Category: CMS

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.

From the Desk of the Dean 2021

Gloria Caddell, Ph. D.Dear CMS Alumni & Friends,

Before I sat down to write this today, I took a break and walked around campus.  I saw the redbud and maple flowers starting to open, the pine trees forming new cones, and the saucer magnolias in bloom.  Although I also saw my favorite bur oak tree whose towering shape had been devastated by the recent ice storm, I felt hopeful after a very challenging year.  And not just because it is spring.  Over the weekend, I attended our Tri-Center Symposium, where students and their faculty mentors from our three interdisciplinary research centers presented posters.  At the symposium, three of our outstanding alumni related to the students how the research opportunities they had at UCO and the close interactions with the faculty had prepared them for success in their Ph.D. programs and careers.  The students were able to share their research because, with safety measures in place, they had continued to work in our research labs and in the field over this past year.  The symposium was in a virtual format, but there were advantages to that.  The posters were viewable for a few days in advance, so attendees could come with questions.  Students gave a short summary of their poster, and many constructive questions were easily asked and answered in the “Chat”.   A group of faculty and staff did an incredible job selecting the virtual platform and planning all the details of this highly successful event.

I was also feeling hopeful today because of some other impressive accomplishments by our students. Kayley McBride, assisted by Mahnoor Ahsan and mentored by Dr. Christina Hendrickson and Dr. Mel Vaughan, received 1st place in the Regional, Community, and Tribal College category at the EPSCoR Research Day at the Capitol for her poster on using dandelion extract to treat cervical cancer.  Also, two of Dr. Nikki Seagraves’ students, Nazgul Nurbyek and Michaela Vance, were among the 60 participants selected from hundreds of applicants to present their research on the effect of phenylalanine, retinoic acid, retinol, and citral on proliferation of O9-1 mouse cranial neural crest cells at the Council for Undergraduate Research’s Posters on the Hill 2021.  Another noteworthy achievement is the growing list of our students accepted to medical and dental schools for this coming fall.

My hope continues to grow because I know that our nursing students and faculty, through their participation in the clinics administering COVID-19 vaccines to our faculty, staff, and students, are helping make it possible for us to return to full face-to-face classes in the fall, as recently announced.  I look forward to noisy hallways and to the Howell Hall Atrium filled with students gathered around whiteboards covered with equations.

Like all universities across the nation, we have had to deal with declining enrollment and resources over the past year. The value of higher education is being questioned. I am confident that, as demonstrated by the above examples, there is tremendous value to a degree from our college. Throughout the pandemic, we have remained steadfast in our commitment to our mission to advance knowledge, prepare students for success and leadership roles, and contribute to the intellectual life, health, and economy of the metropolitan area.  In my letter in the fall newsletter, I said that our “landscape” after the pandemic might not look like it did before. We have learned much, and I suspect that we will retain some positive changes such as faculty holding virtual office hours to make themselves more accessible to students. There will be much good that emerges from this past year.

On behalf of the faculty, staff, and students, I thank you for your continued confidence in and support of our college.  And I wish you a very hopeful spring!

Gloria Caddell, Ph.D.
Interim Dean, College of Mathematics and Science

 

Student Highlight- Maggie Ward

My name is Maggie Ward, and I’m currently a third-year chemistry major here at UCO. I graduated from Broken Arrow High School and started my undergraduate education as a forensic science and biology major. However, as I started doing research in inorganic chemistry as a freshman, I soon discovered my love for research. Now, I intend to go to graduate school to get my doctorate in organic or inorganic chemistry.

The current project in my research group centers around using the Evans Method to calculate the number of unpaired electrons in a particular sample. We insert a sealed capillary tube containing a solvent and its deuterated counterpart into an NMR tube containing our complex of interest. The extra solvent tube inside creates a large solvent peak in the 1H-NMR spectrum, and we can calculate the number of unpaired electrons from the distance between the solvent peak and the peak from our sample.

Program Highlight- PSM

Computational Problem Solving: Engineers’ soft skill for the 21st Century

Engineering is defined as the application of math and science to solve problems and engineers are often defined as critical thinkers. Transformational changes in computer technology and extensive use of computers may expand this definition to computational thinkers and computational problem solvers.

The term “computational thinking” was initially associated only with computer scientists, computer engineers, or software engineers. In recent years we saw a paradigm shift. Computational thinking and computational literacy made inroads into all science and engineering disciplines. Integration of computational principles and tools into science and engineering enhances the way of solving complex problems.

So, what actually is computational thinking? Does it mean knowing how to use a computer and the internet? Does it mean knowing a programming language or coding?

Computational thinking is a thought process involved in problem-solving.  It is strategically designing a solution in a form that can be effectively carried out by a computer.

Sorting, searching, clustering, basic mathematical operations like addition, subtraction, multiplication can easily be performed by computers in a very short amount of time. The first step in computational problem solving is called algorithm development, which is converting your problem into a suitable form that computers can recognize. Furthermore, it is developing a set of instructions or sequences which can be easily executed by computers.

To program a computer to execute a step-by-step procedure, an algorithm needs to be translated into a machine language that can be read by a computer. Programming or coding can be explained as translating higher-level human language (i.e: English) to a machine language (i.e: Python, C, Java, etc.).  Programming is a fundamental part of computational problem-solving. It needs creativity and the ability to communicate in writing a code that humans can easily read while computers can still properly execute it.

Among the programming languages, Python has clearly come a long way since the 1990s; it now has one of the most crowded developer communities and is the second most used language on GitHub. The availability of specific Python libraries and frameworks make it an easy choice for all kinds of projects in Web development, artificial intelligence, data analysis, and scientific computing.

Many middle and high schools in the U.S. are now teaching Python as part of their curriculum. Engineering schools are looking for ways to incorporate computational thinking and programming in their curriculum. Computational Engineering and Computational Science graduate programs are gaining popularity among students as they have greater potential to better prepare them for 21st Century job market.

The University of Central Oklahoma is leading the way in developing computational science and engineering curriculum by offering the one and only Computational Science and Engineering Professional Science Master’s degree in Oklahoma. Professional Science Master’s (PSM) degrees are the fastest-growing type of master’s degree in the United States. It is partly a technical science master’s degree (think statistics, engineering, or computer science) with communications and business courses added to the mix.

The PSM degree is designed to train the next generation of STEM (Science, Technology, Engineering, Mathematics) professionals for the integrator and technical leadership roles in science-intensive industries.

Student Highlight: Mukesh Tumbapo and Matthew Henry

Two Engineering Physics Master’s Recipients Present Research on Phosphorene and Silicene:

Mukesh Tumbapo and Matthew Henry both completed Master’s degrees in Engineering – Physics last December. Their research was conducted under the direction of UCO Associate Professor Dr. Benjamin Tayo. Ever since the isolation and controlled exploration of the two-dimensional (2D) crystal graphene was made possible (leading to the Nobel Prize in Physics in 2010), the scientific community has taken great interest in the possibilities graphene offers for new approaches to DNA sequencing. Despite several major advances, sequencing DNA using graphene has not yet been demonstrated. One of the major hindrances is the hydrophobic nature of graphene’s surface which causes DNA bases to stick to its surface. Matthew and Mukesh have demonstrated, using computational studies, that phosphorene and silicene are promising alternatives to graphene.

Binding energy (in electron-volt) for GNP, PNP, and SNP.

The above figure from their work shows that binding energies of the 4 DNA bases Guanine (G), Adenine (A), Cytosine (C), and Thymine (T) for interaction with graphene nanopore (GNP) are much higher than those for phosphorene nanopore (PNP) and silicene nanopore (SNP). This shows a minimal tendency for bases to stick on phosphorene and silicene, compared to graphene.  Hence the problem of DNA bases sticking to graphene’s surface is not expected for phosphorene and silicone. These results were presented at three national conferences and at two regional conferences, and are also the subject of a manuscript that has been accepted for publication in the journal AIP Advances.

Matthew accepted a position as a Systems Engineer at Boeing, and Mukesh is considering whether to move into the industry or continue his studies in pursuit of a doctorate.