The mentor, Mark Knepper, M.D., Ph.D., is a Biomedical Engineer who uses systems biology-based approaches to study how the kidney regulates water excretion. This involves use of large-scale data acquisition techniques, such as protein mass spectrometry and 'next-generation' nucleotide sequencing technologies to discover molecular mechanisms involved in renal water transport. Much of the focus is on regulation of molecular water channels called "aquaporins" by the hormone vasopressin. The Epithelial Systems Biology Laboratory is a small close-knit group of scientists devoted to development and exploitation of cutting-edge experimental and computational tools for these studies.
The objective is to carry out an experimental study that the student can pursue independently of other ongoing laboratory studies, generating a publication with the BESIP student as first author. The current opportunity for a BESIP student is in the category of proteomics and mathematical modeling in renal physiology. The student will develop a Bayesian Network Model of intracellular signaling mechanisms in kidney collecting duct cells to explain to the regulation of osmotic water transport by vasopressin. The work will have both wet lab components (proteomics using targeted mass spectrometry) and computational components (construction of an ‘agent-based’ mathematical model of vasopressin signaling). The goal is to identify the critical protein kinases and phosphatases in the regulation of renal water excretion and to identify potential drug targets in water balance disorders. The student will learn basic biochemical techniques and the principles of protein mass spectrometry. He/she will also learn about strategies for bioinformatic analysis of mass spectrometry data. The student will be closely supervised by the mentor to assure rapid progress with the goal of preparing and publishing a paper based on his/her data.
Recent papers by undergraduate BME students (Sachs, Harbaugh, Zhao, Huling, Liu, Hageman, Han, Claxton, Corcoran, Grady, Deshpande) and undergraduate ChE students (Jacob, Feric, Sanghi, Pickering, Gilmer) in the lab include:
- Sachs AN, Pisitkun T, Hoffert, JD, Yu MJ, Knepper MA. LC-MS/MS analysis of differential centrifugation fractions from native inner medullary collecting duct of rat. Am J Physiol Renal Physiol, 2008; 295: F 1799-806.
- Jacob VA, Harbaugh CM, Dietz JR Fenton RA, Kim SM, Castrop H, Schnermann J, Knepper MA, Chou CL, Anderson SA. Magnetic resonance imaging of urea transporter knockout mice shows renal pelvic abnormalities. Kidney Int., 2008; 74: 1202-8.
- Feric M, Zhao B, Hoffert JD, Pisitkun T, Knepper MA. Large-scale phosphoproteomic analysis of membrane proteins in renal proximal and distal tubule. Am J Physiol Cell Physiol. 2011; 300: C755-70.
- Huling JC, Pisitkun T, Song JH, Yu MJ, Hoffert JD, Knepper MA. Gene expression databases for kidney epithelial cells. Am J Physiol Renal Physiol. 2012;302:F401-7.
- Zhao B, Knepper MA, Chou CL, Pisitkun T. Large-scale phosphotyrosine proteomic profiling of rat renal collecting duct epithelium reveals predominance of proteins involved in cell polarity determination. Am J Physiol Cell Physiol. 2012;302:C27-45
- Claxton JS, Sandoval PC, Liu G, Chou CL, Hoffert JD, Knepper MA. Endogenous carbamylation of renal medullary proteins. PLoS One. 2013 Dec 26;8(12):e82655.
- Sanghi A, Zaringhalam M, Corcoran CC, Saeed F, Hoffert JD, Sandoval P, Pisitkun T, Knepper MA. A knowledge base of vasopressin actions in the kidney. Am J Physiol Renal Physiol. 2014;307:F747-55.
- Pickering CM, Grady C, Medvar B, Emamian M, Sandoval PC, Zhao Y, Yang CR, Jung HJ, Chou CL, Knepper MA. Proteomic profiling of nuclear fractions from native renal inner medullary collecting duct cells. Physiol Genomics. 2016; 48:154-66.
- Gilmer GG, Deshpande V, Chou CL, Knepper MA., Chou CL, Knepper MA. Flow Resistance along the Rat Renal Tubule. Am J Physiol Renal Physiol. 2018 [Epub ahead of print].
- Chou CL, Hwang G, Hageman DJ, Han L, Agrawal P, Pisitkun T, Knepper MA. Identification of UT-A1- and AQP2-interacting proteins in rat inner medullary collecting duct. Am J Physiol Cell Physiol. 2018 Jan 1;314(1):C99-C117.