Category: CIBER

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); and the other under review. The research has been also presented at several local and national conferences.

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.

UCO Professors Collaborate on U. of Kansas NSF EPSCoR Grant

Drs. Robert Brennan and Sean Laverty are part of a multi-institutional NSF EPSCoR grant to research tick-borne diseases including Lyme disease and Rocky Mountain spotted fever. The four-year $3,921,229 grant, “Marshalling Diverse Big Data Streams to Understand Complexity of Tick-borne Diseases in the Southern Great Plains,”  is a collaboration among six universities in Kansas and Oklahoma, with the University of Kansas (KU) serving as the lead institution. Along with KU and UCO, the consortium includes Kansas State University, Pittsburgh State University, Oklahoma State University and the University of Oklahoma. According to the project abstract, major components of the research include assembling detailed large-scale datasets on the occurrences of different tick species, genomes of the ticks and pathogens, and environmental variation across the region. Dr. Brennan, biology professor, director of the Center for Interdisciplinary Biomedical Education and Research (CIBER) and associate dean of the UCO College of Mathematics and Science, serves as a Co-Principal Investigator on the grant. Dr. Laverty, associate professor of mathematics and statistics and CIBER member, will provide data analysis.  


CMS Faculty Receive OK-INBRE Grants

Three CMS faculty have received OK-INBRE grants totaling $189,160 for the 2020-2021 academic year.

Dr. Mohammad Hossan, Associate Professor of Engineering & Physics, received a Research Principal Investigator grant for $189,160. His project “Flow Analysis of a Bioresorbable Pipeline Embolization Device for Treatment of Aneurysms,” involves the design and development of bioresorbable pipeline embolization devices (PEDs) that will control aneurysm-specific hemodynamic parameters and degrade after completely dissolving the aneurysm.

Dr. Hari Kotturi, Professor of Biology, received a $31,389 grant for his project, “Incorporation of Mycobacteriophages in Electrospun Nanofiber.” The goal of the study is to develop an antimicrobial dressing by incorporating bacteriophages that can kill Mycobacterium abscessus, a common causative agent of soft tissue infections in hospitals. Dr. Kotturi’s research team will be able to enhance the antimicrobial property of polycaprolactone/collagen I (PCL/Col I) nanofiber by integrating mycobacteriophages into the nanofiber used as a wound dressing.

Dr. Christina Hendrickson, Coordinator of the Human Physiology Lab in the Department of Biology, was funded $27,083 for her project, “Investigating Anti-carcinogenic Effects of Taraxacum officinale.” The specific aims of the research are to: determine cancer cell viability and apoptosis; determine whether cancer cell apoptosis is activated by intrinsic or extrinsic pathways, and whether leakage of pro-apoptotic factors from mitochondria or induction of oxidative stress on cancer cells are involved in induced cell death; and determine cancer cell migration and invasion.