Genomics and Bioinformatics Facility advances high-tech faculty and student research
CLEMSON — Genetics and biochemistry professor James Morris, a leading expert on the parasite that causes African sleeping sickness, made an important discovery in 2018 that is helping scientists unravel the mysteries surrounding this devastating disease, which infects both humans and livestock, particularly in sub-Saharan Africa.
According to Morris, this discovery was made possible, in large part, because of the RNA sequence analysis support he received from the Clemson University Genomics and Bioinformatics Facility (CUGBF), a partnership facility recently established by the College of Science and the NIH-Eukaryotic Pathogens Innovation Center (EPIC) COBRE training grant.
CUGBF’s mission is to make genomic investigations and analyses accessible to Clemson investigators at all levels through educational partnerships and mentoring experiences. In Morris’ case, CUGBF provided the bioinformatic expertise to turn a mountain of abstruse data into a biological resource.
“We had sequenced the RNA the cells were making to know what the parasite was up to,” said Morris, a faculty member in EPIC. “The staff was able to take our incredibly large datasets and distill them down into some biologically relevant observations. There was absolutely no way I could have done that without the help of the CUGBF.”
CUGBF provides Clemson scientists and engineers with knowledge and training to bring genomic resources to bear on research addressing a variety of issues, including pork quality, coastal ecosystem health, obesity, hazardous waste management, and parasitic diseases.
CUGBF molecular lab technician Jaime Randise (right) mentoring Microbiology undergraduate student Alexis McCollum (left) on the experimental set-up using droplet digital PCR technology.
A fee-for-service facility, CUGBF has experienced and knowledgeable staff, as well as powerful DNA/RNA sequencing tools such as the Agilent Bioanalyzer, Illumina NextSeq 550 sequencer, access to an Illumina NovaSeq 6000, and a droplet digital polymerase chain reaction (ddPCR) machine for examining gene abundance and expression.
The facility also owns two large memory nodes on Clemson’s Palmetto Cluster, a high-performance supercomputer that handles computationally demanding genomic datasets.
While some researchers may prefer to send their genomic data to a commercial warehouse for sequencing, CUGBF can perform preliminary sequencing quickly and guide bioinformatic analyses to enable focused research studies that become the foundation for million-dollar grants.
Biological sciences assistant professor Zhicheng Dou, who studies the basic biology of the Toxoplasma parasite in order to combat toxoplasmosis, a widespread human infectious disease, worked with CUGBF staff to perform RNA sequencing and differential gene expression analysis.
“I’m a biologist, not a bioinformatics scientist, so I focus on the genes,” Dou said. “The report they provided enables me to decide which genes to study based on their interactions with other genes.”
Dou’s collaboration with the CUGBF resulted in a published paper in PLOS Pathogens and a $1.8 million research proposal to the National Institutes of Health (NIH). Bioinformatics research associate Rooksana “Rooksie” Noorai also deposited Dou’s raw data files of transcriptomic sequencing into the NIH Gene Expression Omnibus (GEO) database, so it is accessible to scientists conducting gene expression studies worldwide.
According to Morris, CUGBF’s computational and statistical expertise is a real strength for the Clemson campus.
In a multi-university collaboration, Morris and his colleagues are trying to identify useful drug targets for pathogenic free-living amoeba, including the rare but deadly Naegleria fowleri that infects people swimming in warm lakes by entering their nose and eventually destroying their brain tissue.
Having a quality reference genome for the pathogens is key, said Morris, noting that some of the current genome sequences are in poor shape.
“We provided Rooksie with datasets from all over the world that had not been properly annotated or managed largely because it is such a challenge to do this,” said Morris, who is submitting a new funding proposal to NIH to exploit this work. “She took other people’s data and was able to distill down the good and bad parts and help us assemble genomes that were useful to identify targets.”
In addition to working with established research faculty, CUGBF provides hands-on learning and mentorship experiences, especially for student investigators.
“I was very intimidated by genomics and bioinformatics when I started my Ph.D. at Clemson,” said Melissa Heintz, an environmental toxicology doctoral student who used the facility for her studies on the relationship between metabolic enzymes and obesity.
Noorai taught her how to use an RNAseq (transcriptomics) pipeline and explained how to apply it to her own data. “I now feel very comfortable with transcriptomics and feel as though it is now one of my strengths coming out of my Ph.D.,” Heintz said.
While Noorai provides the bioinformatics expertise, molecular lab technician Jaime Randise works with users on the sequencing side, from performing nucleic acid isolation to full sequencing and teaching researchers various molecular biology techniques.
“The staff was helpful running samples through the bioanalyzer to get RIN values to see if the samples were of high enough quality to be sent off for sequencing,” said Heintz who worked with Randise to process RNA samples.
By guiding students through both the wet-lab and bioinformatic sides of genomic analyses, CUGBF hopes to convey a comprehensive understanding and sense of ownership to students that they might otherwise miss out on.
More recently, CUBGF staff have also conducted hands-on workshops for Clemson faculty, students and post-doctoral researchers as well as student-to-student mentoring in bioinformatic analyses.
“An on-campus genomics and bioinformatics facility is paramount for our faculty and students’ research programs to be competitive in the life sciences funding arena,” said CUGBF interim director Christopher Parkinson, a professor of biological sciences and forestry and environmental conservation. “Being able to generate and analyze ‘Big Data’ data sets in a timely manner with the students learning how to carry out their own analyses helps create a ‘can do attitude’ and advances SciForward and ClemsonForward.”
During 2019, CUGBF staffers have worked with 38 faculty from four colleges on campus, with over 75 percent of the faculty coming from the College of Science. In all, they have assisted 141 researchers.
In addition to offering a full-service genomics lab and bioinformatics team, the Clemson University Genomics and Bioinformatics Facility provides training to students, post-docs and faculty in genomic and bioinformatic techniques. Outside of the lab, CUGBF also offers training and informational workshops to Clemson’s diverse scientific community. Researchers can register for upcoming bioinformatics/RNAseq and Illumina workshops as they are announced. The RNAseq bioinformatics workshop will be held multiple times in the Spring, dates/times TBD, enrollment is through Tiger Training at: https://clemson.bridgeapp.com/learner/programs/f2c173e4/enroll.
To learn more about CUGBF or request a consultation, visit the facility’s new website or contact them at firstname.lastname@example.org. The CUGBF is located in 160E Life Sciences Building at 190 Collings Street.