On the pixel selection criterion for the calculation of the Pearson's correlation coefficient in fluorescence microscopy.

Colocalisation microscopy analysis provides an intuitive and straightforward way of determining if two biomolecules occupy the same diffraction-limited volume. A popular colocalisation coefficient, the Pearson's correlation coefficient (PCC), can be calculated using different pixel selection criteria: PCCALL includes all image pixels, PCCOR only pixels exceeding the intensity thresholds for either one of the detection channels, and PCCAND only pixels exceeding the intensity thresholds for both detection channels. Our results show that PCCALL depends on the foreground to background ratio, producing values influenced by factors unrelated to biomolecular association. PCCAND focuses on areas with the highest intensities in both channels, which allows it to detect low levels of colocalisation, but makes it inappropriate for evaluating spatial cooccurrence between the signals. PCCOR produces values influenced both by signal proportionality and spatial cooccurrence but can sometimes overemphasise the lack of the latter. Overall, PCCAND excels at detecting low levels of colocalisation, PCCOR provides a balanced quantification of signal proportionality and spatial coincidence, and PCCALL risks misinterpretation yet avoids segmentation challenges. Awareness of their distinct properties should inform their appropriate application with the aim of accurately representing the underlying biology.

Mosquito Microbiomes of Rwanda: Characterizing Mosquito Host and Microbial Communities in the Land of a Thousand Hills.

Mosquitoes are a complex nuisance around the world and tropical countries bear the brunt of the burden of mosquito-borne diseases. Rwanda has had success in reducing malaria and some arboviral diseases over the last few years, but still faces challenges to elimination. By building our understanding of in situ mosquito communities in Rwanda at a disturbed, human-occupied site and at a natural, preserved site, we can build our understanding of natural mosquito microbiomes toward the goal of implementing novel microbial control methods. Here, we examined the composition of collected mosquitoes and their microbiomes at two diverse sites using Cytochrome c Oxidase I sequencing and 16S V4 high-throughput sequencing. The majority (36 of 40 species) of mosquitoes captured and characterized in this study are the first-known record of their species for Rwanda but have been characterized in other nations in East Africa. We found significant differences among mosquito genera and among species, but not between mosquito sexes or catch method. Bacteria of interest for arbovirus control, Asaia, Serratia, and Wolbachia, were found in abundance at both sites and varied greatly by species.

Stacking-induced fluorescence increase reveals allosteric interactions through DNA.

From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently attached Cy3 dye undergoes strong enhancement of fluorescence intensity and lifetime when stacked in a nick, gap or overhang region in duplex DNA. This is used to probe hybridization dynamics of a DNA hairpin down to the single-molecule level. We also show that varying the position of a single abasic site up to 20 base pairs away modulates the dye-DNA interaction, indicative of through-backbone allosteric interactions. The phenomenon of stacking-induced fluorescence increase (SIFI) should find widespread use in the study of the structure, dynamics and reactivity of nucleic acids.

Fluorescence correlation and lifetime correlation spectroscopy applied to the study of supported lipid bilayer models of the cell membrane.

Supported Lipid Bilayers (SLBs) are versatile models capable of mimicking some of the key properties of the cell membrane, including for example lipid fluidity, domain formation and protein support, without the challenging complexity of the real biological system. This is important both from the perspective of understanding the behaviour and role of the lipid membrane in cell structure and signalling, as well as in development of applications of lipid membranes across domains as diverse as sensing and drug delivery. Lipid and protein diffusion within the membrane is vital to its function and there are several key experimental methods used to study membrane dynamics. Amongst the optical methods are Fluorescence Recovery After Photobleaching (FRAP), single particle tracking and Fluorescence Correlation (and Fluorescence Lifetime Correlation) Spectroscopy (FCS/FLCS). Each of these methods can provide different and often complementary perspectives on the dynamics of the fluid membrane. Although FCS is well established, FLCS is a relatively new technique and both methods have undergone a number of extensions in recent years which improve their precision and accuracy in studying supported lipid bilayers, most notably z-scan methods. This short review focusses on FCS and FLCS and their recent applications, specifically to artificial lipid bilayer studies addressing key issues of cell membrane behaviour.

Fluorescence enhancement of a fluorescein derivative upon adsorption on cellulose.

9-[1-(2-Methyl-4-methoxyphenyl)]-6-hydroxy-3H-xanthen-3-one (2-Me-4-OMe TG) is a fluorescein derivative dye whose photophysical properties show a remarkable pH dependence. In aqueous solution the fluorescence quantum yield (Φf) of its anionic species is nearly a hundred times higher than that of its neutral species. Such a large difference in Φf makes 2-Me-4-OMe TG useful as an "on-off" pH indicator. Here we report that adsorption on the surface of microcrystalline cellulose exerts a profound effect upon the photophysical properties of 2-Me-4-OMe TG. On the solid only the dye neutral species is observed and its Φf is 0.31 ± 0.10, which is approximately thirty times higher than the value found for the neutral species in aqueous solution (Φf = 0.01). 2-Me-4-OMe TG and Dabcyl (DB) were co-adsorbed on the surface of microcrystalline cellulose to study the transfer of excitation energy from the former to the latter. In the absence of the dye, the formation of DB aggregates is observed at concentrations greater than 0.34 µmol per gram of cellulose, while in the presence of 2-Me-4-OMe TG the formation of DB aggregates is thoroughly inhibited. The quenching of fluorescence of 2-Me-4-OMe TG by DB reaches efficiencies as high as 90% for the most concentrated samples.

O-glycosylation of the transcription factor SPATULA promotes style development in Arabidopsis.

O-linked ß-N-acetylglucosamine (O-GlcNAc) and O-fucose are two sugar-based post-translational modifications whose mechanistic role in plant signalling and transcriptional regulation is still largely unknown. Here we investigated how two O-glycosyltransferase enzymes of Arabidopsis thaliana, SPINDLY (SPY) and SECRET AGENT (SEC), promote the activity of the basic helix-loop-helix transcription factor SPATULA (SPT) during morphogenesis of the plant female reproductive organ apex, the style. SPY and SEC modify amino-terminal residues of SPT in vivo and in vitro by attaching O-fucose and O-GlcNAc, respectively. This post-translational regulation does not impact SPT homo- and heterodimerization events, although it enhances the affinity of SPT for the kinase PINOID gene locus and its transcriptional repression. Our findings offer a mechanistic example of the effect of O-GlcNAc and O-fucose on the activity of a plant transcription factor and reveal previously unrecognized roles for SEC and SPY in orchestrating style elongation and shape.

A molecular mechanosensor for real-time visualization of appressorium membrane tension in Magnaporthe oryzae.

The rice blast fungus Magnaporthe oryzae uses a pressurized infection cell called an appressorium to drive a rigid penetration peg through the leaf cuticle. The vast internal pressure of an appressorium is very challenging to investigate, leaving our understanding of the cellular mechanics of plant infection incomplete. Here, using fluorescence lifetime imaging of a membrane-targeting molecular mechanoprobe, we quantify changes in membrane tension in M. oryzae. We show that extreme pressure in the appressorium leads to large-scale spatial heterogeneities in membrane mechanics, much greater than those observed in any cell type previously. By contrast, non-pathogenic melanin-deficient mutants, exhibit low spatially homogeneous membrane tension. The sensor kinase ∆sln1 mutant displays significantly higher membrane tension during inflation of the appressorium, providing evidence that Sln1 controls turgor throughout plant infection. This non-invasive, live cell imaging technique therefore provides new insight into the enormous invasive forces deployed by pathogenic fungi to invade their hosts, offering the potential for new disease intervention strategies.

Effects of the anion salt nature on the rate constants of the aqueous proton exchange reactions.

The proton-transfer ground-state rate constants of the xanthenic dye 9-[1-(2-methyl-4-methoxyphenyl)]-6-hydroxy-3H-xanthen-3-one (TG-II), recovered by Fluorescence Lifetime Correlation Spectroscopy (FLCS), have proven to be useful to quantitatively reflect specific cation effects in aqueous solutions (J. M. Paredes, L. Crovetto, A. Orte, J. M. Alvarez-Pez and E. M. Talavera, Phys. Chem. Chem. Phys., 2011, 13, 1685-1694). Since these phenomena are more sensitive to anions than to cations, in this paper we have accounted for the influence of salts with the sodium cation in common, and the anion classified according to the empirical Hofmeister series, on the proton transfer rate constants of TG-II. We demonstrate that the presence of ions accelerates the rate of the ground-state proton-exchange reaction in the same order than ions that affect ion solvation in water. The combination of FLCS with a fluorophore undergoing proton transfer reactions in the ground state, along with the desirable feature of a pseudo-dark state when the dye is protonated, allows one unique direct determination of kinetic rate constants of the proton exchange chemical reaction.

The Use of a Replicating Virus Vector For in Planta Generation of Tobacco Mosaic Virus Nanorods Suitable For Metallization.

The production of designer-length tobacco mosaic virus (TMV) nanorods in plants has been problematic in terms of yields, particularly when modified coat protein subunits are incorporated. To address this, we have investigated the use of a replicating potato virus X-based vector (pEff) to express defined length nanorods containing either wild-type or modified versions of the TMV coat protein. This system has previously been shown to be an efficient method for producing virus-like particles of filamentous plant viruses. The length of the resulting TMV nanorods can be controlled by varying the length of the encapsidated RNA. Nanorod lengths were analyzed with a custom-written Python computer script coupled with the Nanorod UI user interface script, thereby generating histograms of particle length. In addition, nanorod variants were produced by incorporating coat protein subunits presenting metal-binding peptides at their C-termini. We demonstrate the utility of this approach by generating nanorods that bind colloidal gold nanoparticles.

Photophysics of the interaction between a fluorescein derivative and Ficoll.

Ficoll has been widely used as a crowding agent to mimic intracellular media because it is believed to be noninteracting and is composed of mixed sizes such that smaller and larger diffusing solutes can be studied. Due to the interest that the fluorescent dye 9-[1-(2-methyl-4-methoxyphenyl)]-6-hydroxy-3H-xanthen-3-one (TG-II) as a fluorometric probe of phosphate ions in intracellular media could generate, we describe the spectral characteristics of the system TG-II-Ficoll in aqueous solution by means of absorption spectroscopy, steady-state fluorescence, time-resolved fluorescence, time-resolved emission spectroscopy, and fluorescence lifetime correlation spectroscopy. The spectral characteristics found are consistent with the formation of an adsorption complex on the surface of Ficoll, probably due to hydrogen bonding between TG-II and Ficoll. In addition, the diffusion coefficient calculated for the association was similar to the diffusion coefficient previously recovered for Ficoll in the same experimental conditions. Therefore, our overall data clearly demonstrate that Ficoll is not an inert crowding agent when in the presence of fluorescein derivative dyes.

Trapping of Rhodamine 6G excitation energy on cellulose microparticles.

Rhodamine 6G (R6G) was adsorbed on cellulose microparticles and fluorescence quantum yields and decays were measured as a function of dye loading. Though no spectroscopic evidence of dye aggregation was found, a noticeable decrease of quantum yield--after correction for reabsorption and reemission of fluorescence--and shortening of decays were observed at the highest loadings. These effects were attributed to the dissipation of the excitation energy by traps constituted by R6G pairs, leading to static and dynamic quenching produced by direct absorption of traps and non-radiative energy transfer from monomers, respectively. Regarding the nature of traps, two extreme approaches were considered: (a) equilibrium between monomers slightly interacting in the ground state and (b) randomly distributed monomers located below a critical distance (statistical traps). Both approaches accounted quantitatively for the observed facts. The effect of energy migration was evaluated through computational simulations. As the concentration of traps could only be indirectly inferred, in some experiments an external energy transfer quencher, Methylene Blue, was coadsorbed and the results were compared with those obtained with pure R6G.

The lateral diffusion and fibrinogen induced clustering of platelet integrin αIIbß3 reconstituted into physiologically mimetic GUVs.

Platelet integrin αIIbß3 is a key mediator of platelet activation and thrombosis. Upon activation αIIbß3 undergoes significant conformational rearrangement, inducing complex bidirectional signalling and protein recruitment leading to platelet activation. Reconstituted lipid models of the integrin can enhance our understanding of the structural and mechanistic details of αIIbß3 behaviour away from the complexity of the platelet machinery. Here, a novel method of αIIbß3 insertion into Giant Unilamellar Vesicles (GUVs) is described that allows for effective integrin reconstitution unrestricted by lipid composition. αIIbß3 was inserted into two GUV lipid compositions that seek to better mimic the platelet membrane. First, "nature's own", comprising 32% DOPC, 25% DOPE, 20% CH, 15% SM and 8% DOPS, intended to mimic the platelet cell membrane. Fluorescence Lifetime Correlation Spectroscopy (FLCS) reveals that exposure of the integrin to the activators Mn(2+) or DTT does not influence the diffusion coefficient of αIIbß3. Similarly, exposure to αIIbß3's primary ligand fibrinogen (Fg) alone does not affect αIIbß3's diffusion coefficient. However, addition of Fg with either activator reduces the integrin diffusion coefficient from 2.52 ± 0.29 to µm(2) s(-1) to 1.56 ± 0.26 (Mn(2+)) or 1.49 ± 0.41 µm(2) s(-1) (DTT) which is consistent with aggregation of activated αIIbß3 induced by fibrinogen binding. The Multichannel Scaler (MCS) trace shows that the integrin-Fg complex diffuses through the confocal volume in clusters. Using the Saffman-Delbrück model as a first approximation, the diffusion coefficient of the complex suggests at least a 20-fold increase in the radius of membrane bound protein, consistent with integrin clustering. Second, αIIbß3 was also reconstituted into a "raft forming" GUV with well defined liquid disordered (Ld) and liquid ordered (Lo) phases. Using confocal microscopy and lipid partitioning dyes, αIIbß3 showed an affinity for the DOPC rich Ld phase of the raft forming GUVs, and was effectively excluded from the cholesterol and sphingomyelin rich Lo phase. Activation and Fg binding of the integrin did not alter the distribution of αIIbß3 between the lipid phases. This observation suggests partitioning of the activated fibrinogen bound αIIbß3 into cholesterol rich domains is not responsible for the integrin clustering observed.

Bulk and single-molecule fluorescence studies of the saturation of the DNA double helix using YOYO-3 intercalator dye.

We report a thorough photophysical characterization of the interactions between double-stranded DNA (dsDNA) and the trimethine cyanine homodimer dye YOYO-3. The fluorescence emission of this dye is enhanced by intercalation within the DNA double helix. We have explored the saturation of the dsDNA by bound YOYO-3 at the single-molecule level by studying the single-pair Förster resonance energy transfer (FRET) from an energy donor, Alexa Fluor 488, tagged at the 5' end of the double helix and the energy acceptor, YOYO-3, bound to the same DNA molecule. The spontaneous binding of YOYO-3 gives rise to an effective distribution of different FRET efficiencies and, therefore, donor-acceptor (D-A) distances. These distributions reveal the existence of multiple states of YOYO-3. Steady-state and time-resolved fluorescence and circular dichroism confirmed the presence of a DNA-bound aggregate of YOYO-3, conspicuous at high dye/base pair ratios. The spectral features of the aggregate suggest that it may have the structure of a parallel H-aggregate.