VCU GREAT to provide students from underrepresented backgrounds with research training, opportunities.

The program aims to diversify the field of behavioral research and enhance undergraduate student success.

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VCU Guided Research Experiences & Applied Training, or VCU GREAT, grew out of Spit for Science, an ongoing universitywide research project at VCU that creates unique, cross-disciplinary opportunities for students to work with leading researchers in substance use and emotional health. (Courtesy photo)

A newly established program at Virginia Commonwealth University will provide undergraduate students from underrepresented backgrounds with the opportunity to gain research skills training, work in campus research labs and receive mentorship from VCU faculty researchers.

The program, VCU Guided Research Experiences & Applied Training, or VCU GREAT, is funded by a recently awarded $486,000 grant from the National Institute on Alcohol Abuse and Alcoholism that has a goal of not only training young researchers but also to diversify the pipeline of scientists working in the fields of substance use and genetics research.

“We know there is a lack of diversity among scientists engaged in biomedical and behavioral research,” said Danielle M. Dick, Ph.D., a professor in the Department of Psychology in the College of Humanities and Sciences and the Department of Human and Molecular Genetics in the School of Medicine. “This grant focuses on introducing students from a diversity of backgrounds to the research process, with the long-term goal of creating a more diverse scientific workforce.”

The program grew out of Spit for Science, an ongoing universitywide project at VCU that creates unique, cross-disciplinary opportunities for students to work with leading researchers in substance use and emotional health, along with other research opportunities offered through the College Behavioral and Emotional Health Institute, in partnership with the Undergraduate Research Opportunities Program.

As part of VCU GREAT, roughly 10 students each summer will participate in an eight-week research experience — consisting of structured training and individual mentorship — designed to provide young researchers with foundational research skills, experiential learning and responsible conduct of research training.

“We want to use Spit for Science as a means to engage undergraduates in the importance of research,” said Dick, director of Spit for Science and the College Behavioral and Emotional Health Institute, or COBE. “And to that end, with VCU being such a diverse university, another real opportunity that we have here is to increase representation of historically underrepresented groups in the sciences.”

Participants in VCU GREAT will spend one week with the Spit for Science research team in a summer “boot camp” followed by seven weeks of supervised research in the lab of a VCU Spit for Science faculty collaborator.

“The idea is that over those eight weeks the students will gain research skills and, with our help, propel themselves into other research experiences with the eventual goal of entering academia and increasing diversity,” said Amy Adkins, Ph.D., an assistant professor in the Department of Psychology and director of undergraduate research at COBE.

Applications to take part in VCU GREAT will open in December and run through early March. It is aimed at students from disadvantaged backgrounds, students with disabilities, and students who are of underrepresented ethnicities, including blacks or African-Americans, Hispanics or Latinos, American Indians or Alaska Natives, and Native Hawaiians and other Pacific Islanders.

Following the eight-week experience, participants will continue to have access to monthly professional and career development meetings, networking opportunities and mentorship.

Herb Hill, director of undergraduate research opportunities in the Office of Academic Affairs, said the Undergraduate Research Opportunities Program will contribute to VCU GREAT by expanding on what it already provides for all undergraduates who are interested in engaging with research experience at VCU: access and support for student/mentor collaboration.

“With VCU GREAT, we have the opportunity to recruit and train undergraduates who are underrepresented in the behavioral sciences and assist them toward careers in science and research,” he said. “Along the way we will work to support them in disseminating their research via publications and conference presentations, identifying potential graduate programs, and generally building a network of support that the GREAT students can rely upon.”

VCU GREAT is an extension of a previous Spit for Science research course taught by Adkins. It builds on the previous course by adding mentorship from researchers working with the Spit for Science registry, which includes de-identified genotypic data (DNA extracted from spit) and other health information (from questionnaires) voluntarily provided by VCU students.

More than 12,300 VCU students have participated in the Spit for Science registry, with roughly 70 percent of incoming freshmen participating in years that data has been collected.

“It all goes into a huge database that is being used by researchers across the campus to understand risk and protective factors related to behavioral and emotional health and well-being,” Dick said. “And then the COBE Institute focuses on how can we translate that research to feedback and benefit our students and our broader university and community. So this grant is one piece of that mission that is specifically related to engaging undergraduates in research.”

More than 75 faculty from 27 departments across VCU, along with more than 65 additional trainees — graduate or post-doctoral researchers — work with Spit for Science data. A number of these faculty members will serve as mentors through VCU GREAT. More than 250 undergraduates have participated in research opportunities associated with Spit for Science.

“We have tremendous faculty expertise at VCU in behavioral and emotional health — everything from faculty who work on genetics and substance use, like our group, to faculty who work on mindfulness, sleep, depression and anxiety, parent-child relationships, romantic relationships, and how all of these factors ultimately influence college outcomes,” Dick said. “I could go on and on about the amazing work that is ongoing.”

Included among the VCU GREAT faculty mentors are:

Ananda Amstadter, Ph.D., associate professor in the Virginia Institute for Psychiatric and Behavioral Genetics

Bethany Coston, Ph.D., assistant professor in the Department of Gender, Sexuality and Women’s Studies

Chelsea Derlan, Ph.D., assistant professor in the Department of Psychology

Mignonne Guy, Ph.D., assistant professor in the Department of African American Studies

Wendy Kliewer, professor in the Department of Psychology

Joshua Langberg, associate professor in the Department of Psychology

Elizabeth Prom-Wormley, Ph.D., assistant professor in the Department of Family Medicine and Population Health in the School of Medicine

Jessica Salvatore, Ph.D., assistant professor in the Department of Psychology

Jasmin Vassileva, Ph.D., associate professor in the Department of Psychiatry

Scott Vrana, Ph.D., professor in the Department of Psychology

Call for Positions: VCU Work Study Research Assistant Program

We are happy to again call upon faculty for position descriptions for work study research assistants for the upcoming academic year.  The VCU Work-Study Research Assistantship Program (WSRA) was designed to give undergraduates the opportunity to gain experience with the research process while providing assistance to faculty mentors and research groups.  UROP collaborates with the Office of Financial Aid to utilize federal work-study funds to support undergraduate research assistants for VCU mentors.  There are two important points that mentors and department chairs should note before emailing a position description:

  1. I am pleased to announce VCU will be maintaining the 5% budget funding match that we started in 2017-2018. This means, employers will pay 5% of the total funding a student receives through the Federal Work Study program. The maximum award for the 2018-2019 year is $4000, meaning the maximum an employer could expect to pay is $200 per student. ($4000 x 0.05% = $200). This year the Work Study Office will bill each department, in December and in May, for the 5% funding.
  1. Mentors or a designated departmental staff member must be trained in VCU Realtime in order to approve hours worked by each work study research assistant.

Interested mentors should check with their dept. chair before moving forward.  We are asking mentors to submit a brief position description that outlines your expectations of a UROP RA to  Students are currently able to apply for positions and will accept offers quickly, so it is best to submit a position as soon as you are able to do so.  Please see the attached Faculty Guidance document linked below the flyer for more information and feel to direct any questions or concerns to me.

VCU students in the Undergraduate Research Opportunities Program are studying everything from archaeology to zebrafish

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Undergraduates present study findings at the annual VCU Poster Symposium for Undergraduate Research and Creativity. (Photos by Kevin Morley, University Relations)

Understanding the secrets of Skeleton Lake, using zebrafish to study neuron development and mapping tick infestations seem to be unrelated. But they are all tied together as topics researched by students in the Undergraduate Research Opportunities Program.

The program, an initiative of the Office of Research and Innovation, gives undergraduate students a unique chance to conduct real-world studies alongside nationally and internationally recognized faculty. It often represents one of the biggest highlights of their undergraduate careers.

Aishwarya Nugooru, a biology student in the College of Humanities and Sciences and pre-medicine, said conducting research and presenting findings gave her valuable experience translating research to the public.

“[The program] prepares undergraduates to be future scientists and researchers,” she said. “I believe that being able to clearly articulate your research to all audiences is crucial. UROP gives students the opportunity to do this before entering their careers.”

Many undergraduates introduced to faculty mentors have the opportunity to work in research settings in the UROP work study program. UROP funds a limited number of undergraduate student fellowships for research produced under faculty mentorship. The program also hosts the annual VCU Poster Symposium for Undergraduate Research and Creativity, part of the eighth annual Research Weeks in April. The event is a chance for undergraduate researchers to present research across disciplines in the arts, humanities, math and science.

VCU News interviewed several UROP researchers about their work:

The allure of Skeleton Lake

William Swilley is uncovering the secrets of the Skeleton Lake archaeological site in India.
William Swilley is uncovering the secrets of the Skeleton Lake archaeological site in India.

“That sounds like the name of a death metal band,” William Swilley said when he first heard about Roopkund Lake, a mysterious archaeological site more than 16,000 feet high in the Himalayas in northeast India. The site is more popularly known as Skeleton Lake.

Swilley, a senior who studies anthropology in the School of World Studies in the College of Humanities and Sciences, learned about the site from his mentor, Bernard Means, Ph.D., a VCU instructor of anthropology and director of the Virtual Curation Laboratory. The lab specializes in 3-D scanning and 3-D printing artifacts for museums and archaeological sites across the country. Means worked with archaeologist Vinod Nautiyal, Ph.D., of Hemvati Nandan Bahuguna Garhwal University, to 3-D scan and print skulls from Roopkund Lake.

The small lake, with a depth of about 6.5 feet, is known for the bones and artifacts strewn across its shore. The remains are remarkably well-preserved and dated more than 1,000 years ago to roughly 850 A.D. But not much else is known about the possibly nomadic group that died in the harsh extremities of the mountains.

“The fact that all of these people have expired on this mountain is tragic, but it’s actually a bittersweet moment for the archaeological community,” Swilley said. “At over 16,000 feet you have cold and dry conditions that preserve hair, skin and leather excellently. It’s almost like mummification.”

The site was discovered in the early 1940s by a British forest ranger. The remains were first suspected to be that of a Japanese invasion force but the absence of firearms, mess kits and uniforms suggested otherwise. An archaeologist dated the remains and discovered they belonged to individuals indigenous to the area and another ethnic group. Growing popularity of the site coincided with a movement to promote tourism of Indian cultural and ecological sites following the country’s independence in 1947. The remarkably well-preserved condition of the remains has allowed archaeologists to generate a number of competing theories about what killed the trekkers.

After researching the theories, Swilley agrees with the popular hypothesis that some members of the group died instantly when struck by large hailstones, or lost consciousness after impact and died from exposure.

Swilley hopes future studies will provide more information on the specific ethnic groups represented by the remains. But the removal of artifacts from the site by tourists could hamper research efforts, Swilley said.

“The removal of any artifact, eco-fact, feature or human remains without proper examination and notation can create errors in research,” he said. “It’s like taking pieces out of a puzzle box before the puzzle is complete. I can understand the desire to bring a trinket back from vacation, but gift shops exist for a reason.”


Zebrafish and development

Aishwarya Nugooru explains the impact of nesprin proteins on human development.
Aishwarya Nugooru explains the impact of nesprin proteins on human development.

Aishwarya Nugooru, a senior studying biology in the College of Humanities and Sciences and pre-medicine, is investigating how abnormalities and mutations in nesprin proteins might affect neural development. Nesprins are found in the nuclear membrane, which encases the nucleus of cells. The proteins are responsible for maintaining the structural integrity of the nuclear cell membrane. Mutations in the nesprin gene are associated with some forms of muscular dystrophies.

Nugooru investigated the role of nesprins in neural and muscular development using a zebrafish model in the neural development lab of Gregory Walsh, assistant professor in the Department of Biology in the College of Humanities and Sciences in collaboration with Daniel E. Conway, assistant professor in the Department of Biomedical Engineering in the College of Engineering. The researchers hypothesize that the inactivation of nesprin could result in defects in neuronal migration, or movement of neurons from origin to final position in the brain that occurs during an embryo’s gestation. Neuronal migration is essential for the assembly of neural circuits during brain development. Defects in neuronal migration could lead to several disorders.

Studying the impact of nesprin abnormalities in zebrafish models could later be translated to clinical settings to better devise therapeutic strategies for patients with mutations in nesprin.

Nugooru was responsible for much of the benchwork of the study, which included regulating nesprin expression in the embryos, imaging, embryo microscopy and breeding the zebrafish.

“In class I had learned about neurons and their functions but applying my knowledge by performing experiments and working on the in vivo model definitely helped me to further grasp the concepts,” she said. “It felt so much more abstract when learning in the classroom and from textbooks. But now I really understand the molecular mechanisms behind it and the connections to real-life applications.”


Pro sexual health practices

Jackie Offeh researches pro sexual health attitudes among young African-American women.
Jackie Offeh researches pro sexual health attitudes among young African-American women.

When Jacqueline Offeh volunteered as a facilitator for Voices, a program that promotes student discussion of safe sex and self-advocacy, she was excited about the opportunity to help other local college students. But Offeh was stunned to find that many women in the program were not aware of low-cost or free reproductive health services and current HIV preventive therapeutics. They also were less likely to negotiate condom usage with their partners and were not aware of various condom types, such as female condoms.

The senior, who studies psychology in the College of Humanities and Sciences, decided to examine the issue and found that self-advocacy in sexual situations, or pro sexual health, and awareness of sexual health resources was lowest among poor, African-American women.

“I found that many of these young adults, especially in the Richmond area, are less likely to emphasize pro sexual health in their lives,” Offeh said. “Pro sexual health is knowing that you’re able to say no, knowing that you are able to demand that your partner wear a condom, and that there are different types of condoms to use in different situations.”

The Voices program mostly serves African-American students attending Virginia Commonwealth and Virginia Union universities. Participants attend pro sexual health discussion groups with students of the same sexual orientation. In her role as facilitator, Offeh was able to gather information from consenting students to inform her conclusions. She collected demographic information from the participants, including race, gender, income level, housing location and where they attended high school.

“African-American women of lower socioeconomic backgrounds, who attended high school in economically disadvantaged districts, tended to be less likely to negotiate with partners on condom use, insist on STI and HIV testing for their partners and to have less knowledge of HIV preventative therapeutics.”

Socioeconomic barriers to health care, housing and HIV prevention education have been linked to increased risk of HIV transmission, especially among African Americans, according to the Centers for Disease Control and Prevention. African Americans are less likely to be connected with care providers, which prevents access to viral suppression therapies. The CDC also notes that in 2016, African Americans accounted for 44 percent of HIV diagnoses but comprise 12 percent of the population.

During her senior year, Offeh plans to continue facilitating Voices and aims to help expand the program to other college students, sexually active teenagers and other local stakeholders. Offeh was led in her study by mentor Mona L. Quarless, a doctoral student studying psychology; and Faye Belgrave, Ph.D., professor of health psychology and social psychology. Both are part of the Center for Cultural Experiences in Prevention.


Ticks and white-tailed deer

Emma Davis is studying tick biodiversity and the population of white-tailed deer.
Emma Davis is studying tick biodiversity and the population of white-tailed deer.

Emma Davis, who graduated on Saturday with an undergraduate degree in biology in the College of Humanities and Sciences, wants to help visitors of the James River Park System avoid tick-borne diseases. She is currently working with Anne Wright, outreach director at the Center for Environmental Studies and an assistant professor in the Department of Biology, to determine if there is a correlation between tick biodiversity and high numbers of white-tailed deer in the park system.

For part of years 2016-18, Davis used wildlife cameras to record deer activity in the parks and observed more instances of white-tailed deer movement than any other mammal. The cameras were installed four years ago by Wright to document the biodiversity of animal species within the parks. Davis and Wright suspect that tick biodiversity in the James River Park System, which reflects the number and variety of tick species present, is tied to the location of white-tailed deer populations.

“We are thinking that when there are more white-tailed deer in the area, they will act as hosts for ticks, which could be carriers of bacteria they get from deer which could spread to humans,” Davis said.

Lyme disease spreads when ticks take blood meals from animals infected with disease-causing bacterium, which is transferred to humans by latching ticks.

The researchers noted that the Pony Pasture and Wetlands sections of the park system, located to the south, had the highest numbers of white-tailed deer. In March, Davis attempted to collect ticks in those areas by running pieces of white denim material over grassy areas. Scientists use this method to detect ticks that are questing, or raising their front legs in search of warm bodies on which to latch. Davis was not able to find any ticks and suspects it was because the weather was unseasonably cold.

She plans to continue the search this summer and will use coarser material, which she suspects will allow the ticks to better adhere. Davis and Wright hope to eventually gather enough data to produce a map of areas within the park system most infested with ticks.

“We could hopefully put signage in those areas and encourage people to stay on trails, keep their dogs on a leash and other helpful hints to avoid ticks,” she said. “Hopefully we can keep people a little safer.”

Summer Research Opportunities with VCU Virginia Institute for Psychiatric and Behavioral Genetics

Dr. Ruth Brown is looking for one to two undergraduate students to assist with research focused on trauma, stress, and mental health of children and adults with intellectual and developmental disabilities. Dr. Brown is currently conducting two studies. One will use clinical interviews and self-report questionnaires to identify DNA methylation associated with stress and depression in people with Down syndrome. The other study will evaluate the effectiveness of a workshop to train healthcare professionals to use trauma-informed approaches to help adults with intellectual disabilities who have experienced trauma.

Duties may include contacting potential research participants by phone and email, preparing marketing material, scheduling research participants, assisting with administration of research surveys, assisting with event registration, data entry, literature searches, and creating data tables. Students will have the opportunity to learn about human subjects research and receive mentorship on CV development, graduate school or job applications, and other professional development skills. Students may have opportunities to prepare and present research at local and national conferences and publication of research findings.

Applicants should have a minimum GPA of 3.2. Ideal candidates will be able to commit 10 – 15 hours a week for at least one year on the project, be detail-oriented, motivated, outgoing, and willing to learn. Students seeking degrees in psychology, psychiatry, social work, rehabilitation, public health, or related degrees are preferred. Prior experience interacting with people with intellectual and developmental disabilities is desired.

Interested applicants should contact Dr. Ruth Brown at

Congratulations to our Outstanding Faculty Mentor Awardees for 2018!

Each year, the VCU Undergraduate Research Opportunities Program accepts nominations from students for our “Outstanding Faculty Mentor” Awards. Undergraduate researchers are asked to identify a professor or faculty mentor who regularly goes above and beyond to create and engage students in research opportunities.

Students provide a written statement that describes why the chosen nominee deserves an outstanding mentorship award, including specific examples that detail their nominee’s contribution to undergraduate research at VCU.  The main criteria for these nominations include; how the faculty member has enhanced the skills related to undergraduate research in their discipline, how the nominee has expanded the knowledge base of student researchers, the ways in which the mentor has assisted undergraduates in their engagement with research, the lasting impression the mentor has made on students’ future academic and professional plans.

Please join us in recognizing our 2018 Outstanding Faculty Mentors!

Dr. Bridget T. McInnes, Dept. of Computer Science, VCU School of Engineering – Student: Clint Cuffy

“Professor Bridget T. McInnes has insurmountable drive to learn, knowledge to achieve, and demonstrates impeccable skills in the art of machine learning; as a result, my knowledge set in the subject has increased as well, especially regarding neural networks.  In the beginning she oversaw my research, then slowly but surely she was able to see the fruits of my labor from her guidance. Since then, we’ve been able to accomplish many aspects of research. Some have even been published.  I’ve always looked towards getting a job pursuing my interest in programming.  However, under the guidance of Dr. McInnes, I slowly transitioned, seeing myself graduating and continuing towards my graduate degree or PHD and pursuing research. The more I research and spend time in the natural language processing lab amongst other researchers, the more that idea changes from possibility to actuality. This would have not been possible without her intervention”.

Dr. Esra Sahingur, Dept. of Periodontics, VCU School of Dentistry – Student: Nitika Gupta

“Dr. Sahingur has invested her time in enhancing my education. She has suggested classes to take that will aid me in performing research. Moreover, my passion for molecular and cellular biology and biochemistry has grown exponentially while working in the lab. She helped me relate the information I learned in class to the experiments I was performing in lab. However, Dr. Sahingur’s extent of increasing my education did not stop in the classroom, rather she continuously exposed me to the current work done in the periodontal field. From emailing me articles to introducing me to techniques and common practices in the field, my depth of knowledge has increased significantly.  More than serving as an instructor, Dr. Sahingur has fulfilled the role of a coach – she believed in me.  She also kept her expectations high, which only pushed me to surpass them.  As a result of the bar being raised, I worked harder to receive admission into a top 10 dental school. As of fall 2018, I will be attending the University of Pennsylvania School of Dental Medicine.  Although Dr. Sahingur has an abundance of responsibilities as a researcher, professor, and Periodontist, she never forgets about her mentees. The unique relationship I have built with Dr. Sahingur encompasses endless motivation, inspiration, and support.  Dr. Sahingur has served an integral part of my career. I hope to inspire others the way she has inspired me”.

Dr. Sarah Seashols-Williams, Dept. of Forensic Science – Student: Christian Renwick

“During my second semester volunteering in her laboratory, Dr. Williams assigned me to contribute to a project regarding DNA stability after Raman exposure, under the tutelage of a more senior undergraduate student. From the guidance of both Dr. Williams and the other students in her lab, through projects such as the Raman study, I was exposed to materials that I would never have been solely through my coursework. Exploration of not only analytical methods, such as Raman spectroscopy and melt curve analysis but the underlying principles on which they operate has been a key benefit to my college career.  I not only learned real-life applications of materials that had been covered only theoretically in class, such as DNA quantitation, capillary electrophoresis, and STR analysis. I also had the gained exposure to the extremely crucial aspects of troubleshooting, which I believe can only be acquired through trial and error.   It is all these aspects which have culminated in the most impactful experience I have had during college. Dr. Williams is deserving of the UROP Faculty Mentorship Award for not only her support of my growth, but for the growth of each undergraduate student who has or is yet to pass through her lab”.

Student researcher finds that medicinal Chinese herbs are unsafe when not skillfully and carefully prepared

Featured photo
Julia Grzymkowski.

As part of Research Weeks (April 6–27) we are highlighting the work of six undergraduates whose work was made possible by VCU’s Undergraduate Research Opportunities ProgramGlobal Education OfficeDivision for Inclusive Excellence and guidance from faculty members.

Research Weeks takes place on both campuses and features a wide variety of projects in multiple disciplines.

See more stories by clicking on links in the “Related stories” section or learn more about the lineup of events for this year’s Research Weeks.

Sales of Chinese herbs in the U.S. have increased in recent years, with many people viewing them as a less expensive, and more effective alternative to traditional pharmaceutics with fewer adverse side effects. However, medicinal teas brewed from these herbs are unsafe if not properly administered, VCU student Julia Grzymkowski has found in her research.

A senior majoring in forensic science and chemistry, Grzymkowski tested various brewing methods to determine their ability to eliminate bacterial cultures, and identified bacterial species found on medicinal Chinese herbs. Grzymkowski works in the lab of Michelle Peace, Ph.D., associate professor of forensic science in the College of Humanities and Sciences, who has published a number of studies on the properties of natural and plant-based materials.

The case of a woman who died after ingesting a traditional remedy without consulting her doctor piqued Grzymkowski’s interest in the possible deleterious effects of Chinese herbs. The woman sought relief from symptoms related to irritable bowel syndrome and became ill when the herbs counteracted each other. She experienced flu-like symptoms and died from multiple organ failure during surgery. Post-mortem microbial toxicology analysis of sampled lung tissue revealed a common pneumonia-causing bacteria.

Grzymkowski said that while Chinese herbal remedies can be effective, they should be administered under the guidance of a licensed professional, or at the very least, the accompanying brewing instructions followed.

It’s important to use high temperatures to kill the bacteria.

“These are unsterilized substances that come from the earth and are handled by a variety of people before they make it to you,” she said. “It’s important to use high temperatures to kill the bacteria. You would rather be safe than sorry.”

Grzymkowski analyzed 11 Chinese herbs known for their analgesic, anticonvulsant, sedative or hypnotic effects.

She tested the efficacy of three brewing methods in killing bacteria by exposing samples of the herbs to Bacillus cereus — a bacteria that contributes to foodborne illness — to determine if the germ would survive brewing. While brewing instructions accompanying every herb eliminated some bacteria, a method prescribed by an herbal pharmacist to steep herbs in boiling water for 1.5 hours was the most effective at decontamination. Steeping the herbs for only a few minutes, as is done with many western teas, was less effective.

The fastest brewing method did not kill all of the spores placed on the herbs. Upwards of 3,000 bacterial cells with growth viability still existed in the tea.

“Any bacterial colony that can grow on a plate can potentially grow on human tissue,” Grzymkowski said. “It only takes one viable bacteria cell to start growth.”

In subsequent tests, she did not add bacteria to the herbs but classified existing bacteria on herb samples taken directly from packaging. She cultured the bacteria and identified species by isolating their individual fatty acid chains, which are important and unique structural features of their cell membranes.

Grzymkowski identified disease-causing bacteria such as Bacillus cereus and Bacillus anthracis, the latter of which is a known bioterrorism agent.

She found the work rewarding because it expanded her knowledge of microbiology.

“After mostly studying chemistry, I dove into a different discipline with this microorganism study,” she said. “I learned a lot of new techniques I would not have otherwise.”

Peace urged Grzymkowski to undertake the project to add to a previous student’s work identifying the drug-like compounds in Chinese herbs. Peace is helping Grzymkowski publish two papers, one on Chinese herbs and the other on the properties of kratom; a plant-based drug that can act as a stimulant or depressant, depending on how much is taken.

Peace encourages Grzymkowski to pursue a doctoral degree and sees a bright future for the budding scientist.

“Anything Julia sets her mind to, she just devours!” Peace said. “She is so efficient, so competent and just brilliant.”

Engineering student researches machine learning for language processing

Using computers to comb the vast sea of biomedical literature could be key to identifying relationships among concepts.

Featured photo
Clint Cuffy.

As part of Research Weeks (April 6–27) we are highlighting the work of six undergraduates whose work was made possible by VCU’s Undergraduate Research Opportunities ProgramGlobal Education OfficeDivision for Inclusive Excellence and guidance from faculty members.

Research Weeks takes place on both campuses and features a wide variety of projects in multiple disciplines.

See more stories by clicking on links in the “Related stories” section or learn more about the lineup of events for this year’s Research Weeks.

Clint Cuffy has always been interested in machine learning — the area of computer science in which computers use data to learn how to perform tasks, rather than being specifically programmed to do those tasks. But he lacked the opportunity to delve into the subject.

“It seemed like a daunting task without a finite starting point, especially when it comes to neural networks,” said the senior, who is majoring in computer science at the Virginia Commonwealth University School of Engineering. “Learning the inner workings and how to implement algorithmic approaches of modeling how the human mind works seemed far-fetched at best.”

Then Bridget McInnes, Ph.D., assistant professor in the Department of Computer Science, approached him with an opportunity to research machine learning with regard to natural language processing, and the rest is history, Cuffy said.

“My research project [‘Identifying relations in biomedical text for literature-based discovery’] entails using a neural network, an algorithm modeled after how the mind functions in regards to a-cyclical connected neurons, to learn unique relationships between concepts through predications and represent them in semantic space as concept vectors,” Cuffy said. “That is to say, considering an example such as ‘aspirin treats headaches,’ we can see the relationships between all three of these terms. ‘Aspirin’ and ‘headaches’ are related through the word ‘treats.’ Semantic similarity and relatedness defines how words can be similar to each other, such as ‘liver-organ,’ or related, such as ‘aspirin-headache,’ through predicate relationships. Using the previous examples, ‘liver is an organ,’ since liver is a more specific subset of an organ they are similar, but aspirin is not a headache so they are not similar. Since aspirin is used to treat headaches, they are related by the ‘treats’ predication.

“With this knowledge, we [use] a neural network that learns how to define representations of concepts in semantic space, in terms of similarity and relatedness, by the hypothesis words that can be defined by the context which surrounds it.”

Biomedical research publications are being published at an astounding rate, Cuffy noted. These publications could hold keys to potentially important relationships in literature-based discovery, but keeping up by reading a single document at a time and identifying possible relationships poses a daunting task, he said.

However, researchers have consequently found relationships among concepts through accidental or investigative reading of these publications. Attempts have been made to automate the process, but in order to identify meaningful relationships that are presently unknown, Cuffy and McInnes are building a foundation by identifying those that already exist within semantic space. They are training a neural network using data from the National Institutes of Health — which contains a Semantic Predication Database with more than 91.6 million examples of predication triplets — to generate term vectors that define the concepts and predicates with high levels of accuracy.

“The significance to this could be the key to unlocking more meaningful relationships,” Cuffy said. “Rather than investigative or accidental relationships being discovered, we could potentially automate this process.”

Providing undergraduate students the opportunity to conduct research is an important part of their education, McInnes said. “Experiential learning initiatives have been shown to aid in the development of undergraduates’ professional habits and promote scientific and critical thinking.” Cuffy said the project has further fueled his drive to see the limits of machine learning and its practicality. “Performing research at the undergraduate level is a blessing in disguise,” Cuffy said. “You find yourself exposed to information, briefly discussed or taught at the classroom level, taken steps further into practical application. … Research can be a very challenging, but rewarding, experience. Not only are you increasing your knowledge-set and learning invaluable information, but there is always the possibility of having a positive impact on the lives of others through your research.”

A study in unpredictability: VCU senior learns that when it comes to public health research, planning is only part of the process

Featured photo
Noelle Pooler.

As part of Research Weeks (April 6–27) we are highlighting the work of six undergraduates whose work was made possible by VCU’s Undergraduate Research Opportunities ProgramGlobal Education OfficeDivision for Inclusive Excellence and guidance from faculty members.

Research Weeks takes place on both campuses and features a wide variety of projects in multiple disciplines.

See more stories by clicking on links in the “Related stories” section or learn more about the lineup of events for this year’s Research Weeks.

In her office at the 500 Academic Centre building on Virginia Commonwealth University’s Monroe Park Campus, Joann Richardson, Ph.D., has a framed thank you letter from a Jamaican woman who participated in a health study led by a VCU student.

“Thank you for choosing me to participate in the study,” the letter says. “I have learned so much about my health and now am educating my family from what I have learned from the survey. I have impacted other lives from it because they are eating properly, exercising and taking better care of themselves.”

Richardson, an associate professor in VCU’s Department of Kinesiology and Health Sciences, served as the faculty adviser for an Undergraduate Research and Creative Scholarship study that started in 2016. Last year, physical education and exercise science senior Noelle Pooler picked up where the original study left off. The purpose of the study was influencing attitudes and behaviors toward health, with an ultimate goal of preventing and controlling the development of hypertension and diabetes among rural, medically underserved Jamaican women of childbearing age.

Noncommunicable diseases are the leading cause of death globally, according to the World Health Organization. Jamaica’s Ministry of Health indicates that the diseases, which include hypertension and diabetes, account for about 60 percent of deaths among men and 75 percent of deaths among women. Pooler’s research focused on the fact that hypertension and diabetes can be reduced with educational interventions that change lifestyle risk factors. In her research proposal, she hypothesized that informing people about the seriousness, risks and preventive measures to control hypertension and diabetes could help their society and communities function optimally.

“The study was focused on empowering people through knowledge so that they can improve their health,” Pooler said.

Pooler traveled to Jamaica last summer to conduct the first phase of research. Prior to starting the Undergraduate Research Opportunities Program study, she had not conducted research independently.

“I was really overwhelmed at first,” she said.

Before traveling to Jamaica, the New Jersey native researched Jamaican culture and government to prepare for identifying with and relating to the study participants. “I wanted to be culturally competent when I arrived,” she said.

In Jamaica, she recruited 15 women to participate in the study. The women, who ranged in age from 15 to 44 years old, first completed a survey that quantified their knowledge about hypertension and diabetes. They then participated in an informational session — led by Pooler — about the effect of exercise and nutrition on development of the diseases. “Being able to empower someone with knowledge that way was very humbling,” Pooler said. The women were later asked to complete surveys that assessed the effectiveness of the informational session.

The second and third phases of the study involved collecting post-session surveys in the months following the information session, but Pooler ran into obstacles in completing those phases.

“The personality and nature of the Jamaican women is that they do better in a personal environment,” Richardson said. “Trying to do a study long distance just didn’t work for them.”

Though Pooler was not able to complete the study, she said she still learned a lot from participating.

“Dr. Richardson warned me in advance that the nature of public health research is that it is unpredictable,” Pooler said. “You have to be prepared to roll with the punches.”

While she does not foresee a future career in public health research, Pooler was grateful for the opportunity to learn more about the research experience and be immersed in a culture unfamiliar to her.

“Doing this research solidified the fact that I like working with people and want to work with a diverse population,” Pooler said. “It is important to have a diverse array of knowledge and experiences working with different types of people from different cultures.”

Infection detection: VCU student researcher is using the latest DNA sequencing technologies to pinpoint a malaria parasite

Analyzing DNA data of mosquitoes has been “an amazing window into the world of malaria research and its importance to global health,” Megan Mair said.

Featured photo
Megan Mair.

As part of Research Weeks (April 6–27) we are highlighting the work of six undergraduates whose work was made possible by VCU’s Undergraduate Research Opportunities ProgramGlobal Education OfficeDivision for Inclusive Excellence and guidance from faculty members.

Research Weeks takes place on both campuses and features a wide variety of projects in multiple disciplines.

See more stories by clicking on links in the “Related stories” section or learn more about the lineup of events for this year’s Research Weeks.

A Virginia Commonwealth University student researcher is perfecting methods of detecting a malaria parasite in mosquitoes in the Brazilian Amazon.

Megan Mair and mentor Luiz Shozo Ozaki, Ph.D., associate professor in the VCU Center for the Study of Biological Complexity, use the latest DNA sequencing technologies to identify plasmodium, the malaria parasite in anopheline mosquitoes. The insect transmits the parasite to humans.

Mair, a senior studying bioinformatics, is working with Ozaki and collaborators at the institutions Fiocruz Rondonia in Brazil, and the Liverpool School of Tropical Medicine in England, to determine if new DNA sequencing technologies can help better identify the malaria parasite than more commonly used methods. Researchers typically identify a particular protein or examine DNA fragments of the parasite, but this does not always paint a complete picture, Mair said.

“These methods have the potential to lead to false positives and false negatives due to lack of specificity,” she said. “If we can determine infection of the parasite based on sequencing reads, and if the cost and complexity of sequencing goes down in the next few years, this could be a sound method to utilize in the field.”

Mair said the work gave her a compelling experience in tropical diseases.

This has been an amazing window into the world of malaria research and its importance to global health.

“I had never put much thought into malaria research because it doesn’t affect a lot of people in the United States,” Mair said. “This has been an amazing window into the world of malaria research and its importance to global health.”

Mair analyzed DNA sequencing data of mosquitoes collected by colleagues in the village Vila Amazonas, a village in the Brazilian state of Rondonia, where in 2008 researchers attempted to eliminate malaria by directly eliminating the parasite in the human host. Ozaki and his collaborators are concurrently characterizing the genetic profile of two populations of mosquitoes captured before and after malaria was eliminated in the village.

Mair spent much of last summer sorting DNA sequences from more than 1,000 mosquitoes. She compared sequences from the total DNA of the mosquitoes to those in a database of plasmodium DNA to determine which mosquitoes were infected.

Mair and collaborators found additional confirmation that malaria elimination efforts in Vila Amazonas were effective. Before the disease was eliminated, there was higher incidence of the malaria parasite within mosquitoes.

The researchers are also confirming evidence they found of a species of malaria parasite not previously documented in the region.

“If that is true, this could really change the way malaria is treated in Brazil because that parasite isn’t currently screened for in humans,” Mair said. “We are hoping this isn’t the case. Hopefully, more DNA sequencing would confirm this with certainty.”

Mair said she would like to work with another graduate researcher in bioinformatics to continue interpreting the mosquito data. Ozaki said Mair’s technical skills and approach to scientific research will serve her well in this and future endeavors.

“Her computational skills are impressive. For instance, she is able to quickly write an algorithm to sort specific files from millions in a database,” he said. “What most impresses me is her inquisitive mind, new ideas and original conclusions.”