NSF-REU Mentors and Projects

Dr. Mike Cowley

Epigenetics, toxicology and liver lipid metabolism. How do epigenetic mechanisms in the liver regulate gene transcription and ultimately liver function? Little is known about the role of epigenetic mechanisms in liver function and lipid metabolism.  Students in the Cowley group will use external triggers to perturb the epigenome of the liver and interrogate its relationship to the transcriptomehttps://facultyclusters.ncsu.edu/people/macowley/


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Dr. Patricia Estes

Transcriptomics and the role of single-minded neurons in energy balance. A team of two students will join the Estes’s group to understand how sim neurons in the fruit fly brain regulate energy balance and longevity in the fly. Preliminary results show that silencing PI sim neurons with tetanus toxin causes flies to increase food intake as larvae and become obese as adults. Moreover, these flies die ~10 days after reaching adulthood, whereas control flies live ~30-60 days.  Students will identify transcriptional differences between wild type flies and flies with silenced sim neurons throughout development using RNA-seq. http://www4.ncsu.edu/~paestes/


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Dr. Ben Reading

Metagenomics and caviar science.  Since caviar is a “living food” comprised of fish roe, salt, fungi and bacteria, the Reading group intends to characterize the microbial communities present by metagenomic analysis.  The project is an exciting one that bridges food science, basic ecology, and fisheries science. Little is known about the colonization of microbial flora on fish eggs. The research goal is, in part, for students to discover the microbial communities that naturally live in raw and preserved sturgeon roes (caviars) and also, more generally, to understand the microbes that live on fishes. How are they transferred to the eggs once they are laid or harvested (i.e., do they live on the fish or elsewhere)?  https://appliedecology.cals.ncsu.edu/faculty/benjamin-j-reading/

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Dr. Seth Faith

Forensics and wildlife protection.  Illegal wildlife trade is decimating certain animal populations (e.g., rhinoceros and elephants), destabilizing some regional economies and supporting criminal enterprises that threaten global security.  NGS technology, promises to open doors to low-cost, multi-species approaches for DNA analysis.  First, DNA markers that provide identity, kinship and biogeographical origins across numerous wildlife species need to be characterized. Students in the Faith group will help discover single-nucleotide polymorphisms (SNP), short tandem repeats (STR) and haplotypic loci that can be used for an NGS approach to i) identify animals ii) determine kinship and iii) predict geographic origin.  Students will contribute to sample collection, DNA extractions, sequencing, bioinformatics, databasing, and data analysis using our Cloud-based computing system. http://www.genomicidlab.com

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Dr. Robert Kelly

Transcriptomics, bio-based fuels and thermophile metabolic engineering. Thermophilic microorganisms, which grow optimally at high temperatures--at or above 70°C-- have been studied for decades because of their unique ability to thrive in extreme environments. The rise of new genetic engineering tools has greatly expanded the potential use of thermophiles for the production of bio-based fuels and chemicals. The BIT SURE student team will focus on metabolic engineering of two extreme thermophiles: Sulfolobus acidocaldarius (Topt 75°C, pHopt 3.0) and Caldicellulosiruptor bescii (Topt 75°C, pHopt 6.5). Each student will manipulate a single thermophile, yet both students will assess and compare the impact of metabolic engineering using RNA sequencing technology. https://www.cbe.ncsu.edu/extremophiles/

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Dr. Santosh Mishra

Transcriptomics to identify novel receptors for itch sensation. Itch is an unpleasant sensation that affects millions of people suffering worldwide from a variety of chronic illnesses. Itch sensations are received by receptors expressed in neurons of the dorsal root ganglia (DRG) where the message is relayed to the spinal cord and brain. A few receptors involved in itch sensation at the periphery have been characterized; however, traditional approaches for identifying new receptors remain largely ineffective. Two BIT SURE trainees will join the Mishra group and use NGS tools to identify novel receptors in DRG neurons critical for the itch sensation.  This work will contribute to the lab goal of identifying novel receptors involved in acute and chronic itch sensation, which is critical for developing novel therapeutics to cure or treat this debilitating sensation. https://cvm.ncsu.edu/directory/mishra-santosh/

Dr. Ross Whetten

Genomics and mitigation of climate change in forest ecosystems.  Conifers, which are keystone species in northern hemisphere forest ecosystems, are affected to varying degrees by climate change. A better understanding of adaptive genetic variation will be critical to climate change management of forest ecosystems. Over the last decade, genome assemblies have become available for multiple genera of forest trees due to enabling NGS methods (i.e., Ion Torrent and long-read technologies such as Pac Biosciences & Oxford Nanopore). Through an integrated research program utilizing these new technologies and other cutting-edge approaches, students will help the Whetten lab work towards mitigating effects of climate change on forest ecosystems. https://research.cnr.ncsu.edu/sites/moleculartreebreeding/