Genomic profiling and characteristics of a C1 degrading heterotrophic fresh-water bacterium Paracoccus sp. strain DMF.

Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation studies. Here we report, the complete genome analysis of Paracoccus sp. strain DMF (P.

Insight into the metabolic pathways of Paracoccus sp. strain DMF: a non-marine halotolerant methylotroph capable of degrading aliphatic amines/amides.

Paracoccus sp. strain DMF (P. DMF from henceforth) is a gram-negative heterotroph known to tolerate and utilize high concentrations of N,N-dimethylformamide (DMF).

Biotransformation of 2,4,6-trinitrotoluene by Diaphorobacter sp. strain DS2.

Diaphorobacter strain DS2 degrades 3-nitrotoluene and 2-nitrotoluene via ring oxidation with 3-nitrotoluene dioxygenase (3NTDO). In the current study, we hypothesized that 3NTDO might also be involved in the degradation of 2,4,6-trinitrotoluene (TNT), a major nitroaromatic explosive contaminant in soil and groundwater. Strain DS2 transforms TNT as a sole carbon and nitrogen source when grown on it.

A spectrophotometric trimethylamine monooxygenase assay.

Trimethylamine monooxygenase (Tmm, EC-1.14.13.

Effect of the Standardized ZnO/ZnO-GO Filter Element Substrate driven Advanced Oxidation Process on Textile Industry Effluent Stream: Detailed Analysis of Photocatalytic Degradation Kinetics.

A simple process of synthesizing coated filter element substrates (FES) containing zinc oxide (ZnO) nanorods and ZnO graphene-oxide nanocomposite for a pilot-scale industrial dye-effluent treatment plant is proposed. This work reports a detailed analysis of the photocatalysis mechanism on real industrial effluent streams containing a mixture of dyes. The analysis is very relevant for conducting advanced oxidation process-assisted effluent remediation at a field-level treatment operation.

Transformation of 2, 4, 6-trinitrotoluene by Stenotrophomonas strain SG1 under aerobic and anaerobic conditions.

TNT, or 2,4,6-trinitrotoluene, is a common explosive that can contaminate soil and groundwater in production sites, military training areas, and disposal locations. The compound is highly toxic; therefore, there is an urgent need to rehabilitate the impacted environments. Harnessing the microbial ability to biodegrade TNT into environmentally harmless compound(s) is one approach to remediating contaminated sites.

Inhibition effect of 2,4,6-trinitrotoluene (TNT) on RDX degradation by rhodococcus strains isolated from contaminated soil and water.

2,4,6-trinitrotoluene (TNT) is a highly toxic explosive that contaminates soil and water and may interfere with the degradation of co-occurring compounds, such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). We proposed that TNT may influence RDX-degrading bacteria via either general toxicity or a specific effect on the |RDX degradation mechanisms. Thus, we examined the impact of TNT on RDX degradation by Rhodococcus strains YH1, T7, and YY1, which were isolated from an explosives-polluted environment.

Integrated DEP Assisted Detection of PCR Products With Metallic Nanoparticle Labels Through Impedance Spectroscopy.

Electrochemical impedance spectroscopy (EIS) is gaining immense popularity in the current times due to the ease of integration with microelectronics. Keeping this aspect in mind, various detection schemes have been developed to make impedance detection of nucleic acids more specific. In this context, the current work makes a strong case for specific DNA detection through EIS using nanoparticle labeling approach and also an added selectivity step through the use of dielectrophoresis (DEP), which enhances the detection sensitivity and specificity to match the detection capability of quantitative polymerase chain reaction (qPCR) in real-time context as compared to the individually amplified DNA (Liu et al.

Comparison of CryoEM and X-ray structures of dimethylformamidase.

Dimethylformamidase (DMFase) catalyzes the hydrolysis of dimethylformamide, an industrial solvent, introduced into the environment by humans. Recently, we determined the structures of dimethylformamidase by electron cryo microscopy and X-ray crystallography revealing a tetrameric enzyme with a mononuclear iron at the active site. DMFase from Paracoccus sp.

A 2-Tyr-1-carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase.

N,N-dimethyl formamide (DMF) is an extensively used organic solvent but is also a potent pollutant. Certain bacterial species from genera such as Paracoccus, Pseudomonas, and Alcaligenes have evolved to use DMF as a sole carbon and nitrogen source for growth via degradation by a dimethylformamidase (DMFase). We show that DMFase from Paracoccus sp.

Synchronized Electromechanical Shock Wave-Induced Bacterial Transformation.

We report a simple device that generates synchronized mechanical and electrical pressure waves for carrying out bacterial transformation. The mechanical pressure waves are produced by igniting a confined nanoenergetic composite material that provides ultrahigh pressure. Further, this device has an arrangement through which a synchronized electric field (of a time-varying nature) is initiated at a delay of ≈85 μs at the full width half-maxima point of the pressure pulse.

Crosslinking of agar by diisocyanates.

In the present study, crosslinking of agar using diisocyanate (DI) was demonstrated to limit the high water absorption property of agar. In addition, the efficacy of aromatic diisocyanate, DDI (4, 4 diphenyl diisocyanate) and aliphatic diisocyanate, HDI (1, 6 hexamethylene diisocyanate) on crosslinked agar properties was compared. The water uptake was successfully reduced by crosslinking and its minimum values observed for DDI and HDI crosslinked agar was 33.

Structural and functional studies of ferredoxin and oxygenase components of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2.

3-nitrotoluene dioxygenase (3NTDO) from Diaphorobacter sp. strain DS2 catalyses the conversion of 3-nitrotoluene (3NT) into a mixture of 3- and 4-methylcatechols with release of nitrite. We report here, X-ray crystal structures of oxygenase and ferredoxin components of 3NTDO at 2.

Impact of surface roughness on Dielectrophoretically assisted concentration of microorganisms over PCB based platforms.

This article presents a PCB based microfluidic platform for performing a dielectrophoretic capture of live microorganisms over inter-digitated electrodes buried under layers of different surface roughness values. Although dielectrophoresis has been extensively studied earlier over silicon and polymer surfaces with printed electrodes the issue of surface roughness particularly in case of buried electrodes has been seldom investigated. We have addressed this issue through a layer of spin coated PDMS (of various surface roughness) that is used to cover the printed electrodes over a printed circuit board.

Effect of methylene group insertions on the structural rigidity of Aib containing helices.

Nonprotein amino acids are being extensively used in the design of synthetic peptides to create new structure mimics. In this study we report the effect of methylene group insertions in a heptapeptide Boc-Ala1-Leu2-Aib3-Xxx4-Ala5-Leu6-Aib7-OMe which nicely folds into a mixed 310 -/α-helical structure when Xxx= Ala. Analogs of this peptide have been made and studied by replacing central Xxx4 residue with Glycine (α-residue), β-Alanine (β-Αla), γ-aminobutyric acid (Gaba), and ε-aminocaproic acid (ε-Aca).

Structures, stability and hydrogen bonding in inositol conformers.

Various ab initio calculations using the density-functional (DFT), the second order Möller-Plesset perturbation (MP2) and self-consistent reaction field (SCRF) theories were performed on thirteen theoretically possible inositol stereoisomers. Gas phase calculations reveal that the myo- and neo-isomers of inositol (bearing one and two axial hydroxyl groups, respectively) are marginally more stable (by 0.5 kcal mol(-1)) than the all equatorially substituted scyllo-inositol.

Structures and conformation of a benzo-12-crown-4 containing dipeptide.

Crystal structures of the dipeptide Boc-12-Crown-4-L-DOPA-Gly-OMe (chi) and Boc-12-Crown-4-D/L-DOPA-Gly-OMe (rac) were solved by single crystal X-ray diffraction. Analysis of the packing differences in the crystal reveals that the presence of a water molecule in chi enables intermolecular contacts with the solvent that result in a different conformation of the dipeptide backbone itself. An uncommon N-H…N interaction stabilizes the peptide in its solid state.

Expression, purification and substrate specificities of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2.

3-Nitotoluene dioxygenase (3-NTDO) is the first enzyme in the degradation pathway of 3-nitrotoluene (3-NT) by Diaphorobacter sp. strain DS2. The complete gene sequences of 3-NTDO were PCR amplified from genomic DNA of Diaphorobacter sp.

Integrated sorting, concentration and real time PCR based detection system for sensitive detection of microorganisms.

The extremely low limit of detection (LOD) posed by global food and water safety standards necessitates the need to perform a rapid process of integrated detection with high specificity, sensitivity and repeatability. The work reported in this article shows a microchip platform which carries out an ensemble of protocols which are otherwise carried in a molecular biology laboratory to achieve the global safety standards. The various steps in the microchip include pre-concentration of specific microorganisms from samples and a highly specific real time molecular identification utilizing a q-PCR process.

3-Nitrotoluene dioxygenase from Diaphorobacter sp. strains: cloning, sequencing and evolutionary studies.

The first step in the degradation of 3-nitrotoluene by Diaphorobacter sp. strain DS2 is the dihydroxylation of the benzene ring with the concomitant removal of nitro group. This is catalyzed by a dioxygenase enzyme system.

Biomineralization of 3-nitrotoluene by Diaphorobacter species.

Three bacterial strains utilizing 3-nitrotoluene (3-NT) as a sole source of carbon, nitrogen and energy were isolated from an industrial wastewater treatment plant. Biochemical tests and 16S rDNA sequence analysis revealed that the isolated strains belonged to Diaphorobacter sp. Detailed studies were carried out with Diaphorobacter sp.

Excited state relaxation dynamics of model green fluorescent protein chromophore analogs: evidence for cis-trans isomerism.

Two green fluorescent protein (GFP) chromophore analogs (4Z)-4-(N,N-dimethylaminobenzylidene)-1-methyl-2-phenyl-1,4-dihydro-5H-imidazolin-5-one (DMPI) and (4Z)-4-(N,N-diphenylaminobenzylidene)-1-methyl-2-phenyl-1,4-dihydro-5H-imidazolin-5-one (DPMPI) were investigated using femtosecond fluorescence up-conversion spectroscopy and quantum chemical calculations with the results being substantiated by HPLC and NMR measurements. The femtosecond fluorescence transients are found to be biexponential in nature and the time constants exhibit a significant dependence on solvent viscosity and polarity. A multicoordinate relaxation mechanism is proposed for the excited state relaxation behavior of the model GFP analogs.

Biomineralization of N,N-dimethylformamide by Paracoccus sp. strain DMF.

N,N-dimethylformamide (DMF) is a man-made compound that is widely used as a solvent for the synthesis of various organic compounds. In this study, a bacterial strain Paracoccus sp. DMF capable of using DMF as the sole carbon, nitrogen and energy source, was isolated from an enrichment culture developed using activated sludge from domestic waste water treatment unit as the source inoculum.

Mineralization of 4-aminobenzenesulfonate (4-ABS) by Agrobacterium sp. strain PNS-1.

A bacterial strain, PNS-1, isolated from activated sludge, could utilize sulphanilic acid (4-ABS) as the sole organic carbon and energy source under aerobic conditions. Determination and comparison of 16S r DNA sequences showed that the strain PNS-1 is closely related to the species of Agrobacterium genus. Growth on 4-ABS was accompanied with ammonia and sulfate release.

Truncated thioredoxin (Trx80) exerts unique mitogenic cytokine effects via a mechanism independent of thiol oxido-reductase activity.

Recently we discovered that a naturally occurring C-terminally truncated thioredoxin (Trx80) is a potent mitogenic cytokine stimulating IL-12 production from CD40(+) monocytes. To further characterise Trx80 we have engineered cysteine to serine mutants of Trx80 corresponding to the active site cysteines of Trx (Trx80SGPS) and to the structural cysteine at position 72 (Trx80C72S). Trx80SGPS and Trx80C72S retained the cell stimulatory activity of Trx80 and increased peripheral blood mononuclear cell (PBMC) proliferation three- to five-fold in vitro (P<0.