Microbial community in packed bed bioreactor involved in nitrate remediation from low level radioactive waste.

Nitrate is the second largest contaminant of agriculture soil after pesticides. It also is a major pollutant from nuclear and metallurgical operations. Conventional methods for nitrate removal suffers from high cost and complexity leaving bioremediation as a viable alternative strategy. A pilot plant of 2.5 m(3)/day capacity has been functioning since 2005 based on microbial consortia treating actual effluent from nuclear power plant having pH of 7-8.5 (optimum) with N:C ratio of 1:1.7. The maximum biodegradable nitrate concentration of 3000 ppm could be reduced to below permissible limit (44.2 ppm) within 24 h in presence of sodium acetate as carbon source. Culture independent analysis (16S rDNA based) revealed clones having closest identity with uncultured bacterium, Pseudomonas stutzeri and Azoarcus sp. The existence of dissimilatory pathway of nitrate reduction in the community DNA is indicated by presence of nirS and nirK gene. Though the microbial mass was developed using municipal sewage, absence of Mycobacterium sp was confirmed using PCR. The understanding of the molecular identification of the consortium would help in developing the preservation strategy of the microbial mass for replication and perpetuation of the system.

Presence of a human Hyaluronan binding protein 1 (HABP1) pseudogene-like sequence in Methanosarcina barkeri suggests its linkage in evolution.

The gene encoding Hyaluronan binding protein 1 (HABP1) and its homologs have been reported across eukaryotes, from yeast to human. We have reported the presence of processed pseudogenes in several human chromosomes, along with the location of the HABP1 gene on chromosome 17p12-p13. In this study, we report not only the presence of HABP1 pseudogene in other animal species, but also the presence of a homologous sequence in Methanosarcina barkeri, an ancient life form. This sequence has 44.8% homology to the human HABP1 cDNA and 45.3% homology with the HABP1 pseudogene in human chromosome 21. This sequence has a high G + C content (57%), characteristic of archaea, a family to which M. barkeri belongs. The presence of this HABP1 cDNA like fragment in M. barkeri might enable us to shed light on the evolution of the HABPl gene and whether it was present in a common ancestral organism before the lineages separated.

Vitamin C and vitamin E protect the rat testes from cadmium-induced reactive oxygen species.

Cadmium is an environmental and industrial pollutant that affects the male reproductive system of humans and animals. However, the mechanism of its adverse effect on Leydig cell steroidogenesis remains unknown. The present study points to the possible involvement of oxidative stress in the suppression of steroidogenesis. Cadmium administration caused an increase in reactive oxygen species (ROS) by elevating testicular malondialdehyde (MDA) and decreasing the activities of testicular antioxidant enzymes such as glutathione peroxidase and superoxide dismutase. The mRNA of Steroid Acute Regulatory (StAR) protein was substantially reduced. The activities of testicular delta5-3beta and 17-beta-hydroxysteroid dehydrogenases (HSD) as well as serum testosterone level were also lowered, suggesting that cadmium-induced ROS inhibit testicular steroidogenesis. Supplementation with vitamin C (VC) and or vitamin E (VE) reduced testicular ROS and restored normal testicular function in Cd-exposed rats. We conclude that VC and VE prevent oxidative stress and play vital roles in co-regulating StAR gene expression and steroid production in cadmium-exposed rats.

Draft Genome Sequence of Ammonia-Producing Acinetobacter sp. Strain MCC2139 from Dairy Effluent.

We report the draft genome sequence of an ammonia-producing, esculin-hydrolyzing, catalase-positive, gram-negative bacterium, Acinetobacter sp. strain MCC2139. This bacterium, isolated from dairy sludge and with optimum growth at 37°C, has a genome size of 2,967,280 bp with a G+C content of 42.3%.

Draft Genome Sequence of the Nitrate- and Phosphate-Accumulating Bacillus sp. Strain MCC0008.

Here, we report the draft genome sequence of the nitrate- and phosphate-accumulating Bacillus sp. strain MCC0008, isolated from a consortium enriched from municipal sewage in nitrate broth (HiMedia M439). The total size of the genome is 5,609,456 bp, with a G+C content of 35.1%.

Draft Genome Sequence of Ammonia-Producing Aeromonas sp. MDS8 Strain MCC2167 from Sludge of a Dairy Effluent Treatment Plant.

The draft genome sequence of an amylase-, protease-, lipase-, oxidase-, and catalase-producing Gram-negative bacillus (Aeromonas sp. MDS8 strain MCC2167) with the ability to produce ammonia during 16 h of growth at 37°C, isolated from dairy sludge, with a size of 4,841,753 bp and a G+C content of 63.1%, is reported here.

Draft Genome Sequence of a Phosphate-Accumulating Bacillus sp., WBUNB004.

The draft genome sequence of a nitrate- and phosphate-removing, Gram-positive Bacillus sp. with optimum growth at 37°C and pH 7 in nitrate broth (HiMedia M439) isolated from rhizosphere of a water lily, with a genome size of 5,465,157 bp and a G+C content of 35.0%, is reported here.

Draft Genome Sequence of a Nitrate- and Phosphate-Removing Bacillus sp., WBUNB009.

The draft genome sequence (5,868,741 bp) of a nitrate- and phosphate-removing Bacillus sp., WBUNB009, isolated from a raw sewage canal in nitrate broth (Himedia M439) with a G+C content of 34.9% is reported. It removes 60.23% nitrate and 96% phosphate within 16 h at 37°C.

Analysis of Delta-Notch interaction by molecular modeling and molecular dynamic simulation studies.

Notch is a single-pass transmembrane receptor protein. Delta (member of the DSL protein family), a Notch ligand, is also single-pass transmembrane protein that can interact with Notch to form the Delta-Notch complex. It has been demonstrated that of the 36 Epidermal Growth Factor (EGF) repeats of Notch, 11th and 12th are sufficient to mediate interactions with Delta. Crystal structure of mammalian Notch1 extracellular ligand binding domain shows the presence of 11th and 12th EGF-like repeats. Here a portion of the Drosophila Delta protein, known to interact with Notch extracellular domain, has been modeled using homology modeling. The structure of the Delta-Notch complex was subsequently modeled by protein-docking method using GRAMM. Molecular dynamic simulations of the modeled structures were performed. The probable structures for Delta-Notch complex have been proposed based on interaction energy parameter and planarity studies.

Two models of Smad4 and Hoxa9 complex are proposed: structural and interactional perspective.

Transforming growth factor-beta superfamily growth factors (TGF-ß) regulate a diverse range of cellular functions, including proliferation, differentiation, extracellular matrix secretion and cell adhesion. TGF-ß is also one of the most abundant of the known growth factors. Osteopontin (OPN), the major non-collagenous bone matrix protein is a secreted, arginine-glycine-aspertate containing phosphorylated glycoprotein. Analysis of the OPN promoter sequence reveals both Hoxc8 and Hoxa9 (mouse homeotic gene) recognize and utilize the same consensus TAAT motif in the binding sequence to mediate the repression. Hoxa9 functions as a strong transcriptional repressor, similar to Hoxc-8 (X. Shi, X. Yang, D. Chen, Z. Chang, and X. Cao, J Biol Chem 274, 13711-13717, 1999). The DNA-binding protein Hoxa9 interacts with Smad4 (X. Shi, S. Bai, L. Li and X, and Cao X, J Biol Chem 276, 850-855, 2001), but not with Smad3 (which binds to OPN promoter), and the interaction between Smad4 and Hoxa9 results in the transcriptional activation of OPN in response to TGF- stimulation. In this paper we have proposed two possible model structures of Hoxa9 and Smad4 complex. These have been modeled based on homology modeling and a new method has been used to model the flexible loop part. Manual docking has been used to achieve the final model involving the Hoxa9 -Smad4 complex which tallies with the experimental results. We have mutated some selective important residues and looked at their effect in terms of interaction energy in complex formation in both the models.

Molecular modeling and molecular dynamics simulation studies of Delta-Notch complex.

Notch is a single-pass transmembrane receptor protein which is composed of a short extracellular region, a single-pass transmembrane domain and a small intracellular region. Notch ligand like Delta, member of the DSL protein family, is also single-pass transmembrane protein. It has been demonstrated that of the 36 EGF repeats of Notch, 11th and 12th are sufficient to mediate interactions with Delta. Crystal structure of mammalian Notch extracellular ligand binding domain contains 11 and 12 EGF-like repeats. Here a portion of the Delta protein of Drosophila, known to interact with Notch extracellular domain (ECD) has been modeled using homology modeling. The structure of the Delta-Notch complex was subsequently modeled by protein docking method using GRAMM. MD simulations of the modeled structures were performed. The structure for Delta-Notch complex has been proposed based on interaction energy parameter and planarity studies.

20ns molecular dynamics simulation of the antennapedia homeodomain-DNA complex: water interaction and DNA structure analysis.

Homeodomains are one of the important families of eukaryotic DNA-binding motifs and provide an important model system for studying protein-DNA interactions. The crystal structure and NMR structure of the antennapedia homeodomain-DNA complex and comparison between them is available. Although earlier works have shown that the direct contacts and water mediated contacts are important for the binding and specificity. The detail dynamical structural characteristics of the complex, water mediating interactions in the complex and also the detail study of the free DNA and protein has not done. In the present paper we have reported the results of 20ns MD simulation of this complex with the presence of explicit water and also the 20ns MD simulation of the protein and the DNA separately in explicit water. The results show that the complex remains stable during the last 8ns of the simulation. The part of the protein which is interacting with the DNA has fewer fluctuations than other part of the protein. The pattern of water distribution around the interacting center has a typical pattern for this complex and it is quite different from the free protein and the free DNA. Water molecules penetrate into the interacting center during the simulation. Several water bridges have been identified which is responsible for recognition but not observed in the crystal structure. The recognized DNA sequence (14 mer) has been characterized by helical and step parameters. The correlated motions of the DNA and the protein in the complexed form and the free form has been analyzed.

Uptake of Pb(2+ )by a cyanobacterium belonging to the genus Synechocystis, isolated from East Kolkata Wetlands.

East Kolkata Wetlands is a conserved wetland utilizing sewage and garbage, generated by Kolkata Municipal Corporation area for cultivation purpose. Cyanobacteria are the photosynthetic prokaryotes having bioremedial capacity. We have isolated a cyanobacterium from the sewage recycling fish-pond of East Kolkata Wetlands. Partial sequence of 16S rDNA gene of the isolated strain showed 100% similarity with that of genus Synechocystis. Isolated strain and Synechocystis sp. PCC6803 survived up to 300 mug ml(-1) Pb(2+ )and growth was completely inhibited at 400 mug ml(-1) Pb(2+). All experiments were carried out with 100 mug ml(-1) Pb(2+) in which growth was the maximum. 91.67% of the total Pb(2+) got adsorbed to the outer surface of the cell and 1% of the total Pb(2+) entered the cell of the isolated strain as estimated by atomic absorption spectrometry, but in Synechocystis sp. PCC6803 72.72% adsorbed and 0.96% penetrated. Intracellular and periplasmic depositions of Pb(2+) were observed in both the strain. A filamentous structure developed outside the cell wall of the isolated cyanobacterium, but very little change was observed in Synechocystis sp. PCC6803. ZiaR-SmtB like regulator gene was expressed in both the strains after Pb(2+) induction. The cDNA sequence of ZiaR of the isolated cyanobacterium shows 100% homology with that of Synechocystis sp. PCC6803. Upon Pb(2+) induction, expression of SOD gene increased. cDNA sequence of the SOD gene from the isolated strain showed 98% homology with that of Synechocystis sp. PCC6803. Enzymatic activity of catalase and SOD was also increased. No DNA damage was monitored upon induction with Pb(2+).

Effect of heavy ion irradiation on DNA DSB repair in Methanosarcina barkeri.

Archaea are expected to be highly repair proficient since they survived the vicious onslaught of radiation damage at the time of their early appearance. The DNA double strand break repairing ability of mesophilic archaea Methanosarcina barkeri (DSM 804) was studied using (7)Li, (12)C and (16)O heavy ions and compared with that of (60)Co gamma-rays. They can repair double strand breaks and, as in eukaryotes, the nature as well as extent of induction and its subsequent repair were dependent on the linear energy transfer of the radiation source.