Amplified protein sensing using deep purple fluorophores on homogeneous Au substrates

We report here the first observation of appreciable enhancement of fluorescence induced by large Au colloids. Au monolayers with Au colloids of 40 nm, 59 nm, and 81 nm in radii, were formed on silane modified glass surfaces, respectively. The nanoparticle densities were varied by varying the deposition times and documented by scanning electron microscopy. Two types of samples were prepared, with large inter-particle distance and hence little or no inter-particle coupling and small inter-particle distance with inter-particle coupling. The fluorescence enhancement was examined by using a self assembled monolayer of the fluorophore-protein conjugate with Deep Purple as a fluorophore and Bovine Serum Albumin as protein (DP-BSA). The data show the over 15 fold enhancement under optimized conditions and reveal strong variations with both inter-particle distance and particle size. Nanostructures of appropriate size with optimized inter-particle distance thus prepared can produce promising substrates for decent fluorescence enhancement. We demonstrated that the Au colloid monolayers on glass surfaces are promising substrates for fluorescence enhancement with outstanding macroscopic homogeneity. This important feature will pave the way for the application of our substrates in biotechnology and life sciences such as imaging and sensing of biomolecules in proteomics.     

Polarization sensing of fluorophores in tissues for drug compliance monitoring.

We used a new method, polarization sensing, to monitor the concentration of the fluorophore rhodamine 800 in an intralipid suspension and in chicken tissue. Rhodamine 800 (Rh800) could be excited at 648 nm using a laser pointer. We developed a simple device for measuring the combined emission from a highly polarized reference film and the unpolarized or orthogonally polarized emission of Rh800 from the scattering intralipid or tissue. The concentration of Rh800 in this medium was revealed by large changes in the polarization (P) with values of P ranging from 0.8 to -0.9. It is possible to vary the sensitive Rh800 concentration range by variation of the detected emission wavelengths, orientation of the excitation polarizer, or fluorophore concentration in the reference film. Polarization sensing of fluorophores in tissue requires only steady-state detection, and can be accomplished with simple and/or portable electronics. Such devices may find use in electronic detection of ingested medicines based on transdermal detection of nontoxic long-wavelength fluorophores.     

Latent fluorophores based on a self-immolative linker strategy and suitable for protease sensing

The self-immolative spacer para-aminobenzyl alcohol (PABA) was used as a key component in the design of new protease-sensitive fluorogenic probes whose parent phenol-based fluorophore is released through an enzyme-initiated domino reaction. First, the conjugation of the phenylacetyl moiety to 7-hydroxycoumarin (umbelliferone) and 7-hydroxy-9 H-(9,9-dimethylacridin-2-one) (DAO) by means of the heterobifunctional PABA linker has led to pro-fluorophores 6a and 6d whose enzyme activation by penicillin amidase was demonstrated. The second part of this study was devoted to the extension of this latent fluorophore strategy to the caspase-3 protease, a key mediator of apoptosis in mammalian cells. Fluorogenic caspase-3 substrates 11 and 13 derived from umbelliferone and DAO, respectively, were prepared. It was demonstrated that pro-fluorophore 11 is a sensitive fluorimetric reagent for the detection of this cysteine protease. Furthermore, in vitro assays with fluorogenic probe 13 showed a deleterious effect of biological thiols on fluorescence of the released acridinone fluorophore DAO that, to our knowledge, had not been reported until now.     

Rejuvenating old fluorophores with new chemistry

The field of organic chemistry began with 19th century scientists identifying and then expanding upon synthetic dye molecules for textiles. In the 20th century, dye chemistry continued with the aim of developing photographic sensitizers and laser dyes. Now, in the 21st century, the rapid evolution of biological imaging techniques provides a new driving force for dye chemistry. Of the extant collection of synthetic fluorescent dyes for biological imaging, two classes reign supreme: rhodamines and cyanines. Here, we provide an overview of recent examples where modern chemistry is used to build these old-but-venerable classes of optically responsive molecules. These new synthetic methods access new fluorophores, which then enable sophisticated imaging experiments leading to new biological insights.     

Lighting up cells: labelling proteins with fluorophores

During the past decade, rapid improvements have been made in the tools available for labelling proteins within cells, which has increased our ability to unravel the finer details of cellular events. One significant reason for these advances has been the development of fluorescent proteins that can be incorporated into proteins by genetic fusion to produce a fluorescent label. In addition, new techniques have made it possible to label proteins with small organic fluorophores and semiconductor nanocrystals.     

Local motions of fluorophores

Summary We further describe the general formulation of fluorescence depolarization in which the depolarization results from exchanges between a number of oscillator orientations in thermal equilibrium. Temperature and pressure affect the polarization by changing the relative populations of the allowed orientations as well as the rate of exchanges during the fluorescence lifetime. This treatment satisfactorily describes the limited motions that fluorophores undergo when they are either attached to a macromolecule such as the local tryptophan rotations in proteins, or embedded in a biological membrane.     

Lipofuscin-like fluorophores originated from malondialdehyde

The accumulation of fluorescent age pigment or lipofuscin is a frequently observed age-associated cellular alteration in a variety of post-mitotic cells of many species. These pigments are observed within granules composed, in part, of damaged protein and lipid. In the present mini-review, I provide a comprehensive summary of fluorescent adducts originated from malondialdehyde (MDA).     

Site-specific labeling of RNA with fluorophores and other structural probes

Site-specific probes provide a powerful tool for structure and function studies of nucleic acids, especially in elucidating tertiary structures of large ribozymes and other folded RNA molecules. Among many types of extrinsic labels, fluorophores are most attractive because they can provide structural information at millisecond time resolution, thus allowing real-time observation of structural transition during biological function. Methods for introducing fluorophores in RNA molecules are summarized here. These methods are robust and readily applicable to the labeling of other types of probes. However, as each case of RNA modification is unique, fine tuning of the general methodology is beneficial.     

Toward a forest biomass reference measurement system for remote sensing applications

Forests contribute to climate change mitigation through carbon storage and uptake, but the extent to which this carbon pool varies in space and time is still poorly known. Several Earth Observation missions have been specifically designed to address this issue, for example, NASA's GEDI, NASA-ISRO's NISAR and ESA's BIOMASS. Yet, all these missions' products require independent and consistent validation. A permanent, global, in situ, site-based forest biomass reference measurement system relying on ground data of the highest possible quality is therefore needed. Here, we have assembled a list of almost 200 high-quality sites through an in-depth review of the literature and expert knowledge. In this study, we explore how representative these sites are in terms of their coverage of environmental conditions, geographical space and biomass-related forest structure, compared to those experienced by forests worldwide. This work also aims at identifying which sites are the most representative, and where to invest to improve the representativeness of the proposed system. We show that the environmental coverage of the system does not seem to improve after at least the 175 most representative sites are included, but geographical and structural coverages continue to improve as more sites are added. We highlight the areas of poor environmental, geographical, or structural coverage, including, but not limited to, Canada, the western half of the USA, Mexico, Patagonia, Angola, Zambia, eastern Russia, and tropical and subtropical highlands (e.g. in Colombia, the Himalayas, Borneo, Papua). For the proposed system to succeed, we stress that (1) data must be collected and processed applying the same standards across all countries and continents; (2) system establishment and management must be inclusive and equitable, with careful consideration of working conditions; and (3) training and site partner involvement in downstream activities should be mandatory.     

Location of monitorial fluorophores inCandida utilis

Summary The fluorescent spectra of whole broth, cell-free broth and resuspended cells were compared during the fermentation ofCandida utilis growing in ethanol for the purposes of identifying the location of monitorial fluorophores in cellular systems. Four cellular fluorophores, tryptophan, pyridoxine, NADH and riboflavin were examined. The results indicated that the fluorescence signal of tryptophan and NADH came mainly from intracellular fluorophores, and the fluorescence signal of pyridoxine and riboflavin mainly came from extracellular fluorophores. The contributions of intracellular and extracellular fluorophores to culture fluorescence signals were found to change during the fermentation.     

Inactivation of acetylcholinesterase by various fluorophores

The inhibition of recombinant mouse acetylcholinesterase (rMAChE) and electric eel acetylcholinesterase (EEAChE) by seven, structurally different chromophore-based (dansyl, pyrene, dabsyl, diethylamino- and methoxycoumarin, Lissamine rhodamine B, and Texas Red) propargyl carboxamides or sulfonamides was studied. Diethylaminocoumarin, Lissamine, and Texas Red amides inhibited rMAChE with IC₅₀ values of 1.00 μM, 0.05 μM, and 0.70 μM, respectively. Lissamine and Texas Red amides inhibited EEAChE with IC₅₀ values of 3.57 and 10.4 μM, respectively. The other chromophore amides did not inhibit either AChE. The surprising inhibitory potency of Lissamine was examined in further detail against EEAChE and revealed a mixed-type inhibition with K_i?=?11.7 μM (competitive) and K_i′?=?24.9 μM (noncompetitive), suggesting that Lissamine binds to free enzyme and enzyme–substrate complex.     

Inhibition of quorum sensing regulated bacterial functions by plant essential oils with special reference to clove oil

Aims:  To evaluate quorum sensing (QS) inhibitory activity of plant essential oils using strains of Chromobacterium violaceum (CV12472 and CVO26) and Pseudomonas aeruginosa (PAO1).
Methods and Results:  Inhibition of QS-controlled violacein production in C. violaceum was assayed using disc diffusion and agar well diffusion method. Of the 21 essential oils, four oils showed varying levels of anti-QS activity. Syzygium aromaticum (Clove) oil showed promising anti-QS activity on both wild and mutant strains with zones of pigment inhibition 19 and 17 mm, respectively, followed by activity in cinnamon, lavender and peppermint oils. The effect of clove oil on the extent of violacein production was estimated photometrically and found to be concentration dependent. At sub-MICs of clove oil, 78·4% reduction in violacein production over control and up to 78% reduction in swarming motility in PAO1 over control were recorded. Gas chromatography–mass spectrometry analysis of clove oil indicated presence of many phytocompounds. Eugenol, the major constituent of clove oil could not exhibit anti-QS activity.
Conclusions:  Presence of anti-QS activity in clove oil and other essential oils has indicated new anti-infective activity. The identification of anti-QS phytoconstituents is needed to assess the mechanism of action against both C. violaceum and Ps. aeruginosa .
Significance and Impact of the study:  Essential oils having new antipathogenic drugs principle because of its anti-QS activity might be important in reducing virulence and pathogenicity of drug-resistant bacteria in vivo .     

Visualizing single fluorophores in live cells

The methods have been described that can be used to visualize single fluorescent molecules in live cells: laser epifluorescent, confocal, near-field, two-photon, and total internal reflection microscopy. Each method has its own advantages and limitations. We showed that total internal reflection microscopy is a method of choice for single fluorophore visualisation near substrate-medium interface. It can be used to study receptors, ion channels, and many cytoskeleton or signalling molecules located at or in close proximity to basal cell membrane. It was shown that it is very important to use rigorous criteria for single fluorophore identification since these objects emit a limited number of photons before irreversible photo-bleaching, and their fluorescence is often obscured by cell auto-fluorescence and out-of-focus fluorescence. Methods used for lateral mobility studies of single molecules floating on cell membrane were also described.     

Mouse transgenesis in a single locus with independent regulation for multiple fluorophores

A major barrier to complex experimental design in mouse genetics is the allele problem: combining three or more alleles is time-consuming and inefficient. Here, we solve this problem for transgenic animals with a simple modification of existing BAC transgenesis protocols, and generate triple-colored 'prism' mice in which the major cell types of the brain: neurons, astrocytes, and oligodendrocytes, are each labeled with a distinct fluorophore. All three fluorophores are expressed from the same locus, yet each fluorophore is expressed in an independent temporal and spatial pattern. All three transgenes are generally co-inherited across multiple generations with stable genomic copy number and expression patterns. This generic solution should permit more sophisticated experimental manipulations to assess functional interactions amongst populations of cell types in vivo in a more rapid and efficient manner.     

Combinatorial discovery of fluorophores and fluorescent probes

The properties of organic fluorophores are difficult to predict, even in simple cases. Fluorescent probes--which combine fluorescent properties with the equally challenging problem of molecular recognition--are even more difficult to develop. Combinatorial approaches to the development of such molecules are a new but promising endeavor, and reviewing the state of the art delineates the near-and long-term possibilities.     

Solid-phase oligonucleotide synthesis and flow cytometric analysis with microspheres encoded with covalently attached fluorophores

A novel combinatorial approach to synthesize oligonucleotides on fluorescently encoded microspheres based on flow sorting and segmental solid-phase synthesis is described. BODIPY dyes were covalently attached to polystyrene (8.8 microm, 55% DVB) microsphere particles to generate four fluorescently encoded sets. 20-mer oligonucleotide sequences can be synthesized on these microspheres with yields comparable to conventional CPG supports (80% overall yield, average stepwise yield = 99%). The concept of segmental solid-phase synthesis by flow sorting was demonstrated by synthesizing unique 20-mer oligonucleotide sequences on each of four fluorescently encoded microsphere sets by including a flow sorting step (after first eight base additions) and flow cytometric detection of sequences synthesized on each microsphere set by hybridization with fluorescently labeled complementary sequence.     

Peptide tags for labeling membrane proteins in live cells with multiple fluorophores

We describe a method to label specific membrane proteins with fluorophores for live imaging. Fusion proteins are generated that incorporate into their extracellular domains short peptide sequences (13-38 amino acids) recognized with high affinity and specificity by protein ligands, alpha-bungarotoxin (BTX), or streptavidin (SA). Many fluorophore- and enzyme-conjugated derivatives of both ligands are commercially available. To demonstrate the general utility of the methods, we tagged a vesicle-associated protein (VAMP2), a receptor tyrosine kinase [muscle-specific kinase (MuSK)], and receptors for three neurotransmitters: acetylcholine (nAChR alpha3), glutamate (mGluR2), and gamma-aminobutyric acid (GABA(A) alpha3). In all cases, we could selectively label surface-exposed proteins without interference from intracellular pools. By successive pulse-labeling with different fluorophore conjugates of a single ligand, we were able to monitor endocytosis of tagged molecules. By combining the two ligands, we could assess co-localization of synaptic components in cells. This strategy for epitope tagging provides a useful adjunct to green fluorescent protein (GFP)-tagging, which fails to distinguish intracellular from extracellular pools, sometimes interferes with protein localization or function, and requires a separate construct for each color.     

Visualization of single fluorophores in living cells

Methods applicable to visualizing single fluorophores in living cells are described, namely, laser epifluorescence, confocal, near-field, two-photon, and total internal reflection microscopy. It is demonstrated that total internal reflection microscopy is the most appropriate for visualizing single fluorophores near the substrate-medium interface. This method can be used for studying receptors, ion channels, and numerous cytoskeletal and signal molecules located on or near the basal cell membrane. It is demonstrated that stringent criteria are necessary when identifying single molecules, as these objects emit a limited number of photons before irreversible photobleaching and their fluorescence is obscured by autofluorescence or out-of-focus fluorescence. The methods used for studying the lateral mobility of single molecules floating on the cell membrane are also described.