Peptide-Guided Surface-Enhanced Raman Scattering Probes for Localized Cell Composition Analysis

The ability to control the localization of surface-enhanced Raman scattering (SERS) nanoparticle probes in bacterial cells is critical to the development of analytical techniques that can nondestructively determine cell composition and phenotype. Here, selective localization of SERS probes was achieved at the outer bacterial membrane by using silver nanoparticles functionalized with synthetic hydrophobic peptides.     

Synoptic determination of living/dead and active/dormant bacterial fractions in marine sediments

The most widely used methods for the estimation of the living/dead fractions of bacterial cells involve specific stains that are able to reveal membrane integrity. Here, we have compared two different probes (propidium iodide and ethidium homodimer-2) that have different molecular weights and steric hindrance effects. We have also combined this method with the staining/destaining procedure that is currently used in the identification of potentially active cells. The procedure for marine sediments described here allows the synoptic (i.e. from the same filter) identification of: (i) the number of living bacteria; (ii) the number of active vs. dormant cells within this living fraction; (iii) the bacterial fraction with an intact nucleoid region without membrane integrity; and (iv) dead cells (devoid of the nucleoid region and without membrane integrity). Our results demonstrate that the concentration of propidium is crucial for the correct estimation of the dead bacterial fraction, ethidium homodimer-2 allows efficient and accurate estimates that are independent of the concentrations used and the sample storage. The active bacterial fraction represented c. 40% of the total bacterial abundance, the inactive/dormant fraction c. 30%, and the dead fraction was, on average, c. 30%. This method allows the processing of a large number of samples with high precision and at relatively low cost, and thus it provides additional synoptic insights into the metabolic state of bacteria in marine sediments.     

Cytoplasmic membrane polarization in Gram-positive and Gram-negative bacteria grown in the absence and presence of tetracycline

The ability of numerous diverse compounds and ions to cross the bacterial cytoplasmic membrane by diffusion and active transport is highly dependent on cytoplasmic membrane fluidity, which can be measured using fluorescent probes to estimate membrane polarization values. However, membrane polarization data are lacking for most bacterial species. The cytoplasmic membrane polarization values for Arthrobacter sp. ATCC 21908, Bacillus cereus NRC 3045, Pseudomonas fluorescens R2F, Pseudomonas putida NRC 2986 and Escherichia coli C600 bacterial cells were spectrofluorometrically measured over a temperature range from 10 to 50 degrees C, and in the absence and presence of 1 microg/ml tetracycline, using the fluorescent probe 1,6-diphenyl-1,3,5-hexatriene (DPH) to obtain new information on their membrane fluidity. At an assay temperature of 10 degrees C, E. coli cells grown in the absence of tetracycline exhibited the highest cytoplasmic membrane polarization value (least fluid membrane) of 0.446, followed by values of 0.392, 0.371, 0.344 and 0.293, respectively, for B. cereus, Arthrobacter sp., P. fluorescens and P. putida. At an assay temperature of 30 degrees C, the polarization values ranged from 0.357 to 0.288 for cells grown in the absence of tetracycline, regardless of the species. B. cereus grown in the presence of 1 microg/ml tetracycline had lower polarization values than when grown in the absence of this antibiotic at all assay temperatures. Regardless of the absence or presence of 1 microg/ml tetracycline in the growth medium, all bacterial species generally exhibited a more fluid membrane as the assay temperature increased from 10 to 50 degrees C. To our knowledge, these are some of the first cytoplasmic membrane polarization values reported for these Gram-negative and Gram-positive bacteria over a broad temperature range and also for cells grown in the presence of tetracycline.     

Enzyme-targeted fluorescent small-molecule probes for bacterial imaging

Molecular imaging methods to visualize myriad biochemical processes in bacteria have traditionally been dependent upon molecular biology techniques to incorporate fluorescent biomolecules (e.g., fusion proteins). Such methods have been instrumental in our understanding of how bacteria function but are not without drawbacks, including potential perturbation to native protein expression and function. To overcome these limitations, the use of fluorescent small-molecule probes has gained much attention. Here, we highlight examples from the recent literature that showcase the utility of small-molecule probes for the fluorescence imaging of bacterial cells, including electrophilic, metabolic, and enzyme-activated probes. Although the use of these types of compounds for bacterial imaging is still relatively new, the selected examples demonstrate the exciting potential of these critical tools in the exploration of bacterial physiology.     

Targeted pancreatic beta cell imaging for early diagnosis

Pancreatic beta cells are important in blood glucose level regulation. As type 1 and 2 diabetes are getting prevalent worldwide, we need to explore new methods for early detection of beta cell-related afflictions. Using bioimaging techniques to measure beta cell mass is crucial because a decrease in beta cell density is seen in diseases such as diabetes and thus can be a new way of diagnosis for such diseases. We also need to appraise beta cell purity in transplanted islets for type 1 diabetes patients. Sufficient amount of functional beta cells must also be determined before being transplanted to the patients. In this review, indirect imaging of beta cells will be discussed. This includes membrane protein on pancreatic beta cells whereby specific probes are designed for different imaging modalities mainly magnetic resonance imaging, positron emission tomography and fluorescence imaging. Direct imaging of insulin is also explored though probes synthesized for such function are relatively fewer. The path for successful pancreatic beta cell imaging is fraught with challenges like non-specific binding, lack of beta cell-restricted targets, the requirement of probes to cross multiple lipid layers to bind to intracellular insulin. Hence, there is an urgent need to develop new imaging techniques and innovative probing constructs in the entire imaging chain of bioengineering to provide early detection of beta cell-related pathology.     

Determination of lipid raft partitioning of fluorescently-tagged probes in living cells by Fluorescence Correlation Spectroscopy (FCS)

In the past fifteen years the notion that cell membranes are not homogenous and rely on microdomains to exert their functions has become widely accepted. Lipid rafts are membrane microdomains enriched in cholesterol and sphingolipids. They play a role in cellular physiological processes such as signalling, and trafficking but are also thought to be key players in several diseases including viral or bacterial infections and neurodegenerative diseases. Yet their existence is still a matter of controversy. Indeed, lipid raft size has been estimated to be around 20 nm, far under the resolution limit of conventional microscopy (around 200 nm), thus precluding their direct imaging. Up to now, the main techniques used to assess the partition of proteins of interest inside lipid rafts were Detergent Resistant Membranes (DRMs) isolation and co-patching with antibodies. Though widely used because of their rather easy implementation, these techniques were prone to artefacts and thus criticized. Technical improvements were therefore necessary to overcome these artefacts and to be able to probe lipid rafts partition in living cells. Here we present a method for the sensitive analysis of lipid rafts partition of fluorescently-tagged proteins or lipids in the plasma membrane of living cells. This method, termed Fluorescence Correlation Spectroscopy (FCS), relies on the disparity in diffusion times of fluorescent probes located inside or outside of lipid rafts. In fact, as evidenced in both artificial membranes and cell cultures, probes would diffuse much faster outside than inside dense lipid rafts. To determine diffusion times, minute fluorescence fluctuations are measured as a function of time in a focal volume (approximately 1 femtoliter), located at the plasma membrane of cells with a confocal microscope (Fig. 1). The auto-correlation curves can then be drawn from these fluctuations and fitted with appropriate mathematical diffusion models. FCS can be used to determine the lipid raft partitioning of various probes, as long as they are fluorescently tagged. Fluorescent tagging can be achieved by expression of fluorescent fusion proteins or by binding of fluorescent ligands. Moreover, FCS can be used not only in artificial membranes and cell lines but also in primary cultures, as described recently. It can also be used to follow the dynamics of lipid raft partitioning after drug addition or membrane lipid composition change.     

Correlations between fatty acid distribution in phospholipids and the temperature dependence of membrane physical state

Cytoplasmic membranes of an unsaturated fatty acid auxotroph of Escherichia coli have been studied using spin labeled hydrocarbon probes. These studies reveal that the membrane lipids undergo changes of state at critical temperatures which reflect the physical properties of the fatty acid supplement supplied to the cells during growth. The critical temperatures observed in spin labeled membranes correlate with characteristic temperatures in membrane functions. Lipid analysis reveals that fatty acid composition and distribution in membrane phospholipids are primary determinants of the temperatures at which changes of state are observed in membrane lipids. Fatty acid composition and distribution can also produce unique interactions between certain spin label probes and their lipid environment.     

Profiling the membrane proteome of Shewanella oneidensis MR-1 with new affinity labeling probes

The membrane proteome plays a critical role in electron transport processes in Shewanella oneidensis MR-1, a bacterial organism that has great potential for bioremediation. Biotinylation of intact cells with subsequent affinity-enrichment has become a useful tool for characterization of the membrane proteome. As opposed to these commonly used, water-soluble commercial reagents, we here introduce a family of hydrophobic, cell-permeable affinity probes for extensive labeling and detection of membrane proteins. When applied to S. oneidensis cells, all three new chemical probes allowed identification of a substantial proportion of membrane proteins from total cell lysate without the use of specific membrane isolation method. From a total of 410 unique proteins identified, approximately 42% are cell envelope proteins that include outer membrane, periplasmic, and inner membrane proteins. This report demonstrates the first application of this intact cell biotinylation method to S. oneidensis and presents the results of many identified proteins that are involved in metal reduction processes. As a general labeling method, all chemical probes we introduced in this study can be extended to other organisms or cell types and will help expedite the characterization of membrane proteomes.     

Development of a Robust Flow Cytometric Assay for Determining Numbers of Viable Bacteria

Several fluorescent probes were evaluated as indicators of bacterial viability by flow cytometry. The probes monitor a number of biological factors that are altered during loss of viability. The factors include alterations in membrane permeability, monitored by using fluorogenic substrates and fluorescent intercalating dyes such as propidium iodide, and changes in membrane potential, monitored by using fluorescent cationic and anionic potential-sensitive probes. Of the fluorescent reagents examined, the fluorescent anionic membrane potential probe bis-(1,3-dibutylbarbituric acid)trimethine oxonol [DiBAC(inf4)(3)] proved the best candidate for use as a general robust viability marker and is a promising choice for use in high-throughput assays. With this probe, live and dead cells within a population can be identified and counted 10 min after sampling. There was a close correlation between viable counts determined by flow cytometry and by standard CFU assays for samples of untreated cells. The results indicate that flow cytometry is a sensitive analytical technique that can rapidly monitor physiological changes of individual microorganisms as a result of external perturbations. The membrane potential probe DiBAC(inf4)(3) provided a robust flow cytometric indicator for bacterial cell viability.     

A DIE responsive NIR-fluorescent cell membrane probe

It is challenging to achieve selective off to on modulation of the emissive state of a fluorophore within a complex and heterogeneous cellular environment. Herein we show that the dis-assembly of a non-fluorescent aggregate to produce individual fluorescent molecules, termed disaggregation induced emission (DIE), can be utilised to achieve this goal with an amphiphilic BF₂-azadipyrromethene (NIR-AZA) probe. Optical near-infrared properties of the NIR-AZA probe used in this study include absorption and emission maxima at 700 and 726 nm respectively when in the emissive non-aggregated state. Key to the success of the probe is the bis-sulfonic acid substitution of the NIR-AZA fluorophore, which is atypical for membrane probes as it does not contain zwitterionic lipid substituents. The aggregation/disaggregation properties of the NIR-fluorophore have been investigated in model surfactant and synthetic liposomal systems and shown to be emissive responsive to both. Real-time live cell imaging experiments in HeLa Kyoto and MC3T3 cells showed a rapid switch on of emission specific to the plasma membrane of viable and apoptotic cells attributable to a disaggregation-induced emission of the probe. Image analysis software confirmed localisation of fluorescence to the plasma membrane. Cell membrane staining was also effective for formaldehyde fixed cells, with staining possible either before or after fixation. This study adds new and important findings to recent developments of DIE responsive probes and further applications of this controllable emission-switching event are anticipated.     

Advanced functional fluorescent probes for cell plasma membranes

Imaging the plasma membrane (PM) by fluorescence techniques using molecular fluorescent probes enable cell segmentation, studying membrane organization and dynamics, formation, and tracking of vesicles. Rational molecular design brings fluorescent PM probes to a new level, providing PM probes with new functions beyond basic PM staining and imaging. We herein review the latest advances in fluorescent PM probes for chemical and biophysical sensing as well as for super-resolution imaging.     

Rapid detection, identification, and enumeration of Escherichia coli cells in municipal water by chemiluminescent in situ hybridization

A new chemiluminescent in situ hybridization (CISH) method provides simultaneous detection, identification, and enumeration of culturable Escherichia coli cells in 100 ml of municipal water within one working day. Following filtration and 5 h of growth on tryptic soy agar at 35 degrees C, individual microcolonies of E. coli were detected directly on a 47-mm-diameter membrane filter using soybean peroxidase-labeled peptide nucleic acid (PNA) probes targeting a species-specific sequence in E. coli 16S rRNA. Within each microcolony, hybridized, peroxidase-labeled PNA probe and chemiluminescent substrate generated light which was subsequently captured on film. Thus, each spot of light represented one microcolony of E. coli. Following probe selection based on 16S ribosomal DNA (rDNA) sequence alignments and sample matrix interference, the sensitivity and specificity of the probe Eco16S07C were determined by dot hybridization to RNA of eight bacterial species. Only the rRNA of E. coli and Pseudomonas aeruginosa were detected by Eco16S07C with the latter mismatch hybridization being eliminated by a PNA blocker probe targeting P. aeruginosa 16S rRNA. The sensitivity and specificity for the detection of E. coli by PNA CISH were then determined using 8 E. coli strains and 17 other bacterial species, including closely related species. No bacterial strains other than E. coli and Shigella spp. were detected, which is in accordance with 16S rDNA sequence information. Furthermore, the enumeration of microcolonies of E. coli represented by spots of light correlated 92 to 95% with visible colonies following overnight incubation. PNA CISH employs traditional membrane filtration and culturing techniques while providing the added sensitivity and specificity of PNA probes in order to yield faster and more definitive results.     

Solid-phase polymerase chain reaction: applications for direct detection of enteric pathogens in waters.

The techniques in current use for detection of pathogens in environmental samples are restricted to those organisms whose replication in either culture media or cell culture is feasible. These methods lack the selectivity and sensitivity necessary for their unequivocal detection and identification. We have developed an assay for the detection of bacterial cells in large volumes of water. Low concentrations of cells containing target sequences were concentrated on membrane filters and were subjected to amplification directly using a stepwise polymerase chain reaction. This procedure, together with nucleic acid probes, has enhanced the limit of detection to the level of a single bacterial cell. This technique could be used for the detection of any bacteria or virus in water or air.     

Distinction between changes in membrane potential and surface charge upon chemotactic stimulation of Escherichia coli.

Galactose and other chemotactic attractants have been shown to trigger an apparent hyperpolarization in Escherichia coli (Eisenbach, M., 1982, Biochemistry, 21:6818-6825). The probe used to measure membrane potential in that study, tetraphenylphosphonium (TPP+), may respond also to surface-charge changes in the membrane. The distinction between true changes in membrane potential and changes in the surface charge of the membrane is crucial for the study of this phenomenon in bacterial chemotaxis. To distinguish between these parameters, we compared the response to galactose with different techniques: K+ distribution in the presence of valinomycin (measured with a K+-selective electrode), TPP+ distribution (measured with a TPP+-selective electrode) at different ionic strengths, absorbance changes of bis(3-phenyl-5-oxoisoxazol-4-yl)pentamethineoxonol (oxonol V), and fluorescence changes of three probes with different mechanisms of response. All the techniques revealed stimulation by galactose of transient hyperpolarization, of comparable magnitude. This indicates the involvement of ion currents rather than alterations of local surface properties.     

Lipid domains in bacterial membranes

The recent development of specific probes for lipid molecules has led to the discovery of lipid domains in bacterial membranes, that is, of membrane areas differing in lipid composition. A view of the membrane as a patchwork is replacing the assumption of lipid homogeneity inherent in the fluid mosaic model of Singer and Nicolson (Science 1972, 175: 720–731). If thus membranes have complex lipid structure, questions arise about how it is generated and maintained, and what its function might be. How do lipid domains relate to the functionally distinct regions in bacterial cells as they are identified by protein localization techniques? This review assesses the current knowledge on the existence of cardiolipin (CL) and phosphatidylethanolamine (PE) domains in bacterial cell membranes and on the specific cellular localization of certain membrane proteins, which include phospholipid synthases, and discusses possible mechanisms, both chemical and physiological, for the formation of the lipid domains. We propose that bacterial membranes contain a mosaic of microdomains of CL and PE, which are to a significant extent self‐assembled according to their respective intrinsic chemical characteristics. We extend the discussion to the possible relevance of the domains to specific cellular processes, including cell division and sporulation.     

Volume recovery, surface properties and membrane integrity of Lactobacillus delbrueckii subsp. bulgaricus dehydrated in the presence of trehalose or sucrose

AIMS: Although the practical importance of adding sugars before drying is well known, the mechanism of protection of bacteria by sugars is not clear. The response of the dehydrated micro-organisms to rehydration is analysed in terms of structural and functional changes, and correlated with their potentiality to grow in rich media. These aspects are related with the membrane integrity and the metabolic state of the rehydrated bacteria, measured by means of surface properties and permeability. To attain this objective, Lactobacillus delbrueckii subsp. bulgaricus was dehydrated in the presence and in the absence of sucrose and trehalose. The bacterial response upon rehydration was investigated by determining: (i) the lag time of the bacterial growing in rich media, (ii) the restoration of the surface properties and the cellular volume and (iii) the membrane integrity. METHODS AND RESULTS: Lactobacillus delbrueckii subsp. bulgaricus was grown in MRS at 37 degrees C overnight [De Man et al. (1960)J Appl Bacteriol 23, 130] and then dehydrated for 10, 20 and 30 min at 70 degrees C in a vacuum centrifuge. The lag time of micro-organisms was determined by optical density changes after rehydration. The surface properties were determined by measuring the zeta potential of the bacteria suspended in aqueous solution. The cellular volume recovery was measured, after stabilization in saline solution, by light scattering and by the haematocrit method [Alemohammad and Knowles (1974)J Gen Microbiol 82, 125]. Finally, the membrane integrity has been determined by using specific fluorescent probes [SYTO 9 and propidium iodide, (PI)] that bind differentially depending on the integrity of the bacterial membrane. The lag time of Lact. delbrueckii subsp bulgaricus, dehydrated by heat in the presence of sucrose or trehalose and after that rehydrated, was significantly shortened, when compared with that obtained for bacteria dried in the absence of sugars. In these conditions, trehalose and sucrose maintained the zeta potential and the cell volume close to the control (nondried) cells. However, the membrane integrity, measured with fluorescent probes, was maintained only when cells were dehydrated for 10 min in the presence of sugars. For larger times of dehydration, the membrane integrity was not preserved, even in the presence of sugars. CONCLUSIONS: When the micro-organisms are dehydrated in the absence of protectants, the membrane damage occurs with a decrease in the absolute value of the zeta potential and a decrease in the cellular volume recovered after rehydration. In contrast, when the zeta potential and the cellular volume are restored after rehydration to that corresponding to nondried cells, the micro-organisms are able to recover and grow with a reduced lag time. This can only be achieved when the dehydration is carried out in the presence of sugars. At short dehydration times, the response is associated with the preservation of the membrane integrity. However, for longer times of dehydration the zeta potential and volume recovery occurs in the presence of sugars in spite of a severe damage at membrane level. In this condition, cells are also recovered. In conclusion, to predict the ability of growing after dehydration, other bacterial structural parameters besides membrane integrity, such as zeta potential and cellular volume, should be taken into account. SIGNIFICANCE AND IMPACT OF THE STUDY: The correlation of the lag time with the surface and permeability properties is of practical importance because the correlation of these two parameters with cell viability, allow to determine the potential bacterial capacity to grow in a rich medium after the preservation procedure, without necessity of performing a kinetic curve of growth, which is certainly time-consuming.     

Applying Multiphoton Imaging to the Study of Membrane Dynamics in Living Cells

The endomembrane system of a cell is a highly dynamic, ephemeral structure that is difficult to visualize. Reconstructions from sections of fixed material can provide high-resolution information on intercellular membrane architecture, but such techniques are fraught with artifacts and are of little help in understanding the dynamics of intracellular membrane traffic. Recently, the availability of fluorescent membrane probes and the development of techniques for optically sectioning intact specimens have allowed glimpses of membrane dynamics to be visualized in living tissue. In this review we discuss the potential of a new optical sectioning technique, multiphoton imaging, for visualizing membrane dynamics in living cells. Multiphoton microscopy offers an unparalleled ability to obtain images from deep within specimens while minimizing the effects of phototoxicity.     

Electron Spin Resonance and Fluorescence Observations on Erythrocytes,Erythrocyte Membranes, 13762 Mat-A Ascites Adenocarcinoma Cells,and Their Membranes,Effects of Membrane Perturbations

Membranes from erythrocytes or MAT-A 13762 tumor cells were labeled with the fatty acid spin probe I(5,10) or ANS and examined by spin resonance (ESR) or fluorescence polarization in the presence or absence of the perturbants EDTA, trypsin, glutaraldehyde, and dodecylsulfate. Extraction of cell membranes with hypotonic EDTA produced fragments in which the order parameters and fluorescence polarization values increased. Fluorescence polarization values using membranes labeled with diphenylhexatriene showed an apparent increase in membrane fluidity. A large portion of both I(5,10) and both fluorescence probes coextract with the peripheral membrane proteins in both membrane systems. Paramagnetic quenching of tryptophan fluorescence with I(5,10) and the spectral characteristics of ANS in these membranes indicated further that significant amounts of both probes bind either at or near the protein-lipid interface or directly to protein moieties. Trypsinization of cell membranes, which preferentially cleaves the large cytoskeletal proteins, fragmented the membranes and reduced the ESR order parameter. Glutaraldehyde immobilized I(5,10) in both types of membranes. These studies suggest that the association of cytoskeletal proteins with the membrane does not have any pronounced, consistent effect on biophysical properties of the bilayer.

Attempts to apply these same probes to studies of the plasma membranes of intact cells were not successful because of the diffusion of the probes into the cells. These studies also point out some difficulties in using probe-group techniques to determine the nature of changes in bilayer structural parameters and emphasize the need for a better understanding of probe-group localization and behavior in such studies.     

Expression of epidermal growth factor in the rat kidney. An immunocytochemical and in situ hybridization study

The renal localization and the site of synthesis of epidermal growth factor (EGF) were investigated in the rat kidney by immunohistochemistry and in situ hybridization techniques. EGF was localized in the cells of the thick ascending limb of Henle (TAL) and distal convoluted tubule (DCT). At the ultrastructural level, EGF immunoreactivity was distributed on the apical membrane and trans-Golgi complex of the TAL and DCT cells. These segments of the rat nephron also hybridized to prepro-EGF cRNA probes in a specific manner, indicating that TAL and DCT are the sites of EGF synthesis in the rat kidney.     

Efficient and Innocuous Live‐Cell Delivery: Making Membrane Barriers Disappear to Enable Cellular Biochemistry

The confluence of protein engineering techniques and delivery protocols are providing new opportunities in cell biology. In particular, techniques that render the membrane of cells transiently permeable make the introduction of nongenetically encodable macromolecular probes into cells possible. This, in turn, can enable the monitoring of intracellular processes in ways that can be both precise and quantitative, ushering an area that one may envision as cellular biochemistry. Herein, the author reviews pioneering examples of such new cell‐based assays, provides evidence that challenges the paradigm that cell penetration is a necessarily damaging and stressful event for cells, and highlights some of the challenges that should be addressed to fully unlock the potential of this nascent field.