Dr. Bill McLaughlin
Geisinger Commonwealth School of Medicine, Scranton, PA
A Stand-Alone Integration Platform for the Annotations of Protein Structures That Enables Disease to Medication Searches
Data integration and validation efforts aid in ensuring that biomedical information from primary and secondary sources is both accurate and comprehensive. Our collaborative partners have developed software for the retrieval, parsing, and mapping of the functional annotations of protein structures as part of the Structural Biology Knowledgebase. We have implemented a complementary platform that further integrates the disease associations and the functional annotations of the protein structures. Here we describe here a stand-alone program which merges these two efforts. Challenges that were overcome include the combining of the software components and the creation of means to automatically identify errors in the data. We discuss our collaborative efforts with the curators of the biomedical resources to resolve the identified errors. We also discuss a means to access to the cleaned information according to disease-specific queries using the KB-Rank tool . Ranking and prioritization of the search results is done using the functions of the retrieved protein structures. Example searches are highlighted that navigate from a disease description to the involved protein structures to known and putative treatments.
Dr. William Terzaghi
Wilkes University, Wilkes-Barre, PA
Using Bioinformatics and Synthetic Biology for Bioremediation of Atrazine and to Develop Novel Treatments for Kidney Stones
We are using bioinformatics to identify genes that may be useful for various purposes, and then we use synthetic biology to construct organisms with the desired properties. We will describe how we are using this approach to develop plants that can detoxify atrazine, the second most widely used herbicide in the US, and to alleviate kidney stones. We are taking three approaches to alleviating kidney stones. The first is to identify, clone and purify enzymes shown to degrade oxalate, and we have cloned several of these enzymes. A second approach is to attempt creating probiotic bacteria that will degrade oxalate in the human digestive tract. For this end we are creating a strain of E. coli that takes up oxalate because we have added an oxalate transporter gene, and then degrades oxalate because we have added an enzyme that degrades oxalate. The third is to clone and characterize the human oxalate transporter in CHO cells in order to identify small molecules or other ways to inhibit its activity.
PrimBio Research Institute, Exton, PA
Characterizing human microbiome with 16S rRNA profiling
There are about three times as many microbial cells in the human body than there are human cells. Yet how the composition of the microbiota community impacts human health is still elusive. The fast developing high-throughput sequencing technologies allow us to examine and analyze millions of microbial genomes simultaneously. Several approaches, including microbial whole genome sequencing, transcriptome sequencing, and 16S ribosomal RNA gene sequencing, have been applied to profile the microbiota community. In this study, we developed a bioinformatic tool to fast characterize the bacteria population from sequencing of microbe mixtures. Raw data was obtained using the Ion Torrent PGM platform and targeting specific hypervariable regions of the bacterial rRNA gene. With the new tool, we were able to quickly identify bacteria in a complex population down to genus, or even species level.
Dr. Wonpil Im
IMMSTECH, LLC, Bethlehem, PA
CHARMM-GUI for Biomolecular Modeling and Simulation, and Its Commercialization Path.
This talk will provide an overview and commercialization plan of CHARMM-GUI , ST-analyzer , and G-LoSA that has been developed in the Im lab. CHARMM-GUI provides a web-based, user-friendly interface with functional modules that reliably build various complex biological systems for molecular modeling and simulation. While CHARMM-GUI uses software named CHARMM (a simulation program originally developed in the Karplus lab at Harvard University), the end products of CHARMM-GUI are the complex molecular system and input files that can be readily used in many other simulation programs. CHARMM-GUI is a well-recognized tool in biomolecular modeling and simulation research and has been used by many researchers worldwide . The Im lab has also developed ST-analyzer to provide a web-based platform to analyze simulation trajectories. ST-analyzer can be combined with the CHARMM-GUI technology to provide a complete simulation pipeline from system building to simulation analysis. As a separate effort, the Im lab has developed G-LoSA , a structural bioinformatics tool to align a protein local structure onto another (local) structure and to measure their structural similarity. G-LoSA is highly effective in detecting local regions on a given protein to which specific molecules or chemical fragments likely bind and thus can be used to predict ligand binding sites and ligand structures for computer-aided drug design.
Michael J. Smith
Geisinger Health Plan, Danville, PA
Informatics and their Importance in Healthcare Today
A discussion on the importance of using informatics and being properly trained for a career in healthcare.
Medtrics Lab LLC , Lewisburg, PA
Hidden Costs of Healthcare: Administrative Time and Waste
This presentation will focus on the hidden inefficiencies behind the scenes of healthcare that are not often seen by those outside of the industry. Such as highly paid physicians spending their time doing copy and paste work instead of treating their patients because two software systems are incapable of communicating.
The presentation will also highlight some potential solutions to these issues, while discussing some of the factors that make implementing them difficult.
Dr. Del Lucent
Wilkes University, Wilkes Barre PA
Protein Folding and Design: Interdisciplinary Science in a Digital Laboratory
Science is driven by experiments, and it is indeed through our ability to validate hypotheses in the laboratory that we have begun to understand the mysteries of our universe. There are however, certain phenomena that elude the keen observational gaze of scientists and confound even the most sophisticated experimental apparatus. It is for these phenomena that our laboratories become the processors of computers and our experimental tools become computer programs. This is particularly true for studying the assembly and function of the molecules that constitute all life: proteins. After they are assembled, proteins must somehow know how to fold into the correct shape needed to sustain all of the processes of life. Using state of the art data science techniques combined with cloud computing, we are now beginning to understand this fundamental biological process. This knowledge will potentially enable treatment a myriad of human diseases including Alzheimer’s Disease, Parkinson’s Disease, Huntington’s Disease, cystic fibrosis, type 2 diabetes and even some forms of cancer. Furthermore, we can apply our protein folding knowledge to the field of bioengineering, allowing us to design proteins with great potential to rectify national and global problems. Two examples include the design of custom enzymes for bioremediation, and the design of super-capacitors from protein crystals. Research and engineering endeavors of this sort require a synthesis of biology, chemistry, and physics as well as a marriage of digital and physical experiments.