Laboratory for Fluorescence Dynamics

A NIH research center for biomedical fluorescence spectroscopy at the 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 Institutes of Health (2P41GM103540) and UCI."

2016

  1. Fong AH, Romero-López M, Heylman CM, Keating M, Tran D, Sobrino A, Tran AQ, Pham HH, Fimbres C, Gershon PD, Botvinick EL, George SC, Hughes CCW.
    Three-Dimensional adult cardiac extracellular matrix promotes maturation of human induced pluripotent stem cell-derived cardiomyocytes.
    Tissue Eng Part A. 2016; 22(15-16): 1016-1025. PMCID: PMC4991595
  2. Steinhardt RC, O’Neill JM, Rathbun CM, McCutcheon DC, Paley MA, Prescher JA.
    Design and synthesis of an Alkynyl Luciferin analogue for bioluminescence imaging.
    Chem Eur J. 2016; 22(11): 3671-3675.

2015

  1. Rahim MK, Kota R, Haun JB.
    Enhancing reactivity for bioorthogonal pretargeting by unmasking antibody-conjugated trans-cyclooctenes.
    Bioconjug Chem. 2015; 26(2): 352-360.

2014

  1. Kim MY, Li DJ, Pham LK, Wong BG, Hui EE.
    Microfabrication of high-resolution porous membranes for cell culture.
    J Memb Sci. 2014; 452: 460-469. PMCID: PMC3931465
  2. Lu D, Kan JJ, Fullerton EE, Liu Z.
    Enhancing spontaneous emission rates of molecules using nanopatterned multilayer hyperbolic metamaterials.
    Nat Nanotechnol. 2014; 9(1): 48-53.

2013

  1. Gibbons E, Pickett KR, Streeter MC, Warcup AO, Nelson J, Judd AM, Bell JD.
    Molecular details of membrane fluidity changes during apoptosis and relationship to phospholipase A2 activity.
    Biochim Biophys Acta. 2013; 1828(2): 887-895. PMCID: PMC3529823

2012

  1. Andrews LM.
    Understanding the intracellular dynamics of endogenous ribonucleic acid species in living cells.
    PhD in University of Western Sydney, 2012.
    Advisor: Mark Jones
  2. Lei TC, Glazner GF, Duffy M, Scherrer L, Pendyala S, Lib B, Wang X, Wang H, Huang Z.
    Optical properties of hematoporphyrin monomethyl ether (HMME), a PDT photosensitizer.
    Photodiagnosis Photodyn Ther. 2012; 9(3): 232-242.
  3. McCutcheon DC, Paley MA, Steinhardt RC, Prescher JA.
    Expedient synthesis of electronically modified luciferins for bioluminescence imaging.
    J Am Chem Soc. 2012; 134(18): 7604-7607. PMCID: PMC3613990

2011

  1. Hellriegel C, Caiolfa VR, Corti V, Sidenius N, Zamai M.
    Number and brightness image analysis reveals ATF-induced dimerization kinetics of uPAR in the cell membrane.
    FASEB J. 2011; 25(9): 2883-2897. PMCID: PMC3157682
  2. Coppola S.
    Ruolo del Citoscheletro nel Trafficking Intracellulare di Nanovettori per il Trasporto Genico.
    Laurea in Facoltà di Scienze Matematiche Fisiche e Naturali, La Sapienza Università di Roma, Italy, 2011.
    Advisor: Giulio Caracciolo

2010

  1. Carrion B, Huang CP, Ghajar CM, Kachgal S, Kniazeva E, Jeon NL, Putnam AJ.
    Recreating the perivascular niche ex vivo using a microfluidic approach.
    Biotechnol Bioeng. 2010; 107(6): 1020-1028. PMCID: PMC3367510
  2. Weise K, Triola G, Janosch S, Waldmann H, Winter R.
    Visualizing association of lipidated signaling proteins in heterogeneous membranes - Partitioning into subdomains, lipid sorting, interfacial adsorption, and protein association.
    Biochim Biophys Acta. 2010; 1798(7): 1409-1417.

2009

  1. Spring BQ Clegg RM.
    Image analysis for denoising full-field frequency-domain fluorescence lifetime images.
    J Microsc. 2009; 235(2): 221-237.
  2. Kang I, Reem RE, Kaczmarowski AL, Malpeli JG.
    Contrast sensitivity of cats and humans in scotopic and mesopic conditions.
    J Neurophysiol. 2009; 102(2): 831-840. PMCID: PMC2724355
  3. Bailey RW, Nguyen T, Robertson L, Gibbons E, Nelson J, Christensen RE, Bell JP, Judd AM, Bell JD.
    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. Clegg RM.
    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. Stott BM, Vu MP, McLemore CO, Lund MS, Gibbons E, Brueseke TJ, Wilson-Ashworth HA, Bell JD.
    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
  2. Heiner AL, Gibbons E, Fairbourn JL, Gonzalez LJ, McLemore CO, Brueseke TJ, Judd AM, Bell JD.
    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
  3. Bailey RW.
    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
  4. Buranachai C, Kamiyama D, Chiba A, Williams BD, Clegg RM.
    Rapid frequency-domain FLIM spinning disk confocal microscope: lifetime resolution, image improvement and wavelet analysis.
    J Fluoresc. 2008; 18(5): 929-942.
  5. Buranachai C.
    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. Duncan KA Huber SC.
    Sucrose synthase oligomerization and F-actin association are regulated by sucrose concentration and phosphorylation.
    Plant Cell Physiol. 2007; 48(11): 1612-23.
  2. Bailey RW, Olson ED, Vu MP, Brueseke TJ, Robertson L, Christensen RE, Parker KH, Judd AM, Bell JD.
    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. Guest CB, Hartman ME, O'Connor JC, Chakour KS, Sovari AA, Freund GG.
    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. Cuevas FJ, Jameson DM, Sotomayor CP.
    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. Fidorra M, Duelund L, Leidy C, Simonsen AC, Bagatolli LA.
    Absence of fluid-ordered/fluid-disordered phase coexistence in ceramide/POPC mixtures containing cholesterol.
    Biophys J. 2006; 90(12): 4437-51. PMCID: PMC1471871
  3. Breusegem SY, Levi M, Barry NP.
    Fluorescence correlation spectroscopy and fluorescence lifetime imaging microscopy.
    Nephron Exp Nephrol. 2006; 103(2): e41-e49.
  4. Jeng ES, Moll AE, Roy AC, Gastala JB, Strano MS.
    Detection of DNA hybridization using the near-infrared band-gap fluorescence of single-walled carbon nanotubes.
    Nano Lett. 2006; 6(3): 371-375.
  5. Vest RS, Wallis R, Jensen LB, Hawes AC, Callister J, Brimhall B, Judd AM, Bell JD.
    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. Liu J Lu Y.
    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. Liu J Lu Y.
    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. Madhavan N, Robert EC, Gin MS.
    A highly active anion-selective aminocyclodextrin ion channel.
    Angew Chem Int Ed Engl. 2005; 44(46): 7584-7.
  2. Woodyer R, Zhao H, van der Donk WA.
    Mechanistic investigation of a highly active phosphite dehydrogenase mutant and its application for NADPH regeneration.
    FEBS J. 2005; 272(15): 3816-27.
  3. Aathimanikandan SV, Sandanaraj BS, Arges CG, Bardeen CJ, Thayumanavan S.
    Effect of guest molecule flexibility in access to dendritic interiors.
    Org Lett. 2005; 7(14): 2809-12.
  4. Breusegem SY, Halaihel N, Inoue M, Zajicek HK, Lederer E, Barry NP, Sorribas V, Levi M.
    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. Relyea HA, Vrtis JM, Woodyer R, Rimkus SA, van der Donk WA.
    Inhibition and pH dependence of phosphite dehydrogenase.
    Biochemistry. 2005; 44(17): 6640-9.
  6. Jensen LB, Burgess NK, Gonda DD, Spencer E, Wilson-Ashworth HA, Driscoll E, Vu MP, Fairbourn JL, Judd AM, Bell JD.
    Mechanisms governing the level of susceptibility of erythrocyte membranes to secretory phospholipase A2.
    Biophys J. 2005; 88(4): 2692-2705. PMCID: PMC1305365
  7. Woodyer R, Wheatley JL, Relyea HA, Rimkus SA, van der Donk WA.
    Site-directed mutagenesis of active site residues of phosphite dehydrogenase.
    Biochemistry. 2005; 44(12): 4765-74.

2004

  1. Arnulphi C, Jin L, Tricerri MA, Jonas A.
    Enthalpy-driven apolipoprotein A-I and lipid bilayer interaction indicating protein penetration upon lipid binding.
    Biochemistry. 2004; 43(38): 12258-64.
  2. Payton JE, Perrin RJ, Woods WS, George JM.
    Structural determinants of PLD2 inhibition by α-synuclein.
    J Mol Biol. 2004; 337(4): 1001-9.
  3. Vest RS, Gonzales LJ, Permann SA, Spencer E, Hansen LD, Judd AM, Bell JD.
    Divalent cations increase lipid order in erythrocytes and susceptibility to secretory phospholipase A2.
    Biophys J. 2004; 86(4): 2251-2260. PMCID: PMC1304075
  4. Murphy MC, Rasnik I, Cheng W, Lohman TM, Ha T.
    Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy.
    Biophys J. 2004; 86(4): 2530-2537. PMCID: PMC1304100

2003

  1. Liu J Lu Y.
    Improving fluorescent DNAzyme biosensors by combining inter- and intramolecular quenchers.
    Anal Chem. 2003; 75(23): 6666-72.
  2. Düzgünes N, Bagatolli LA, Meers P, Oh YK, Straubinger RM.
    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. Lu Y, Liu J, Li J, Bruesehoff PJ, Pavot CMB, Brown AK.
    New highly sensitive and selective catalytic DNA biosensors for metal ions.
    Biosens Bioelectr. 2003; 18(5-6): 529-40.
  4. Bagatolli LA.
    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. Liu J Lu Y.
    FRET study of a trifluorophore-labeled DNAzyme.
    J Am Chem Soc. 2002; 124(51): 15208-16.
  2. da Poian AT, Johnson JE, Silva JL.
    Protein-RNA interactions and virus stability as probed by the dynamics of Tryptophan side chains.
    J Biol Chem. 2002; 277(49): 47596-47602.
  3. Snow CD, Nguyen H, Pande VS, Gruebele M.
    Absolute comparison of simulated and experimental protein-folding dynamics.
    Nature. 2002; 420(6911): 102-106.
  4. Smith A, Chaïeb S, Aql Aa, Alsalhi M, Nayfeh MH.
    Observation of assembly of fluorescent Si nanoparticles under the influence of electric current.
    J Nanosci Nanotechnol. 2002; 2(5): 471-3.
  5. Harris FM, Best KB, Bell JD.
    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. Bagatolli LA, Binns DD, Jameson DM, Albanesi JP.
    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. Didenko YT Suslick KS.
    The energy efficiency of formation of photons, radicals and ions during single-bubble cavitation.
    Nature. 2002; 418(6896): 394-397.
  8. Nag K, Pao JS, Harbottle RR, Possmayer F, Petersen NO, Bagatolli LA.
    Segregation of saturated chain lipids in pulmonary surfactant films and bilayers.
    Biophys J. 2002; 82(4): 2041-51. PMCID: PMC1301999
  9. Agree AKB, Tricerri MA, Arnvig-McGuire K, Tian Sm, Jonas A.
    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. Harris FM, Smith SK, Bell JD.
    Physical properties of erythrocyte ghosts that determine susceptibility to secretory phospholipase A2.
    J Biol Chem. 2001; 276(25): 22722-22731.
  2. Vijayendran RA Leckband DE.
    A quantitative assessment of heterogeneity for surface-immobilized proteins.
    Anal Chem. 2001; 73(3): 471-80.

2000

  1. Sotomayor CP, Aguilar LF, Cuevas FJ, Helms MK, Jameson DM.
    Modulation of pig kidney Na+/K+-ATPase activity by cholesterol: role of hydration.
    Biochemistry. 2000; 39(35): 10928-35.
  2. Bondosa SE, Sligar SG, Jonas J.
    High-pressure denaturation of apomyoglobin.
    Biochim Biophys Acta. 2000; 1480(1-2): 353-64.
  3. Casavola C.
    Application of near infra-red spectroscopy to the non-invasive measurement of relevant physiological parameters: the blood flow and the oxygen consumption in the skeletal muscle.
    PhD in Physics, University of Bari, Italy, 2000.
    Advisor: Pietro Mario Lugarà

1999

  1. Jean JM, Clerte C, Hall KB.
    Global and local dynamics of the human U1A protein determined by tryptophan fluorescence.
    Protein Sci. 1999; 8(10): 2110-2120. PMCID: PMC2144131
  2. Benci S, Vaccari S, Mozzarelli A, Cook PF.
    Time-resolved fluorescence of O-acetylserine sulfhydrylase.
    Biochim Biophys Acta. 1999; 1429(2): 317-30.

1998

  1. Xiao M, Li H, Snyder GE, Cooke R, Yount RG, Selvin PR.
    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. Blackman SM, Piston DW, Beth AH.
    Oligomeric state of human erythrocyte band 3 measured by fluorescence resonance energy homotransfer.
    Biophys J. 1998; 75(2): 1117-1130. PMCID: PMC1299786
  3. Helms MK, Malencik DA, Anderson SR.
    Flexibility involving the intermolecular dityrosyl cross-links of enzymatically polymerized calmodulin.
    Biochemistry. 1998; 37(23): 8378-84.
  4. Pyles EA Lee JC.
    Escherichia coli cAMP receptor protein-DNA complexes. 2. Structural asymmetry of DNA bending.
    Biochemistry. 1998; 37(15): 5201-10.

1997

  1. Pilas B Durack G.
    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. Helms MK, Petersen CE, Bhagavan NV, Jameson DM.
    Time-resolved fluorescence studies on site-directed mutants of human serum albumin.
    FEBS Lett. 1997; 408(1): 67-70.
  3. Weaver DJ Jr, Durack G, Voss EW 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. Carrero J, Mallender WD, Voss EW Jr.
    Anti-metatype antibody stabilization of Fv 4-4-20 variable domain dynamics.
    J Biol Chem. 1996; 271(19): 11247-52.
  2. Mallender WD, Carrero J, Voss EW 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. Carrero J Voss EW 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. DeLong LJ Nichols JW.
    Time-resolved fluorescence anisotropy of fluorescent-labeled lysophospholipid and taurodeoxycholate aggregates.
    Biophys J. 1996; 70(3): 1466-71. PMCID: PMC1225073
  5. Ehrhardt MR, Erijman L, Weber G, Wand AJ.
    Molecular recognition by calmodulin: pressure-induced reorganization of a novel calmodulin-peptide complex.
    Biochemistry. 1996; 35(5): 1599-1605.

1995

  1. Dreger ZA, Lang JM, Drickamer HG.
    Unusual phosphorescence and its pressure dependence in 4-N,N-dimethylaminobenzonitrile dissolved in solid polymers.
    Chem Phys Lett. 1995; 232(4): 351-356.

1993

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

1992

  1. Royer CA, Ropp T, Scarlata SF.
    Solution studies of the interactions between the histone core proteins and DNA using fluorescence spectroscopy.
    Biophys Chem. 1992; 43(2): 197-211.
  2. Bedzyk WD, Swindlehurst CA, Voss EW 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. Coelho-Sampaio T, Ferreira ST, Benaim G, Vieyra A.
    Dissociation of purified erythrocyte Ca(2+)-ATPase by hydrostatic pressure.
    J Biol Chem. 1991; 266(33): 22266-72.
  2. Nemecz G Schroeder F.
    Selective binding of cholesterol by recombinant fatty acid binding proteins.
    J Biol Chem. 1991; 266(26): 17180-6.
  3. Nemecz G, Jefferson JR, Schroeder F.
    Polyene fatty acid interactions with recombinant intestinal and liver fatty acid-binding proteins. Spectroscopic studies.
    J Biol Chem. 1991; 266(26): 17112-23.
  4. Swindlehurst CA Voss EW Jr.
    Fluorescence measurements of immune complexes of Mab 4-4-20 with isomeric haptens.
    Biophys J. 1991; 59(3): 619-28. PMCID: PMC1281226
  5. Stayton PS Sligar SG.
    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. Wald JH, Krul ES, Jonas A.
    Structure of apolipoprotein A-I in three homogeneous, reconstituted high density lipoprotein particles.
    J Biol Chem. 1990; 265(32): 20037-43.
  2. MacDonald RI.
    Characteristics of self-quenching of the fluorescence of lipid-conjugated rhodamine in membranes.
    J Biol Chem. 1990; 265(23): 13533-9.
  3. Kao YL, Chong PLG, Huang CH.
    Time-resolved fluorometric and differential scanning calorimetric investigation of dehydroergosterol in 1-stearoyl-2-caprylphosphatidylcholine bilayers.
    Biochemistry. 1990; 29(5): 1315-22.

1989

  1. Ferreira ST.
    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. Dombrink-Kurtzman MA Voss EW Jr.
    Cryoprecipitation properties of a high-affinity monoclonal IgM anti-fluorescyl antibody.
    Mol Immunol. 1988; 25(12): 1309-20.
  2. Stayton PS, Fisher MT, Sligar SG.
    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.