Laboratory for Fluorescence Dynamics

A NIH research resource center for biomedical fluorescence spectroscopy at the University of California, Irvine

Publications

LFD is supported by

National Center for Research Resources

University of California, Irvine


Publications Acknowledging the LFD

The Laboratory for Fluorescence Dynamics (LFD) should be acknowledged in any publications arising from the data collected in the LFD using the following text:

"The experiments reported in this paper were performed at the Laboratory for Fluorescence Dynamics (LFD) at the University of California, Irvine (UCI). The LFD is supported jointly by the National Center for Research Resources of the National Institutes of Health (PHS 5 P41-RR003155) and UCI."

2009

  1. Brian Q Spring and Robert M Clegg.
    Image analysis for denoising full-field frequency-domain fluorescence lifetime images.
    J Microsc. 2009; 235(2): 221-237.
  2. Incheol Kang, Rachel E Reem, Amy L Kaczmarowski, and Joseph G Malpeli.
    Contrast sensitivity of cats and humans in scotopic and mesopic conditions.
    J Neurophysiol. 2009; 102(2): 831-840. PMCID: PMC2724355
  3. Rachel W Bailey, Thaothanh Nguyen, Leslie Robertson, Elizabeth Gibbons, Jennifer Nelson, Ryan E Christensen, Jacob P Bell, Allan M Judd, and John D Bell.
    Sequence of physical changes to the cell membrane during glucocorticoid-induced apoptosis in S49 lymphoma cells.
    Biophys J. 2009; 96(7): 2709-2718. PMCID: PMC2711280
  4. Robert M Clegg.
    Förster Resonance Energy Transfer - FRET what is it, why do it, and how it's done.
    FRET and FLIM Techniques (Laboratory Techniques in Biochemistry and Molecular Biology, Vol. 33). By TWJ Gadella (Editors). Elsevier Science, pp. 1-57, 2009. ISBN: 9780080549583

2008

  1. Francesco Cutrale.
    PALM. Photo-activated localization microscopy.
    Laurea in Fisica e Tecnologie Biomediche. Università degli studi di Trento, 2008.
    Advisor: Renzo Antolini
  2. Brian M Stott, Mai P Vu, Chisako O McLemore, M Shaun Lund, Elizabeth Gibbons, Taylor J Brueseke, Heather A Wilson-Ashworth, and John D Bell.
    Use of fluorescence to determine the effects of cholesterol on lipid behavior in sphingomyelin liposomes and erythrocyte membranes.
    J Lipid Res. 2008; 49(6): 1202-1215. PMCID: PMC2386901
  3. Anne L Heiner, Elizabeth Gibbons, Jeremy L Fairbourn, Laurie J Gonzalez, Chisako O McLemore, Taylor J Brueseke, Allan M Judd, and John D Bell.
    Effects of cholesterol on physical properties of human erythrocyte membranes: impact on susceptibility to hydrolysis by secretory phospholipase A2.
    Biophys J. 2008; 94(8): 3084-3093. PMCID: PMC2275687
  4. Rachel W Bailey.
    Mechanisms by which apoptotic membranes become susceptible to secretory phospholipase A2.
    Master in Physiology and Developmental Biology, Brigham Young University, 2008.
    Advisor: John D Bell
  5. Chittanon Buranachai, Daichi Kamiyama, Akira Chiba, Benjamin D Williams, and Robert M Clegg.
    Rapid frequency-domain FLIM spinning disk confocal microscope: lifetime resolution, image improvement and wavelet analysis.
    J Fluoresc. 2008; 18(5): 929-942.
  6. Chittanon Buranachai.
    Multi scale fluorescence studies: The spinning disk confocal fluorescence lifetime imaging microscopy & single molecule nano-metronome & single molecule study of tetramethyrhodamine-DNA interaction.
    PhD in Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 2008.
    Advisor: Robert M Clegg

2007

  1. Kateri A Duncan and Steven C Huber.
    Sucrose synthase oligomerization and F-actin association are regulated by sucrose concentration and phosphorylation.
    Plant Cell Physiol. 2007; 48(11): 1612-23.
  2. Rachel W Bailey, Erin D Olson, Mai P Vu, Taylor J Brueseke, Leslie Robertson, Ryan E Christensen, Kristen H Parker, Allan M Judd, and John D Bell.
    Relationship between membrane physical properties and secretory phospholipase A2 hydrolysis kinetics in S49 cells during ionophore-induced apoptosis.
    Biophys J. 2007; 93(7): 2350-62. PMCID: PMC1965435
  3. Christopher B Guest, Matthew E Hartman, Jason C O'Connor, Kenneth S Chakour, Ali A Sovari, and Gregory G Freund.
    Phagocytosis of cholesteryl ester is amplified in diabetic mouse macrophages and is largely mediated by CD36 and SR-A.
    PLoS One. 2007; 2(6): e511. PMCID: PMC1876806

2006

  1. Francisco J Cuevas, David M Jameson, and Carlos P Sotomayor.
    Modulation of reconstituted pig kidney Na+/K(+)-ATPase activity by cholesterol in endogenous lipid vesicles: role of lipid domains.
    Biochemistry. 2006; 45(46): 13855-68.
  2. M Fidorra, L Duelund, C Leidy, A C Simonsen, and Luis A Bagatolli.
    Absence of fluid-ordered/fluid-disordered phase coexistence in ceramide/POPC mixtures containing cholesterol.
    Biophys J. 2006; 90(12): 4437-51. PMCID: PMC1471871
  3. Sophia Y Breusegem, Moshe Levi, and Nicholas P Barry.
    Fluorescence correlation spectroscopy and fluorescence lifetime imaging microscopy.
    Nephron Exp Nephrol. 2006; 103(2): e41–e49.
  4. Esther S Jeng, Anthonie E Moll, Amanda C Roy, Joseph B Gastala, and Michael S Strano.
    Detection of DNA hybridization using the near-infrared band-gap fluorescence of single-walled carbon nanotubes.
    Nano Lett. 2006; 6(3): 371-375.
  5. Rebekah S Vest, Rachel Wallis, Lauren B Jensen, Andrea C Hawes, Joseph Callister, Brent Brimhall, Allan M Judd, and John D Bell.
    Use of steady-state Laurdan fluorescence to detect changes in liquid ordered phases in human erythrocyte membranes.
    J Membrane Biol. 2006; 211(1): 15-25.
  6. Juewen Liu and Yi Lu.
    Fluorescent DNAzyme biosensors for metal ions based on catalytic molecular beacons.
    Fluorescent Energy Transfer Nucleic Acid Probes Designs and Protocols (Methods in Molecular Biology, Vol. 335). By VV Didenko (Editors). Humana Press, pp. 275-288, 2006. ISBN: 9781588293800
  7. Juewen Liu and Yi Lu.
    Multi-fluorophore fluorescence resonance energy transfer for probing nucleic acids structure and folding.
    Fluorescent Energy Transfer Nucleic Acid Probes Designs and Protocols (Methods in Molecular Biology, Vol. 335). By VV Didenko (Editors). Humana Press, pp. 257-71, 2006. ISBN: 9781588293800

2005

  1. Nandita Madhavan, Erin C Robert, and Mary S Gin.
    A highly active anion-selective aminocyclodextrin ion channel.
    Angew Chem Int Ed Engl. 2005; 44(46): 7584-7.
  2. Ryan Woodyer, Huimin Zhao, and Wilfred A van der Donk.
    Mechanistic investigation of a highly active phosphite dehydrogenase mutant and its application for NADPH regeneration.
    FEBS J. 2005; 272(15): 3816-27.
  3. Sivakumar V Aathimanikandan, Britto S Sandanaraj, Christopher G Arges, Christopher J Bardeen, and S Thayumanavan.
    Effect of guest molecule flexibility in access to dendritic interiors.
    Org Lett. 2005; 7(14): 2809-12.
  4. Sophia Y Breusegem, Nabil Halaihel, Makoto Inoue, Hubert K Zajicek, Eleanor Lederer, Nicholas P Barry, Victor Sorribas, and Moshe Levi.
    Acute and chronic changes in cholesterol modulate Na-Pi cotransport activity in OK cells.
    Am J Physiol Renal Physiol. 2005; 289(1): F154-65.
  5. Heather A Relyea, Jennifer M Vrtis, Ryan Woodyer, Stacey A Rimkus, and Wilfred A van der Donk.
    Inhibition and pH dependence of phosphite dehydrogenase.
    Biochemistry. 2005; 44(17): 6640-9.
  6. Lauren B Jensen, Nancy K Burgess, Denise D Gonda, Emily Spencer, Heather A Wilson-Ashworth, Erin Driscoll, Mai P Vu, Jeremy L Fairbourn, Allan M Judd, and John D Bell.
    Mechanisms governing the level of susceptibility of erythrocyte membranes to secretory phospholipase A2.
    Biophys J. 2005; 88(4): 2692-2705. PMCID: PMC1305365
  7. Ryan Woodyer, Joshua L Wheatley, Heather A Relyea, Stacey A Rimkus, and Wilfred A van der Donk.
    Site-directed mutagenesis of active site residues of phosphite dehydrogenase.
    Biochemistry. 2005; 44(12): 4765-74.

2004

  1. Cristina Arnulphi, Lihua Jin, M Alejandra Tricerri, and Ana Jonas.
    Enthalpy-driven apolipoprotein A-I and lipid bilayer interaction indicating protein penetration upon lipid binding.
    Biochemistry. 2004; 43(38): 12258-64.
  2. Jacqueline E Payton, Richard J Perrin, Wendy S Woods, and Julia M George.
    Structural determinants of PLD2 inhibition by α-synuclein.
    J Mol Biol. 2004; 337(4): 1001-9.
  3. Rebekah S Vest, Laurie J Gonzales, Seth A Permann, Emily Spencer, Lee D Hansen, Allan M Judd, and John D Bell.
    Divalent cations increase lipid order in erythrocytes and susceptibility to secretory phospholipase A2.
    Biophys J. 2004; 86(4): 2251-2260. PMCID: PMC1304075
  4. Mary C Murphy, Ivan Rasnik, Wei Cheng, Timothy M Lohman, and Taekjip Ha.
    Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy.
    Biophys J. 2004; 86(4): 2530–2537. PMCID: PMC1304100

2003

  1. Juewen Liu and Yi Lu.
    Improving fluorescent DNAzyme biosensors by combining inter- and intramolecular quenchers.
    Anal Chem. 2003; 75(23): 6666-72.
  2. Nejat Düzgünes, Luis A Bagatolli, Paul Meers, Yu-Kyuong Oh, and Robert M Straubinger.
    Fluorescence methods in liposome research.
    Liposomes 2nd ed: A Practical Approach (The Practical Approach Series, Vol. 264). By V Torchilin and V Weissig (Editors). Oxford University Press, USA, pp. 105-147, 2003. ISBN: 9780199636549
  3. Yi Lu, Juewen Liu, Jing Li, Peter J Bruesehoff, Caroline M-B Pavot, and Andrea K Brown.
    New highly sensitive and selective catalytic DNA biosensors for metal ions.
    Biosens Bioelectr. 2003; 18(5-6): 529-40.
  4. Luis A Bagatolli.
    Direct observation of lipid domains in free standing bilayers: from simple to complex lipid mixtures.
    Chem Phys Lipids. 2003; 122(1-2): 137-45.

2002

  1. Juewen Liu and Yi Lu.
    FRET study of a trifluorophore-labeled DNAzyme.
    J Am Chem Soc. 2002; 124(51): 15208-16.
  2. Andrea T Da Poian, John E Johnson, and Jerson L Silva.
    Protein-RNA interactions and virus stability as probed by the dynamics of Tryptophan side chains.
    J Biol Chem. 2002; 277(49): 47596-47602.
  3. Christopher D Snow, Houbi Nguyen, Vijay S Pande, and Martin Gruebele.
    Absolute comparison of simulated and experimental protein-folding dynamics.
    Nature. 2002; 420(6911): 102-106.
  4. Adam Smith, Sahraoui Chaïeb, A al Aql, M Alsalhi, and Munir H Nayfeh.
    Observation of assembly of fluorescent Si nanoparticles under the influence of electric current.
    J Nanosci Nanotechnol. 2002; 2(5): 471-3.
  5. Faith M Harris, Katrina B Best, and John D Bell.
    Use of laurdan fluorescence intensity and polarization to distinguish between changes in membrane fluidity and phospholipid order.
    Biochim Biophys Acta. 2002; 1565(1): 123-128.
  6. Luis A Bagatolli, Derk D Binns, David M Jameson, and Joseph P Albanesi.
    Activation of dynamin II by POPC in giant unilamellar vesicles: a two-photon fluorescence microscopy study.
    J Protein Chem. 2002; 21(6): 383-391.
  7. Yuri T Didenko and Kenneth S Suslick.
    The energy efficiency of formation of photons, radicals and ions during single-bubble cavitation.
    Nature. 2002; 418(6896): 394-397.
  8. Kaushik Nag, Jin-Si Pao, Robert R Harbottle, Fred Possmayer, Nils O Petersen, and Luis A Bagatolli.
    Segregation of saturated chain lipids in pulmonary surfactant films and bilayers.
    Biophys J. 2002; 82(4): 2041-51. PMCID: PMC1301999
  9. Andrea K Behling Agree, M Alejandra Tricerri, Kirsten Arnvig-McGuire, Shao-min Tian, and Ana Jonas.
    Folding and stability of the C-terminal half of apolipoprotein A-I examined with a Cys-specific fluorescence probe.
    Biochim Biophys Acta. 2002; 1594(2): 286-96.

2001

  1. Faith M Harris, Samantha K Smith, and John D Bell.
    Physical properties of erythrocyte ghosts that determine susceptibility to secretory phospholipase A2.
    J Biol Chem. 2001; 276(25): 22722-22731.
  2. Ravi A Vijayendran and Deborah E Leckband.
    A quantitative assessment of heterogeneity for surface-immobilized proteins.
    Anal Chem. 2001; 73(3): 471-80.

2000

  1. Carlos P Sotomayor, Luis F Aguilar, Francisco J Cuevas, Michael K Helms, and David M Jameson.
    Modulation of pig kidney Na+/K+-ATPase activity by cholesterol: role of hydration.
    Biochemistry. 2000; 39(35): 10928-35.
  2. Sarah E Bondosa, Stephen G Sligar, and Jiri Jonas.
    High-pressure denaturation of apomyoglobin.
    Biochim Biophys Acta. 2000; 1480(1-2): 353-64.

1999

  1. John M Jean, Caroline Clerte, and Kathleen B Hall.
    Global and local dynamics of the human U1A protein determined by tryptophan fluorescence.
    Protein Sci. 1999; 8(10): 2110-2120. PMCID: PMC2144131
  2. Sara Benci, Simona Vaccari, Andrea Mozzarelli, and Paul F Cook.
    Time-resolved fluorescence of O-acetylserine sulfhydrylase.
    Biochim Biophys Acta. 1999; 1429(2): 317-30.

1998

  1. Ming Xiao, Handong Li, Gregory E Snyder, Roger Cooke, Ralph G Yount, and Paul R Selvin.
    Conformational changes between the active-site and regulatory light chain of myosin as determined by luminescence resonance energy transfer: The effect of nucleotides and actin.
    Proc Natl Acad Sci USA. 1998; 95(26): 15309-15314. PMCID: PMC28039
  2. Scott M Blackman, David W Piston, and Albert H Beth.
    Oligomeric state of human erythrocyte band 3 measured by fluorescence resonance energy homotransfer.
    Biophys J. 1998; 75(2): 1117-1130. PMCID: PMC1299786
  3. Michael K Helms, Dean A Malencik, and Sonia R Anderson.
    Flexibility involving the intermolecular dityrosyl cross-links of enzymatically polymerized calmodulin.
    Biochemistry. 1998; 37(23): 8378-84.
  4. Erica A Pyles and J Ching Lee.
    Escherichia coli cAMP receptor protein-DNA complexes. 2. Structural asymmetry of DNA bending.
    Biochemistry. 1998; 37(15): 5201-10.

1997

  1. Barbara Pilas and Gary Durack.
    A flow cytometric method for measurement of intracellular chloride concentration in lymphocytes using the halide-specific probe 6-methoxy-N-(3-sulfopropyl) quinolinium (SPQ).
    Cytometry. 1997; 28(4): 316-22.
  2. Michael K Helms, Charles E Petersen, Nadhipuram V Bhagavan, and David M Jameson.
    Time-resolved fluorescence studies on site-directed mutants of human serum albumin.
    FEBS Lett. 1997; 408(1): 67-70.
  3. Donald J Weaver Jr, Gary Durack, and Edward W Voss Jr.
    Analysis of the intracellular processing of proteins: application of fluorescence polarization and a novel fluorescent probe.
    Cytometry. 1997; 28(1): 25-35.

1996

  1. Jenny Carrero, William D Mallender, and Edward W Voss Jr.
    Anti-metatype antibody stabilization of Fv 4-4-20 variable domain dynamics.
    J Biol Chem. 1996; 271(19): 11247-52.
  2. William D Mallender, Jenny Carrero, and Edward W Voss Jr.
    Comparative properties of the single chain antibody and Fv derivatives of mAb 4-4-20. Relationship between interdomain interactions and the high affinity for fluorescein ligand.
    J Biol Chem. 1996; 271(10): 5338-46.
  3. Jenny Carrero and Edward W Voss Jr.
    Temperature and pH dependence of fluorescein binding within the monoclonal antibody 9-40 active site as monitored by hydrostatic pressure.
    J Biol Chem. 1996; 271(10): 5332-7.
  4. Laura J DeLong and J Wylie Nichols.
    Time-resolved fluorescence anisotropy of fluorescent-labeled lysophospholipid and taurodeoxycholate aggregates.
    Biophys J. 1996; 70(3): 1466-71. PMCID: PMC1225073
  5. Mark R Ehrhardt, Leonardo Erijman, Gregorio Weber, and A Joshua Wand.
    Molecular recognition by calmodulin: pressure-induced reorganization of a novel calmodulin-peptide complex.
    Biochemistry. 1996; 35(5): 1599-1605.

1993

  1. Tatiana Coelho-Sampaio and Edward W Voss Jr.
    Pressure-induced dissociation of fluorescein from the anti-fluorescein single-chain antibody 4-4-20.
    Biochemistry. 1993; 32(41): 10929-35.

1992

  1. Catherine A Royer, Traci Ropp, and Suzanne F Scarlata.
    Solution studies of the interactions between the histone core proteins and DNA using fluorescence spectroscopy.
    Biophys Chem. 1992; 43(2): 197-211.
  2. William D Bedzyk, Cathy A Swindlehurst, and Edward W Voss Jr.
    Relative binding properties of fluorescein and 9-hydroxyphenylfluoron (HPF) with murine monoclonal anti-fluorescein antibodies.
    Biochim Biophys Acta. 1992; 1119(1): 27-34.

1991

  1. Tatiana Coelho-Sampaio, Sérgio T Ferreira, G Benaim, and A Vieyra.
    Dissociation of purified erythrocyte Ca(2+)-ATPase by hydrostatic pressure.
    J Biol Chem. 1991; 266(33): 22266-72.
  2. Gyorgy Nemecz and Friedhelm Schroeder.
    Selective binding of cholesterol by recombinant fatty acid binding proteins.
    J Biol Chem. 1991; 266(26): 17180-6.
  3. Gyorgy Nemecz, John R Jefferson, and Friedhelm Schroeder.
    Polyene fatty acid interactions with recombinant intestinal and liver fatty acid-binding proteins. Spectroscopic studies.
    J Biol Chem. 1991; 266(26): 17112-23.
  4. Cathy A Swindlehurst and Edward W Voss Jr.
    Fluorescence measurements of immune complexes of Mab 4-4-20 with isomeric haptens.
    Biophys J. 1991; 59(3): 619-28. PMCID: PMC1281226
  5. Patrick S Stayton and Stephen G Sligar.
    Structural microheterogeneity of a tryptophan residue required for efficient biological electron transfer between putidaredoxin and cytochrome P-450CAM.
    Biochemistry. 1991; 30(7): 1845-51.

1990

  1. Jennifer H Wald, Elaine S Krul, and Ana Jonas.
    Structure of apolipoprotein A-I in three homogeneous, reconstituted high density lipoprotein particles.
    J Biol Chem. 1990; 265(32): 20037-43.
  2. Ruby I MacDonald.
    Characteristics of self-quenching of the fluorescence of lipid-conjugated rhodamine in membranes.
    J Biol Chem. 1990; 265(23): 13533-9.
  3. Yvonne Lin Kao, Parkson L G Chong, and Ching Hsien Huang.
    Time-resolved fluorometric and differential scanning calorimetric investigation of dehydroergosterol in 1-stearoyl-2-caprylphosphatidylcholine bilayers.
    Biochemistry. 1990; 29(5): 1315-22.

1989

  1. Sérgio T Ferreira.
    Fluorescence studies of the conformational dynamics of parvalbumin in solution: lifetime and rotational motions of the single tryptophan residue.
    Biochemistry. 1989; 28(26): 10066-10072.

1988

  1. Mary Ann Dombrink-Kurtzman and Edward W Voss Jr.
    Cryoprecipitation properties of a high-affinity monoclonal IgM anti-fluorescyl antibody.
    Mol Immunol. 1988; 25(12): 1309-20.
  2. Patrick S Stayton, Mark T Fisher, and Stephen G Sligar.
    Determination of cytochrome b5 association reactions. Characterization of metmyoglobin and cytochrome P-450cam binding to genetically engineered cytochrome B5.
    J Biol Chem. 1988; 263(27): 13544-8.