the 5th day of incubation in the culture medium, and GC-ECD studies confirmed that lindane removal did not occur via adsorption on the fungal biomass. Degradation studies using different medium compositions showed that nitrogen/carbon limiting conditions (stress conditions) and presence of veratryl alcohol, induced the secretion of extracellular oxidative enzymes, which enhanced the rate of lindance biodegradation. Under optimum nutrient-limiting conditions, GC-ECD and GC-MS analysis showed complete absence of any degradation metabolite, indicating that lindane was completely mineralized. Assays for tannic acid utilization and lignin peroxidase showed similar enzymatic profiles between Conidiobolus 03-1-56 and standard white rot fungi Pleurotus ostreatus 1200 and Trametes versicolor 1086. Although Conidiobolus 03-1-56 showed a reduced enzyme activity compared to white rot fungi, preliminary evidence indicates that enzymes responsible for lignin degradation by white rots play a key role in lindane degradation by Conidiobolus 03-1-56.

Taguchi approach significantly increases bioremediation process efficiency: a case study with Hg (II) removal by Pseudomonas aeruginosa.

AIM: Optimization of process parameters for mercury removal by an Hg (II)-reducing Pseudomonas aeruginosa strain. METHODS AND RESULTS: A strain of Ps. aeruginosa was found to reduce 10 mg l(-1) Hg (II) to Hg0 with 70% efficiency in 24 h. To optimize process performance, a statistical tool--Taguchi design of experiments (DOE)--was used to carry out 18 well-defined experiments (L18 Orthogonal array) with eight variable parameters (viz. agitation, temperature, pH, carbon source, medium volume: flask volume ratio and concentrations of Hg (II), ammonium sulfate and yeast extract). When data obtained were analyzed using specialized software for Taguchi design, Qualitek-4 (Nutek Inc., MI, USA), Hg (II) reduction efficiency was predicted to be 95% in 24 h under the optimized process parameters (also suggested by the software). In the validation experiment, Hg (II) removal of 99.29% in 24 h was indeed obtained. CONCLUSIONS: Using Taguchi DOE, Hg (II) reduction (and hence its removal) using Ps. aeruginosa could be improved by 29.3%. SIGNIFICANCE AND IMPACT OF THE STUDY: Taguchi approach could be employed as an efficient and time-saving strategy for parameter optimization in bioremediation processes.

Microbial synthesis of semiconductor CdS nanoparticles, their characterization, and their use in the fabrication of an ideal diode.

Cadmium sulfide nanoparticles were synthesized intracellularly by a Schizosaccharomyces pombe strain when challenged with 1 mM cadmium in solution. The nanoparticles, a known semiconducting material, exhibited an absorbance maximum at 305 nm. X-ray scattering data showed that the nanoparticles had a Wurtzite (Cd(16)S(20))-type hexagonal lattice structure and most of the nanoparicles were in the size range of 1-1.5 nm. The nanoparticles were used in the fabrication of a heterojunction with poly (p-phenylenevinylene). The diode exhibited approximately 75 mA/cm(2) current at 10 V when forward biased and the breakdown occurred at approximately 15 V in the reverse biased mode. These characteristics are considered ideal for a diode.

Arsenic (III) oxidizing Microbacterium lacticum and its use in the treatment of arsenic contaminated groundwater.

AIMS: To develop a microbially-assisted process for the removal of arsenic from contaminated groundwater. METHODS AND RESULTS: A culture of Microbacterium lacticum oxidizing up to 50 mmol l(-1) arsenic (III) was isolated from municipal sewage by an enrichment culture technique. Using culture immobilized on brick pieces and packed in a glass column, complete oxidation of As (III) from groundwater could be quickly achieved at neutral pH and ambient temperature with methanol as substrate. The oxidized As species were removed from groundwater using three different methods: zero valent iron, activated charcoal and ferric chloride. CONCLUSIONS: The oxidation of groundwater As (III) by a M. lacticum-immobilized column, followed by its removal using activated carbon, could be an efficient method for the treatment of As (III)-contaminated groundwater. SIGNIFICANCE AND IMPACT OF THE STUDY: The study will be useful in developing a combined microbiological-chemical process for treating arsenic-contaminated groundwater.

Comparative studies on metal biosorption by two strains of Cladosporium cladosporioides.

Two strains of a fungus, Cladosporium cladosporioides 1 and C. cladosporioides 2 showed different metal biosorption properties. Strain 1 showed preferential sorption of gold and silver, while strain 2 could bind metals such as copper and cadmium in addition to gold and silver. Strain 1 had a cell-wall hexosamine content of 0.1%. X-ray photoelectron spectroscopy (XPS) and Fourier transform infra-red spectroscopy (FTIR) analyses indicated that nitrogen was not involved in metal biosorption by the strain. In strain 2 the cell-wall hexosamine content was 150 times that of strain 1. These results indicated that hexosamine was responsible for non-specific metal binding while cell-wall polymers other than hexosamines had a role in conferring selectivity in precious-metal binding.

Biodetoxification of silver-cyanide from electroplating industry wastewater.

A bacterial consortium capable of utilizing metal-cyanides as a source of nitrogen was used to develop a microbiological process for the detoxification of silver-cyanide from electroplating wastewater. When the treatment was carried out in a 27-l rotating biological contactor (R3C) in continuous mode, the system could achieve > 99.5% removal of 0.1 mmol l(-1) silver-cyanide (approximately 5 mg l(-1) cyanide and 10 mg l(-1) silver) in 10 h with sugarcane molasses (0.1 ml l(-1)) as carbon source. The silver ions set free during biodegradation were efficiently adsorbed by the bacterial biomass. The RBC-treated effluent was found to be safe for discharge into the environment, as confirmed by chemical analysis and fish bioassay studies.

Biosorption of lead, cadmium, and zinc by Citrobacter strain MCM B-181: characterization studies.

The biosorption process for removal of lead, cadmium, and zinc by Citrobacter strain MCM B-181, a laboratory isolate, was characterized. Effects of environmental factors and growth conditions on metal uptake capacity were studied. Pretreatment of biomass with chemical agents increased cadmium sorption efficiency; however, there was no significant enhancement in lead and zinc sorption capacity. Metal sorption by Citrobacter strain MCM B-181 was found to be influenced by the pH of the solution, initial metal concentration, biomass concentration, and type of growth medium. The metal sorption process was not affected by the age of the culture or change in temperature. Equilibrium metal sorption was found to fit the Langmuir adsorption model. Kinetic studies showed that metal uptake by Citrobacter strain MCM B-181 was a fast process, requiring <20 min to achieve >90% adsorption efficiency. The presence of cations reduced lead, zinc, and cadmium sorption to the extent of 11. 8%, 84.3%, and 33.4%, respectively. When biomass was exposed to multimetal solutions, metals were adsorbed in the order Co2+ < Ni2+ < Cd2+ < Cu2+ < Zn2+ < Pb2+. Among various anions tested, only phosphate and citrate were found to hamper metal sorption capacity of cells. Biosorbent beads prepared by immobilizing the Citrobacter biomass in polysulfone matrix exhibited high metal loading capacities. A new mathematical model used for batch kinetic studies was found to be highly useful in prediction of experimentally obtained metal concentration profiles as a function of time. Metal desorption studies indicated that Citrobacter beads could, in principle, be regenerated and reused in adsorption-desorption cycles. In an expanded scale trial, biosorbent beads were found to be useful in removal/recovery of metals such as lead from industrial wastewaters.

Comparative performance of pearl millet- and sorghum- based diets vs. wheat- and rice-based diets for trace metal bioavailability.

Pearl millet and sorghum offer a cheap source of energy compared to wheat and rice and are widely consumed by rural communities in many parts of the world. Due to the low consumption of vegetables and animal foods, millets also are the major suppliers of micronutrients especially for low-income groups. It is of prime importance to study how millets perform in terms of bioavailable contents of trace metals. Investigations were carried out using weanling mice which offer a model for the initial testing of bioavailability of trace metals before human trials. Four isocaloric diets differing only in the type of cereal, i.e. pearl millet, sorghum, wheat and rice, were prepared representing habitual dietary patterns observed by National Nutrition Monitoring Bureau (NNMB) of India. Mice were allocated randomly to 4 groups of 8 mice each, and housed individually in metal free metabolic cages. A fifth group of 8 mice fed a balanced synthetic diet served as control. All the groups were fed ad libitum. The absorption of zinc and iron averaged for 3 periods of 5 days each was significantly higher for the wheat and pearl millet group than for the other 2 experimental groups (p < 0.05), as were also the levels of liver zinc and iron. The weight gain was also highest (6.9 +/- 1.2 g) in the pearl millet group as compared to sorghum (1.58 +/- 0.59 g), wheat (1.66 +/- 1.27 g) and rice (-0.72 +/- 0.62 g) groups. The levels of liver copper were comparable in all the 5 groups. These results further confirm our earlier in vitro results indicating the superiority of pearl millet but not sorghum in bioavailability of zinc and iron.