Predicting the behaviour and selectivity of fluorescent probes for lysosomes and related structures by means of structure-activity models

The potential of phenothiazinium dyes as cytotoxicity markers in cisplatin-treated cells

Assessing the in vitro toxicity of compounds on cell cultures is an important step during the screening of candidate molecules for diverse applications. Among the strategies employed to determine cytotoxicity, MTT, neutral red, and resazurin are commonly used. Methylene blue (MB), a phenothiazinium salt, has several uses, such as dye, redox indicator, and even as treatment for human disease and health conditions, such as malaria and methemoglobinemia. However, MB has only been sparsely used as a cellular toxicity indicator. As a viability indicator, MB is mostly applied to fixed cultures at high concentrations, especially when compared to MTT or neutral red. Here we show that MB and its related compounds new methylene blue (NMB), toluidine blue O (TBO), and dimethylmethylene blue (DMMB) can be used as cytotoxicity indicators in live (non-fixed) cells treated for 72 h with DMSO and cisplatin. We compared dye uptake between phenothiazinium dyes and neutral red by analyzing supernatant and cell content via visible spectra scanning and microscopy. All dyes showed a similar ability to assess cell toxicity compared to either MTT or neutral red. Our method represents a cost-effective alternative to in vitro cytotoxicity assays using cisplatin or DMSO, indicating the potential of phenothiazinium dyes for the screening of candidate drugs and other applications.

Impact assessment of metals realeased by aluminium-based galvanic anode on the physiology of the abalone Haliotis tuberculata in controlled conditions

To protect metal structures immersed in the sea from corrosion, the galvanic anode cathodic protection system (GACP) is often applied. However, this association leads to continuous oxidation of the galvanic anode and therefore to a release of a metal cocktail in the forms of ions or oxy-hydroxides. Therefore, the main objective of our study was to investigate the toxicity of elements released from the dissolution of an aluminium-based galvanic anode (∼95% Al, ∼5% Zn, <0.1% for In, Cu, Cd, Mn, Fe) on a grazing gastropod, the abalone Haliotis tuberculata. The present study was carried out in complement to other research currently in submission. Gastropods were exposed for 16 weeks (12 weeks of exposure and 4 weeks of decontamination phase) to 6 conditions including a control, 4 concentrations based on total aluminium level (86, 425, 1096 and 3549 µg L^-1) and a trophic control, corresponding to abalones placed in non-contaminated natural seawater but fed with contaminated algae. The effects of metals on growth, glycogen levels, brix index of hemolymph, MDA levels in digestive gland and gills, hemocyte phagocytic activity, ROS production, lysosomal system and the progress of gametogenesis were investigated throughout the entire exposure allowing the realization of kinetics. The results revealed that the aluminium-based anode does not seem to have an effect on the health status of the individuals for environmentally realistic concentrations. However, in extreme conditions strong effects were reported on the growth, immune system and reproduction of abalone.

Dynamic Visualization of Endoplasmic Reticulum Stress in Living Cells via a Two-Stage Cascade Recognition Process

The endoplasmic reticulum (ER) is crucial for the regulation of multiple cellular processes, such as cellular responses to stress and protein synthesis, folding, and posttranslational modification. Nevertheless, monitoring ER physiological activity remains challenging due to the lack of powerful detection methods. Herein, we built a two-stage cascade recognition process to achieve dynamic visualization of ER stress in living cells based on a fluorescent carbon dot (CD) probe, which is synthesized by a facile one-pot hydrothermal method without additional modification. The fluorescent CD probe enables two-stage cascade ER recognition by first accumulating in the ER as the positively charged and lipophilic surface of the CD probe allows its fast crossing of multiple membrane barriers. Next, the CD probe can specifically anchor on the ER membrane via recognition between boronic acids and o-dihydroxy groups of mannose in the ER lumen. The two-stage cascade recognition process significantly increases the ER affinity of the CD probe, thus allowing the following evaluation of ER stress by tracking autophagy-induced mannose transfer from the ER to the cytoplasm. Thus, the boronic acid-functionalized cationic CD probe represents an attractive tool for targeted ER imaging and dynamic tracking of ER stress in living cells.

A hybrid aggregate FRET probe from the mixed assembly of cyanine dyes for highly specific monitoring of mitochondria autophagy

Mitochondria autophagy, also known as mitophagy, is a process in which mitochondria are wrapped by autophagosomes and fused with lysosomes for degradation. This process is essential for mitochondrial quality control. Here, we developed a hybrid aggregate FRET probe through mixed assembly of two cyanine dyes FMOTY and AMTC. In live cells, FMOTY and AMTC exist independently in lysosomes and mitochondria and will not produce interfering FRET background signals. The FRET signal is only generated when mitochondria is transported to lysosomes during mitophagy. This allows the hybridized aggregate to be used as a highly specific probe for monitoring mitophagy.

Antagonistic cytoprotective effects of C60 fullerene nanoparticles in simultaneous exposure to benzo[a]pyrene in a molluscan animal model

The hypothesis that C₆₀ fullerene nanoparticles (C₆₀) exert an antagonistic interactive effect on the toxicity of benzo[a]pyrene (BaP) has been supported by this investigation. Mussels were exposed to BaP (5, 50 & 100μg/L) and C₆₀ (C₆₀-1mg/L) separately and in combination. Both BaP and C₆₀ were shown to co-localize in the secondary lysosomes of the hepatopancreatic digestive cells in the digestive gland where they reduced lysosomal membrane stability (LMS) or increased membrane permeability, while BaP also induced increased lysosomal lipid and lipofuscin, indicative of oxidative cell injury and autophagic dysfunction. Combinations of BaP and C₆₀ showed antagonistic effects for lysosomal stability, mTORC1 (mechanistic target of rapamycin complex 1) inhibition and intralysosomal lipid (5 & 50μg/L BaP). The biomarker data (i.e., LMS, lysosomal lipidosis and lipofuscin accumulation; lysosomal/cell volume and dephosphorylation of mTORC1) were further analysed using multivariate statistics. Principal component and cluster analysis clearly indicated that BaP on its own was more injurious than in combination with C₆₀. Use of a network model that integrated the biomarker data for the cell pathophysiological processes, indicated that there were significant antagonistic interactions in network complexity (% connectance) at all BaP concentrations for the combined treatments. Loss of lysosomal membrane stability probably causes the release of intralysosomal iron and hydrolases into the cytosol, where iron can generate harmful reactive oxygen species (ROS). It was inferred that this adverse oxidative reaction induced by BaP was ameliorated in the combination treatments by the ROS scavenging property of intralysosomal C₆₀, thus limiting the injury to the lysosomal membrane; and reducing the oxidative damage in the cytosol and to the nuclear DNA. The ROS scavenging by C₆₀, in combination with enhanced autophagic turnover of damaged cell constituents, appeared to have a cytoprotective effect against the toxic reaction to BaP in the combined treatments.

Polyelectrolyte stiffness on gold nanorods mediates cell membrane damage

Charge and surface chemistry of gold nanorods (AuNRs) are often considered the predictive factors for cell membrane damage. Unfortunately, extensive research on AuNR passivated with polyelectrolyte (PE) ligand shell (AuNR-PE) has hitherto left a vital knowledge gap between the mechanical stability of the ligand shell and the cytotoxicity of AuNR-PEs. Here, the agreement between unbiased coarse-grained molecular dynamics (CGMD) simulation and empirical outcomes on hemolysis of red blood cells by AuNR-PEs demonstrates for the first time, a direct impact of the mechanical stability of the PE shell passivating the AuNRs on the lipid membrane rupture. Such mechanical stability is ultimately modulated by the rigidity of the PE components. The CGMD simulation results also reveal the mechanism where the PE chain adsorbs near the surface of the lipid bilayer without penetrating the hydrophobic core of the bilayer, which allows the hydrophobic AuNR core to be in direct contact with the hydrophobic interior of the lipid bilayer, thereby perforating the lipid membrane to induce membrane damage.

Label-free chlorine and nitrogen-doped fluorescent carbon dots for target imaging of lysosomes in living cells

Lysosomes with a single-layered membrane structure are mainly involved in the scavenging of foreign substances and play an important role in maintaining normal physiological functions of living cells. In this work, near-neutrally charged fluorescent carbon dots (CDs) were prepared with lipophilicity through a facile one-pot hydrothermal carbonization of chloranil and triethylenetetramine at 160 °C for 3 h. The as-obtained CDs are proved to have good photostability, low cost, and excellent biocompatibility. Importantly, the as-prepared CDs with high quantum yield of 30.8% show excitation-dependent emission with great stability, and thus, they can be well used for the long-term target imaging of lysosomes in living cells without further modification. Meanwhile, the CDs can quickly enter into the lysosomes within 30 min, and the green fluorescence (FL) of CDs reaches the plateau when incubated for 60 min. By comparing the fluorescent intensity, the information about distribution and amount of lysosomes in different cells can be obtained. The proposed CD-based strategy demonstrates great promise for label-free target imaging of lysosomes in living cells. Graphical abstract The near-neutral carbon dots (CDs) with lipophilicity are used as label-free fluorescent nanoprobes for the long-term imaging of lysosomes in living cells.

Lysosomes, Autophagy, and Hormesis in Cell Physiology, Pathology, and Age-Related Disease

Autophagy has been strongly linked with hormesis, however, it is only relatively recently that the mechanistic basis underlying this association has begun to emerge. Lysosomal autophagy is a group of processes that degrade proteins, protein aggregates, membranes, organelles, segregated regions of cytoplasm, and even parts of the nucleus in eukaryotic cells. These degradative processes are evolutionarily very ancient and provide a survival capability for cells that are stressed or injured. Autophagy and autophagic dysfunction have been linked with many aspects of cell physiology and pathology in disease processes; and there is now intense interest in identifying various therapeutic strategies involving its regulation. The main regulatory pathway for augmented autophagy is the mechanistic target of rapamycin (mTOR) cell signaling, although other pathways can be involved, such as 5'-adenosine monophosphate-activated protein kinase. Mechanistic target of rapamycin is a key player in the many highly interconnected intracellular signaling pathways and is responsible for the control of cell growth among other processes. Inhibition of mTOR (specifically dephosphorylation of mTOR complex 1) triggers augmented autophagy and the search is on the find inhibitors that can induce hormetic responses that may be suitable for treating many diseases, including many cancers, type 2 diabetes, and age-related neurodegenerative conditions.

Visual monitoring of the lysosomal pH changes during autophagy with a red-emission fluorescent probe

Autophagy plays crucial roles in maintaining normal intracellular homeostasis. Molecular probes capable of monitoring lysosomal pH changes during autophagy are still highly required yet challenging to develop. Here, a lysosome-targeting fluorescent pH probe, RML, is presented by introducing a methylcarbitol unit as the lysosome-targeting group to rhodamine B, which is highly sensitive to pH changes. RML exhibits remarkable pH-dependent behavior at 583 nm with a fluorescent enhancement of more than 148-fold. The pK_a value is determined as 4.96, and the linear response with pH changes from 4.50-5.70, which is favorable for lysosomal pH imaging. We also confirm that RML diffuses selectively into lysosomes using confocal fluorescence microscopy. Using RML, we have successfully visualized autophagy by monitoring the lysosomal pH changes.

Coumarin Tröger's base derivatives with cyanine substitution as selective and sensitive fluorescent lysosomal probes

The fluorescent probes based on Tröger's base motive with both coumarin and cyanine substitution 11-13 have been synthesized by multi-step synthesis in high overall yields. Intracellular localization of prepared probes have been tested using four different cell lines (HF-P4, BLM, U-2 OS and A-2058). Prepared probes have intensive green and red fluorescence. Co-localization with commercial lysosome specific marker LysoTracker Blue DND 22 has been confirmed that all prepared fluorescent probes labeled lysosomal compartment with high selectivity and probes show excellent brightness at low concentration.

Quirks of dye nomenclature. 9. Fluorescein

Adolf Baeyer announced the discovery of fluorescein in 1871 and named it after its most striking property, i.e., fluorescence. I describe here the synthesis of fluorescein. There are seven molecular species in both the solid state or in solution. I also summarize some of the diverse applications of the dye, both medical and nonmedical, which depend mostly on the facile detection of fluorescein at low concentration. Both animal and human toxicity are examined.

Monitoring autophagy in live cells with a fluorescent light-up probe for G-quadruplex structures

Monitoring autophagy in live cells with a fluorescent light-up probe for G-quadruplex structures.

Emergent synergistic lysosomal toxicity of chemical mixtures in molluscan blood cells (hemocytes)

The problem of effective assessment of risk posed by complex mixtures of toxic chemicals in the environment is a major challenge for government regulators and industry. The biological effect of the individual contaminants, where these are known, can be measured; but the problem lies in relating toxicity to the multiple constituents of contaminant cocktails. The objective of this study was to test the hypothesis that diverse contaminant mixtures may cause a greater toxicity than the sum of their individual parts, due to synergistic interactions between contaminants with different intracellular targets. Lysosomal membrane stability in hemocytes from marine mussels was used for in vitro toxicity tests; and was coupled with analysis using the isobole method and a linear additive statistical model. The findings from both methods have shown significant emergent synergistic interactions between environmentally relevant chemicals (i.e., polycyclic aromatic hydrocarbons, pesticides, biocides and a surfactant) when exposed to isolated hemocytes as a mixture of 3 & 7 constituents. The results support the complexity-based hypothesis that emergent toxicity occurs with increasing contaminant diversity, and raises questions about the validity of estimating toxicity of contaminant mixtures based on the additive toxicity of single components. Further experimentation is required to investigate the potential for interactive effects in mixtures with more constituents (e.g., 50-100) at more environmentally realistic concentrations in order to test other regions of the model, namely, very low concentrations and high diversity. Estimated toxicant diversity coupled with tests for lysosomal damage may provide a potential tool for determining the toxicity of estuarine sediments, dredge spoil or contaminated soil.

Quinolizinium as a new fluorescent lysosomotropic probe

We have synthesized a collection of quinolizinium fluorescent dyes for the purpose of cell imaging. Preliminary biological studies in human U2OS osteosarcoma cancer cells have shown that different functional groups appended to the cationic quinolizinium scaffold efficiently modulate photophysical properties but also cellular distribution. While quinolizinium probes are known nuclear staining reagents, we have identified a particular quinolizinium derivative salt that targets the lysosomal compartment. This finding raises the question of predictability of specific organelle targeting from structural features of small molecules.

Mitochondrial Dynamics Tracking with Two-Photon Phosphorescent Terpyridyl Iridium(III) Complexes

Mitochondrial dynamics, including fission and fusion, control the morphology and function of mitochondria, and disruption of mitochondrial dynamics leads to Parkinson's disease, Alzheimer's disease, metabolic diseases, and cancers. Currently, many types of commercial mitochondria probes are available, but high excitation energy and low photo-stability render them unsuitable for tracking mitochondrial dynamics in living cells. Therefore, mitochondrial targeting agents that exhibit superior anti-photo-bleaching ability, deep tissue penetration and intrinsically high three-dimensional resolutions are urgently needed. Two-photon-excited compounds that use low-energy near-infrared excitation lasers have emerged as non-invasive tools for cell imaging. In this work, terpyridyl cyclometalated Ir(III) complexes (Ir1-Ir3) are demonstrated as one- and two-photon phosphorescent probes for real-time imaging and tracking of mitochondrial morphology changes in living cells.

In vivo selective imaging and inhibition of leukemia stem-like cells using the fluorescent carbocyanine derivative, DiOC5(3)

Elimination of leukemia stem cells (LSCs) is necessary for the destruction of malignant cell populations. Owing to the very small number of LSCs in leukemia cells, xenotransplantation studies are difficult in terms of functionally and pathophysiologically replicating clinical conditions of cell culture experiments. There is currently a limited number of lead compounds that target LSCs. Using the LSC-xenograft zebrafish screening method we previously developed, we found that the fluorescent compound 3,3'-dipentyloxacarbocyanine iodide (DiOC5(3)) selectively marked LSCs and suppressed their proliferation in vivo and in vitro. DiOC5(3) had no obvious toxicity to human umbilical cord blood CD34+ progenitor cells and normal zebrafish. It accumulated in mitochondria through organic anion transporter polypeptides that are overexpressed in the plasma membrane of LSCs, and induced apoptosis via ROS overproduction. DiOC5(3) also inhibited the nuclear translocation of NF-κB through the downregulation of LSC-selective pathways, as indicated from DNA microarray analysis. In summary, DiOC5(3) is a new type of anti-LSC compound available for diagnostic imaging and therapeutics that has the advantage of being a single fluorescent chemical.

Electrochemical detection of intracellular and cell membrane redox systems in Saccharomyces cerevisiae

Redox mediators can interact with eukaryote cells at a number of different cell locations. While cell membrane redox centres are easily accessible, the redox centres of catabolism are situated within the cytoplasm and mitochondria and can be difficult to access. We have systematically investigated the interaction of thirteen commonly used lipophilic and hydrophilic mediators with the yeast Saccharomyces cerevisiae. A double mediator system is used in which ferricyanide is the final electron acceptor (the reporter mediator). After incubation of cells with mediators, steady state voltammetry of the ferri/ferrocyanide redox couple allows quantitation of the amount of mediator reduced by the cells. The plateau current at 425 mV vs Ag/AgCl gives the analytical signal. The results show that five of the mediators interact with at least three different trans Plasma Membrane Electron Transport systems (tPMETs), and that four mediators cross the plasma membrane to interact with cytoplasmic and mitochondrial redox molecules. Four of the mediators inhibit electron transfer from S. cerevisiae. Catabolic inhibitors were used to locate the cellular source of electrons for three of the mediators.

Using lysosomal membrane stability of haemocytes in Ruditapes philippinarum as a biomarker of cellular stress to assess contamination by caffeine, ibuprofen, carbamazepine and novobiocin

Although pharmaceuticals have been detected in the environment only in the range from ng/L to microg/L, it has been demonstrated that they can adversely affect the health status of aquatic organisms. Lysosomal membrane stability (LMS) has previously been applied as an indicator of cellular well-being to determine health status in bivalve mussels. The objective of this study is to evaluate LMS in Ruditapes philippinarum haemolymph using the neutral red retention assay (NRRA). Clams were exposed in laboratory conditions to caffeine (0.1, 5, 15, 50 microg/L), ibuprofen (0.1, 5, 10, 50 microg/L), carbamazepine and novobiocin (both at 0.1, 1, 10, 50 microg/L) for 35 days. Results show a dose-dependent effect of the pharmaceuticals. The neutral red retention time measured at the end of the bioassay was significantly reduced by 50% after exposure to environmental concentrations (p < 0.05) (caffeine = 15 microg/L; ibuprofen = 10 microg/L; carbamazepine = 1 microg/L and novobiocin = 1 microg/L), compared to controls. Clams exposed to these pharmaceuticals were considered to present a diminished health status (retention time < 45 min), significantly worse than controls (96 min) (p < 0.05). The predicted no environmental effect concentration (PNEC) results showed that these pharmaceuticals are very toxic at the environmental concentrations tested. Measurement of the alteration of LMS has been found to be a sensitive technique that enables evaluation of the health status of clams after exposure to pharmaceuticals under laboratory conditions, thus representing a robust Tier-1 screening biomarker.

Stability of lysosomal membrane in Carcinus maenas acts as a biomarker of exposure to pharmaceuticals

The presence of pharmaceuticals in the environment is now a major concern given their potential adverse effects on organisms, particularly human beings. Because the feeding style and habitat of the crab Carcinus maenas make this species vulnerable to organic contaminants, it has been used previously in ecotoxicological studies. Lysosomal membrane stability (LMS) in crabs is a general indicator of cellular well-being and can be visualized by the neutral red retention (NRR) assay. LMS in crab hemolymph has been evaluated as a cellular biomarker of adverse effects produced by exposure to pharmaceutical compounds. Crabs were exposed in the laboratory to four different pharmaceuticals for 28 days in a semistatic 24-h renewal assay. Filtered seawater was spiked every 2 days with various concentrations (from 0.1 to 50 μg · L(-1)) of caffeine, ibuprofen, carbamazepine, and novobiocin. Results showed that NRR time, measured at day 28, was significantly reduced (p < 0.05) after exposure to environmental concentrations of each pharmaceutical (caffeine = 15 μg · L(-1); carbamazepine = 1 μg · L(-1); ibuprofen = 5 μg · L(-1); and novobiocin = 0.1 μg · L(-1)) when compared with control organisms. The predicted "no environmental effect" concentration/measured environmental concentration results showed that the selected pharmaceuticals are toxic at environmental concentrations and need further assessment. LMS monitoring in crabs is a sensitive tool for evaluating exposure to concentrations of selected drugs under laboratory conditions and provides a robust tier 1 testing approach (screening biomarker) for rapid assessment of marine pollution and environmental impact assessments for analyzing pharmaceutical contamination in aquatic environments.

Uptake and localisation of small-molecule fluorescent probes in living cells: a critical appraisal of QSAR models and a case study concerning probes for DNA and RNA

Small-molecule fluorochromes are used in biology and medicine to generate informative microscopic and macroscopic images, permitting identification of cell structures, measurement of physiological/physicochemical properties, assessment of biological functions and assay of chemical components. Modes of uptake and precise intracellular localisation of a probe are typically significant factors in its successful application. These processes and localisations can be predicted using quantitative structure activity relations (QSAR) models, which correlate aspects of the physicochemical properties of the probes (expressed numerically) with the uptake/localisation. Pay-offs of such modelling include better understanding and trouble-shooting of current and novel probes, and easier design of future probes ("guided synthesis"). Uptake models discussed consider adsorptive (to lipid or protein domains), phagocytic and pinocytotic endocytosis, as well as passive diffusion. Localisation models discussed include those for cytosol, endoplasmic reticulum, Golgi apparatus, lipid droplets, lysosomes, mitochondria, nucleus and plasma membrane. A case example illustrates how such QSAR modelling of probe interactions can clarify localisation and mode of binding of probes to intracellular nucleic acids of living cells, including not only eukaryotic chromatin DNA and ribosomal RNA, but also prokaryote chromosomes.

The novel approach to enhance seed security: dual anti-counterfeiting methods applied on tobacco pelleted seeds

Seed security is of prime importance for agriculture. To protect true seeds from being faked, more secure dual anti-counterfeiting technologies for tobacco (Nicotiana tabacum L.) pelleted seed were developed in this paper. Fluorescein (FR), rhodamine B (RB), and magnetic powder (MP) were used as anti-counterfeiting labels. According to their different properties and the special seed pelleting process, four dual-labeling treatments were conducted for two tobacco varieties, MS Yunyan85 (MSYY85) and Honghua Dajinyuan (HHDJY). Then the seed germination and seedling growth status were investigated, and the fluorescence in cracked pellets and developing seedlings was observed under different excitation lights. The results showed that FR, RB, and MP had no negative effects on the germination, seedling growth, and MDA content of the pelleted seeds, and even some treatments significantly enhanced seedling dry weight, vigor index, and shoot height in MS YY85, and increased SOD activity and chlorophyll content in HHDJY as compared to the control. In addition, the cotyledon tip of seedlings treated with FR and MP together represented bright green fluorescence under illumination of blue light (478 nm). And the seedling cotyledon vein treated with RB and MP together showed red fluorescence under green light (546 nm). All seeds pelleted with magnetic powder of proper concentration could be attracted by a magnet. Thus, it indicated that those new dual-labeling methods that fluorescent compound and magnetic powder simultaneously applied in the same seed pellets definitely improved anti-counterfeiting technology and enhanced the seed security. This technology will ensure that high quality seed will be used in the crop production.

Location-dependent coronary artery diffusive and convective mass transport properties of a lipophilic drug surrogate measured using nonlinear microscopy

PURPOSE

Arterial wall mass transport properties dictate local distribution of biomolecules or locally delivered dugs. Knowing how these properties vary between coronary artery locations could provide insight into how therapy efficacy is altered between arterial locations.

METHODS

We introduced an indocarbocyanine drug surrogate to the lumens of left anterior descending and right coronary (LADC; RC) arteries from pigs with or without a pressure gradient. Interstitial fluorescent intensity was measured on live samples with multiphoton microscopy. We also measured binding to porcine coronary SMCs in monoculture.

RESULTS

Diffusive transport constants peaked in the middle sections of the LADC and RC arteries by 2.09 and 2.04 times, respectively, compared to the proximal and distal segments. There was no statistical difference between the average diffusivity value between LADC and RC arteries. The convection coefficients had an upward trend down each artery, with the RC being higher than the LADC by 3.89 times.

CONCLUSIONS

This study demonstrates that the convective and diffusive transport of lipophilic molecules changes between the LADC and the RC arteries as well as along their length. These results may have important implications in optimizing drug delivery for the treatment of coronary artery disease.

MTT assay for cell viability: Intracellular localization of the formazan product is in lipid droplets

Although MTT is widely used to assess cytotoxicity and cell viability, the precise localization of its reduced formazan product is still unclear. In the present study the localization of MTT formazan was studied by direct microscopic observation of living HeLa cells and by colocalization analysis with organelle-selective fluorescent probes. MTT formazan granules did not colocalize with mitochondria as revealed by rhodamine 123 labeling or autofluorescence. Likewise, no colocalization was observed between MTT formazan granules and lysosomes labeled by neutral red. Taking into account the lipophilic character and lipid solubility of MTT formazan, an evaluation of the MTT reaction was performed after treatment of cells with sunflower oil emulsions to induce a massive occurrence of lipid droplets. Under this condition, lipid droplets revealed a large amount of MTT formazan deposits. Kinetic studies on the viability of MTT-treated cells showed no harmful effects at short times. Quantitative structure-activity relations (QSAR) models were used to predict and explain the localization of both the MTT tetrazolium salt and its formazan product. These predictions were in agreement with experimental observations on the accumulation of MTT formazan product in lipid droplets.

Calcium rubies: a family of red-emitting functionalizable indicators suitable for two-photon Ca2+ imaging

We designed Calcium Rubies, a family of functionalizable BAPTA-based red-fluorescent calcium (Ca(2+)) indicators as new tools for biological Ca(2+) imaging. The specificity of this Ca(2+)-indicator family is its side arm, attached on the ethylene glycol bridge that allows coupling the indicator to various groups while leaving open the possibility of aromatic substitutions on the BAPTA core for tuning the Ca(2+)-binding affinity. Using this possibility we now synthesize and characterize three different CaRubies with affinities between 3 and 22 μM. Their long excitation and emission wavelengths (peaks at 586/604 nm) allow their use in otherwise challenging multicolor experiments, e.g., when combining Ca(2+) uncaging or optogenetic stimulation with Ca(2+) imaging in cells expressing fluorescent proteins. We illustrate this capacity by the detection of Ca(2+) transients evoked by blue light in cultured astrocytes expressing CatCh, a light-sensitive Ca(2+)-translocating channelrhodopsin linked to yellow fluorescent protein. Using time-correlated single-photon counting, we measured fluorescence lifetimes for all CaRubies and demonstrate a 10-fold increase in the average lifetime upon Ca(2+) chelation. Since only the fluorescence quantum yield but not the absorbance of the CaRubies is Ca(2+)-dependent, calibrated two-photon fluorescence excitation measurements of absolute Ca(2+) concentrations are feasible.

Tracking living decapod larvae: mass staining of eggs with neutral red prior to hatching

Mass staining of decapod females carrying eggs, with subsequent identification of hatched larvae in the environment, is a research tool with great potential for field ecologists wishing to track the movements of larvae. For this to be achieved, however, numerous requirements must be met. These include adequate dye solubility, short staining time, dye penetration through different tissues, dye retention within the organism, absence of toxic and behavioral effects, low visibility to predators of stained larvae, no loss of staining owing to preservatives and low cost. The dye, neutral red, appears to meet most of these requirements. This dye was used in aliquots of 0.7 g/770 ml seawater applied to the females of Norway lobster (Nephrops norvegicus) and European lobster (Homarus gammarus) for 10 min. This procedure stained lobster eggs and embryos so that hatched larvae could be distinguished easily by fluorescence microscopy from larvae that hatched from unstained eggs. Stained larvae that were preserved in 4% formaldehyde in seawater were still stained after 1 year. Larvae should not come in contact with ethanol, because it extracts the dye rapidly.

Cell death causes relocalization of photosensitizing fluorescent probes

When cultured cells are treated with fluorescent organelle probes or photosensitizer agents, a characteristic redistribution of fluorescence in cell structures occurs frequently after light irradiation. It is currently assumed that such changes, referred to as relocalizations of the fluorescent compounds, represent an important aspect of the photodynamic process, which is based on the excitation of photosensitizers by light in the presence of oxygen. As cell damage and death result from the oxidative stress induced by photodynamic treatments, we have studied here the redistribution of acridine orange (AO) and 3,3'-dimethyl-oxacarbocyanine (DiOC(1)(3)) fluorescence after incubation of HeLa cell cultures with these compounds followed by blue light irradiation to achieve lethal effects. The relocalization of dyes from their original labeling sites (AO: lysosomes, DiOC(1)(3): mitochondria) to nucleic acid-containing structures (cytoplasm, nuclei and nucleoli) appeared clearly associated with cell death. Therefore, the relocalization phenomenon simply reflects fluorescence changes due to the different affinity of these dyes for living and damaged or dead cells. As fluorescent probes are often photosensitizers, prolonged light exposures using fluorescence microscopy will produce lethal photodynamic effects with relocalization of the fluorescent signal and changes in the cell morphology.

Machine vision-assisted analysis of structure-localization relationships in a combinatorial library of prospective bioimaging probes

With a combinatorial library of bioimaging probes, it is now possible to use machine vision to analyze the contribution of different building blocks of the molecules to their cell-associated visual signals. For this purpose, cell-permeant, fluorescent styryl molecules were synthesized by condensation of 168 aldehyde with 8 pyridinium/quinolinium building blocks. Images of cells incubated with fluorescent molecules were acquired with a high content screening instrument. Chemical and image feature analysis revealed how variation in one or the other building block of the styryl molecules led to variations in the molecules' visual signals. Across each pair of probes in the library, chemical similarity was significantly associated with spectral and total signal intensity similarity. However, chemical similarity was much less associated with similarity in subcellular probe fluorescence patterns. Quantitative analysis and visual inspection of pairs of images acquired from pairs of styryl isomers confirm that many closely-related probes exhibit different subcellular localization patterns. Therefore, idiosyncratic interactions between styryl molecules and specific cellular components greatly contribute to the subcellular distribution of the styryl probes' fluorescence signal. These results demonstrate how machine vision and cheminformatics can be combined to analyze the targeting properties of bioimaging probes, using large image data sets acquired with automated screening systems.

Lysosomes and autophagy in aquatic animals

The lysosomal-autophagic system appears to be a common target for many environmental pollutants, as lysosomes accumulate many toxic metals and organic xenobiotics, which perturb normal function and damage the lysosomal membrane. In fact, autophagic reactions frequently involving reduced lysosomal membrane integrity or stability appear to be effective generic indicators of cellular well-being in eukaryotes: in social amoebae (slime mold), mollusks and fish, autophagy/membrane destabilization is correlated with many stress and toxicological responses and pathological reactions. Prognostic use of adverse lysosomal and autophagic reactions to environmental pollutants can be used for predicting cellular dysfunction and health in aquatic animals, such as shellfish and fish, which are extensively used as sensitive bioindicators in monitoring ecosystem health; and also represent a significant food resource for at least 20% of the global human population. Explanatory frameworks for prediction of pollutant impact on health have been derived encompassing a conceptual mechanistic model linking lysosomal damage and autophagic dysfunction with injury to cells and tissues. Methods are described for tracking in vivo autophagy of fluorescently labeled cytoplasmic proteins, measuring degradation of radiolabeled intracellular proteins and morphometric measurement of lysosomal/cytoplasmic volume ratio. Additional methods for the determination of lysosomal membrane stability in lower animals are also described, which can be applied to frozen tissue sections, protozoans and isolated cells in vivo. Experimental and simulated results have also indicated that nutritional deprivation (analogous in marine mussels to caloric restriction)-induced autophagy has a protective function against toxic effects mediated by reactive oxygen species (ROS). Finally, coupled measurement of lysosomal-autophagic reactions and simulation modelling is proposed as a practical toolbox for predicting toxic environmental risk.

Rapid doxorubicin efflux from the nucleus of drug-resistant cancer cells following extracellular drug clearance

PURPOSE

Following extracellular drug clearance, we analyzed the rate of doxorubicin efflux from the nucleus of three human leukemic cells (K562, Molt4 and CCRF-CEM) and related it to their differential sensitivity to this drug, after a short drug pulse.

RESULTS

For many pulse-chase regimes, K562 cell viability was least affected by doxorubicin. In K562 cells, nuclear drug accumulation was greatest, but nuclear drug egress was also greatest. P-glycoprotein over-expression in a doxorubicin-resistant, K562/DOX sub-line did not facilitate doxorubicin efflux from the nucleus. In K562 cells, doxorubicin accumulated in multivesicular bodies (MVBs) through a pH-dependent mechanism. Inhibiting drug sequestration in MVBs did not affect nuclear efflux. The rates of doxorubicin efflux from the nuclei of live and digitonin-permeabilized K562 cells were similar. However, extracting cytoplasmic membranes with Triton X-100 significantly inhibited nuclear drug efflux following extracellular drug clearance.

CONCLUSION

Our results are consistent with drug efflux from the nucleus being primarily mediated by an ATP-independent, passive diffusion mechanism. The effect of membrane extraction suggests that nonspecific drug absorption to cytoplasmic membranes plays a role in facilitating nuclear efflux in K562 cells, perhaps by lowering the concentration of free doxorubicin from a perinuclear diffusion boundary layer.

Mitochondriotropics: A review of their mode of action, and their applications for drug and DNA delivery to mammalian mitochondria

Since compounds targeting mitochondria exhibit diverse accumulation mechanisms and chemical features, various questions arise. Do such "mitochondriotropics" have a characteristic chemistry? What are mitochondrial uptake mechanisms? Do mitochondriotropics necessarily accumulate in mitochondria or merely have access? Is the concept "mitochondriotropic" of any practical value? To seek answers, a non-biased sample of >100 mitochondriotropics was generated from the review literature. This dataset was examined using: physicochemical classification; quantitative structure-activity relations (QSAR) models; and a Fick-Nernst-Planck physicochemical model. The ability of the latter two approaches to predict mitochondriotropic behaviour was assessed, and comparisons made between methods, and with current assumptions. All approaches provided instructive pictures of the nature of mitochondriotropics. Thus although lipophilic cations are regarded as the commonest structural type, only a third were such. Much the same proportion were acids, potentially or actually anions. Many mitochondriotropics were electrically neutral compounds. All categorizations involved overall molecular properties, not the presence of "mitochondriotropic tags"--again contrary to literature concepts. Selective mitochondrial accumulation involved electric potential, ion-trapping, and complex formation with cardiolipin; non-specific accumulation involved membrane partitioning. Non-specific access required only low lipophilicity. Mitochondrial targeting did not preclude additional accumulation sites, e.g. lysosomes. The concept "mitochondriotropic" remains useful, although may imply access, not accumulation. QSAR and Fick-Nernst-Planck approaches are complementary--neither is universally applicable. Using both approaches enabled the mitochondriotropic behavior of >80% of the dataset to be predicted, and the physicochemistry of mitochondriotropics to be specified in some detail. This can facilitate guided syntheses and selection of optimal mitochondriotropic structures.

Lysosomal sequestration of amine-containing drugs: analysis and therapeutic implications

Amine-containing drugs represent a very important class of therapeutic agents, with the majority of all drugs containing at least one basic nitrogen. For many decades, it has been known that weakly basic compounds can be sequestered into acidic organelles such as lysosomes. Some amines can achieve very high concentrations and induce a dramatic expansion (vacuolization) of the compartment. In the early 70s, Nobel laureate and discoverer of lysosomes, Christian de Duve et al. wrote an elegant commentary describing the theoretical basis for lysosomal sequestration of amines, referring to the process as pH-partitioning and the substrates as lysosomotropics. Recently, a resurgence of interest in the intracellular distribution of drugs has occurred considering its therapeutic importance. Specifically, lysosomal sequestration of amines has received considerable attention for reasons including its involvement in drug resistance, inducement of phospholipidosis, and its influence on whole body distribution/pharmacokinetics. Moreover, the sequestration phenomenon has been recently exploited in the development of a novel drug targeting strategy. This review will focus on these occurrences/developments and conclude with a commentary on the expected impact that knowledge regarding the intracellular distribution of drugs will likely have on future drug development processes.

Role of acidic cell organelles in the higher nonmelanoma retention of melanoma markers based on N-(2-dialkylaminoethyl)benzamides and the cytotoxicity of alkylating benzamides

Melanoma markers based on both N-(2-dialkylaminoethyl)benzamides and lysosomotropic agents comprise a N-(2-dialkylaminoethyl)aminocarbamoyl pharmacophore, suggesting that benzamides and lysosomotropic probes should show affinity to melanoma and acidic cell organelles. We prepared novel fluorescent N-(2-dialkylaminoethyl)benzamides to prove this presumption. Lysosomotropic probes showed a melanin affinity comparable to benzamides. Lysosomal markers and benzamides colocalized in acidic organelles. Various nonmelanoma cell lines showed equal benzamide uptake and retention compared with melanoma cells. In nonmelanoma cells the amount of retained benzamides correlates with the number of acidic cell organelles. Benzamides almost completely failed to accumulate in melanoma cells with neutralized acidic organelles but normal melanin content. In melanoma retention of benzamides, acidic cell organelles are the main determinant. N-(2-dialkylaminoethyl)benzamides are lysosomotropic probes with high accumulation in nonmelanoma tumors with many acidic cell organelles. Alkylating benzamides were reported previously to show a melanoma unselective, in general enhanced cytotoxicity. Alkylating benzamides can act as lysosomotropic detergents or as DNA alkylators. The ability of alkylating benzamides to disrupt the membrane of lysosomes and cause liberation of lysosomal-trapped fluorescent dyes was demonstrated by fluorescence microscopy. Whether they act as an alkylating agent or a lysosomotropic detergent in a specific cell line is dependent on the amount of acidic cell organelles. In cell lines with small amounts of acidic cell organelles alkylating benzamides act as alkylating agents, whereas in cell lines with many acidic cell organelles they act as lysosomotropic detergents. In cell lines with high amounts of acidic cell organelles they do not reach the nucleus.

A Cheminformatic Toolkit for Mining Biomedical Knowledge

PURPOSE

Cheminformatics can be broadly defined to encompass any activity related to the application of information technology to the study of properties, effects and uses of chemical agents. One of the most important current challenges in cheminformatics is to allow researchers to search databases of biomedical knowledge, using chemical structures as input.

MATERIALS AND METHODS

An important step towards this goal was the establishment of PubChem, an open, centralized database of small molecules accessible through the World Wide Web. While PubChem is primarily intended to serve as a repository for high throughput screening data from federally-funded screening centers and academic research laboratories, the major impact of PubChem could also reside in its ability to serve as a chemical gateway to biomedical databases such as PubMed.

CONCLUSION

This article will review cheminformatic tools that can be applied to facilitate annotation of PubChem through links to the scientific literature; to integrate PubChem with transcriptomic, proteomic, and metabolomic datasets; to incorporate results of numerical simulations of physiological systems into PubChem annotation; and ultimately, to translate data of chemical genomics screening efforts into information that will benefit biomedical researchers and physician scientists across all therapeutic areas.

Structure−Function Correlation of Chloroquine and Analogues as Transgene Expression Enhancers in Nonviral Gene Delivery

To understand how chloroquine (CQ) enhances transgene expression in polycation-based, nonviral gene delivery systems, a number of CQ analogues with variations in the aliphatic amino side chain or in the aromatic ring are synthesized and investigated. Our studies indicate that the aliphatic amino moiety of CQ is essential to provide increased gene expression. Further, the enhancements are more dramatically affected by changes to the aromatic ring and are positively correlated to the strength of intercalation between DNA and the CQ analogues. Quinacrine (QC), a CQ analogue with a fused acridinyl structure that can strongly intercalate DNA, enhances transfection similarly to CQ at a concentration 10 times lower, while N(4)-(4-pyridinyl)-N(1),N(1)-diethyl-1,4-pentanediamine (CP), a CQ analogue that has a weakly intercalating pyridinyl ring, shows no effect on gene expression. Subtle change on the 7-substituent of the chloroquine aromatic structure can also greatly affect the ability of the CQ analogues to enhance transgene expression. Transfection in the presence of N(4)-(7-trifluoromethyl-4-quinolinyl)-N(1),N(1)-diethyl-1,4-pentanediamin e (CQ7a) shows expression efficiency 10 times higher than in the presence of CQ at same concentration, while transfection in the presence of N(4)-(4-quinolinyl)-N(1),N(1)-diethyl-1,4-pentanediamine (CQ7b) does not reveal any enhancing effects on expression. Through a number of comparative studies with CQ and its analogues, we conclude that there are at least three mechanistic features of CQ that lead to the enhancement in gene expression: (i) pH buffering in endocytic vesicles, (ii) displacement of polycations from the nucleic acids in polyplexes, and (iii) alteration of the biophysical properties of the released nucleic acid.

Pathological reactions and recovery of hepatopancreatic digestive cells from the marine snail Littorina littorea following exposure to a polycyclic aromatic hydrocarbon

The aim of this study was to investigate the cellular pathological responses of hepatopancreatic digestive cells from the periwinkle Littorina littorea exposed to the polycyclic aromatic hydrocarbon (PAH) fluoranthene and to ascertain whether any injurious effects were reversible within the experimental time scale. A secondary objective was to establish the relationship of the various reactions to animal health status, using lysosomal stability as an index of well-being. Exposure of snails to a concentration of 335 microgl(-1) (1.7 microM) fluoranthene (seawater renewed and spiked daily with fluoranthene) for 5 days resulted in a reduction in lysosomal stability (neutral red retention) and endocytosis; and an increase in smooth endoplasmic reticulum (ER) and 7-ethoxycoumarin-o-deethylase (ECOD; measured as cyano-ECOD) activity measured in isolated live digestive cells. Exposed snails treated with clean seawater for a further 8 days resulted in a return to control levels of lysosomal stability, ECOD and ER; endocytosis showed only a partial recovery. Multi-variate and uni-variate analysis showed that there were strong correlations between the various cellular biomarker responses. These findings are interpretable within the current framework of molluscan biomarker responses to PAHs. Principal component analysis was used to derive the first principal component for endocytosis, ER and ECOD reactions and these were plotted against lysosomal stability as a measure of cellular well-being. The resulting significant regression represents the mapping of the individual biomarkers within health status space for a gradient of fluoranthene toxicity. From this analysis, we concluded that endocytosis is an indicator of healthy snails while proliferation of ER and to a lesser extent induced ECOD are indicative of dysfunction and reduced health. Finally, the results indicate that stress induced by chronic exposure to a PAH is reversible.