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Last Updated: June 21, 2017

Students are actively involved in all stages of research. Undergraduate authors are underlined, and graduate-student authors are italicized.

PEER-REVIEWED PUBLICATIONS

19) J. Maltas, D. Palo, S. Stefan, J. O'Connor, J. Folz, D. Kinn, and P. Urayama. in preparation. [on demonstrating applications of spectrum-shape based metabolic monitoring]

18) D. Palo, J. Maltas, L. Risal, and P. Urayama. Sensing NADH conformation using phasor analysis on fluorescence spectra, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 186: 105-111 (2017). doi:10.1016/j.saa.2017.06.013

17) J. Maltas, L. Amer, Z. Long, D. Palo, A. Oliva, J. Folz, and P. Urayama. Autofluorescence from NADH conformations associated with different metabolic pathways monitored using nanosecond-gated spectroscopy and spectral phasor analysis, Analytical Chemistry, 87: 5117-5124 (2015). doi:10.1021/ac504386x

16) Z. Long, J. Maltas, M.C. Zatt, J. Cheng, E.J. Alquist, A. Brest, and P. Urayama. The real-time quantification of autofluorescence spectrum shape for the monitoring of mitochondrial metabolism, Journal of Biophotonics, 8:247-257 (2015). doi:10.1002/jbio.201300207

15) J. Maltas, Z. Long, A. Huff, R. Maloney, J. Ryan, and P. Urayama. A micro-perfusion system for use during real-time physiological studies under high pressure, Review of Scientific Instruments, 85: 106106 (2014). doi: 10.1063/1.4899121

14) J. Ryan, P. Urayama. Characterizing the dual-wavelength dye indo-1 for calcium-ion sensing under pressure, Analytical Methods, 4: 80-84 (2012). doi: 10.1039/C1AY05486D

13) P. Urayama, E.W. Frey, and S.R. Savage. Fluorescent probe dyes for metabolic-ion sensing under high hydrostatic pressures, Annals of the New York Academy of Sciences, 1189: 104-112 (2010). doi:10.1111/j.1749-6632.2009.05184.x

12) H.M. DePedro, P. Urayama. Using LysoSensor Yellow/Blue DND-160 to sense acidic pH under high hydrostatic pressures, Analytical Biochemistry, 384: 359-361 (2009). doi:10.1016/j.ab.2008.10.007

11) S.B. Keller, J.A. Dudley, K. Binzel, J. Jasensky, H.M. DePedro, E.W. Frey, P. Urayama. A calibration approach for rapid fluorescence lifetime determination for applications using time-gated detection and finite pulse width excitation, Analytical Chemistry, 80: 7876-7881 (2008). doi:10.1021/ac801252q

10) P. Urayama, E.W. Frey, M.J. Eldridge. A fluid handling system with finger-tightened connectors for biological studies at kilo-atmosphere pressures, Review of Scientific Instruments, 79: 046103 (2008). doi:10.1063/1.2907245 Listed in the April 15, 2008 edition of the Virtual Journal of Biological Physics Research.

9) T. Haver, E.C. Raber, P. Urayama. An application of spatial deconvolution to a capillary-based high-pressure chamber for fluorescence microscopy imaging, Journal of Microscopy, 230: 363-371 (2008). doi:10.1111/j.1365-2818.2008.01994.x

8) M. Salerno, J. J. Ajimo, J. A. Dudley, K. Binzel, P. Urayama. Characterization of dual-wavelength SNAFL and SNARF dyes for pH sensing under high hydrostatic pressures, Analytical Biochemistry, 362: 258-267 (2007). doi:10.1016/j.ab.2006.12.042

7) E.C. Raber, J. A. Dudley, M. Salerno, P. Urayama. A capillary-based, high-pressure chamber for fluorescence microscopy imaging, Review of Scientific Instruments, 77: 096106 (2006). doi:10.1063/1.2349303 Listed in the October 1, 2006 edition of the Virtual Journal of Biological Physics Research.


6) P. Urayama, W. Zhong, J.A. Beamish, F.K. Minn, R.D. Sloboda, K.H. Dragnev, E. Dmitrovsky, and M.-A. Mycek. A UV-visible-NIR fluorescence lifetime imaging microscope for laser-based biological sensing with picosecond resolution, Applied Physics B, 76: 483-496 (2003). doi:10.1007/s00340-003-1152-4

5) W. Zhong, P. Urayama, M.-A. Mycek. Imaging fluorescence lifetime modulation of a ruthenium-based dye in living cells: the potential for oxygen sensing, Journal of Physics D: Applied Physics, 36: 1689-1695 (2003). doi:10.1088/0022-3727/36/14/306

4) P. Urayama, S.M. Gruner, and G.N. Phillips Jr. Probing substates in sperm whale myoglobin using high pressure crystallography, Structure, 10: 51-60 (2002). doi:10.1016/S0969-2126(01)00699-2

3) D.A. Hajduk, P. Urayama, S.M. Gruner, S. Erramilli, R. Register, K. Brister, and L. J. Fetters. High pressure effects on the disordered phase of block copolymer melts, Macromolecules, 28: 7148-7156 (1995). doi:10.1021/ma00125a017

2) P. Urayama and G. Benford. Modeling energy flow in turbulent beam-plasma experiments, Physics of Plasmas, 2: 2117-2121 (1995). doi:10.1063/1.871298

1) W.W. Heidbrink, D. Adams, S. Drum, K. Evans, J. Manson, T. Price, P. Urayama, F. J. Wessel. Propagation of a narrow plasma beam in an oblique magnetic field, Physics of Fluids B, 4: 3454-3456 (1992). doi:10.1063/1.860475

BOOK CHAPTERS

1)   P. Urayama and M.-A. Mycek: Fluorescence lifetime imaging microscopy of endogenous biological fluorescence, in Handbook of Biomedical Fluorescence, M.-A. Mycek and B. W. Pogue, eds. Marcel Dekker: New York, 2003, pp.211-236.

FICTION

1)   "Living in a Stranger," Analog Science Fiction and Fact, October 1998.

MASTER'S THESIS

15) Laxmi Risal, M.S., 2016. "Study of pressure dependence of molecular conformation of NADH using spectral phasor analysis."

14) Millicent N. Gikunda, M.S., 2016. "An improved sample loading technique for cellular metabolic response monitoring under pressure."

13) Madhu S. Gaire, M.S., 2016. "Exploring the autofluorescence response to cyanide using spectral phasor analysis."

12) Maha M. Aljohani, M.S., 2016. "Spectral phasor analysis on absorbance spectra for quantifying the content of dye mixtures."

11) Jeffrey A. Maltas, M.S., 2014. "The spectral phasor approach as a tool for monitoring the autofluorescence of mitochondrial metabolism and its application to high pressure studies."

10) Zac Long, M.S., 2013. "Towards a system for nanosecond-gated, fluorescence based monitoring of cellular responses to high hydrostatic pressures."

9) Zachariah P. Callahan, M.S., 2013. "Utilization of a dual-wavelength dye for the characterization of pH buffers under hydrostatic pressure."

8) Alison Huff, M.S., 2012. "A hydrostatic pressure perfusion system for biological systems."

7) Jun Cheng, M.S., 2011. "Monitoring metabolic responses in Saccharomyces cerevisiae using fluorescence-based detection of NADH conformation."

6) Erik J. Alquist, M.S., 2010. "The effects of high hydrostatic pressure on NADH conformation."

5) M. Junaid Farooqi, M.S., 2009. "Methods for in situ piezophysiological studies: Optical sectioning via structured illumination and fluorescence-based characterization of NADH conformation."

4) Hector Michael DePedro, M.S., 2008. "Characterization of the low pH sensing dye, LysoSensor Yellow/Blue DND-160, under high hydrostatic pressures."

3) Thomas Haver, M.S., 2007. "The assessment and application of point spread function deconvolution to high pressure fluorescence microscopy imaging."

2) Erica Raber, M.S., 2006. "Spatial resolution characterization of images taken from a capillary-based high pressure chamber for biological imaging studies."

1) Jacob J. Ajimo, M.S. 2005. "A UV-Visible-NIR, Time-Resolved Fluorescence Spectrometer for High-Pressure Biological Studies."

HONORS THESIS

6) James O'Connor, B.S., 2016. "Monitoring Changes in Cellular Conformations of NADH in Yeast During Metabolic Transitions Induced by Alcohols." Honors, Department of Chemistry and Biochemistry.

5) Michael Zatt, B.A., 2013. Honors, Department of Microbiology.

4) Erik Rotterman, B.S., 2011. "Testing and implementation of a titration technique for use in the determination of Ca2+ binding constants." University Honors with Distinction; Department Honors.

3) Lauren A. Regueyra, B.S., 2010. "High Pressure Effects on the Solvent Denaturation of NADH probed via Fluorescence Spectroscopy" Department Honors.

2) Eric W. Frey, B.S., 2008. "Fluorescence-based calcium ion sensing at high hydrostatic pressures." University Honors with Distinction; Department Honors.

1) Michael J. Maffett, B.S., 2008. "Computations on the role of electrostatics in understanding the effects of pressure on myoglobin structure." University Honors with Distinction; Department Honors.