R. Nagarajan | Gvl Website

Dr. Raman Nagarajan - Project Scientist

Research Interests

My research focuses on environmental DNA (eDNA) methods and CRISPR-based detection technologies, along with UC Davis colleagues and government agency collaborators. We are actively working on CRISPR-based detection of aquatic eDNA for single species as well as multispecies detection of fishes and aquatic invertebrates using eDNA metabarcoding. I am also interested in molecular methods development for conservation genetics and environmental management, including possible future methods using transcriptomics and epigenomics.

B.S. Microbiology, Indiana University

Ph.D. Genetics, UC Davis

Selected Publications

Nagarajan, RP, Sanders L, Kolm N, Perez A, Senegal T, Mahardja B, Baerwald M, & Schreier A. CRISPR-Based Environmental

DNA Detection for a Rare Endangered Estuarine Species. Manuscript under review.

Nagarajan, RP, Bedwell, M., Holmes, A.E. et al. Environmental DNA Methods for Ecological Monitoring and Biodiversity

Assessment in Estuaries. Estuaries and Coasts 45, 2254–2273 (2022). https://doi.org/10.1007/s12237-022-01080-y

Nagarajan RP, Goodbla A, Graves E, Baerwald M, Holyoak M, Schreier A. (2020) Non-invasive genetic monitoring for the

threatened valley elderberry longhorn beetle. PLoS One. 2020 Jan 17;15(1):e0227333. https://doi.org/10.1371/journal.pone.0227333

Baerwald MR, Meek MH, Stephens MR, Nagarajan RP, Goodbla AM, Tomalty KM, Thorgaard GH, May B, Nichols KM. (2016)

Migration-related phenotypic divergence is associated with epigenetic modifications in rainbow trout. Molecular Ecology 25(8):1785-1800.

Bell RJ, Rube HT, Kreig A, Mancini A, Fouse SD, Nagarajan RP, Choi S, Hong C, He D, Pekmezci M, Wiencke JK, Wrensch MR,

Chang SM, Walsh KM, Myong S, Song JS, Costello JF. (2015) The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer. Science 348(6238):1036-1039.

Nagarajan RP*, Zhang B*, Bell RJ, Johnson BE, Olshen AB, Sundaram V, Li D, Graham AE, Diaz A, Fouse SD, Smirnov I, Song J,

Paris PL, Wang T, Costello JF. (2014) Recurrent epimutations activate gene body promoters in primary glioblastoma. Genome Research 24(5), 761-774.

* these authors contributed equally

Maunakea AK*, Nagarajan RP*, Bilenky M, Ballinger TJ, et al. (2010) Conserved Role of Intragenic DNA Methylation in

Regulating Alternative Promoters. Nature 466(7303), 253-257.

* these authors contributed equally

Current

1. CRISPR-SHERLOCK for species identification and environmental DNA detection

(Collaborators: US Bureau of Reclamation), US Fish and Wildlife Service)

2. Tidal wetland restoration monitoring using eDNA metabarcoding - with Leigh Sanders

(Collaborators: Fish Restoration Program (FRP))

Past

Developing an eDNA metabarcoding protocol to improve fish and mussel monitoring in the San Francisco Estuary.

Resource: custom reference sequence database for San Francisco Estuary fishes and invertebrates - link to publicly available Dryad dataset

Using fecal DNA survey protocols to optimize traditional exit hole surveys and increase detection rates for the Valley Elderberry Longhorn Beetle (VELB)

Publication: https://doi.org/10.1371/journal.pone.0227333