Author: Beverly Endicott

Biology Alumna featured in Association of American Medical Colleges Students and Residents Website

Christiana Obioma, a 2018 Biology-Biomedical Sciences graduate and current student at the University of Oklahoma College of Medicine, is featured in the online “Anatomy of an Applicant” series of the Association of American Medical Colleges. While at UCO, Christiana worked with Dr. Caroline Bentley, health professions advisor and associate professor of biology, to take the appropriate courses to fulfill medical school pre-requisites. She enlisted in the Army during her junior year, taking two semesters off while training to become an emergency medical technician. During her senior year, Christiana participated in a research project on wound healing with Dr. Melville Vaughan, professor of biology, and presented her research at the National Conference for Undergraduate Research (NCUR) and the Oklahoma Louis Stokes Alliance for Minority Participation conference (OK-LSAMP). Christiana was named the Outstanding Biology Senior in 2018 and graduated cum laude.

Read more about Christana’s journey on the AAMC Students and Residents website, Compassionate Caregiver to Military Medic: Christiana’s Path to Medical School.

UCO’s Buddy Supercomputer is Accelerating Research in DNA Sequencing and Bioinformatics

 

The progress toward cheaper and faster sequencing has been very impressive since the Human Genome Project first sequenced the human genome using the classical Sanger method. The Sanger procedure is time consuming due to the slow throughput with DNA fragment separation in gels. The need for cheaper and faster techniques drove scientists and companies to work on new sequencing technologies. Recently, Oxford Nanopore Technologies developed a sequencing device based on protein nanopores. Despite this progress, there are still several challenges with DNA sequencing using protein nanopores such as: 1) high startup and consumables costs; 2) short read length, which limits the ability to analyze large scale structural variations; 3) sensitivity of pore to environmental conditions e.g., temperature, pH, and applied voltage; and 4) high error rate (~15%). Due to these challenges, the need for cheaper and faster approaches with the focus on label-free, single-nucleotide, long read length automated sequencing using a minimum amount of consumables is very crucial. Two-dimensional (2D) crystals such as graphene have emerged as revolutionary materials for fast, single-nucleotide, direct-read DNA sequencing with a minimum amount of consumables. Among the large family of 2D materials, graphene remains the most widely explored for DNA sequencing applications. Due to its single-layer nature (comparable to the interbase distance in single-stranded DNA), graphene has strong potentials to be used for designing nanodevices for fast, single-nucleotide resolution, label-free DNA sequencing using a limited number of consumables. Despite its remarkable properties, sequencing DNA using graphene is experimentally very challenging. One of the major hindrances is the hydrophobic nature of graphene’s surface, which causes DNA bases to stick to its surface, making it difficult to translocate DNA through graphene nanopores. Due to this challenge, the scientific community has turned its attention to other single-layer materials similar to graphene (e.g. phosphorene and silicene). Using UCO’s Buddy Supercomputer, Dr. Benjamin Tayo’s students carried out computational studies to study the interaction of DNA bases with phosphorene and silicene. These studies reveal that phosphorene and silicene show a lower tendency (less binding energy) to bind with DNA bases (see Figure), and hence are promising alternatives to graphene for use in next-generation DNA sequencing devices. Furthermore, the hydrophilicity and biocompatibility of phosphorene makes it an important material for biological applications. Dr. Tayo’s group has partnered with leading experimentalists in the field who will provide more data for benchmarking their theoretical predictions. This research has led to two peer-reviewed journal articles, one published (AIP Advances 11, 035324 (2021); https://doi.org/10.1063/5.0043000) and the other under review. The research has been also presented at several local and national conferences.

Dr. Christopher Butler Receives Texas Parks and Wildlife Department Grant

Dr. Christopher Butler, professor of biology, has received a four-year $332,100 grant from the Texas Parks and Wildlife Department. His project, “Comparing detectability and efficiency of multiple methods for surveying rails,” will improve detection rates of Black Rail and King Rail species on the Texas Gulf Coast.
The specific objectives of the project are: to conduct present-absence surveys using multiple approaches that include both detection and occupancy rates for rail species; evaluate whether FLIR-equipped (thermal) UAVs may be used to detect multiple rail species; refine a survey technique for long-term monitoring that, afterwards, might be continued by TPWD staff for various rail species; and assess potential habitat associations that relate back to management practices conducted on state and federal lands.

 

Dr. Andrew Taylor Receives OK Department of Wildlife Conservation Grant

Dr. Andrew Taylor, assistant professor of biology, received a $119,361 grant from the Oklahoma Department of Wildlife Conservation. Dr. Christopher Butler, professor of biology will serve as a Co-Principal Investigator on the grant. The two-year project, “Detection and Occupancy of Bluntface Shiner (Cyprinella camura) in Wadeable Streams of Northeastern Oklahoma,” will update the known distribution and habitat associations of Bluntface Shiner. The extent of the species’ current geographic distribution is unknown. This project will perform targeted field collections of Bluntface Shiner across streams in 15 north central and northeastern Oklahoma counties. Over the course of the project, sampling will be focused among locations within the Verdigris River basin, upper Arkansas River basin, and the Ozark Mountains ecoregion.

Dr. Gang Xu’s Research Continues after U.S. Dept. of Energy Grant

In summer 2019, Dr. Gang Xu received funding from the U.S. Department of Energy for his proposal, “Flagella-Driven Cellular Motility, Transport, & Biomixing: Computational Studies.”  The funding provided Dr. Xu and two of his former research assistants, Erin Drewke and Joseph Wagner, with full support to spend 10 weeks working at the Lawrence Berkeley National Lab in Berkeley, California.  There they worked with Drs. Ann Almgren and Johannes Blaschke in its Center for Computational Sciences and Engineering to develop a novel simulation capability based on combining state-of-the-art algorithms with empirical models for beating flagella and swimming cells. The new codes are ideally suitable for high-performance computing resources such as those at the Berkeley Lab and also UCO. The results will improve the understanding on the hydrodynamic impacts of flagellar beating and flagella-actuated cell swimming, and provide biophysical and mechanistic basis for development of novel microfluidic and biofuel devices. This experience paved the way for continued collaboration and expanded Dr. Xu’s research capacity.  Erin, a 2020 UCO biomedical engineering graduate, is pursuing her Ph.D. in biomedical engineering at the University of Arkansas. Joseph, a prospective 2021 mechanical engineering graduate, is planning to pursue a Ph.D.

Research Group Investigates Gene Transfer in Bacteria

Biology professor Dr. Jim Bidlack and his research group are investigating gene transfer in bacteria. Better understanding of how bacteria become multidrug resistant can help researchers develop new techniques that can control bacterial infections and save human lives. Coincidently, a new gene locus encoding for bile salt sensitivity in bacteria appears to be the same gene locus responsible for antibiotic resistance. Dr. Bidlack’s students are currently isolating that gene locus so that it can be sequenced and determine what part of the DNA encodes for antibiotic resistance. If successful, it may be possible to use that information to develop new drugs that will be more effective in fighting bacterial infections.