Current Fellows

Edward Chuang, Ph.D. Department of Molecular Biology and Biochemistry, Rutgers University Nelson Labs, Piscataway, NJ edward.chuang@rutgers.edu

Education

B.A. in Biochemistry and B.A. in Mathematics – Colby College, Waterville, ME

Ph.D. in Pharmacology – University of Pennsylvania, Philadelphia, PA

INSPIRE fellow, Department of Molecular Biology and Biochemistry – Rutgers University, New Brunswick, NJ

Research

Research Mentor: Dr. Monica Driscoll, Ph.D. 
 
My broad research interests are in cellular protein quality control pathways and how misfolded and aggregated proteins are sorted into various pathways of protein folding and degradation. I am currently exploring how various protein substrates are sorted into neuronal exophers for removal from the soma using C. elegans as a model organism.

Teaching

Teaching Mentor: N/A

Teaching Interests: Chemistry, Biochemistry, and Molecular Biology
 
Publications:
 

Jones, R.D., C. Enam, R. Ibarra, H.R. Borror, K.E. Mostoller, E.K. Fredrickson, J. Lin, E. Chuang, Z. March, J. Shorter, T. Ravid, G. Kleiger, and R.G. Gardner. (2020). The extent of Ssa1/Ssa2 Hsp70 chaperone involvement in nuclear protein quality control degradation varies with the substrate. Mol. Biol. Cell. 31(3):221-233.

Michalska, K.*, K. Zhang*, Z.M. March*, C. Hatzos-Skintges, G. Pintilie, L. Bigelow, L.M. Castellano, L.J. Miles, M.E. Jackrel, E. Chuang, R. Jedrzejczak, J. Shorter, W. Chiu, and A. Joachimiak. (2019). Structure of Calcarisporiella thermophila Hsp104 disaggregase that antagonizes diverse proteotoxic misfolding events. Structure. 27(3):4490463. (*Co-first author).

Chuang, E.*, A.M. Hori*, C.D. Hesketh*, and J. Shorter. (2018). Amyloid assembly and disassembly. J. Cell. Sci. doi: 10.1242/jcs.189928. (*Co-first author).

Gates, S.N*., A.L. Yokom*, J. Lin, M.E. Jackrel, A.N. Rizo, N.M. Kendsersky, C.E. Buell, E.A. Sweeny, K.L. Mack, E. Chuang, M.P. Torrente, M. Su, J. Shorter, and D.R. Southworth. (2017). Ratchet-like polypeptide translocation mechanism of the AAA+ disaggregase Hsp104. Science. 357(6348):273-279. (*Co-first author).

Torrente, M.P., E. Chuang, M.M. Noll, M.E. Jackrel, M.S. Go, and J. Shorter. (2016). Mechanistic insights into Hsp104 potentiation. J. Biol. Chem. 291(10):5101-5115.

Millard, J.T., E. Chuang, J.S. Lucas, E.E. Nagy, and G.T. Davis. (2013). Case-Study Investigation of Equine Maternity via PCR-RFLP: A Biochemistry Laboratory Experiment. J Chem Educ. 90(11). doi: 10.1021/ed300740r.

Alexander Cope, Ph.D. Department of Genetics Rutgers University Life Sciences Building, Piscataway, NJ alexander.cope@rutgers.edu

Education

B.S. in Mathematics and Computer Science – Centre College, Danville, KY

Ph.D. Genome Science and Technology – University of Tennessee, Knoxville, TN

INSPIRE fellow, Department of Genetics — Rutgers University, Piscataway, NJ

Research

Research Mentor: Premal Shah, Ph.D. 
 
My research primarily focuses on applying models rooted in evolutionary theory to extract biological information from omics datasets. I have interests in studying the evolution and mechanisms of mRNA translation dynamics (including post-transcriptional and post-translational regulation) and the evolution of secreted proteins.

Teaching

Teaching Interests: Evolutionary genetics, computational biology, bioinformatics

 
Publications:

A.L. Cope, S. Vellappan, J.S. Favate, K.S. Skalenko, S.S. Yadavalli, P. Shah; Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling. In: Dassi E. (eds) Post-Transcriptional Gene Regulation. Methods in Molecular Biology, vol 2404. Humana, New York, NY, 2022, doi: https://doi.org/10.1007/978-1-0716-1851-6_5 


I.A. Nikonorova, J. Wang, A.L. Cope, P. Tilton, K.M. Power, J.D. Walsh, J.S. Akella, P. Shah, M.M. Barr; Tracking extracellular vesicle (EV) cargo as a platform for studying EVomics, signaling, and targeting in vivo, bioRxiv, September 2021, doi: https://doi.org/10.1101/2021.09.23.461577 (Accepted: Current Biology) 


A.L. Cope, P. Shah; Intragenomic variation in mutation biases causes underestimation of selection on synonymous codon usage, bioRxiv, November 2021, doi: https://doi.org/10.1101/2021.10.29.466462 (In Review: Plos Genetics) 

Cope, A.L., Gilchrist M.A. (2021). Quantifying shifts in natural selection on codon usage between protein regions: A population genetics approach. bioRxiv. (In review: BMC Genomics)

Cope, A.L, Anderson, F., Favate, J., Jackson, M., Mok, A., Kurowska, A., MacKenzie, E., Shivakumar, V., Tilton, P., Winterbourne, S.M., Xue, S., Kavoussanakis, K., Lareau, L.F., Shah, P., Wallace, E.W.J. (2021). riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow. bioRxiv. (Accepted: Bioinformatics, https://doi.org/10.1093/bioinformatics/btac093).

Skalenko, K.S., Li, L., Zhang, Y., Vvedenskaya, I.O., Winkelman, J.T., Cope, A.L., Taylor, D.M., Shah, P., Ebright, R.H., Kinney, J.B., Zhang, Y., Nickels, B.E. (2021). Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli. PNAS, 118(27), e2106388118.

Poudel, S., Cope, A.L., O’Dell, K.B., Guss, A.M, Seo, H, Trinh, C.T., Hettich, R.L. (2021). Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets. Biotechnology for biofuels, 14(1), 1-19.   

Cope, A.L, O’Meara, B.C., Gilchrist, M.A. (2020). Gene expression of functionally-related genes coevolves across fungal species: detecting coevolution of gene expression using phylogenetic comparative methods. BMC Genomics, 21, 1-17.

Cope, A.L., Hettich, R.L., Gilchrist, M.A. (2018). Quantifying codon usage in signal peptides: Gene ecpression and amino acid usage explain apparent selection for inefficient codons. Biochimica et Biophysica Acta – Biomembranes, 1860(12), 2479-2485.

Landerer, C., Cope, A., Zaretzki, R. Gilchrist M.A. (2018). AnaCoDa: analyzing codon data with Bayesian mixture models. Bioinformatics, 34(14), 2496-2498.

Katherine Jacobs, Ph.D. 

kj490@rwjms.rutgers.edu 

Department:  Genetics/HGINJ 

Research Topic:  I study relationships between extracellular matrix, sensory cilia and extracellular vesicles with the aim of understanding how ECM impacts ciliary function. 

Education:  PhD, Genetics and Genomics, Duke University. BA, Biology, Dartmouth College. 

Research Mentor:  Dr. Maureen Barr 

Teaching Mentor:  Dr. Reed Carroll 

Teaching Interests:  Cell Biology, Genetics, Biochemistry, Physiology 

Melanie Johnston 

mlj114@rutgers.edu 

Department:  Pharmacology, Physiology, and Neuroscience 

Research Topic:  Tuberculosis drug discovery, including studying inhibitors of fatty acid metabolism and mycobacterial drug uptake and metabolism 

Education:  B.S. Chemistry and Biochemistry and B.A. Creative Writing - Purdue University, West Lafayette, IN.  

Ph.D. Biochemistry, Cellular, and Molecular Biology - Johns Hopkins School of Medicine, Baltimore, MD. 

Research Mentor:  Dr. Joel Freundlich 

Teaching Mentor:  Dr. Margaret Carroll 

Teaching Interests:  Biochemistry, Metabolism, Microbiology 

Publications:  

Johnston ML, Bonett EM, DeColli AA, and Freel Meyers CL (2022). Antibacterial target DXP Synthase catalyzes the cleavage of D-xylulose 5-phosphate: a study of ketose phosphate binding and the ketol transfer reaction. Biochemistry, 61(17): 1810–1823. doi: 10.1021/acs.biochem.2c00274. & Johnston ML and Freel Meyers CL (2021). Revealing Donor Substrate-Dependent Mechanistic Control on DXPS, an Enzyme in Bacterial Central Metabolism. Biochemistry, 60 (12): 929–39. doi: 10.1021/acs.biochem.1c00019. 

Katherine Maniates, Ph.D. Department of Genetics Rutgers University Waksman Institute of Microbiology, Piscataway, NJ maniates@waksman.rutgers.edu

Education

B.A. in Biology and B.S. in Public Health- St. Catherine University, St. Paul, MN

Ph.D. in Biology- Marquette University, Milwaukee, WI

INSPIRE Fellow, Waksman Institute of Microbiology- Rutgers University, New Brunswick, NJ

Research

Research Mentor: Andrew Singson

Research Topic: Identification of genes and molecular mechanisms for fertilization in C. elegans.

I am working to identify additional genes involved in both the egg and sperm in C. elegans which are required for fertilization, egg, or sperm activation.

Teaching

Teaching Interests: Genetics, Development, General Biology

 
Publications:
 

Katherine A Maniates, Benjamin S Olson, Allison L Abbott, Sperm fate is promoted by the mir-44 microRNA family in the Caenorhabditis elegans hermaphrodite germline, Genetics, Volume 217, Issue 1, January 2021, iyaa006, https://doi.org/10.1093/genetics/iyaa006

Vik Meadows, Ph.D.

vik.meadows@rutgers.edu 

Department:  Pharmacology, Physiology, and Neuroscience 

Research Topic:  Paneth Cells and the gut-liver axis 

Education:  

PhD Biochemistry and Molecular Biology Indiana University School of Medicine, MS Biochemistry and Molecular Biology Oregon Health & Science University, BS Cell Biology/Spanish University of Mary Hardin-Baylor 

Research Mentor:  Nan Gao, Ph.D. 

Teaching Mentor:  Emily Monroe Waldburger, Ph.D. 

Teaching Interests:  Cellular and Molecular Biology, Physiology 

Publications:  PMID: 36410025, PMID: 34164827, PMID: 37442156 

Karen Olson, Ph.D. Department of Biological Sciences, Rutgers University Boyden Hall, Newark, NJ olsonvkaren@gmail.com

Education

B.S. – University of Florida, Gainesville FL

M.A. – University of Kansas, Lawrence KS

Ph.D. – University of Kansas, Lawrence KS

INSPIRE fellow, Department of Biological Sciences — Rutgers University, New Brunswick, NJ

Research

Research Mentor: Angelo Soto-Centeno, Ph.D. 

I study bat and cave microbiomes in the Caribbean and South Pacific islands, population genomics of island mammals, and genomics of invasive species.

 
Publications:

Olson KV, Alexander AM, Campbell LP, Brown RM. (In revision). Processes governing patterns of genomic differentiation at fine versus broad spatial scales in an iconic archipelago system. Molecular Ecology.

Wood PL, Xianguang G, Travers SL, Su YC, Olson KV, Bauer AM, Grismer LL, Siler CD, Moyle RG, Andersen MJ, Brown RM. (2020). Parachute geckos free fall into synonomy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements. Molecular Phylogenetics and Evolution, 146, 106731.

Ingenloff K, Hensz CM, Anamza T, Barve V, Campbell LP, Cooper JC, Komp E, Jimenez L, Olson KV, Osorio-Olvera L, Owens HL. (2017). Predictable invasion dynamics in North American populations of the Eurasian collared dove Streptopelia decaocto. Proceedings of the Royal Society B: Biological Sciences, 284(1862), 20171157.

Alexander AM, Su YC, Oliveros CH, Olson KV, Travers SL, Brown RM. (2017). Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow-mouth frogs. Evolution, 71, 475-488.

Mathis VL, Ascunce MS, Logan-López KG, DeYoung RW, Honeycutt RL, Olson KV, Kassu G, Silvy NJ, Reed DL. (2017). Insights into the genetic diversity of the whitetailed deer (Odocoileus virginianus) population at the Guantanamo Naval Base. Caribbean Naturalist, 45, 1-20.

Brown RM, Weghorst JA, Olson KV, Duya MR, Barley AJ, Duya MV, Shekelle M, Neri-Arboleda I, Esselstyn JA, Dominy NJ, Ong PS. (2014). Conservation genetics of the Philippine tarsier: Cryptic genetic variation restructures conservation priorities for an island archipelago primate. PLoS One, 9(8), e104340.

Benton Purnell, Ph.D. Neurosurgery, Rutgers University School of Public Health, Piscataway, NJ benton-purnell@uiowa.edu

Education

Psychology, B.A. – University of Maine, Orono, ME

Neuroscience. PhD – University of Iowa, Iowa City, IA (pending defense- Oct 13^th, 2020)

INSPIRE fellow, Neurosurgery — Rutgers University, New Brunswick, NJ

Research

Research Mentor: Detlev Boison, Ph.D. 
 
I study the role of the purine metabolite and neuromodulator adenosine in seizure-induced respiratory arrest and sudden unexpected death in epilepsy (SUDEP).

Teaching 
Teaching Interests: I am interested in teaching classes related to anatomy and physiology, neuroscience, research methods, cell biology, and computer science.
 
Publications:

Purnell, B., Buchanan G. (2020) Free-running Circadian Breathing Rhythms Are Eliminated by Suprachiasmatic Nucleus Lesion. Journal of Applied Physiology. 129: 49-57.

Petrucci, A., Joyal, K., Purnell, B., Buchanan, G. (2020) Serotonin and sudden unexpected death in epilepsy. Experimental Neurology. 325, 113-145.

Kruse, S., Dayton, K.., Purnell, B., Rosner, J., & Buchanan, G. (2019) Effect of monoamine reuptake inhibition and α1 blockade on respiratory arrest and death following electroshock-induced seizures in mice. Epilepsia. 60: 495–507.

Purnell, B., Thijs, R., & Buchanan, G. (2018) Dead in the night: Sleep-wake and time-of-day influences on sudden unexpected death in epilepsy. Frontiers in Neurology. 9: 1079

Smith, H., Leibold, N. K., Rappoport, D., Ginapp, C., Purnell, B., Bode, N., Alberico S., Kim K., Audero E., Gross C., & Buchanan, G. (2018). Dorsal raphe serotonin neurons mediate CO2-induced arousal from sleep. Journal of Neuroscience, 38(8), 1915-1925.

Purnell, B., Hajek, M., & Buchanan, G. (2017). Time of day influences on respiratory sequelae following maximal electroshock induced seizures in mice. Journal of Neurophysiology. 118(5): 2592-2600

Caroline Schwaner

caroline.schwaner@rutgers.edu

Department:  Genetics 

Research Topic:  The genetic mechanisms underlying digit evolution in tetrapods 

Education:  PhD in Marine Science Stony Brook University; MEM in Coastal Environmental Management Duke University; BS in Environmental Science-Emory University 

Research Mentor:  Dr. Tetsuya Nakamura 

Teaching Interests:  Biology 

Publications:   

Schwaner C, Farhat S, Boutet I, Tanguy A, Barbosa M, Grouzdev D, Pales Espinosa E, Allam B. 2023. Combination of RNAseq and RADseq to identify physiological and adaptive responses to acidification in the eastern oyster (Crassostrea virginica). Marine Biotechnology. Doi:10.1007/s1-126-023-10255-y.;  

Schwaner C, Barbosa M, Schwemmer TG, Pales Espinosa E, Allam B. 2023. Increased food resources help eastern oyster mitigate the negative impacts of coastal acidification. Animals, 13, 1161. Doi:10.3390/ani13071161;  

Schwaner C, Farhat S, Haley J, Pales Espinosa E, Allam B. 2022. Proteomic and transcriptomic responses enable clams to correct the pH of calcifying fluids and sustain biomineralization in acidic environments. International Journal of Molecular Sciences: Organic, Inorganic and Natural Molecules in Biomineralization. 23, 16066. DOI:10.3390/ijms232416066;  

Schwaner C, Farhat S, Haley J, Pales Espinosa E, Allam B. 2022. Transcriptomic, proteomic, and functional assays underline the dual role of extrapallial hemocytes in immunity and biomineralization in the hard clam Mercenaria mercenaria. Frontiers in Immunology: Innate immunity in a biomineralized context. DOI:10.3389/fimmu.2022.838530  

Schwaner C, Barbosa M, Connors P, Park TJ, de Silva D, Griffith A, Gobler C, Espinosa EP, Allam B. 2020. Experimental Acidification Increases susceptibility to infection of Mercernaria mercenaria to infection by Vibrio spp. Marine Environmental Research. DOI:10.1016/j.marenvres.2019.104872. 

Timothy J. Stanek, Ph.D. Human Genetics Institute of New Jersey, Rutgers University Nelson Laboratories, Piscataway, NJ timothy.stanek@rutgers.edu

Education

B.S., The College of New Jersey, Ewing, NJ

Ph.D., Thomas Jefferson University, Philadelphia, PA

INSPIRE fellow, Genetics, Rutgers University, New Brunswick, NJ

Research

Research Mentor: Chris Ellison, Ph.D.
 
My research focuses on the role of R-loops in regulating chromatin architecture in Drosophila melanogaster.

Teaching

Teaching Interests: Genetics, Genomics, and Biochemistry

Publications:

Stanek, T.J., Gennaro, V.J., Tracewell, M.A., Di Marcantonio, D., Pauley, K.L., Butt, S., McNair, C., Wang, F., Kossenkov, A.V., Knudsen, K.E., Butt, T., Sykes, S.M., McMahon, S.B. (2021). The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22. EMBO J Jun 22;e102509.  doi: 10.15252/embj.2019102509

Gennaro, V.J., Stanek, T.J., Peck, A.R., Sun, Y., Wang, F., Qie, S., Knudsen, K.E., Rui, H., Butt, T., Diehl, J.A., McMahon, S.B. (2018). Control of CCND1 ubiquitylation by the catalytic SAGA subunit USP22 is essential for cell cycle progression through G1 in cancer cells. PNAS 75(1);272-86.

Rappaport, J.A., Entezari, A.A., Caspi, A., Caksa, S., Jhaveri, A.V., Stanek, T.J., Ertel, A., Kupper, J., Fortina, P.M., McMahon, S.B., Jaynes, J.B., Snook, A.E., Waldman, S.A. (2021). A β-catenin-TCF-sensitive locus control region mediates GUCY2C ligand loss in colorectal cancer. Cell Mol Gastroenterol Hepatol Dec 22;S2352-345X(21)00264-2.  doi: 10.1016/j.jcmgh.2021.12.014. Online ahead of print.

 McCann, J.J., Vasilevskaya I.A., Neupane, N.P., Shafi, A.A., McNair, C., Dylgjeri, E., Mandigo, A.C., Schiewer, M.J., Schrecengost, R.S., Gallagher, P., Stanek, T.J., McMahon, S.B., Berman-Booty, L.D., Ostrander, W.F. Jr, Knudsen, K.E. (2020). USP22 Functions as an Oncogenic Driver in Prostate Cancer by Regulating Cell Proliferation and DNA Repair. Cancer Res. 80(3):430-443.

 Schrecengost, R.S., Dean, J.L., Goodwin, J.F., Schiewer, M.J., Urban, M.W., Stanek, T.J., Sussman, R.T., Hicks, J.L., Birbe, R.C., Draganova-Tacheva, R.A., Visakorpi, T., Demarzo, A.M., McMahon, S.B., Knudsen, K.E. (2014). USP22 Regulates Oncogenic Signaling Pathways to Drive Lethal Cancer Progression. Cancer Res 74(1);272-86.

Sussman, R.T., Stanek, T.J., Esteso, P., Gearhart, J.D., Knudsen, K.E., McMahon, S.B. (2013). The epigenetic modifier Ubiquitin Specific Protease 22 (Usp22) regulates embryonic stem cell differentiation via transcriptional repression of Sex determining region Y-box (Sox2). J Biol Chem 288(33);24234-46.

Casimiro, M.C., Crosariol, M., Loro, E., Ertel, A., Yu, Y., Dampier, W., Saria, E.A., Papanikolaou, A., Stanek, T.J., Li, Z., Wang, C., Fortina, P., Addya, S., Tozeren, A., Knudsen, E.S., Arnold, A., Pestell, R.G. (2012). ChIP sequencing of cyclin D1 reveals a transcriptional role in chromosomal instability in mice. J Clin Invest 122(3);833-43.

Zhang, X.Y., Pfeiffer, H.K., Mellert, H.S., Stanek, T.J., Sussman, R.T., Kumari, A., Yu, D., Rigoutsos, I., Thomas-Tikhonenko, A., Seidel, H.E., Chodosh, L.A., Packham, G., Baserga, R., McMahon, S.B. (2011). Inhibition of the single downstream target BAG1 activates the latent apoptotic potential of MYC. Mol Cell Bio 31(24);5037-45.

Mellert, H.S., Stanek, T.J., Sykes, S.M., Rauscher, F.J. 3rd, Schultz, D.C., McMahon, S.B. (2011). Deacetylation of the DNA-binding domain regulates p53-mediated apoptosis. J Biol Chem 11;286(6):4264-70.

Sykes, S.M., Stanek, T.J., Frank, A., Murphy, M.E., McMahon, S.B. (2009). Acetylation of the DNA binding domain regulates transcription-independent apoptosis by p53. J Biol Chem 24;284(30):20197-205.

Gwyndolin Vail, Ph.D. Pharmacology, Physiology, and Neuroscience Rutgers University Medical Science Building, Newark, NJ gvail@gsbs.rutgers.edu

Education

BA in Cell Biology and Neuroscience, Rutgers University, New Brunswick

Ph.D. in Toxicology, Rutgers University, New Brunswick

INSPIRE fellow, Pharmacology, Physiology, and Neuroscience — Rutgers University, Newark, NJ

Research

Research Mentor: Vanessa Routh, Ph.D.
 
Research Topic: Sex differences in central sensing and regulation of glucose during exercise. 

Teaching:

Teaching Interests: Endocrinology, Neuroscience, Neuroendocrinology, Histology/Pathology 

Publications:

Garcia, S., Hirschberg, P., Sarkar, P., Siegel, D., Teegala, S., Vail, GM., and Routh, VH. (2021). Insulin actions on hypothalamic glucose-sensing neurons. J. Neuroendocrinology, 33(4), e12937.

Vail, GM., and Roepke, TA. (2020). Organophosphate flame retardants excite arcuate melanocortin circuitry and increase neuronal sensitivity to ghrelin in adult mice. Endocrinology, 161(11), bqaa168.

Vail GM., Walley SN., Yasrebi A., Maeng A., Conde KM., and Roepke TA. (2020). The interactions of diet-induced obesity and organophosphate flame retardant exposure on energy homeostasis in adult male and female mice. J. Toxicological and Environmental Health A. 83(11-12):438-455.

Vail, GM., and Roepke, TA. (2018). Membrane-initiated signaling via Gq-coupled GPCR in the central nervous system. Steroids, 142, 77-83.

Chen, J., Chen, Y., Vail, GM., Chow, H., Zhang, Y., Louie, L., Li, J., Hart, R., Plummer, M. and Herrup, K. (2016). The impact of glutamine supplementation on the symptoms of ataxia-telangiectasia: a preclinical assessment. Molecular Neurodegeneration, 11, 60.

Vail, GM., Cheng, A., Han, YR., Zhao, T., Du, S., Loy, M., Herrup, K., and Plummer, M. (2016). ATM protein is located on presynaptic vesicles and its deficit leads to failures in synaptic plasticity. J. Neurophysiology, 116(1), 201-209