Zeitschrift für Informatik und Systembiologie

Bixin is a natural dye and a high commercial important compound, produced from Bixin synthetic pathway in case of Bixa orellana plant. The particular enzyme Lycopene cleavage Oxygenase catalyzes the fi rst step of reaction pathways from Trans-lycopene to Bixin synthesis. The 3D structure of the enzyme was predicted by MODELLER program and the missing side chains were verifi ed by SCRWL4 tool. Model validation was done by using the output of PROCHECK and DOPE score. The Ramachandran plot for the model was observed as 87.3 percentages of residues is in favourable regions that indicate the model is reliable. Molecular dynamics simulation of the model protein was performed in water 5 lakh times for 1000 Pico second and at 300K by GROMACS software in a high performance computing environment. The energy value and RMSD (Root men square deviation) fl uctuation of Carbon alpha back bone of the model was computed that confi rms the stability of the model protein.

The 3D structure of a protein is a prerequisite for structure based drug design as well as for identifying the conformational epitopes that are essential for the designing vaccines. A 3-dimensional model (3D) was developed for the nucleocapsid protein of Japanese encephalitis virus. A homology modeling method was used for the prediction of the structure. For the modeling, one template proteins were obtained by mGenTHERADER, namely the high-resolution X-ray crystallography structure of NS3 protease helicase of murry vally encephalitis virus(2WV9). By comparing the template protein a rough model was constructed for the target protein using SWISSMODEL, a program for comparative modelling. The model was validated using protein structure checking tools such as Verify3D for reliability. The total of 138 such epitope regions/sites have been identified by kolaskar and tongaokar method. Conformational epitopes are mapped from the 3D structure of nucleocapsid protein of Japanese encephalitis virus modeled using the concept of an antigenic domain. The information thus discussed provides insight to the molecular understanding of nucleocapsid protein of JE virus. The predicted 3-D model may be further used in characterizing the protein in wet laboratory.

Completed genome sequences are rapidly increasing for Rickettsia but most the genes in them does not have an assigned function. The present investigation mainly focused only on identifying the function of hypothetical proteins of Rickettsia massiliae MTU5 that were conserved in Rickettsia species. Nearly, 114 conserved hypothetical proteins were selected that were conserved in Rickettsia species. Function annotation was carried out by using databases like SMART, Interproscan, Pfam, JAFA, COG, and BLAST. Among 114 conserved hypothetical proteins only 35 proteins were annotated. The study motivated us to thoroughly study the genome of Rickettsia massiliae MTU5 by bioinformatics approach for categorizing the proteins whose function was unknown.

The improvement of production processes to achieve commercially viable production levels is a prerequisite to any bioprocess. Currently, production strains are enhanced using a combination of random and targeted approach. By combining metabolomics technology and genome data analysis, it is possible to replace empirical target-selection strategies with a more scienti fi c approach. All steps of biotechnological development, from up-stream and mid-stream to down-stream processes will bene fi t signi fi cantly by taking systems biotechnological approaches. The prevalence of genome sequence information, in concert with modern molecular biology advances, should have facilitated the easy manipulation of speci fi c genes and pathways for the production of microbial metabolites. A notable success has been made on designing optimized production systems that maximize productivity and minimize raw materials costs for valuable metabolites. A remarkable advantage of this approach up-to-data and its relevant web resources is critically reviewed in this article. Indeed, this alternative approach will not only hopefully be useful for improving the productivity of many meaningful metabolites including antibiotics, enzymes, organic acids, etc. from industrially signi fi cant microorganisms but also will ensure correlation of many experimental reliabilities.

Next Generation Sequencing (NGS) technologies enable the resequencing of entire - genomes or the sampling of entire transcriptomes more effi ciently and economically and with greater depth than ever before. Rather than sequencing individual genomes, now it is possible to sequence hundreds or even thousands of related genomes to sample genetic diversity within and between germplasm pools. Identifying and tracking genetic variation is now so effi cient and precise that thousands of variants can be tracked within large populations. While NGS technologies have signifi cant implications on crop breeding, optimization and availability of appropriate methodologies and tools to analyze, visualize and intrepret NGS data are still in their infancy. With an objective to help crop genetics and breeding community to utilize NGS data for crop improvement, Generation Challenge Programme, Mexico and ICRISAT, India organized an international workshop entitled “Next Generation Sequencing (NGS) Data Analysis” during Jul 21-23, 2009. More than 30 scientists from nine countries (USA, UK, France, Korea, Japan, Australia, Mexico, Philippines and India) participated in the workshop. The workshop had four technical sessions and two brainstorming sessions in which participants shared their experience/views on data generation and analysis by using NGS technologies for accelerating plant genome research to understand genome dynamics as well as to facilitate crop breeding. This article presents a report on this international workshop. All presentations made in this workshop have been made available online (http:// www.icrisat.org/bt-publicdomain-ngs.htm).

A homeomorphic biomechanical model of the eye based on the Incremental Retinal-Defocus Theory (IRDT) was developed to simulate myopic and hyperopic growth under different optical defocus conditions. The IRDT states that the time-integrated reduction in retinal-image defocus magnitude decreases the rate of retinal neuromodulator release, which in turn decreases the rate of proteoglycan synthesis and reduces scleral structural integrity, thus resulting in axial elongation and myopia development. A homeomorphic biomechanical model of the eye was constructed to test the IRDT based only on optical defocus and its resultant contribution to mechanical forces acting on the components of the eye. The Matlab simulation results showed a more fl attened oblate shape for myopic defocus, and a more elongated prolate shape with hyperopic defocus. Thus, the homeomorphic biomechanical model of the eye was able to simulate the emmetropization mechanism using only the forces acting on the masses at the nodes. In addition, neurochemicals injected at local retinal regions modifi ed the spring constants to result in predicted changes in ocular deformation. The fi ndings have clinical implications with respect to basic theories of myopia development, as well as future therapeutic use of direct ocular drug delivery to control human myopia.