De Novo Transcriptome Assembly of Solid Sequencing Data in Cucumis Melo  

Purru Supriya1 and K V Bhat2, 1Indian Agricultural Research Institute, India and 2National Bureau of Plant Genetic Resources, India

ABSTRACT 

As sequencing technologies progress, focus shifts towards solving bioinformatic challenges, of which sequence read assembly is the first task. In the present study, we have carried out a comparison of two assemblers (SeqMan and CLC) for transcriptome assembly, using a new dataset from Cucumis melo. Between two assemblers SeqMan generated an excess of small, redundant contigs where as CLC generated the least redundant assembly. Since different assemblers use different algorithms to build contigs, we followed the merging of assemblies by CAP3 and found that the merged assembly is better than individual assemblies and more consistent in the number and size of contigs. Combining the assemblies from different programs gave a more credible final product, and therefore this approach is recommended for quantitative output.

 KEYWORDS 

De novo assembly, Transcriptome, Contig, RNA-Seq 

More details :- https://airccse.com/bioej/papers/2115bioej02.pdf

https://airccse.com/bioej/vol2.html

Cloning and Extracellular Expression of Recombinant Tissue Plasminogen Activator (RT-PA) Using a Methylotrophic Yeast Pichia Pastoris  

Atul M. Vhanmarathi, Rekha Matlani and Arvind M.Lali, Institute of chemical Technology, India

ABSTRACT 

Tissue plasminogen activator (tPA) has noteworthy application in treatment of acute myocardial infarctions. This study focuses on expression of rt-PA using microbial systems in order to reduce cost without compromising on quality as an alternative to commercial (rt-PA)produced by using mammalian host systems. In the present study, Pichia pastoris X-33strain was used as a host with pICZαA expression vector to obtain extracellular expression of full length tPA gene. Specific primers were designed in such a way to get native tPA protein sequence in subsequent purification steps. Further, construct pICZαA-tPA was developed and electroporated into host to achieve stablert-PA gene by achieving genome integration. The transformants were screened for phenotypic characters.Mut+ phenotypic colony named Pichia tPA-3 showed expression of rt-PA at 66 kDa on SDS PAGE. Size Exclusion Chromatography (SEC) was performed, resulting in product peak at same RT as reference standard. (alteplase).Cloning and expression of rt-PA was successfully achieved in microbial system. Further process optimization at larger scales will surely provide cost effective alternative to mammalian system forrt-PA production.

 KEYWORDS

Tissue plasminogen activator, acute myocardial infarctions, Pichia pastoris, pICZαA, FactorXa protease, SDS PAGE, Size Exclusion Chromatography etc.  

More details :- https://airccse.com/bioej/papers/2115bioej01.pdf

https://airccse.com/bioej/vol2.html

Statistical Based Media Optimization and Production of Clavulanic Acid By Solid State Fermentation in Jackfruit Seed Powder as Novel Substrate Using Streptomyces Clavuligerus MTCC 1142  

Basavaraj M. Vastrad1 and Shivayageeswar E. Neelagund2, 1S.E.Ts College of Pharmacy, India and 2Jnana Sahayadri Kuvempu University, India

Abstract 

Statistics based optimization, Plackett–Burman design (PBD) and response surface methodology (RSM) were employed to screen and optimize the media components for the production of clavulanic acid from Streptomyces clavuligerus MTCC 1142, using solid state fermentation. jackfruit seed powder was used as both the solid support and carbon source for the growth of Streptomyces clavuligerus MTCC 1142. Based on the positive influence of the Pareto chart obtained from PBD on clavulanic acid production, five media components – yeast extract, beef extract, sucrose, malt extract and ferric chloride were screened. Central composite design (CCD) was employed using these five media components- yeast extract 2.5%, beef extract 0.5%, sucrose 2.5%, malt extract 0.25% and ferric chloride nutritional factors at three levels, for further optimization, and the second order polynomial equation was derived, based on the experimental data. Response surface methodology showed that the concentrations of yeast extract 2.5%, beef extract 0.5%, sucrose 2.5%, malt extract 0.25% and ferric chloride 2.5% were the optimal levels for maximal clavulanic acid production (19.37 mg /gds) which were validated through experiments. 

KEYWORDS

Plackett–Burman design, Central composite design, Streptomyces clavuligerus MTCC 1142, clavulanic acid, jackfruit seed powder, solid state fermentation 

More details :- https://airccse.com/bioej/papers/1114bioej05.pdf

https://airccse.com/bioej/vol1.html