Quantitative analysis and characterization of biofunctionalized fluorescent silica particles

A strategy for the production and subsequent characterization of biofunctionalized silica particles is presented. The particles were engineered to produce a bifunctional material capable of both (a) the attachment of fluorescent dyes for particle encoding and (b) the sequential modification of the surface of the particles to couple oligonucleotide probes. A combination of microscopic and analytical methods is implemented to demonstrate that modification of the particles with 3-aminopropyl trimethoxysilane results in an even distribution of amine groups across the particle surface. Evidence is provided to indicate that there are negligible interactions between the bound fluorescent dyes and the attached biomolecules. A unique approach was adopted to provide direct quantification of the oligonucleotide probe loading on the particle surface through X-ray photoelectron spectroscopy, a technique which may have a major impact for current researchers and users of bead-based technologies. A simple hybridization assay showing high sequence specificity is included to demonstrate the applicability of these particles to DNA screening.

Sequence variation can affect the performance of minor groove binder TaqMan probes in viral diagnostic assays

A minor groove binder (MGB) TaqMan real-time PCR assay was developed for the detection of respiratory syncytial virus (RSV) in clinical specimens. Upon evaluation of the assay, notable differences were observed in the overall fluorescent response obtained from RSV positive specimens, with some linear amplification curves deviating only slightly from baseline fluorescence. Sequencing of the probes targets in these RSV strains revealed single base mismatches with the MGB TaqMan probe. overall, these results highlight the usefulness of MGB TaqMan probes for the detection of mismatches, but suggest that MGB Taqman probes have limitations for routine screening for uncharacterised viral strains. (C) 2005 Elsevier B.V. All rights reserved.

Synthesis and application of novel probes for the detection of cysteine sulphenic acids

Cysteine is a thiol containing amino acid that readily undergoes oxidation by reactive oxygen species (ROS) to form sulphenic (R-SOH) sulphinic (RSO2H) and sulphonic (RSO3H) acids. Thiol modifications of cysteine have been implicated as modulators of cellular processes and represent significant biological modifications that occur during oxidative stress and cell signalling. However, the different oxidation states are difficult to monitor in a physiological setting due to the limited availability of experimental tools. Therefore it is of interest to synthesise and use a chemical probe that selectively recognises the reversible oxidation state of cysteine sulphenic acid to understand more about oxidative signalling. The aim of this thesis was to investigate a synthetic approach for novel fluorescent probe synthesis, for the specific detection of cysteine sulphenic acids by fluorescence spectroscopy and confocal microscopy. N-[2-(Anthracen-2-ylamino)-2-oxoethyl]-3,5-dioxocyclohexanecarboxamide was synthesised in a multistep synthesis and characterised by nuclear magnetic resonance spectroscopy. The optimisation of conditions needed for sulphenic acid formation in a purified protein using human serum albumin (HSA) and the commercially available biotin tagged probe 3-(2,4-dioxocyclohexyl)propyl-5-((3aR,6S,6aS)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-6-yl)pentanoate (DCP-Bio1) were identified. This approach was extended to detect sulphenic acids in Jurkat T cells and CD4+ T cells pre- and post-stimulus. Buthionine sulfoximine (BSO) was used to manipulate the endogenous antioxidant glutathione (GSH) in human CD4+ T cells. Then the surface protein thiol levels and sulphenic acid formation was examined. T cells were also activated by the lectin phytohaemagglutinin-L (PHA-L) and formation of sulphenic acid was investigated using SDS-PAGE, western blotting and confocal microscopy. Resting Jurkat cells have two prominent protein bands that have sulphenic acid modifications whereas resting CD4+ T cells have an additional band present. When cells were treated with BSO the number of bands increased whereas activation reduced the number of proteins that were modified. The identities of the protein bands containing sulphenic acids were explored by mass spectrometry. Cysteine oxidation was observed in redox, metabolic and cytoskeletal proteins. In summary, a novel fluorescent probe for detection of cysteine sulphenic acids has been synthesised alongside a model system that introduces cysteine sulphenic acid in primary T cells. This probe has potential application in the subcellular localisation of cysteine oxidation during T cell signalling.

Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale

Peer reviewed

Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale

Peer reviewed

Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study

Fluorescence spectroscopy andmicroscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in thesemembranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3–4 Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using themasmembrane reporters.

RNA-FISH Technique: Probe Cocktails vs Single Probes

RNA-Fluorescence In Situ Hybridization (RNA-FISH) enables to analyze and visualize the microorganisms of interest within microbial communities in their natural environments by fluorescent labelling of specific RNA sequences. Poor accessibility or low content of the RNA target region can cause false positives/negatives due to low fluorescence of the cells. To reduce the chances of this occurring, probe cocktails – i.e. mixture of several probes that hybridize to different regions of the target RNA- has been proposed as an alternative to single probes use for increasing the Fluorescence Intensities (FI). However, is this really a good solution? The key finding of this work was that the use of probe cocktails is not always a good solution for maximizing the FI as at high concentrations the single probe EUK516-6 FAM yielded higher FI than the probe cocktails.

Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study

Fluorescence spectroscopy andmicroscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in thesemembranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3–4 Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using themasmembrane reporters.

Influence Of Fluorescent Dye On Physical-mechanical Properties Of Luting Cements For Confocal Microscopy Analysis.

To evaluate the influence of a fluorescent dye (rhodamine B) on the physical and mechanical properties of three different luting cements: a conventional adhesive luting cement (RelyX ARC, 3M/ESPE), a self-adhesive luting cement (RelyX U-200, 3M/ESPE), and a self-etching and self-adhesive luting cement (SeT PP, SDI). The cements were mixed with 0.03 wt% rhodamine B, formed into bar-shaped specimens (n = 10), and light cured using an LED curing unit (Radii, SDI) with a radiant exposure of 32 J/cm(2) . The Knoop hardness (KHN), flexural strength (FS), and Young's modulus (YM) analyses were evaluated after storage for 24 h. Outcomes were subjected to two-way ANOVA and Tukey's test (P = 0.05) for multiple comparisons. No significant differences in FS or YM were observed among the tested groups (P ≥ 0.05); the addition of rhodamine B increased the hardness of the luting cements tested. The addition of a fluorescent agent at 0.03 wt% concentration does not negatively affect the physical-mechanical properties of the luting cement polymerization behavior.

Localization of ribosomal genes in three Pimelodus species (Siluriformes, Pimelodidae) of the São Francisco River: 5S genes as species markers and conservation of the 18S rDNA sites

Pimelodidae is one of the most representative of Neotropical catfish families. However, these fish are still poorly studied in terms of cytogenetics, especially regarding the application of more accurate techniques such as the chromosomal localization of ribosomal genes. In the present work, fluorescent in situ hybridization with 5S and 18S rDNA probes was employed for rDNA site mapping in Pimelodus sp., P. fur and P. maculatus from the São Francisco River in the Três Marias municipality - MG. The results from the application of the 18S probe confirmed the previous data obtained by silver nitrate staining, identifying a simple nucleolar organizing region system for these species. However, the labeling results from the 5S rDNA probe demonstrated a difference in the number and localization of these sites between the analyzed species. The obtained data allowed inferences on the possible processes involved in the karyotypic evolution of this genus.

Sudan Black B treatment reduces autofluorescence and improves resolution of in situ hybridization specific fluorescent signals of brain sections

Interference by autofluorescence is one of the major concerns of immunofluorescence analysis of in situ hybridization-based diagnostic assays. We present a useful technique that reduces autofluorescent background without affecting the tissue integrity or direct immunofluorescence signals in brain sections. Using six different protocols, such as ammonia/ethanol, Sudan Black B (SBB) in 70% ethanol, photobleaching with UV light and different combinations of them in both formalin-fixed paraffin-embedded and frozen human brain tissue sections, we have found that tissue treatment of SBB in a concentration of 0.1% in 70% ethanol is the best approach to reduce/eliminate tissue autofluorescence and background, while preserving the specific fluorescence hybridization signals. This strategy is a feasible, non-time consuming method that provides a reasonable compromise between total reduction of the tissue autofluorescence and maintenance of specific fluorescent labels.

Charged Kaon Interferometric Probes of Space-Time Evolution in Au plus Au Collisions at s(NN)=200 GeV

Bose-Einstein correlations of charged kaons are used to probe Au+Au collisions at s(NN)=200 GeV and are compared to charged pion probes, which have a larger hadronic scattering cross section. Three-dimensional Gaussian source radii are extracted, along with a one-dimensional kaon emission source function. The centrality dependences of the three Gaussian radii are well described by a single linear function of N(part)(1/3) with a zero intercept. Imaging analysis shows a deviation from a Gaussian tail at r greater than or similar to 10 fm, although the bulk emission at lower radius is well described by a Gaussian. The presence of a non-Gaussian tail in the kaon source reaffirms that the particle emission region in a heavy-ion collision is extended, and that similar measurements with pions are not solely due to the decay of long-lived resonances.

Singlet molecular oxygen trapping by the fluorescent probe diethyl-3,3 '-(9,10-anthracenediyl)bisacrylate synthesized by the Heck reaction

Singlet molecular oxygen O(2)((1)Delta(g)) is a potent oxidant that can react with different biomolecules, including DNA, lipids and proteins. Many polycyclic aromatic hydrocarbons have been studied as O(2)((1)Delta(g)) chemical traps. Nevertheless, a suitable modification in the polycyclic aromatic ring must be made to increase the yield of O(2)((1)Delta(g)) chemical trapping. With this goal, an anthracene derivative, diethyl-3,3 '-(9,10-anthracenediyl)bisacrylate (DADB), was obtained from the reaction of 9,10-dibromoanthracene and ethyl acrylate through the Heck coupling reaction. The coupling of ethyl acrylate with the anthracene ring produced a new lipophilic, esterified, fluorescent probe reactive toward O(2)((1)Delta(g)). This compound reacts with O(2)((1)Delta(g)) at a rate of k(r) = 1.69 x 10(6) M(-1) s(-1) forming a stable endoperoxide (DADBO(2)), which was characterized by UV-Vis, fluorescence, HPLC/MS and (1)H and (13)C NMR techniques. The photophysical, photochemical and thermostability features of DADB were also evaluated. Furthermore, this compound has the potential for great application in biological systems because it is easily synthetized in large amount and generates specific endoperoxide (DADBO(2)), which can be easily detected by HPLC tandem mass spectrometry (HPLC/MS/MS).

2-(4-Methylphenyl)-1H-anthraceno-[1,2-d]imidazole-6,11-dione: a fluorescent chemosensor

In the title compound, C(22)H(14)N(2)O(2), the five rings of the molecule are not coplanar. There is a significant twist between the four fused rings, which have a slightly arched conformation, and the pendant aromatic ring, as seen in the dihedral angle of 13.16 (8)degrees between the anthraquinonic ring system and the pendant aromatic ring plane.

Violet ZnSe/ZnS as an Alternative to Green CdSe/ZnS in Nanocrystal-Fluorescent Protein FRET Systems

Fluorescent proteins from the green fluorescent protein family strongly interact with CdSe/ZnS and ZnSe/ZnS nanocrystals at neutral pH. Green emitting CdSe/ZnS nanocrystals and red emitting fluorescent protein dTomato constitute a 72% efficiency FRET system with the largest alteration of the overall photoluminescence profile, following complex formation, observed so far. The substitution of ZnSe/ZnS for CdSe/ZnS nanocrystals as energy donors enabled the use of a green fluorescent protein, GFP5, as energy acceptor. Violet emitting ZnSe/ZnS nanocrystals and green GFP5 constitute a system with 43% FRET efficiency and an unusually strong sensitized emission. ZnSe/ZnS-GFP5 provides a cadmium-free, high-contrast FRET system that covers only the high-energy part of the visible spectrum, leaving room for simultaneous use of the yellow and red color channels. Anisotropic fluorescence measurements confirmed the depolarization of GFP5 sensitized emission.