Overexpression of Cu/Zn Superoxide Dismutase (Cu/Zn SOD) in Synechococcus elongatus PCC 7942 for Enhanced Azo Dye Removal through Hydrogen Peroxide Accumulation.

Discharge of recalcitrant azo dyes to the environment poses a serious threat to environmental health. However certain microorganisms in nature have developed their survival strategies by degrading these toxic dyes. Cyanobacteria are one such prokaryotic, photosynthetic group of microorganisms that degrade various xenobiotic compounds, due to their capability to produce various reactive oxygen species (ROS), and particularly the hydrogen peroxide (H2O2) when released in their milieu. The accumulation of H2O2 is the result of the dismutation of superoxide radicals by the enzyme superoxide dismutase (SOD). In this study, we have genetically modified the cyanobacterium Synechococcus elongatus PCC 7942 by integrating Cu/Zn SOD gene (sodC) from Synechococcus sp. PCC 9311 to its neutral site through homologous recombination. The overexpression of sodC in the derivative strain was driven using a strong constitutive promoter of the psbA gene. The derivative strain resulted in constitutive production of sodC, which was induced further during dye-treated growth. The genetically engineered Synechococcus elongatus PCC 7942 (MS-sodC+) over-accumulated H2O2 during azo dye treatment with a higher dye removal rate than the wild-type strain (WS-sodC-). Therefore, enhanced H2O2 accumulation through SODs overexpression in cyanobacteria may serve as a valuable bioremediation tool.

SynRio: R and Shiny based application platform for cyanobacterial genome analysis.

UNLABELLED: SynRio is a Shiny and R based web analysis portal for viewing Synechocystis PCC 6803 genome, a cyanobacterial genome with data analysis capabilities. The web based user interface is created using R programming language powered by Shiny package. This web interface helps in creating interactive genome visualization based on user provided data selection along with selective data download options. AVAILABILITY: SinRio is available to download freely from Github - https://github.com/NFMC/SynRio or from http://www.nfmc.res.in/synrio/. In addition an online version of the platform is also hosted at nfmc.res.in/synrio, using shiny server (open source edition) installation.

Cyanobacterial KnowledgeBase (CKB), a Compendium of Cyanobacterial Genomes and Proteomes.

Cyanobacterial KnowledgeBase (CKB) is a free access database that contains the genomic and proteomic information of 74 fully sequenced cyanobacterial genomes belonging to seven orders. The database also contains tools for sequence analysis. The Species report and the gene report provide details about each species and gene (including sequence features and gene ontology annotations) respectively. The database also includes cyanoBLAST, an advanced tool that facilitates comparative analysis, among cyanobacterial genomes and genomes of E. coli (prokaryote) and Arabidopsis (eukaryote). The database is developed and maintained by the Sub-Distributed Informatics Centre (sponsored by the Department of Biotechnology, Govt. of India) of the National Facility for Marine Cyanobacteria, a facility dedicated to marine cyanobacterial research. CKB is freely available at http://nfmc.res.in/ckb/index.html.

Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking.

We present a comparative account on 3D-structures of human type-1 receptor (AT1) for angiotensin II (AngII), modeled using three different methodologies. AngII activates a wide spectrum of signaling responses via the AT1 receptor that mediates physiological control of blood pressure and diverse pathological actions in cardiovascular, renal, and other cell types. Availability of 3D-model of AT1 receptor would significantly enhance the development of new drugs for cardiovascular diseases. However, templates of AT1 receptor with low sequence similarity increase the complexity in straightforward homology modeling, and hence there is a need to evaluate different modeling methodologies in order to use the models for sensitive applications such as rational drug design. Three models were generated for AT1 receptor by, (1) homology modeling with bovine rhodopsin as template, (2) homology modeling with multiple templates and (3) threading using I-TASSER web server. Molecular dynamics (MD) simulation (15 ns) of models in explicit membrane-water system, Ramachandran plot analysis and molecular docking with antagonists led to the conclusion that multiple template-based homology modeling outweighs other methodologies for AT1 modeling.