|Microbial Genome-based Analysis Tool for Post-PKS Tailoring Steps|
We have developed a microbial genome-based analysis system to provide the user with a wealth of information that can be utilized for biosynthetic engineering of enzymes, especially involved in post-PKS tailoring steps. Post-PKS tailoring steps are necessary to add functional groups essential for the biological activity. Our system has sophisticated graphical user interfaces (GUIs) with a wide range of well-tested analytical functions, customized database, and well-maintained user-support applica
|MED-SuMo and MED-Hybridise: exploit all PDB macromolecule structures to design/optimize innovative leads|
Moriaud F., Oguievetskaia K., Adcock S.A., Vorotynsev A.M., Martin L., Doppelt-Azeroual O. and Delfaud F.
Obtaining structural information on fragment-protein target is a key factor and also a major limitation. We’ve used MED-SuMo and MED-Hybridise to query and mine the PDB seeking for similar interaction surfaces. MED-portions were used to design novel scaffolds (GPCR) and decorate a given scaffold (kinase). We have analysed the scaffolds in regard to their diversity, their presence in PubChem, PDB and other libraries.
|A Novel Multiplexed Digital Gene Expression Technology|
Gary K. Geiss1,#, Roger Bumgarner2, Brian Birditt1, Timothy Dahl1, Naeem Dowidar1, Dwayne L. Dunaway1, H. Perry Fell1, Sean Ferree1, Renee D. George1, Tammy Grogan1, Jeffrey J. James1, Malini Maysuria1, Jeffrey D. Mitton1, Paola Oliveri4, Jennifer L. Osborn3, Tao Peng2, Amber L. Ratcliffe1, Philippa J. Webster1, Eric H. Davidson4, and Leroy Hood5
We describe a novel platform, the nCounter Analysis System, for sensitive, highly multiplexed, digital gene expression analysis based on NanoString’s novel molecular barcoding technology. Detection of individual mRNA molecules using an assigned sequence of six different fluorescent spots per probe are detected, and then the number of times that code sequence appears in a sample are counted.
|Dymension 2D Gel Dymension 2D Gel Analysis Software|
Ibogaine, an indole alkaloid present in the root of plant
Tabernanthe iboga has been shown to have anti-addiction
properties against opiates1, 2, stimulants3 and alcohol4. Since the
anti-addiction effect lasts longer than the presence of ibogaine in
the body, metabolic changes are occurring in the brain which
could be studied using a 2D gel based proteomics approach. The
protein profiles could then be used to establish which proteins are
up or down-regulated and may lead to a better under
|No Impact of Dietary Iodine Restriction in Short Term Development of Hypothyroidism Following Fixed Dose Radioactive Iodine Therapy for Graves Disease|
Jubbin J Jacob*, Charles Stephen§, Nihal Thomas*, Regi Oommen¶ and M.S.Seshadri*
To study the outcomes at 6 months after fixed dose 131I therapy for Graves’ disease (GD) with an iodine restricted diet.
|Nutritionally-induced differences in the metabolic profiles of Chlamydomonas reinhardtii and Saccharomyces cerevisae determined by 1H-NMR and cross model validation and permutation testing|
Hank D. Bestman & Jordyn B. Brandsma
Using cross validation, permutation and rank products statistical procedures we identified biomarker regions in proton spectra of polar metabolites extracted from the algae Chlamydomonas reinhardtii (light and dark grown) and from the yeast Saccharomyces cerevisae (aerobically and anaerobically grown).
|Modulation of sporadic colorectal cancer risk by polymorphisms and haplotypes of mismatch repair genes|
Tulupova E., Kumar R.*, Slyskova J., Pardini B., Polakova V., Naccarati A., Vodickova L., Novotny J.**, Hemminki K.*, Vodicka P.
A role of mismatch repair (MMR) in modulating colorectal cancer (CRC) was assessed by genotyping single nucleotide polymorphisms in five MMR genes in hospital-based case- control study. The TAG haplotype in hMSH6 (-556G>T-Ex1-145G>-IVS4-101G>C) decreased a risk of CRC and the GGG haplotype increased a risk of rectal cancer. Although no significant association was found for individual MMR polymorphisms, the hMSH6 haplotypes may modulate the risk of CRC in this population.
|A comparison of siRNA activity predictors using advanced regression techniques|
Simone Sciabola, Qing Cao, Theresa Johnson, Lingling Shen, Robert Stanton, Xiaoyu Jiang, Simon Xi, Jason Hughes, Daniel Caffrey, Shobha Potluri, Steven Haney, Johnathan Cyr, Jeremy Little
Although considerable progress has been made recently in understanding how gene silencing is mediated by the RNAi pathway, the design of effective sequences is still a challenging task. To tackle the efficacy challenge and further improve accuracy for prediction of siRNA potency, we performed a comparison of advanced regression techniques and new in-house generated descriptors in the generation of siRNA efficiency models.
|miRNAs in Treating Cardiomyopathy |
The study aims to design antigomirs against miRNAs involved in Cardiomyopathy. Potential miRNAs involved in the down regulation of certain important genes during this disorder have been identified. All reported miRNAs were scanned using an algorithm against these genes. At three step protocol was followed to take care of false positives and false negatives. Further, HL-1 cells (cardiomyocytes) are been transfected by anti-miRNAs for confirmation.