fluorescent dyes

Summary

Summary: Agents that emit light after excitation by light. The wave length of the emitted light is usually longer than that of the incident light. Fluorochromes are substances that cause fluorescence in other substances, i.e., dyes used to mark or label other compounds with fluorescent tags.

Top Publications

  1. pmc Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)
    Michael J Rust
    Department of Physics, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    Nat Methods 3:793-5. 2006
  2. ncbi Two-photon laser scanning fluorescence microscopy
    W Denk
    School of Applied and Engineering Physics, Department of Physics, Cornell University, Ithaca, NY 14853
    Science 248:73-6. 1990
  3. ncbi A guide to choosing fluorescent proteins
    Nathan C Shaner
    Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Nat Methods 2:905-9. 2005
  4. pmc Ultra-high resolution imaging by fluorescence photoactivation localization microscopy
    Samuel T Hess
    Department of Physics and Astronomy, University of Maine, Orono, ME 04469, USA
    Biophys J 91:4258-72. 2006
  5. pmc Improving the photostability of bright monomeric orange and red fluorescent proteins
    Nathan C Shaner
    Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    Nat Methods 5:545-51. 2008
  6. ncbi High-resolution genotyping by amplicon melting analysis using LCGreen
    Carl T Wittwer
    Department of Pathology, University of Utah Medical School, Salt Lake City, UT 84132, USA
    Clin Chem 49:853-60. 2003
  7. pmc Precise nanometer localization analysis for individual fluorescent probes
    Russell E Thompson
    Cornell University, School of Applied and Engineering Physics, Ithaca, New York 14853, USA
    Biophys J 82:2775-83. 2002
  8. pmc Expanded dynamic range of fluorescent indicators for Ca(2+) by circularly permuted yellow fluorescent proteins
    Takeharu Nagai
    Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    Proc Natl Acad Sci U S A 101:10554-9. 2004
  9. pmc A practical guide to single-molecule FRET
    Rahul Roy
    Department of Physics, University of Illinois at Urbana Champaign, 1110 West Green Street, Urbana, Illinois 61801, USA
    Nat Methods 5:507-16. 2008
  10. ncbi Deep tissue two-photon microscopy
    Fritjof Helmchen
    Department of Neurophysiology, Brain Research Institute, University of Zurich, CH 8057 Zurich, Switzerland
    Nat Methods 2:932-40. 2005

Detail Information

Publications355 found, 100 shown here

  1. pmc Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)
    Michael J Rust
    Department of Physics, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    Nat Methods 3:793-5. 2006
    ..The fluorophore positions obtained from a series of imaging cycles were used to reconstruct the overall image. We demonstrated an imaging resolution of 20 nm. This technique can, in principle, reach molecular-scale resolution...
  2. ncbi Two-photon laser scanning fluorescence microscopy
    W Denk
    School of Applied and Engineering Physics, Department of Physics, Cornell University, Ithaca, NY 14853
    Science 248:73-6. 1990
    ..This technique also provides unprecedented capabilities for three-dimensional, spatially resolved photochemistry, particularly photolytic release of caged effector molecules...
  3. ncbi A guide to choosing fluorescent proteins
    Nathan C Shaner
    Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Nat Methods 2:905-9. 2005
    ....
  4. pmc Ultra-high resolution imaging by fluorescence photoactivation localization microscopy
    Samuel T Hess
    Department of Physics and Astronomy, University of Maine, Orono, ME 04469, USA
    Biophys J 91:4258-72. 2006
    ..This new method suggests a means to address a significant number of biological questions that had previously been limited by microscope resolution...
  5. pmc Improving the photostability of bright monomeric orange and red fluorescent proteins
    Nathan C Shaner
    Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    Nat Methods 5:545-51. 2008
    ..and TagRFP (a monomeric derivative of eqFP578 from Entacmaea quadricolor) that maintain most of the beneficial qualities of the original proteins and perform as reliably as Aequorea victoria GFP derivatives in fusion constructs...
  6. ncbi High-resolution genotyping by amplicon melting analysis using LCGreen
    Carl T Wittwer
    Department of Pathology, University of Utah Medical School, Salt Lake City, UT 84132, USA
    Clin Chem 49:853-60. 2003
    ..Our aim was to develop a closed-tube system for genotyping and mutation scanning that did not require labeled oligonucleotides...
  7. pmc Precise nanometer localization analysis for individual fluorescent probes
    Russell E Thompson
    Cornell University, School of Applied and Engineering Physics, Ithaca, New York 14853, USA
    Biophys J 82:2775-83. 2002
    ..The optimal image magnification depends on the expected number of photons and background noise, but, for most cases of interest, the pixel size should be about equal to the standard deviation of the point spread function...
  8. pmc Expanded dynamic range of fluorescent indicators for Ca(2+) by circularly permuted yellow fluorescent proteins
    Takeharu Nagai
    Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    Proc Natl Acad Sci U S A 101:10554-9. 2004
    ..Our study provides an important guide for the development and improvement of indicators using GFP-based FRET...
  9. pmc A practical guide to single-molecule FRET
    Rahul Roy
    Department of Physics, University of Illinois at Urbana Champaign, 1110 West Green Street, Urbana, Illinois 61801, USA
    Nat Methods 5:507-16. 2008
    ..We also describe how a smFRET-capable instrument can be built at a reasonable cost with off-the-shelf components and operated reliably using well-established protocols and freely available software...
  10. ncbi Deep tissue two-photon microscopy
    Fritjof Helmchen
    Department of Neurophysiology, Brain Research Institute, University of Zurich, CH 8057 Zurich, Switzerland
    Nat Methods 2:932-40. 2005
    ..Here we review fundamental concepts of nonlinear microscopy and discuss conditions relevant for achieving large imaging depths in intact tissue...
  11. ncbi Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays
    S A Bustin
    Academic Department of Surgery, St Bartholomew s and the Royal London School of Medicine and Dentistry, Queen Mary and Westfield College, London E1 1BB, UK
    J Mol Endocrinol 25:169-93. 2000
    ..It illustrates the usefulness of these assays by demonstrating the significantly different levels of transcription between individuals of the housekeeping gene family, glyceraldehyde-3-phosphate-dehydrogenase (GAPDH)...
  12. ncbi Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization
    Ahmet Yildiz
    Center for Biophysics and Computational Biology, University of Illinois, Urbana Champaign, IL 61801, USA
    Science 300:2061-5. 2003
    ..These results strongly support a hand-over-hand model of motility, not an inchworm model...
  13. pmc Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging
    Graham T Dempsey
    Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts, USA
    Nat Methods 8:1027-36. 2011
    ..Our evaluation identified several photoswitchable dyes with good to excellent performance in four independent spectral ranges, with which we demonstrated low-cross-talk, four-color super-resolution imaging...
  14. pmc Fast, three-dimensional super-resolution imaging of live cells
    Sara A Jones
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Methods 8:499-508. 2011
    ..These imaging capabilities open a new window for characterizing cellular structures in living cells at the ultrastructural level...
  15. pmc Far-red fluorescent tags for protein imaging in living tissues
    Dmitry Shcherbo
    Shemiakin Ovchinnikov Institute of Bioorganic Chemistry, Miklukho Maklaya 16 10, Moscow, Russia
    Biochem J 418:567-74. 2009
    ..Together, monomeric mKate2 and pseudo-monomeric tdKatushka2 represent the next generation of extra-bright far-red fluorescent probes offering novel possibilities for fluorescent imaging of proteins in living cells and animals...
  16. ncbi Molecular beacons: probes that fluoresce upon hybridization
    S Tyagi
    Department of Molecular Genetics, Public Health Research Institute, New York, NY 10016, USA
    Nat Biotechnol 14:303-8. 1996
    ..When introduced into living cells, these probes should enable the origin, movement, and fate of specific mRNAs to be traced...
  17. ncbi Real-time DNA sequencing from single polymerase molecules
    JOHN EID
    Pacific Biosciences, 1505 Adams Drive, Menlo Park, CA 94025, USA
    Science 323:133-8. 2009
    ..Consensus sequences were generated from the single-molecule reads at 15-fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore-dependent error rates...
  18. ncbi Shedding light onto live molecular targets
    Ralph Weissleder
    Center for Molecular Imaging Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
    Nat Med 9:123-8. 2003
  19. ncbi Immunofluorescent labeling of cancer marker Her2 and other cellular targets with semiconductor quantum dots
    Xingyong Wu
    Quantum Dot Corporation, 26118 Research Rd, Hayward, CA 94545, USA
    Nat Biotechnol 21:41-6. 2003
    ..The results indicate that QD-based probes can be very effective in cellular imaging and offer substantial advantages over organic dyes in multiplex target detection...
  20. ncbi Reducing the environmental sensitivity of yellow fluorescent protein. Mechanism and applications
    O Griesbeck
    Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0647, USA
    J Biol Chem 276:29188-94. 2001
    ..Citrine is superior to all previous YFPs except when pH or halide sensitivity is desired and is particularly advantageous within genetically encoded fluorescent indicators of physiological signals...
  21. pmc Exploring RNA transcription and turnover in vivo by using click chemistry
    Cindy Y Jao
    Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 105:15779-84. 2008
    ..We find that total transcription rates vary greatly among different tissues and among different cell types within organs...
  22. pmc Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy
    Bo Huang
    Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
    Science 319:810-3. 2008
    ..This development allowed us to resolve the 3D morphology of nanoscopic cellular structures...
  23. pmc In vivo two-photon calcium imaging of neuronal networks
    Christoph Stosiek
    Physiologisches Institut, Ludwig Maximilians Universitat Munchen, Pettenkoferstrasse 12, 80336 Munich, Germany
    Proc Natl Acad Sci U S A 100:7319-24. 2003
    ..Thus, our results demonstrate the suitability of this technique for real-time analyses of intact neuronal circuits with the resolution of individual cells...
  24. ncbi In vivo near-infrared fluorescence imaging
    John V Frangioni
    SL B05 Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA
    Curr Opin Chem Biol 7:626-34. 2003
    ..Recent examples of in vivo near-infrared fluorescence imaging of animals and humans are presented, including imaging of normal and diseased vasculature, tissue perfusion, protease activity, hydroxyapatite and cancer...
  25. pmc Digital PCR
    B Vogelstein
    The Howard Hughes Medical Institute and The Johns Hopkins Oncology Center, Baltimore, MD 21231, USA
    Proc Natl Acad Sci U S A 96:9236-41. 1999
    ..The process provides a reliable and quantitative measure of the proportion of variant sequences within a DNA sample...
  26. ncbi Fluorescence-guided surgery with 5-aminolevulinic acid for resection of malignant glioma: a randomised controlled multicentre phase III trial
    Walter Stummer
    Neurochirurgische Klinik, Heinrich Heine University, Dusseldorf, Germany
    Lancet Oncol 7:392-401. 2006
    ..We aimed to assess the effect of fluorescence-guided resection with 5-aminolevulinic acid on surgical radicality, progression-free survival, overall survival, and morbidity...
  27. ncbi HaloTag: a novel protein labeling technology for cell imaging and protein analysis
    Georgyi V Los
    Promega Corporation, 2800 Woods Hollow Rd, Madison, Wisconsin 53711, USA
    ACS Chem Biol 3:373-82. 2008
    ..The synthetic ligands comprise a chloroalkane linker attached to a variety of useful molecules, such as fluorescent dyes, affinity handles, or solid surfaces...
  28. pmc Simple and inexpensive fluorescence-based technique for high-throughput antimalarial drug screening
    Martin Smilkstein
    Medical Research Service, Department of Veterans Affairs Medical Center, Oregon Health and Science University, Portland, Oregon, USA
    Antimicrob Agents Chemother 48:1803-6. 2004
    ..The results obtained with this new fluorescence assay suggest that it may be an ideal method for high-throughput antimalarial drug screening...
  29. doi Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes
    Mike Heilemann
    Angewandte Laserphysik and Laserspektroskopie, Universitat Bielefeld, Universitatsstrasse 25, 33615 Bielefeld, Germany
    Angew Chem Int Ed Engl 47:6172-6. 2008
  30. pmc The clinical use of indocyanine green as a near-infrared fluorescent contrast agent for image-guided oncologic surgery
    Boudewijn E Schaafsma
    Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
    J Surg Oncol 104:323-32. 2011
    ..Therefore, understanding its advantages and limitations is of significant importance. Although non-targeted and non-conjugatable, ICG appears to be laying the foundation for more widespread use of NIR fluorescence-guided surgery...
  31. ncbi In vivo imaging of quantum dots encapsulated in phospholipid micelles
    Benoit Dubertret
    Center for Studies in Physics and Biology, Laboratory of Molecular Embryology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Science 298:1759-62. 2002
    ..Nanocrystal fluorescence could be followed to the tadpole stage, allowing lineage-tracing experiments in embryogenesis...
  32. ncbi Spontaneously emerging cortical representations of visual attributes
    Tal Kenet
    Department of Neurobiology, The Weizmann Institute of Science, Rehovot 76100, Israel
    Nature 425:954-6. 2003
    ..We suggest that dynamically switching cortical states could represent the brain's internal context, and therefore reflect or influence memory, perception and behaviour...
  33. ncbi Fluorescence imaging with near-infrared light: new technological advances that enable in vivo molecular imaging
    Vasilis Ntziachristos
    Center for Molecular Imaging Research, Massachusetts General Hospital and Harvard Medical School, Building 149, 13th Street 5406, Charlestown MA 02129 2060, USA
    Eur Radiol 13:195-208. 2003
    ..We describe theoretical specifics, and we provide insight into its in vivo capacity and the sensitivity achieved. Finally, we discuss its clinical feasibility...
  34. ncbi In vivo imaging of tumors with protease-activated near-infrared fluorescent probes
    R Weissleder
    Center of Molecular Imaging Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
    Nat Biotechnol 17:375-8. 1999
    ..In vivo imaging showed a 12-fold increase in NIRF signal, allowing the detection of tumors with submillimeter-sized diameters. This strategy can be used to detect such early stage tumors in vivo and to probe for specific enzyme activity...
  35. ncbi Fluorescent and luminescent probes for measurement of oxidative and nitrosative species in cells and tissues: progress, pitfalls, and prospects
    Peter Wardman
    University of Oxford, Gray Cancer Institute, Mount Vernon Hospital, Northwood, Middlesex HA6 2JR, UK
    Free Radic Biol Med 43:995-1022. 2007
    ..Rational use of probes requires understanding and quantitation of the mechanistic pathways involved, and of environmental factors such as oxygen and pH. We can build on this framework of knowledge in evaluating new probes...
  36. ncbi Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data
    Christian Ramakers
    Department of Anatomy and Embryology K2 283, Experimental and Molecular Cardiology Group, Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
    Neurosci Lett 339:62-6. 2003
    ..A computer program to perform this calculation is available on request (e-mail: bioinfo@amc.uva.nl; subject: LinRegPCR)...
  37. pmc Measurement of mitochondrial membrane potential using fluorescent rhodamine derivatives
    R C Scaduto
    Department of Cellular and Molecular Physiology, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033 USA
    Biophys J 76:469-77. 1999
    ....
  38. pmc Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal
    Jing Li
    Department of Biochemistry, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216 4505, USA
    Nucleic Acids Res 33:4649-59. 2005
    ..These models suggest that the biologically relevant structure of the human telomere quadruplex in K+ solution is not the one determined in the published crystalline state...
  39. ncbi Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples
    Manuel F Juette
    Institute for Molecular Biophysics, The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
    Nat Methods 5:527-9. 2008
    ..This method, named biplane (BP) FPALM, combines a double-plane detection scheme with fluorescence photoactivation localization microscopy (FPALM) enabling 3D sub-diffraction resolution without compromising speed or sensitivity...
  40. ncbi Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation
    Jingyi Fei
    Department of Chemistry, Columbia University, New York, NY 10027, USA
    Mol Cell 30:348-59. 2008
    ..Real-time smFRET experiments reveal that the L1 stalk-tRNA interaction persists throughout the translocation reaction, suggesting that the L1 stalk acts to direct tRNA movements during translocation...
  41. pmc A bright and photostable photoconvertible fluorescent protein
    Sean A McKinney
    Howard Hughes Medical Institute, Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, USA
    Nat Methods 6:131-3. 2009
    ..Here we report an EosFP variant that functions well in a broad range of protein fusions for dynamic investigations, exhibits high photostability and preserves the approximately 10-nm localization precision of its parent...
  42. ncbi Quantum-sized carbon dots for bright and colorful photoluminescence
    Ya Ping Sun
    Department of Chemistry and Laboratory for Emerging Materials and Technology, Clemson University, Clemson, South Carolina 29634 0973, USA
    J Am Chem Soc 128:7756-7. 2006
    ..These strongly emissive carbon dots may find applications similar to or beyond those of their widely pursued silicon counterparts...
  43. ncbi A genetically encoded calcium indicator for chronic in vivo two-photon imaging
    Marco Mank
    Max Planck Institute of Neurobiology, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nat Methods 5:805-11. 2008
    ....
  44. ncbi Visualizing secretion and synaptic transmission with pH-sensitive green fluorescent proteins
    G Miesenbock
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nature 394:192-5. 1998
    ..When linked to a vesicle membrane protein, pHluorins were sorted to secretory and synaptic vesicles and reported transmission at individual synaptic boutons, as well as secretion and fusion pore 'flicker' of single secretory granules...
  45. pmc Ratiometric bimolecular beacons for the sensitive detection of RNA in single living cells
    Antony K Chen
    Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 38:e148. 2010
    ..Combined, these attributes enabled RBMBs to exhibit an improved sensitivity for RNA detection in living cells...
  46. pmc Fast 18F labeling of a near-infrared fluorophore enables positron emission tomography and optical imaging of sentinel lymph nodes
    Richard Ting
    Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, USA
    Bioconjug Chem 21:1811-9. 2010
    ..Facile incorporation of (18)F into a NIRF probe should promote many synergistic PET and NIRF combinations...
  47. ncbi A review of NIR dyes in cancer targeting and imaging
    Shenglin Luo
    Institute of Combined Injury, State Key Laboratory of Trauma, Burns and Combined Injury, College of Preventive Medicine, Third Military Medical University, Chongqing, China
    Biomaterials 32:7127-38. 2011
    ..We believe these newly developed multifunctional NIR dyes will broaden current concept of tumor targeted imaging and hold promise to make an important contribution to the diagnosis and therapeutics for the treatment of cancer...
  48. ncbi Alexa dyes, a series of new fluorescent dyes that yield exceptionally bright, photostable conjugates
    N Panchuk-Voloshina
    Molecular Probes, Inc, Eugene, Oregon, USA
    J Histochem Cytochem 47:1179-88. 1999
    Alexa 350, Alexa 430, Alexa 488, Alexa 532, Alexa 546, Alexa 568, and Alexa 594 dyes are a new series of fluorescent dyes with emission/excitation spectra similar to those of AMCA, Lucifer Yellow, fluorescein, rhodamine 6G, ..
  49. ncbi Chemically induced photoswitching of fluorescent probes--a general concept for super-resolution microscopy
    Ulrike Endesfelder
    Biotechnology and Biophysics, Julius Maximilians University Würzburg, Am Hubland, 97074 Wurzburg, Germany
    Molecules 16:3106-18. 2011
    ..Finally, we discuss opportunities to combine fluorescent proteins with organic fluorophores for dual-color photoswitching microscopy...
  50. ncbi Feature point tracking and trajectory analysis for video imaging in cell biology
    I F Sbalzarini
    Institute of Computational Science, ETH Zurich, 8092 Zurich, Switzerland
    J Struct Biol 151:182-95. 2005
    ..The present automated tracking process enables the quantification of dispersive processes in cell biology using techniques such as moment scaling spectra...
  51. ncbi Evaluating the uptake and intracellular fate of polystyrene nanoparticles by primary and hepatocyte cell lines in vitro
    Helinor J Johnston
    Biomedicine and Sport and Exercise Science Research Group, School of Life Sciences, Edinburgh Napier University, Edinburgh EH10 5DT, UK
    Toxicol Appl Pharmacol 242:66-78. 2010
    ..The findings were, in the main, comparable between primary rat hepatocytes and the different human hepatocyte cell lines...
  52. pmc Formation and dissociation of M1 muscarinic receptor dimers seen by total internal reflection fluorescence imaging of single molecules
    Jonathan A Hern
    Division of Physical Biochemistry, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom
    Proc Natl Acad Sci U S A 107:2693-8. 2010
    ..Two-color TIRFM established the dynamic nature of dimer formation with M(1) receptors undergoing interconversion between monomers and dimers on the timescale of seconds...
  53. ncbi Live cell multicolor imaging of lipid droplets with a new dye, LD540
    Johanna Spandl
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 01307 Dresden, Germany
    Traffic 10:1579-84. 2009
    ..Its improved specificity, brightness and photostability support live cell imaging, which was used to demonstrate by two-color imaging lipid droplet motility along microtubules...
  54. pmc Single-dose intravenous toxicity study of IRDye 800CW in Sprague-Dawley rats
    Milton V Marshall
    Baylor College of Medicine, Houston, TX, USA
    Mol Imaging Biol 12:583-94. 2010
    ..Following conjugation or breakdown of a labeled ligand, excess NHS ester is converted to the carboxylate form. To prepare for clinical use as a near-infrared fluorophore, a toxicity study was conducted on IRDye 800CW carboxylate...
  55. pmc Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators
    Hiromi Imamura
    Precursory Research for Embryonic Science, Japan Science and Technology Agency, 5 Sanbancho, Chiyoda ku, Tokyo 102 0075, Japan
    Proc Natl Acad Sci U S A 106:15651-6. 2009
    ..This was also confirmed by an experiment using oligomycin A, an inhibitor of F(o)F(1)-ATP synthase. In addition, it was demonstrated that HeLa cells change ATP-generating pathway in response to changes of nutrition in the environment...
  56. ncbi The fluorescent toolbox for assessing protein location and function
    Ben N G Giepmans
    National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
    Science 312:217-24. 2006
    ..Small organic fluorescent dyes, nanocrystals ("quantum dots"), autofluorescent proteins, small genetic encoded tags that can be ..
  57. pmc Imaging the biogenesis of individual HIV-1 virions in live cells
    Nolwenn Jouvenet
    Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York 10065, USA
    Nature 454:236-40. 2008
    ..These approaches allow a previously unobserved view of the genesis of individual virions and the determination of parameters of viral assembly that are inaccessible with conventional techniques...
  58. pmc NIR dyes for bioimaging applications
    Jorge O Escobedo
    Department of Chemistry, Portland State University, Portland, OR 97207, USA
    Curr Opin Chem Biol 14:64-70. 2010
    b>Fluorescent dyes based on small organic molecules that function in the near infrared (NIR) region are of great current interest in chemical biology...
  59. ncbi Fluorescence navigation with indocyanine green for detecting sentinel lymph nodes in breast cancer
    Toshiyuki Kitai
    Department of Surgery, Nara Social Security Hospital 1 62 Asahicho Yamatokoriyama Nara 639 1013, Japan
    Breast Cancer 12:211-5. 2005
    ..However, intensive training is necessary to obtain a satisfactory detection rate and to avoid false-negative results. This paper presents a novel method using indocyanine green fluorescence imaging to detect sentinel lymph nodes...
  60. pmc Autofluorescent proteins with excitation in the optical window for intravital imaging in mammals
    Michael Z Lin
    Department of Pharmacology, University of California, San Diego, La Jolla, 92093, USA
    Chem Biol 16:1169-79. 2009
    ..The crystal structure of Neptune reveals a novel mechanism for red-shifting involving the acquisition of a new hydrogen bond with the acylimine region of the chromophore...
  61. ncbi Creating new fluorescent probes for cell biology
    Jin Zhang
    Department of Pharmacology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 18 496, Cambridge, Massachusetts 02139, USA
    Nat Rev Mol Cell Biol 3:906-18. 2002
    ....
  62. pmc Novel, rapid, and inexpensive cell-based quantification of antimalarial drug efficacy
    Tyler N Bennett
    Department of Chemistry, Lombardi Cancer Center, Georgetown University, Washington DC 20057, USA
    Antimicrob Agents Chemother 48:1807-10. 2004
    ..g., [3H]hypoxanthine and [3H]ethanolamine)-based assays or P. falciparum lactate dehydrogenase activity-based assays. The assay significantly improves the pace at which antimalarial drug discovery efforts may proceed...
  63. ncbi Fluorophore-conjugated anti-CEA antibody for the intraoperative imaging of pancreatic and colorectal cancer
    Sharmeela Kaushal
    Department of Surgery, University of California San Diego, Moores Cancer Center, 3855 Health Sciences Drive 0987, La Jolla, CA 92093 0987, USA
    J Gastrointest Surg 12:1938-50. 2008
    ..In both of these cancers, complete detection of primary and metastatic lesions at the time of surgery is critical to optimal surgical resection and appropriate patient treatment...
  64. ncbi Fluorescence spectroscopy of single biomolecules
    S Weiss
    Materials Sciences and Physical Biosciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Science 283:1676-83. 1999
    ..The progress in applying these tools to biological studies with the use of fluorophores that are site-specifically attached to macromolecules is reviewed...
  65. ncbi Measuring calcium signaling using genetically targetable fluorescent indicators
    Amy E Palmer
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309 0215, USA
    Nat Protoc 1:1057-65. 2006
    ..An experiment and calibration will probably take a few hours. Finally, the offline data workup can take approximately 1 d depending on the extent of analysis...
  66. pmc Reaction-based small-molecule fluorescent probes for chemoselective bioimaging
    Jefferson Chan
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Nat Chem 4:973-84. 2012
    ..We highlight design criteria for effective chemical tools for use in biological applications as well as gaps for future exploration...
  67. ncbi Single-mismatch detection using gold-quenched fluorescent oligonucleotides
    B Dubertret
    Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Nat Biotechnol 19:365-70. 2001
    ..In competitive hybridization assays, the ability to detect single mismatch is eightfold greater with this probe than with other molecular beacons...
  68. pmc Imaging voltage in neurons
    Darcy S Peterka
    Department of Biological Sciences, Columbia University, New York, New York 10027, USA
    Neuron 69:9-21. 2011
    ....
  69. ncbi Near-infrared fluorescence: application to in vivo molecular imaging
    Scott A Hilderbrand
    Center for Systems Biology, Massachusetts General Hospital Harvard Medical School, Simches Research Center, 185 Cambridge St, Suite 5 210, Boston, MA 02114, USA
    Curr Opin Chem Biol 14:71-9. 2010
    ..Recent advances in our understanding of these variables as they pertain to the application of optical reporters for in vivo imaging are discussed in this review...
  70. pmc Multicolor super-resolution imaging with photo-switchable fluorescent probes
    Mark Bates
    School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
    Science 317:1749-53. 2007
    ..Using this approach, we demonstrate multicolor imaging of DNA model samples and mammalian cells with 20- to 30-nanometer resolution. This technique will facilitate direct visualization of molecular interactions at the nanometer scale...
  71. pmc Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation
    Yee Hwa Yang
    Department of Statistics, Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720 3860, USA
    Nucleic Acids Res 30:e15. 2002
    ..g. differences in labeling efficiency between the two fluorescent dyes). The term normalization refers to the process of removing such variation...
  72. pmc Bright ideas for chemical biology
    Luke D Lavis
    Department of Chemistry, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    ACS Chem Biol 3:142-55. 2008
    ..Here, we examine the chemical and photophysical properties of oft-used fluorophores and highlight classic and contemporary examples in which utility has been built upon these scaffolds...
  73. ncbi A genetically encoded sensor for H2O2 with expanded dynamic range
    Kseniya N Markvicheva
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, RAS, Miklukho Maklaya 16 10, 117997 Moscow, Russia
    Bioorg Med Chem 19:1079-84. 2011
    ..This mutation was previously shown to destabilize interface between monomers in OxyR dimers. However, in HyPer-2, the A233V mutation stabilizes the dimer and expands the dynamic range of the probe...
  74. pmc Extrinsic fluorescent dyes as tools for protein characterization
    Andrea Hawe
    Division of Drug Delivery Technology, Leiden Amsterdam Center for Drug Research, Leiden University, P O Box 9502, 2300 RA, Leiden, The Netherlands
    Pharm Res 25:1487-99. 2008
    Noncovalent, extrinsic fluorescent dyes are applied in various fields of protein analysis, e.g. to characterize folding intermediates, measure surface hydrophobicity, and detect aggregation or fibrillation...
  75. ncbi Measuring localization performance of super-resolution algorithms on very active samples
    Steve Wolter
    Biotechnology and Biophysics, Julius Maximilians Universitat Wurzburg, Germany
    Opt Express 19:7020-33. 2011
    ..6 per square micrometer and that the number of successfully localized fluorophores per frame is limited to 0.2 per square micrometer...
  76. ncbi Fluorescent nucleic acid base analogues
    L Marcus Wilhelmsson
    Department of Chemical and Biological Engineering Physical Chemistry, Chalmers University of Technology, S 41296 Gothenburg, Sweden
    Q Rev Biophys 43:159-83. 2010
    ..Finally, the development and characterization of the first nucleic base analogue FRET pair, tC(O)-tC(nitro), and its possible future uses are discussed...
  77. pmc Molecular mechanism of Thioflavin-T binding to amyloid fibrils
    Matthew Biancalana
    Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Biochim Biophys Acta 1804:1405-12. 2010
    ..These studies have yielded important insights into amyloid structures and the processes of fibril formation, and they also offer guidance for designing the next generation of amyloid assembly diagnostics, inhibitors, and therapeutics...
  78. ncbi Development of novel fluorescence probes that can reliably detect reactive oxygen species and distinguish specific species
    Ken Ichi Setsukinai
    Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    J Biol Chem 278:3170-5. 2003
    ..HPF and APF should be useful as tools to study the roles of hROS and (-)OCl in many biological and chemical applications...
  79. pmc Near-infrared fluorescent type II quantum dots for sentinel lymph node mapping
    Sungjee Kim
    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Nat Biotechnol 22:93-7. 2004
    ..Taken together, the chemical, optical and in vivo data presented in this study demonstrate the potential of near-infrared quantum dots for biomedical imaging...
  80. ncbi Intraoperative laparoscopic fluorescence guidance to the sentinel lymph node in prostate cancer patients: clinical proof of concept of an integrated functional imaging approach using a multimodal tracer
    Henk G van der Poel
    Department of Urology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
    Eur Urol 60:826-33. 2011
    ..Integration of molecular imaging and in particular intraoperative image guidance is expected to improve the surgical accuracy of laparoscopic lymph node (LN) dissection...
  81. ncbi Real-time single-molecule imaging of the infection pathway of an adeno-associated virus
    G Seisenberger
    Department Chemie, , Butenandtstrasse 11, , Germany
    Science 294:1929-32. 2001
    ..The real-time visualization of the infection pathway of single AAVs shows a much faster infection than was generally observed so far...
  82. pmc Expanding the chemical scope of RNA:methyltransferases to site-specific alkynylation of RNA for click labeling
    Yuri Motorin
    Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D 69120 Heidelberg, Germany
    Nucleic Acids Res 39:1943-52. 2011
    ....
  83. ncbi Fluorescence microscopy
    Jeff W Lichtman
    Department of Molecular and Cell Biology, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA
    Nat Methods 2:910-9. 2005
    ..This review attempts to provide a framework for understanding excitation of and emission by fluorophores, the way fluorescence microscopes work, and some of the ways fluorescence can be optimized...
  84. pmc The TTX-resistant sodium channel Nav1.8 (SNS/PN3): expression and correlation with membrane properties in rat nociceptive primary afferent neurons
    Laiche Djouhri
    Department of Physiology, University of Bristol Medical School, Bristol BS8 1TD, UK
    J Physiol 550:739-52. 2003
    ..Thus high levels of Nav1.8 protein may contribute to the longer AP durations (especially in A-fibre neurons) and larger AP overshoots that are typical of nociceptors...
  85. ncbi Oxidative chemistry of fluorescent dyes: implications in the detection of reactive oxygen and nitrogen species
    Balaraman Kalyanaraman
    Department of Biophysics and Free Radical Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
    Biochem Soc Trans 39:1221-5. 2011
    ..Assays using fluorescent-based boronate probes will be more reliable for peroxynitrite determination than those using either dichlorodihydrofluorescein or dihydrorhodamine...
  86. ncbi Tumor paint: a chlorotoxin:Cy5.5 bioconjugate for intraoperative visualization of cancer foci
    Mandana Veiseh
    Clinical Research Division, Fred Hutchinson Cancer Research Center, University of Washington, 1100 Fairview Avenue N, Seattle, WA 98109, USA
    Cancer Res 67:6882-8. 2007
    ..Mouse studies revealed that CTX:Cy5.5 has favorable biodistribution and toxicity profiles. These studies show that CTX:Cy5.5 has the potential to fundamentally improve intraoperative detection and resection of malignancies...
  87. ncbi Superoxide reacts with hydroethidine but forms a fluorescent product that is distinctly different from ethidium: potential implications in intracellular fluorescence detection of superoxide
    Hongtao Zhao
    Biophysics Research Institute and Free Radical Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
    Free Radic Biol Med 34:1359-68. 2003
    ..We conclude that the reaction between superoxide and HE forms a fluorescent marker product that is different from ethidium. Potential implications of this finding in intracellular detection and imaging of superoxide are discussed...
  88. ncbi Imaging synaptic vesicle exocytosis and endocytosis with FM dyes
    Michael A Gaffield
    Neuroscience Program, University of Colorado Medical School, Aurora, Colorado 80045, USA
    Nat Protoc 1:2916-21. 2006
    ..If the preparation is stimulated again, without dye in the chamber, dimming of the preparation provides a measure of exocytosis of labeled vesicles. With a synaptic preparation on hand, this protocol requires 1 day...
  89. ncbi The effect of surface charge on the uptake and biological function of mesoporous silica nanoparticles in 3T3-L1 cells and human mesenchymal stem cells
    Tsai Hua Chung
    Stem Cell Research Center, National Health Research Institutes, Miaoli 350, Taiwan, ROC
    Biomaterials 28:2959-66. 2007
    ..Our results show that MSNs uptake by hMSCs can be regulated by a threshold of positive surface charge but also imply that the modulation of surface charge on MSNs uptake is specific to cell type...
  90. pmc In vivo imaging of membrane-associated glycans in developing zebrafish
    Scott T Laughlin
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Science 320:664-7. 2008
    ..Using a multicolor detection strategy, we performed a spatiotemporal analysis of glycan expression and trafficking and identified patterns that would be undetectable with conventional molecular imaging approaches...
  91. pmc Diels-Alder cycloaddition for fluorophore targeting to specific proteins inside living cells
    Daniel S Liu
    Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
    J Am Chem Soc 134:792-5. 2012
    ..By incorporating the Diels-Alder cycloaddition, we have broadened the panel of fluorophores that can be targeted by lipoic acid ligase...
  92. ncbi Make them blink: probes for super-resolution microscopy
    Jan Vogelsang
    Center for Nano and Molecular Science and Technology and Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, USA
    Chemphyschem 11:2475-90. 2010
    ....
  93. ncbi Thermodynamic analysis of ligand-induced changes in protein thermal unfolding applied to high-throughput determination of ligand affinities with extrinsic fluorescent dyes
    Curtis J Layton
    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
    Biochemistry 49:10831-41. 2010
    ..We analyze cases in which the ligand binds to both the native and denatured state or to the native state only and cases in which protein:ligand stoichiometry needs to treated explicitly...
  94. pmc Model of sarcomeric Ca2+ movements, including ATP Ca2+ binding and diffusion, during activation of frog skeletal muscle
    S M Baylor
    Department of Physiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104 6085, USA
    J Gen Physiol 112:297-316. 1998
    ..We conclude that Ca2+ binding by ATP and diffusion of CaATP make important contributions to the determination of the amplitude and the time course of Delta[Ca2+]...
  95. pmc Acidification of the oxygen scavenging system in single-molecule fluorescence studies: in situ sensing with a ratiometric dual-emission probe
    Xinghua Shi
    Howard Hughes Medical Institute, Department of Physics, and Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Anal Chem 82:6132-8. 2010
    ..This in situ assay should be applicable to a large variety of future single-molecule fluorescence studies...
  96. pmc Assessment and continued validation of the malaria SYBR green I-based fluorescence assay for use in malaria drug screening
    Jacob D Johnson
    Principal Investigator, Department of Parasitology, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD 20910, USA
    Antimicrob Agents Chemother 51:1926-33. 2007
    ..In conclusion, the MSF assay allows for reliable one-plate high-throughput, automated malaria in vitro susceptibility testing without the expense, time consumption, and hazard of other screening assays...
  97. pmc Sentinel lymph node mapping by indocyanin green fluorescence imaging in oropharyngeal cancer - preliminary experience
    Marius G Bredell
    Department of Craniomaxillofacial Surgery, University Hospital of Zurich, Zurich, Switzerland
    Head Neck Oncol 2:31. 2010
    ..The aim of this paper was to evaluate the potential application of Indocyanin Green (ICG) in the mapping and detection of sentinel lymph nodes (SLN) in cancers of the head and neck...
  98. pmc Target-cancer-cell-specific activatable fluorescence imaging probes: rational design and in vivo applications
    Hisataka Kobayashi
    National Institutes of Health, Bethesda, Maryland 20892 1088, USA
    Acc Chem Res 44:83-90. 2011
    ....
  99. ncbi An engineered protein tag for multiprotein labeling in living cells
    Arnaud Gautier
    Institute of Chemical Sciences and Engineering, Ecole Polytechnique Federale de Lausanne, CH 1015 Lausanne, Switzerland
    Chem Biol 15:128-36. 2008
    ..We furthermore show simultaneous pulse-chase experiments to visualize different generations of two different proteins in one sample...
  100. ncbi Diffusion dynamics of glycine receptors revealed by single-quantum dot tracking
    Maxime Dahan
    Laboratoire Kastler Brossel, CNRS UMR 8552, Ecole Normale Supérieure and Université Pierre et Marie Curie, 24 rue Lhomond, 75005 Paris, France
    Science 302:442-5. 2003
    ..The entry of GlyRs into the synapse by diffusion was observed and further confirmed by electron microscopy imaging of QD-tagged receptors...
  101. ncbi Targeting mitochondria with organelle-specific compounds: strategies and applications
    Lema F Yousif
    Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON, M5S 3M2 Canada
    Chembiochem 10:1939-50. 2009
    ..Recently, however, synthetic transporters that show promise for the mito-specific delivery of bioactive cargos have begun to emerge. This review summarizes the most exciting of these developments and discusses their applications...

Research Grants72

  1. Novel Extended Red-Shifted Rhodamine Dyes
    NICHOLAS CAIRNS; Fiscal Year: 2004
    b>Fluorescent dyes that operate in the long visible / near infra-red (NIR) region of the electromagnetic spectrum are excellent reporter components of molecular probes, fluorescent ligands, enzyme substrates, imaging contrast agents and ..
  2. Cellular interactions in asthma
    CHRISTOPHER DAVID CABALLERO ALLEN; Fiscal Year: 2012
    ..visualized by the expression of fluorescent proteins in a lineage-specific fashion, or by labeling with fluorescent dyes or antibodies...
  3. Effects of nerve demyelination on auditory synaptic functions
    Jun Hee Kim; Fiscal Year: 2012
    ..study Ca2+ and Na+ ion concentration changes in the axon and nerve terminal using Ca2+ and Na+ ion sensitive fluorescent dyes. PUBLIC HEALTH RELEVANCE: The proposed research will give us insights into the basic biological processes ..
  4. Tb-FISH (Fluorescent in Situ Hybridization) Assay for Direct Detection of M. tube
    JYOTSNA S SHAH; Fiscal Year: 2010
    ..The assay uses MTB and Mycobacterium genus (M-Genus) specific probes labeled with different fluorescent dyes. The assay is simple, rapid and in-expensive (<$5.00/test and a one time expense of ~$1200 for filters)...
  5. ANALYSIS OF A NOVEL SUBSET OF HUMAN CD8+ MEMORY CELLS WITH STEM CELL QUALITIES
    Stanley R Riddell; Fiscal Year: 2010
    ..These quiescent memory T cells exhibit higher ATP binding cassette (ABC) transporter activity, rapidly efflux fluorescent dyes and chemotherapy drugs and are resistant to cytotoxic chemotherapy in vitro and in vivo compared with the ..
  6. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
    Ignacio Tinoco; Fiscal Year: 2013
    ..Their motion can be seen in a microscope and thus the behavior of the RNA is assessed. FRET: Fluorescent dyes are placed on the RNA or on the molecules it interacts with...
  7. Sox10 Alleles for Functional Analysis of Glial Lineages
    E Michelle Southard-Smith; Fiscal Year: 2013
    ..of these processes have been primarily investigated in cell culture systems that are amenable to loading with fluorescent dyes or transfection by exogenous plasmids...
  8. Integrated imaging of the form and function of the beating embryonic heart
    ANDREW MARTIN ROLLINS; Fiscal Year: 2013
    ..project period, we will complement OCT with optical mapping (OM) using potentiometric and calcium-sensitive fluorescent dyes to reveal patterns of cardiac conduction and calcium signaling...
  9. Biochemical and Genetic Analysis of yFACT, A Novel Nucleosome Reorganizing Factor
    TIMOTHY G FORMOSA; Fiscal Year: 2013
    ..Purified histones and DNA fragments labeled with fluorescent dyes will be used to probe the properties of reorganized nucleosomes, and mutant histone and FACT proteins will be ..
  10. Rapid, Low-Cost Cell-Sorting System for Diagnosis of Candidemia
    Scott Irwin; Fiscal Year: 2010
    ..and fungal species discrimination at the level achievable with Fountain Flow" sorting combined with RNA fluorescent dyes. This research wil be performed by a team of scientists from SoftRay Inc...
  11. Multiplex ALEX-based Test for Protease Activity Profiling in Arthritic Joints
    ARMIN H REITMAIR; Fiscal Year: 2013
    ..Target recognition molecules are tagged with different color fluorescent dyes (and quenchers)...
  12. Multiplex Fluorescent Zdyes for Differential Glycomic Detection
    EDWARD DRATZ; Fiscal Year: 2009
    ..project between Zdye LLC and Montana State University) a new family of ultrasensitive, highly water soluble fluorescent dyes called Zdyes for multicolor, differential labeling--that do not shift the isoelectric points of Zdye-labeled ..
  13. Structure and mechanism of the dynein motor
    Ronald D Vale; Fiscal Year: 2013
    ..Based upon our crystal structure, we will design new recombinant dyneins that will enable placement of fluorescent dyes and other biophysical probes in defined locations on the dynein motor...
  14. Presynaptic GABA-A receptor activation in auditory brainstem axon terminals
    CATHERINE JEANNE CHALENSKI WEISZ; Fiscal Year: 2013
    ..Tools including fluorescent dyes that measure changes in calcium signaling (indicative of cellular activity) and 'optogenetic'tools ..
  15. Multimodal imaging of antibody-mediated therapy during acute viral encephalitides
    William Paul Duprex; Fiscal Year: 2013
    ..the temporal CNS biodistribution of an intravenously delivered existing rhMAb that has been conjugated to fluorescent dyes or the MRI-contrast agent gadolinium...
  16. Dynamic ICG and FA Software
    Timothy Holmes; Fiscal Year: 2009
    Indocyanine Green (ICG) and Sodium Fluorescein (SF) are fluorescent dyes used clinically in eye fundus imaging, primarily for detecting vascular abnormalities in the retina and choroid, which is the layer behind the retina...
  17. Molecularly guided multimodal theranostics for breast cancer
    Amit Joshi; Fiscal Year: 2013
    ..In this project we will develop a near infrared optical tomography scanner to exploit plasmonically enhanced fluorescent dyes for molecular imaging...
  18. Cell Analytics for Viability Experiments (CAVE (TM))
    Melanie M Tomczak; Fiscal Year: 2013
    ..Also, conducting high throughput studies using fluorescent dyes is expensive and requires complex robotics to prepare specimens...
  19. Multiplexed Protein &miRNA Biomarker-based Next-gen Test for Alzheimers Disease
    ARMIN H REITMAIR; Fiscal Year: 2013
    ..molecule fluorescence spectroscopy, whereby target recognition molecules are tagged with different color fluorescent dyes (and quenchers), allowing, on the same platform, ultrasensitive detection of both proteins and nucleic acids (..
  20. Novel Methodology for Rapid Antibiotic Susceptibiility Testing in S. aureus
    Alexis F Sauer Budge; Fiscal Year: 2010
    ..be determined rapidly via fluorescence microscopy when the mechanical stress is applied in the presence of fluorescent dyes which stain the damaged bacteria...
  21. Photonic Crystal Surfaces for Label-Free Detection and Fluorescence Amplification
    LILA OTT VODKIN; Fiscal Year: 2012
    ..Although fluorescent dyes, surface chemistries, spotting robots, hybridization chambers, detection instruments, and data analysis tools ..
  22. Adaptive Optics Instrumentation for Advanced Ophthalmic Imaging
    David R Williams; Fiscal Year: 2012
    ..special capabilities, such as the ability to image ganglion cells in the living human eye without the use of fluorescent dyes, and the ability to optically record neural responses from specific retinal cells...
  23. LIPID AND PROTEIN EFFECTS ON MONOLAYER STABILITY
    JOSEPH ANTHONY ZASADZINSKI; Fiscal Year: 2013
    ..to the subphase using vertical and horizontal optical sectioning with a confocal microscope and multiple fluorescent dyes. We expect that SP-A, B and C promote adsorption;however, we do not know if specific lipids or proteins are ..
  24. Excitability and Mitochondrial Polarization in Ischemic Ventricular Fibrillation
    JUNKO SHIBAYAMA WARREN; Fiscal Year: 2012
    ..The main approach will be confocal imaging using combination of fluorescent dyes in whole hearts...
  25. Plasmodium Genus and P. falciparum - P. vivax FISH Assays
    Jyotsna Shah; Fiscal Year: 2009
    ..The PFV-FISH assay uses PF and PV specific probes labeled with red and green fluorescent dyes, respectively. Thus, PF fluoresces red and PV fluoresces green under specific dual pass filters...
  26. ALEX for fast ultrasensitive multiplexed detection &quantification of microRNAs
    ARMIN H REITMAIR; Fiscal Year: 2013
    ..molecule fluorescence spectroscopy, whereby target recognition molecules are tagged with different color fluorescent dyes (and quenchers)...
  27. Creating Safe Biodegradable Photoluminescent Implant Polymers
    Jian Yang; Fiscal Year: 2013
    ..As alternatives, fluorescent dyes suffer from photobleaching and fluorescent proteins are dim in vivo and hard to manipulate...
  28. Plaque detection with the hydrocyanines
    Niren Murthy; Fiscal Year: 2013
    ..The hydrocyanines are a new family of fluorescent dyes, recently developed in our laboratory, which can detect ROS at nanomolar concentrations, have tunable ..
  29. PROTEOGLYCANS IN GROWTH FACTOR SIGNALING AND DEVELOPMENT
    Scott B Selleck; Fiscal Year: 2010
    ..Our studies of the synapse employ direct measures of endocytosis using fluorescent dyes that are incorporated into endocytosed vesicles, visualization of growth factors critical for synapse ..
  30. pHLIP Nanotechnology Platform for Cancer Imaging and Therapy
    Yana K Reshetnyak; Fiscal Year: 2012
    ..We will introduce a synthetic scheme of simultaneous conjugation of cargo molecules and fluorescent dyes to the C-terminus of pHLIP via a cleavable S-S bond and establish the properties (polarity, shape, charge and ..
  31. Photonic Crystal Enhanced Fluorescence: Development of Sensors Structures and Det
    Richard C Zangar; Fiscal Year: 2013
    ..been recently demonstrated as an effective approach for increasing the output and collection efficiency of fluorescent dyes that are used for protein microarray biomarker detection...
  32. DIETARY & GENETIC CONTROL OF ROS DAMAGE TO THE LENS
    Norman S Wolf; Fiscal Year: 2010
    ..We now seek answers for the following questions, using specific fluorescent dyes with confocal readout in living extirpated lenses, protein specific antibodies in lens tissue sections, ..
  33. Endovascular Cardiac Optical Mapping
    Christian S Eversull; Fiscal Year: 2013
    ..with novel, inexpensive, and scalable electrophysiological mapping technology, using voltage sensitive fluorescent dyes to intuitively visualize both anatomy and electrophysiology...
  34. The Iowa Center for Molecular Auditory Neuroscience
    Steven H Green; Fiscal Year: 2013
    ..using light microscopy and EM: histology, including sectioning, staining, immunofluorescence, EM, and use of fluorescent dyes to label nerve fibers;confocal imaging, including multiphoton, of live or fixed tissue;(2) Genomics core for ..
  35. Short-term plasticity &temporal precision at the inner hair cell ribbon synapse
    Elisabeth Glowatzki; Fiscal Year: 2013
    ..concentration by controlling its spread with specific buffers, and by monitoring its decay time course with fluorescent dyes. Facilitation will also be studied by uncaging Ca2+ in the cytosolic space...
  36. In Vivo Cancer Therapy Monitoring with Diffuse Optical Methods
    Regine Choe; Fiscal Year: 2013
    ..Using new targeted optical fluorescent dyes, one can probe tumor specific metabolism and physiology not accessible by endogenous contrast alone...
  37. PROTOTYPE CATHETER FOR IN VIVO HIGH-RESOLUTION CARDIAC FLUORESCENCE MAPPING
    Miguel Valderrabano; Fiscal Year: 2010
    ..b>Fluorescent dyes have been used to record biological processes from the heart for more than a decade...
  38. Droplet Method for Bilayer Assays
    Gregory W Faris; Fiscal Year: 2010
    ..protein and one self- assembled pore with a transmembrane peptide into the interfacial bilayer and use fluorescent dyes to establish their presence and function...
  39. Single cell analysis of chromatin changes at individual genes
    Oleg N Denisenko; Fiscal Year: 2013
    ..We anticipate that this method will have a broad impact on many areas of basic and medical research, where epigenetic mechanisms play a role. ..
  40. Multiplex Fluorescent Dyes for Ultrasensitive Proteomics
    Edward A Dratz; Fiscal Year: 2010
    ..foundation of Phase I to synthesize and demonstrate a new family of different-colored, highly water soluble fluorescent dyes (Zdyes) that take greatly expanded advantage of the unique ability of multiplexed 2D gels to reveal global ..
  41. Nonlinear Optical Endomicroscopy for Optical Biopsy of Cancer in Internal Organs
    Xingde Li; Fiscal Year: 2013
    ....
  42. Viral tracing of genetically defined neural circuitry
    KEVIN T BEIER; Fiscal Year: 2012
    ..Historically, neural tracers such as wheat germ agglutinin (WGA), nanobeads, and fluorescent dyes have aided this investigation...
  43. Enhanced Dynamic Range Proteomic Analysis: Phase II
    RAND SWANSON; Fiscal Year: 2013
    ..The present Phase II proposal is aimed at greatly enhancing the analysis of multicolor spectral imaging of fluorescent dyes in proteomics to detect changes in protein levels and protein posttranslational modifications in gel ..
  44. Enhanced Dynamic Range Proteomic Analysis: Phase II
    RAND SWANSON; Fiscal Year: 2011
    ..The present Phase II proposal is aimed at greatly enhancing the analysis of multicolor spectral imaging of fluorescent dyes in proteomics to detect changes in protein levels and protein posttranslational modifications in gel ..
  45. Bringing Modern Circular Dichroism Instrumentation to Notre Dame Researchers
    PATRICIA LOUISE CLARK; Fiscal Year: 2010
    ..also an essential technique in the study of chiral-selective properties of small molecules, including drugs, fluorescent dyes, and chemical catalysts designed to mimic enzymatic catalysis...
  46. Selection and Characterization of PSMA Ligands from Phage-Displayed Libraries
    Gary Fujii; Fiscal Year: 2006
    ..Once binding to purified PSMA ectodomain has been verified, anti-PSMA RRPs will be labeled with fluorescent dyes and PSMA specific binding to prostate and other cancer cells will be assessed by fluorescence microscopy, ..
  47. Novel PET Ligands for In Vivo Binding to Amyloid in AD
    Brian J Ciliax; Fiscal Year: 2010
    ..a method for such imaging studies, radiochemists have tried to model candidate tracers for neuroimaging on fluorescent dyes that bind to the beta-pleated sheet structures of the amyloid fibrils of SP...
  48. Thiol Specific Fluorogenic Agents for Laser Scanning Confocal Microscopy
    Xiangming Guan; Fiscal Year: 2010
    ..This proposed application is aimed to develop a method which can be used to detect the status of oxidative stress in intact cells. ..
  49. Oklahoma High-Throughput Serum Analyte System
    Judith A James; Fiscal Year: 2010
    ..The magnetic beads are infused with varying amounts of fluorescent dyes and coated with specific ligands...
  50. Nitric oxide in bladder neural-epithelial signaling
    Lori A Birder; Fiscal Year: 2013
    ..The aim will utilize imaging with fluorescent dyes to study how chemical and physical stimuli stimulate movement and release of transmitters from vesicles in ..
  51. Multifunctional Photosensitizers for Image-guided PDT of Brain Tumors
    Ravindra K Pandey; Fiscal Year: 2012
    ..and pre-clinical validation of novel conjugates of tumor- avid PS carrying unique, near infrared (NIR) fluorescent dyes and the long half-life PET agent 124I...
  52. TB- FISH Assay for Direct Detection of M. tuberculosis in unprocessed sputum
    Jyotsna Shah; Fiscal Year: 2007
    ..The assay uses MTB specific probes labeled with fluorescent dyes. The assay is simple, rapid and in-expensive (~$5.00/test)...
  53. Fluorometric Imaging Plate Reader (FLIPRtetra)
    Louis M Luttrell; Fiscal Year: 2010
    ..The Fluorometric Imaging Plate Reader (FLIPR 1) was originally designed to utilize fluorescent dyes to monitor changes in cell membrane potential...
  54. Novel Europium Based Time-Resolve Fluorophore with Exceptional Intensity and Stab
    NATHANIEL BUTLIN; Fiscal Year: 2010
    ..complexes of lanthanide ions (particularly Terbium and Europium) offer significant advantages over organic fluorescent dyes. Compared with traditional organic fluorescent materials, the lanthanide coordination compounds have the ..
  55. A Wireless Laser Speckle and Fluorescence Imager for In vivo Brain Tumor Imaging
    Arvind P Pathak; Fiscal Year: 2013
    ..optical imaging technique that meets these requirements and does not require the administration of exogenous fluorescent dyes or contrast agents...
  56. All-optical molecular voltmeter for measuring electric fields in proteins
    Aleksander Rebane; Fiscal Year: 2013
    ..laboratory in physics has a long standing research program on two-photon absorption (2PA) properties of fluorescent dyes, the Hughes laboratory in cell biology has been working on fluorescent proteins and channels for two decades, ..
  57. Fluorescent probes for quantitation of secretory protein levels in single cells
    Erik L Snapp; Fiscal Year: 2013
    ..Theoretically, up to four distinct fluorescent dyes can be paired with unique aptamers to report on the expression of four different secretory proteins...
  58. Superior Near-IR Dyes for Bioimaging
    ARUNKUMAR EASWARAN; Fiscal Year: 2009
    ..It is also used increasingly to monitor specific molecular pathways in animals. This latter technique uses fluorescent dyes that absorb and emit near-infrared (NIR) radiation (650-900 nm) a spectral window where hemoglobin and water ..
  59. An Integrated System for DNA Sequencing by Synthesis
    Jingyue Ju; Fiscal Year: 2009
    ..in such a way that after they are incorporated into the growing strand of DNA in the polymerase reaction, the fluorescent dyes are cleaved by irradiation at 355 nm or by specific chemical reagents in a mild condition that is compatible ..
  60. Bright and Stable Near-IR dyes for Bioimaging
    ARUNKUMAR EASWARAN; Fiscal Year: 2009
    ..It is also used increasingly to monitor specific molecular pathways in animals. This latter technique uses fluorescent dyes that absorb and emit near-infrared (NIR) radiation (700-900 nm) a spectral window where hemoglobin and water ..
  61. A MODEL SYSTEM FOR PHYSIOLOGICAL EXOCYTOSIS
    FREDRIC COHEN; Fiscal Year: 2009
    ..Intermediates of fusion will be captured, and assays of the spread of fluorescent dyes and electrical measurements of fusion pores will be employed to follow the steps of fusion and how they can ..
  62. GammaPNA Miniprobes for Telomere FISH
    Tumul Srivastava; Fiscal Year: 2013
    ..The higher affinity of gammaPNA allows shorter 12 base probes to be used, resulting in more fluorescent dyes being delivered to a telomere of a given length. This will allow more reliable analysis of the shortest (i.e...
  63. Polymer Dot Nanoparticles for Detection of Single Molecules in Live Cells
    JASON DOUGLAS MCNEILL; Fiscal Year: 2010
    ..pi-conjugated polymers which provide substantial improvements in brightness as compared to conventional fluorescent dyes and nanoparticles...
  64. High-Speed, Depth-Resolved Images of Cardiac physiology
    Guy Salama; Fiscal Year: 2007
    ..Aim 2 (years 1-5): Drs. Waggoner and Ernst will synthesize new longer wavelength fluorescent dyes to monitor action potentials (APs) or cytosolic free Ca2+(Cai) and Dr...
  65. Fluorescent Organic Nanoparticles that are Monovalent, Ultra-Stable, and Biocompa
    Steven C Zimmerman; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Fluorescent dyes and nanoparticles are widely used in chemistry, biology, and medicine but suffer from poor photostability or toxicity (nanoparticles)...
  66. Charge sensitive optical detection for high throughput study of small molecules
    Nongjian Tao; Fiscal Year: 2013
    ..uses fluorescence labels, which is problematic for small molecules whose sizes are comparable to those of the fluorescent dyes. Various label- free techniques have been developed, but their sensitivity diminishes with the size of the ..
  67. M. tuberculosis Fluorescent In-Situ Hybridization
    Jyotsna Shah; Fiscal Year: 2004
    ..The assay uses MTB and Mycobacterium genus specific probes labeled with different fluorescent dyes. The assay is simple, rapid and in-expensive (< $5...
  68. REGULATION OF SYNAPTIC TRANSMISSION
    Robert Zucker; Fiscal Year: 2002
    ..methods of controlling presynaptic intracellular calcium concentration ([Ca2+]i), and measuring {Ca2+]i with fluorescent dyes, will be used to determine the basic properties of the Ca2+ sensitivity of low levels of transmitter release, ..
  69. Msec Polymerase Chain Reaction with fMolar Detection Sensitivity using SPR
    DONALD ROPER; Fiscal Year: 2007
    ..It yields absorption cross-sections >106-fold higher than fluorescent dyes, allowing label-free detection of DNA as low as 1-500 femtomoles (Goodrich et al...
  70. P.falciparum and P.vivax Fluorescent In Situ Hybridization
    Jyotsna Shah; Fiscal Year: 2006
    ..The assay uses PF and PV specific probes labeled with different fluorescent dyes. Thus, PF and PV shall fluoresce with different colors under specific dual pass filters...
  71. DIGITAL RESOLUTION IMPROVEMENT OF SLO ANGIOGRAMS
    Timothy Holmes; Fiscal Year: 2002
    ..that will provide improved 2D resolving power of vasculature and other structures in the fundus, using fluorescent dyes with the scanning laser ophthalmoscope (SLO)...
  72. Study of Intrinsic Bladder Activity by Optical Imaging
    Anthony Kanai; Fiscal Year: 2007
    ..Rat bladders will be excised, cannulated at the urethra and stained/loaded with the appropriate fluorescent dyes. Intact bladders will be placed in a temperature-regulated bath, connected to a pressure transducer, and ..