Biodegradation of phenanthrene by piezotolerant Bacillus subtilis EB1 and genomic insights for bioremediation.

A marine strain B. subtilis EB1, isolated from Equator water, showed excellent degradation towards a wide range of hydrocarbons. Degradation studies revealed dense growth with 93 % and 83 % removal of phenanthrene within 72 h at 0.1 and 20 MPa, respectively. The identification of phenanthrene degradation metabolites by GC-MS combined with its whole genome analysis provided the pathway involved in the degradation process. Whole genome sequencing indicated a genome size of 3,983,989 bp with 4331 annotated genes. The genome provided the genetic compartments, which includes monooxygenase, dioxygenase, dehydrogenase, biosurfactant synthesis catabolic genes for the biodegradation of aromatic compounds. Detailed COG and KEGG pathway analysis confirmed the genes involved in the oxygenation reaction of hydrocarbons, piezotolerance, siderophores, chemotaxis and transporter systems which were specific to adaptation for survival in extreme marine habitat. The results of this study will be a key to design an optimal bioremediation strategy for oil contaminated extreme marine environment.

An in silico analysis of the impact of POLE mutations on cladribine docking.

OBJECTIVE: Polymerase ε exonuclease (POLE) is an enzyme involved in DNA replication and may be an attractive therapeutic target in various cancers. Here we sought to model the impact of specific POLE mutations on protein function. Due to the lack of a crystal structure, the tertiary structures of the wild type and four common mutants were modeled using I-Tasser server. MATERIALS AND METHODS: Molecular docking and dynamic simulation studies were performed, and the structure and function of the mutants analyzed through residue conservation analysis and protein folding energy changes. RESULTS: All mutants of POLE gene had favorable binding affinities compared with their wild type of counterpart. The P286R variant, but not the other variants, disrupted cladribine binding to the protein. Similarly, dynamics studies revealed instability of the P286R mutant, while V411L, L424V, and L424F appeared to favor cladribine binding. CONCLUSIONS: Since P286R is a hotspot mutation in endometrioid carcinomas, patients with this variant may not respond to cladribine. Population-based pharmacogenomics studies will be required to validate our results.

Genome sequence analysis of deep sea Aspergillus sydowii BOBA1 and effect of high pressure on biodegradation of spent engine oil.

A deep-sea fungus Aspergillus sydowii BOBA1 isolated from marine sediment at a depth of 3000 m was capable of degrading spent engine (SE) oil. The response of immobilized fungi towards degradation at elevated pressure was studied in customized high pressure reactors without any deviation in simulating in situ deep-sea conditions. The growth rate of A. sydowii BOBA1 in 0.1 MPa was significantly different from the growth at 10 MPa pressure. The degradation percentage reached 71.2 and 82.5% at atmospheric and high pressure conditions, respectively, within a retention period of 21 days. The complete genome sequence of BOBA1 consists of 38,795,664 bp in size, comprises 2582 scaffolds with predicted total coding genes of 18,932. A total of 16,247 genes were assigned with known functions and many families found to have a potential role in PAHs and xenobiotic compound metabolism. Functional genes controlling the pathways of hydrocarbon and xenobiotics compound degrading enzymes such as dioxygenase, decarboxylase, hydrolase, reductase and peroxidase were identified. The spectroscopic and genomic analysis revealed the presence of combined catechol, gentisate and phthalic acid degradation pathway. These results of degradation and genomic studies evidenced that this deep-sea fungus could be employed to develop an eco-friendly mycoremediation technology to combat the oil polluted marine environment. This study expands our knowledge on piezophilic fungi and offer insight into possibilities about the fate of SE oil in deep-sea.

Biodegradation of polystyrene by deep-sea Bacillus paralicheniformis G1 and genome analysis.

Polystyrene (PS) films were subjected to in vitro biodegradation by Bacillus paralicheniformis G1 (MN720578) isolated from 3538 m depth sediments of the Arabian Sea. The growth of the isolate was most favourable at pH 7.5, 30 °C and 4% salinity. A series of batch experiments were conducted to investigate the degradation of PS films up to 60 days. The results of this study indicated that the strain degraded 34% of PS film within 60 days of incubation. The complete genome sequence consists of 4,281,959 bp with 45.88% GC content and encodes 4213 protein coding genes. A high number of genes encoding monooxygenase, dioxygenase, peroxidase, esterase and hydrolase involved in the degradation of synthetic polymers were identified. Also genes associated with flagellum dependent motility, chemotaxis, biofilm formation and siderophores biosynthesis were identified in this deep-sea strain G1. This study suggests that B. paralicheniformis G1 could be a potential species for degradation of PS and its genome analysis provides insight into the molecular basis of biodegradation.

Photocatalytic activity of SnO2/Fe3O4 nanocomposites and the toxicity assessment of Vigna radiata, Artemia salina and Danio rerio in the photodegraded solution.

The study was undertaken to design SnO2/Fe3O4 nanocomposite by sonochemical method and to assess the photodegradation of organic dye. Textural, composition and structural features of the bare SnO2 and SnO2/Fe3O4 samples were characterized using scanning electron microscope (SEM), energy dispersive X-ray (EDX), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR). The X-ray diffraction of as-synthesized SnO2/Fe3O4 nanocomposites confirms the presence of tetragonal and cubic structure. The results disclose that the incorporation of Fe3O4 in SnO2 decrease the crystallite size and increase the surface area compared with bare SnO2 nanoparticle. The as-prepared photocatalyst shows higher efficiency than the bare SnO2 under sunlight irradiation. Vigna radiata seeds (VR), Artemia salina (AS) and Zebra fish (Danio rerio (DR) were used to check the toxicity level of the treated and untreated Rhodamine B (RhB) dye solution. These models displayed good consistency for examining the harmfulness of the solutions. The results suggests SnO2/Fe3O4 nanocomposite exhibited a good efficacy in the dye wastewater treatment. Further, the degradation efficiency was confirmed by the toxicity examination.

Publisher Correction: Genome analysis of deep sea piezotolerant Nesiotobacter exalbescens COD22 and toluene degradation studies under high pressure condition.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Genome analysis of deep sea piezotolerant Nesiotobacter exalbescens COD22 and toluene degradation studies under high pressure condition.

A marine isolate, Nesiotobacter exalbescens COD22, isolated from deep sea sediment (2100 m depth) was capable of degrading aromatic hydrocarbons. The Nesiotobacter sp. grew well in the presence of toluene at 0.1 MPa and 10 MPa at a rate of 0.24 h-1 and 0.12 h-1, respectively, in custom designed high pressure reactors. Percentage of hydrocarbon degradation was found to be 87.5% at ambient pressure and it reached 92% under high pressure condition within a short retention period of 72 h. The biodegradation of hydrocarbon was confirmed by the accumulation of dicarboxylic acid, benzoic acid, benzyl alcohol and benzaldehyde which are key intermediates in toluene catabolism. The complete genome sequence consists of 4,285,402 bp with 53% GC content and contained 3969 total coding genes. The complete genome analysis revealed unique adaptation and degradation capabilities for complex aromatic compounds, biosurfactant synthesis to facilitate hydrocarbon emulsification, advanced mechanisms for chemotaxis and presence of well developed flagellar assembly. The genomic data corroborated with the results of hydrocarbon biodegradation at high pressure growth conditions and confirmed the biotechnological potential of Nesiotobacter sp. towards bioremediation of hydrocarbon polluted deep sea environments.

Biodegradation of crude oil using self-immobilized hydrocarbonoclastic deep sea bacterial consortium.

Hydrocarbonoclastic bacterial consortium that utilizes crude oil as carbon and energy source was isolated from marine sediment collected at a depth of 2100 m. Molecular characterization by 16S rRNA gene sequences confirmed that these isolates as Oceanobacillus sp., Nesiotobacter sp., Ruegeria sp., Photobacterium sp., Enterobacter sp., Haererehalobacter sp., Exiguobacterium sp., Acinetobacter sp. and Pseudoalteromonas sp. Self-immobilized consortium degraded more than 85% of total hydrocarbons after 10 days of incubation with 1% (v/v) of crude oil and 0.05% (v/v) of Tween 80 (non-ionic surfactant) at 28 ±â€¯2 °C. The addition of nitrogen and phosphorus sources separately i.e. 0.1% (v/v) of CO (NH2)2 or K2HPO4 enhanced the hydrocarbon utilization percentage. The pathways of microbial degradation of hydrocarbons were confirmed by FTIR, GC-MS, 1H and 13C NMR spectroscopy analyses. These results demonstrated a novel approach using hydrocarbonoclastic self-immobilized deep sea bacterial consortium for eco-friendly bioremediation.

Studies on the antifungal and serotonin receptor agonist activities of the secondary metabolites from piezotolerant deep-sea fungus Ascotricha sp.

The potent antifungal agent sesquiterpenes and serotonin 5-HT2C agonist ascotricin were produced by a newly isolated deep-sea fungus Ascotricha sp. This fungus was isolated from deep-sea sediment collected at a depth of 1235 m and characterized. Piezotolerance was successfully tested under high pressure-low temperature (100 bar pressure and 20ºC) microbial cultivation system. Production of secondary metabolites was enhanced at optimized culture conditions. The in-vivo antifungal activity of sesquiterpenes was studied using the Caenorhabditis elegans - Candida albicans model system. The sesquiterpenes affected the virulence of C. albicans and prolonged the life of the host C. elegans. These findings suggest that sesquiterpenes are attractive antifungal drug candidates. The 5-HT2C receptor agonist is a potential target for the development of drugs for a range of central nervous system disorders. The interaction of 5-HT2C agonist ascotricin with the receptor was studied through bioinformatic analysis. The in silico molecular docking and molecular dynamic simulation studies demonstrated that they fit into the serotonin 5-HT2C active site and the crucial amino acid residues involved in the interactions were identified. To our knowledge, this is first report of in vivo antifungal analysis of sesquiterpenes and in silico studies of serotonin 5-HT2C receptor-ascotricin complex.

Isatin based macrocyclic Schiff base ligands as novel candidates for antimicrobial and antioxidant drug design: In vitro DNA binding and biological studies.

In the present work, five macrocyclic compounds, C18H12N2O4 (1), C38H24N8O6 (1a), C38H24N8O4S2 (1b), C40H32N8O4 (2a) and C48H32N8O4 (2b) have been synthesized and thoroughly characterized by elemental analysis, FT-IR, 1D & 2D NMR and electron spray ionization mass spectral analysis. The DNA binding ability of these compounds were investigated in vitro by UV-Visible, fluorescence, circular dichroism (CD) spectroscopy and viscosity measurements. The results indicate that these compounds possess strong DNA binding affinity via intercalation, while the order of binding strength followed the trend 2b (1.52 ±â€¯0.06 × 105 M-1) > 2a (1.12 ±â€¯0.11 × 105 M-1) > 1b (1.05 ±â€¯0.04 × 105 M-1) > 1a (0.97 ±â€¯0.14 × 104 M-1) > 1 (0.75 ±â€¯0.21 × 104 M-1). The radical scavenging potencies of the compounds were explored by employing DPPH, OH and NO assays, in which 1a exhibited highest inhibitory effect on the radicals (IC50 = 23.59 µM (DPPH), 26.14 µM (OH), 28.41 µM (NO)). The in vitro antibacterial studies showed that these compounds have the potential to arrest the growth of bacteria, among which, 1a was found to be vulnerable against the bacterial stains. In addition, in silico molecular docking stimulations were also performed to position these compounds into the active sites of bacterial membrane proteins. The results of in vitro and in silico investigations reveal that the compounds apprehend the bacterial growth significantly. The data obtained from this piece of work would be helpful to design antibacterial drugs incorporating isatin based macrocyclic frameworks.

Biodegradation of complex hydrocarbons in spent engine oil by novel bacterial consortium isolated from deep sea sediment.

Complex hydrocarbon and aromatic compounds degrading marine bacterial strains were isolated from deep sea sediment after enrichment on spent engine (SE) oil. Phenotypic characterization and phylogenetic analysis of 16S rRNA gene sequences showed the isolates were related to members of the Pseudoalteromonas sp., Ruegeria sp., Exiguobacterium sp. and Acinetobacter sp. Biodegradation using 1% (v/v) SE oil with individual and mixed strains showed the efficacy of SE oil utilization within a short retention time. The addition of non-ionic surfactant 0.05% (v/v) Tween 80 as emulsifying agent enhanced the solubility of hydrocarbons and renders them more accessible for biodegradation. The degradation of several compounds and the metabolites formed during the microbial oxidation process were confirmed by Fourier transform infrared spectroscopy and Gas chromatography-mass spectrometry analyses. The potential of this consortium to biodegrade SE oil with and without emulsifying agent provides possible application in bioremediation of oil contaminated marine environment.

Agriculture and malnutrition in India.

BACKGROUND: Despite the high and relatively stable overall growth of the economy, India's agriculture sector is underperforming and a vast section of the population remains undernourished. OBJECTIVE: To explore the possible interplay between agricultural performance and malnutrition indicators to see whether states that perform better in agriculture record better nutritional outcomes. METHODS: Correlation analysis and a simple linear regression model were used to study the relationship between agricultural performance and malnutrition among children under 5 years of age and adults from 15 to 49 years of age at 20 major states using data from the National Family Health Survey-3 for the year 2005/06 and the national accounts. RESULTS: Indicators of the level of agricultural performance or income have a strong and significant negative relationship with indices of undernutrition among adults and children, a result suggesting that improvement of agricultural productivity can be a powerful tool to reduce undernutrition across the vast majority of the population. In addition to agriculture, access to sanitation facilities and women's literacy were also found to be strong factors affecting malnutrition. Access to healthcare for women and child-care practices, in particular breastfeeding within 1 hour after birth, are other important determinants of malnutrition among adults and children. CONCLUSIONS: Malnutrition is a multidimensional problem that requires multisectoral interventions. The findings show that improving agricultural performance can have a positive impact on nutritional outcomes. However, improvements in agriculture alone cannot be effective in combating malnutrition if several other mediating factors are not in place. Interventions to improve education, health, sanitation and household infrastructure, and care and feeding practices are critical. Innovative strategies that integrate agriculture and nutrition programs stand a better chance of combating the malnutrition problem.

Effect of Ionic Strength on Porphyrin Drugs Interaction with Quadruplex DNA Formed by the Promoter Region of C-myc and Bcl2 Oncogenes.

C-myc and Bcl2 are well characterized oncogenes that are capable of forming G-quadruplex structures. Promoter regions of C-myc and Bcl2 forming G-quadruplex structures are chemically synthesized and G-quadruplex structure is formed in presence of 100 mM potassium ion. Three different porphyrin drugs, namely TMPyP2, TMPyP3, and TMPyP4 are allowed to interact with quadruplex DNA complex and the site and nature of interaction are studied. Drug interactions with quadruplex DNA were carried out in different potassium ionic strengths using fluorescence spectroscopy. It is found that fluorescence hypochromicity decreases with an increase in ionic strength in the case of TMPyP4, TMPyP3, and TMPyP2. Fluorescence titration studies and Job plots indicate that four molecules of TMPyP4, two molecules of TMPyP3 and TMPyP2 are interacting with one molecule of quadruplex DNA.

In situ immobilization of acid protease on mesoporous activated carbon packed column for the production of protein hydrolysates.

The mesoporous activated carbon (MAC) was used as a support material for in situ immobilization of acid protease (AP). The optimum temperature for the activities of both free and immobilized AP was found to be 50 degrees C. The catalytic efficiency of AP-MAC system has significantly been maintained for more than ten consecutive reaction cycles. The functional groups and surface morphology of the AP, MAC and AP-MAC were observed by Fourier transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM). The production of protein hydrolysates was carried out from bovine serum albumin (BSA) using AP-MAC packed column and its properties were studied.

Nanoemulsion drug delivery by ketene based polyester synthesized using electron rich carbon/silica composite surface.

A new carrier matrix for nanoemulsion drug delivery was synthesized from glycine as the raw material, using mesoporous/microporous electron rich carbon-silica composite surface (MAC(800)). MAC(800) was prepared from rice husk in two-stage carbonization. The surface area, pore volume, and pore size distribution of MAC(800) were measured, using nitrogen adsorption isotherms at 77K. The unpaired electron density of MAC(800) was measured in electron spin resonance spectroscopy (ESR), using TEMPOL (4-hydroxy-2,2,6,6-tetramethyl piperidine-1-oxyl) as the reference spin probe. Glycine was converted into ketene at the surface of MAC(800), which further underwent radical polymerization to form a low molecular weight ketene polymer (LMKP) of ester structure. The structure and the properties of LMKP were confirmed through (13)C, (1)H and DEPT nuclear magnetic resonance (NMR) spectroscopy, attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) and size exclusion chromatography (SEC). The two hydrophilic drugs namely ciprofloxacin hydrochloride (CPH) and gentamicin sulphate (GS) were chosen for the nanoemulsion preparation and characterization. They were characterized for morphology, interaction of drugs with the polymer and their crystallinity, using HR-TEM, DSC and XRD, respectively. The encapsulation efficiency of the LMKP towards the drugs ciprofloxacin hydrochloride and gentamicin sulphate were 26% and 12%, respectively. The dissolution studies of the nanoemulsion were carried out for the pH 6.5, 7.4 and 8.0. The cytocompatibility studies were done for LMKP as well as nanoemulsion using Hep2 epithelial cells.

A novel amphiphilic nano hydrogel using ketene based polyester with polyacrylamide for controlled drug delivery system.

A ketene based Low molecular weight polymer (LMKP) having ester functional group was prepared using glycine through surface initiated anionic polymerization. NMR, ATR-FTIR & SEC were used to characterize the LMKP. The LMKP and acrylamide (AAm) were co-polymerised in methyl ethyl ketone to yield semi-IPN nanohydrogels (NHG). Benzoyl peroxide (BPO) was used as an initiator and N,N-methylene bisacrylamide (MBA) as crosslinking agent. Formation of NHG was confirmed through frequency shift in LMKP and poly acrylamide (PAAm) in FTIR spectroscopy. Photon correlation spectroscopy reveals that the sizes of the NHG were in the range of 140-225 nm and Transmission Electron Micrograph (TEM) also confirms the nano dimension of NHG. Biocompatibility of the NHG was confirmed through the cytotoxicity analysis. The swelling and diffusion behaviour of NHG, prepared under various formulations, were evaluated. The swelling pattern of NHG was studied at different pH conditions. The drug delivery capacity of NHG was investigated using ciprofloxacin as a model drug. The drug release kinetics of NHG suggested their anomalous (non-fickian) behaviour.

Effects of nonionic surfactant on hydrolysis and fermentation of protein rich tannery solid waste.

The untanned proteinaceous tannery solid waste, the animal fleshing (ANFL), was used as substrate in the treatment process (hydrolysis and fermentation) involving Synergistes sp. The nonionic surfactant (Tween 80) was evaluated for its ability to influence on microbial growth and enzyme activity in the hydrolysis and fermentation of ANFL. The addition of Tween 80 in the process significantly increased the activities of hydrolytic and fermentative enzymes like protease (338-360 Um l(-1)) and deaminase (187-206 Um l(-1)) compared to that of control (protease 195-220 Um l(-1) and deaminase 70-83 Um l(-1)). The total viable bacterial count was increased more than twofold, compared to the control in the presence of 0.15% Tween 80. The ANFL fermentation and formation of other metabolites were evidenced by Gas Chromatography and Mass Spectroscopy (GC-MS), Proton Nuclear Magnetic Resonance spectroscopy ((1)H NMR) and Fourier transform infra red spectroscopy (FT-IR). The breakdown of fibrillar proteins in ANFL was confirmed by the scanning electron microscopy (SEM) and the transmission electron microscopy (TEM).

Production of alkaline protease by Pseudomonas aeruginosa using proteinaceous solid waste generated from leather manufacturing industries.

Animal fleshing (ANFL), the major proteinaceous solid waste discharged from leather manufacturing industries was used as the substrate for the production of alkaline protease by Pseudomonas aeruginosa. The strain isolated from the tannery wastewater was selected for its ability to produce protease of activity in the range 1160-1175 U ml(-1). The selective removal of non-fibrillar proteins such as albumin and globulin from ANFL by the protease enzyme during the progress of hydrolysis was confirmed using scanning electron microscopy (SEM). The breakdown of ANFL was also confirmed from the amino acid release into the fermentation medium by P. aeruginosa using high performance liquid chromatography (HPLC).

Acidogenic fermentation of proteinaceous solid waste and characterization of different bioconversion stages and extracellular products.

The purpose of this study was to investigate hydrolysis of animal fleshing (ANFL), a predominant tannery solid waste and to characterize the acetogenic fermentation products of anaerobic digestion. The acidogenic digestibility of the tannery solid wastes were evaluated up to 120 h using batch anaerobic digestion tests performed under mesophilic condition at 37 degrees C. The degradation of ANFL starts with non-fibrillar proteins and proceeds with fibrillar proteins. The release of aliphatic amino acid in the early stages of hydrolysis (24 h) and followed by aromatic amino acids (24-72 h) were evidenced by HPLC analysis. The maximum production of propionic and valeric acid were observed in 72 h followed by rapid increase in acetic acid in 96 h using GC-MS. Breakdown of ANFL and formations of other metabolites were evidenced by FT-IR and (1)H-NMR spectroscopy.

Oxidative destabilization of dissolved organics and E. coli in domestic wastewater through immobilized cell reactor system.

Domestic wastewater contains a considerable amount of pathogenic organisms besides non-biodegradable organics. The conventional technologies followed for the treatment of domestic wastewater are less efficient in removing pathogenic organisms despite substantial removal of dissolved organics. The focal theme of the present investigation was to use a chemo-autotrophic activated carbon oxidation (CAACO) system, an immobilized cell reactor using chemoautotrophs (Bacillus sp.) for the treatment of domestic wastewater. The oxidation of organics and Escherichia coli in wastewater is controlled by the parameters space time, O(2)/COD, bed height and cod loading. The scheme comprised of anaerobic treatment, sand filtration and CAACO treatment removed BOD. COD, Total organic carbon (TOC), dissolved protein, total Kjeldhal nitrogen (TKN) and bacterial count (most probable number (MPN)) by 81%, 92%, 84%, 94%, 93% and 99.9997%, respectively. The low concentration of E. coli in the CAACO-treated wastewater was completely eliminated through UV irradiation in 3 min at 254 nm.