|Visualizing the Dynamic Epigenome|
Lydia Steiner (1,2), Thimo Rohlf (2), Joerg Galle (2), Hans Binder (2), Lydia Hopp (2), Henry Wirth (2), Sonja Prohaska (1,2)
A method is presented to visualize genome-wide information from epigenetic data. It is capable to integrate additional information. Applied to mouse data consisting of H3K4, H3K27, and H3K9 trimethylation for 3 different celltypes, the dynamic behavior and interplay was investigated.
|Repurposing Drugs for the Treatment of Multi-Drug Resistant Breast Cance|
David Monaghan, Rachel Griffin, Amie Regan, Enda O’Connell, Howard Fearnhead
In this study, the Johns Hopkins Clinical Compound Library, containing approximately 1,500 FDA and foreign-approved clinical compounds, was used to screen a multi-drug resistant, triple negative breast cancer cell line for drug sensitivity.
|Genome sequenicng and analysis of the emerging pathogen Corynebacterium ulcerans|
Eva Trost, Andreas Tauch
Sequencing of two C. ulcerans isolates and identification of a noval putative virulence factor
|Demethylation and Re-Expression of Tumor Suppressor Genes: A Novel Approach for Cancer Therapy|
Genevieve Housman, Megan A. Mataga, Amrita Devalapalli, Sarah Heerboth, Leah R. Evans, Sibaji Sarkar
In this study, we demonstrated that a combination therapy using suboptimal doses of HDACi and calpeptin, an inhibitor of calpain, produced synergistic type growth inhibition and reduced cancer cell motility in cancer cells. We hypothesize that the re-expression of tumor suppressor genes by demethylation and other mechanisms sensitize the cells and allows for apoptotic death.
|Development and NDA-Level Validation of a Real-Time PCR Procedure for Detection and Quantification of Residual E.coli DNA Contamination of Biopharmaceutical Products|
Dan Papa, Pedro J. Morales and Michael D. Sadick
Escherichia coli (E. coli) has been commonly used for the production of biopharmaceuticals. Among the impurities that must be monitored in biopharmaceuticals is residual host-cell DNA (HCD). This study describes the development and subsequent NDA-level validation of a real time PCR procedure developed in response to a client’s need to improve the sensitivity of detection and quantification of residual E. coli HCD in their drug product.
|Integrated In Silico Analysis of NGS Prostate Cancer Data via High-Resolution RNA-Seq Analysis|
Sandeep Sanga , Antoaneta Vladimirova, Aubree Hoover
The goal: To get novel insights into the mechanisms of prostate adenocarcinoma by leveraging next generation sequencing (NGS) data, particularly human transcriptome data, through in silico data analysis and interpretation by Ingenuity’s IPA® software. CLC Genomics Workbench and CLC Genomics Server helped us assess short read RNA-Seq data.
|DNA Methylation as a Marker of the Intra Uterine Environment |
Carolyn Banister, Devin Koestler, Matthew A. Maccani, E. Andres Houseman, James F. Padbury and Carmen J. Marsit
The placenta functions not only as a conduit for nutrient and waste exchange between mother and fetus, but also as a regulator of the intrauterine environment. Recent work has identified changes in the expression of candidate genes, often through epigeneticalteration, which alter the placenta’s function and impact fetal growth.
|Prognostic Factors for Refeeding Syndrome in Head and Neck Cancer Patients|
James Hare, Rachel Skelly, Samit Ghosh, Terry Jones
Head and neck cancer sufferers are inherently at risk of refeeding syndrome, which had a prevalence of 9.5% in our series. Our results suggest that site of tumour (but not tumour or nodal staging) is a prognostic indicator for developing refeeding syndrome.
|SuperNatural: A Database of Available Natural Compounds|
Melanie Füllbeck, Mathias Dunkel and Robert Preissner
The majority of marketed drugs are natural compounds or derivatives thereof. The compounds availability is often unclear. Therefore we have compiled a database of ~50,000 natural compounds. Starting point for in silico screenings are about 2,500 well-known, classified natural compounds or imported molecules. Possible medical applications can be detected and about three million conformers computed to account for the flexibility during usage of the 3D-superposition algorithm.