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Sage Arbor, Ph.D.
Assistant Professor of Biochemistry

(317) 455-6666
sarbor@marian.edu
Evans Center, room #123

Biography

Dr. Sage ArborSage Arbor, Ph.D. is an assistant professor of biochemistry in the Marian University College of Osteopathic Medicine. His primary area of teaching and research involves biochemistry, pharmacology, and drug design. Dr. Arbor earned his bachelor of science degree in biology and chemistry with a minor in biochemistry from Duke University in North Carolina. After working in a startup biotech helping to sequence the first human genome for the NIH, Dr. Arbor went on to attain his Ph.D. in biochemistry from Washington University School of Medicine where he researched protein structure and developed rigid compounds to act as therapeutics. Prior to coming to Marian University, Dr. Arbor worked as a systems biologist at Pfizer elucidating molecular pathways, drug targets, and describing clinical trial population results due to genomic variation. He then managed an organic and microbial lab at Eurofins Scientific followed by leading the global development of a new LIMS at Pioneer Hi-Bred architecting databases and analytical tools to help with genotyping.

Dr. Arbor has experience teaching in the Molecular Foundations of Medicine as well as organic chemistry lecture and labs. His research aims to improve the human condition through drug design, compound repurposing, and improved electronic medical record use while studying protein misfolding, epigenetics, HIV, cancer, and causal links found via mining datasets.

Sage Arbor is currently living in Carmel, Indiana and in his free time enjoys running, basketball, wood carving, public policy work and, of course, spending time with his beloved wife and colleague, Dr. Tafline Arbor.

Clinical/Research Interests

Sage Arbor's research includes fields ranging from drug design, systems biology, epigenetic database creation, to fitness app development.  This research can make profound contributions to the field yet be done largely in silico and therefore is much less expensive than a classical biochemistry lab.  In addition, the largely computational nature of his research lends itself exceptionally well to students helping move the research forward with more limited or sporadic work hours. Much of Dr. Arbor's research does not require constant dedicated hours by students, such as that required by live eukaryotic cell culture studies.  All of Dr. Arbors wet lab work is simplified with bacteria used for protein expression.  Having mentored many students in the research described above he has found even undergraduates doing computational research to be quickly engaged, productive, and learn programming skills that are useful regardless of the profession they end up in.  The top four lines of research planned are detailed below, with more info on them and other opportunities on Dr. Sage Arbor's research website.

Dr. Arbor's main wet lab project involves developing orthogonal split inteins. Split inteins are recently discovered proteins that bind each other in the cell and splice whatever protein sequences are attached to them together. This is like a natural nanomachine stapler for proteins. Developing split inteins that interact with only one other split intein (that are orthogonal) will allow greater use of them to combinatorially make proteins and investigate and act on pathways in the cell. An example of how these orthogonal inteins could be for what Dr. Arbor terms his "tickertape" in vivo computer, which would "print out" a record of protein interactions in the cell. By tagging the end of a protein with a unique sequence and a split intein, it would allow covalent linkage with the unique tagged sequence and split intein of other proteins it interacts with. Control peptides, also tagged with unique sequence split inteins on their tails, would act as a temporal read out in that they would be incorporated into this ticker-tape at a constant rate. After running an experiment with different stimuli a read out of the peptide tickertape would tell you the timing that your protein of interest interacted with any other protein. This also has the benefit of being a single molecule experiment.

Two database projects have already had multiple student researcher participation.  The most recent project is the development of an epigenetic database containing the odds ratios of activites and compounds on certain outcomes.  The aim of this project is to create a website or app that allows people to rank order the most effective way to achieve their outcome.  For example how does running, vs getting an extra hour of sleep, vs switching from a night time job effect your likelihood of getting breast cancer.  All of these changes reduce your chance, but the database will enable patients and doctors to compare the efficacy of these actionable activities with therapeutics that may have some undesired side effects.  The second project developed a database of learning objectives across all medical disciplines, as created by the national societies from various disciplines.  This resources has already been used to help improve our integrated curriculum.

A social fitness app is being developed for use in physical education classes with the possibility of continued use outside of the classroom.  Student's percent body fat will be tracked with app usage as well as the ability to incentivize activity outside of physical education classes.  Social aspects include functionality such as handicapping of races based on past performance so all participants should "cross the finish line" at the same time.  Another example is real-time bar charts showing groups competing in pushups of situps so each team urges their team members on.  The app is coded in nativescript which allows its deployment to multiple platforms (iPhone, Android, and Windows).

Dr. Arbor has developed an in silico library of constrained cyclic tetrapeptides (CTPs) which model reverse turns in the PDB, and has also shown they can mimic other known pharmacophores. Two interesting compounds mimic structures which could enable them to be used as HIV and diabetes insipidus therapies.  Two additional benefits of Dr. Arbors potential therapeutic is the fact that CTPs are bioavailable and potentially able to be synthesized in vivo by yeast. Therefore, there is the potential to genetically encode a HIV therapy that could be produced by yeast and administered to the developing world merely by making and eating bread. As a systems biologist at Pfizer, Dr. Arbor worked with many pathway mapping tools analyzing all the nexgen data to detail fingerprints, pathways, and possible drug targets. He plans to augment any structural work completed with pathway analysis to help bring novel knowledge to fruition.

Highlighted Publications

Arbor, S.C., LaFontaine, M., and Cumbay, M. (2016). Amyloid-beta Alzheimer targets — protein processing, lipid rafts, and amyloid-beta pores. Yale J Biol Med 89, 5–21.

Scott K. Breeden, Alex Card, Sage Arbor*.  Split Intein Orthogonality Predicted Computationally.  American Chemical Society National Meeting, 2016, Philadelphia.  Poster.

Arbor S, Marshall GR. A virtual library of constrained cyclic tetrapeptides that mimics all four side-chain orientations for over half the reverse turns in the protein data bank. J Comput Aided Mol Des. 2009 Feb;23(2):87-95. doi: 10.1007/s10822-008-9241-4. Epub 2008 Sep 17. 

Arbor S, Kao J, Wu Y, Marshall GR. c[D-pro-Pro-D-pro-N-methyl-Ala] adopts a rigid conformation that serves as a scaffold to mimic reverse-turns. Biopolymers. 2008;90(3):384-93..

Investigator Research Page

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