From Metabolomics to Fluxomics: A Computational Procedure to Translate Metabolite Profiles into Metabolic Fluxes

We describe a believed-novel procedure for translating metabolite profiles (metabolome) into the set of metabolic fluxes (fluxome) from which they originated. Methodologically, computational modeling is integrated with an analytical platform comprising linear optimization, continuation and dynamic analyses, and metabolic control. The procedure was tested with metabolite profiles obtained from ex vivo mice Langendorff-heart preparations perfused with glucose. The metabolic profiles were analyzed using a detailed kinetic model of the glucose catabolic pathways including glycolysis, pentose phosphate (PP), glycogenolysis, and polyols to translate the glucose metabolome of the heart into the fluxome. After optimization, the ability of the model to simulate the initial metabolite profile was confirmed, and metabolic fluxes as well as the structure of control and regulation of the glucose catabolic network could be calculated. We show that the step catalyzed by phosphofructokinase together with ATP demand and glycogenolysis exert the highest control on the glycolytic flux. The negative flux control exerted by phosphofructokinase on the PP and polyol pathways revealed that the extent of glycolytic flux directly affects flux redirection through these pathways, i.e., the higher the glycolytic flux the lower the PP and polyols. This believed-novel methodological approach represents a step forward that may help in designing therapeutic strategies targeted to diagnose, prevent, and treat metabolic diseases.     

Quantifying Cell-Surface Biomarker Expression in Thick Tissues with Ratiometric Three-Dimensional Microscopy

The burgeoning fields of in vivo three-dimensional (3D) microscopy and endomicroscopy, as well as ex vivo tissue cytometry have introduced new challenges for tissue preparation and staining with exogenous molecular contrast agents. These challenges include effective delivery of the agents, and once delivered, distinguishing between bound verses unbound molecular probes. If applied topically, there are additional issues with rinsing off unbound probe, which can be nonuniform and inefficient in thick tissues, thus leading to ambiguous contrast and a large nonspecific background that may obscure molecule-specific staining. Therefore, we have developed a ratiometric 3D microscopy scheme that not only reduces the effects of nonspecific sources of contrast, but also enables quantification of the relative binding affinity of imaging probes to their biomarker targets. Here we demonstrate this ratiometric approach by simultaneously imaging a HER2/neu (erbB2)-targeted monoclonal antibody labeled with one fluorophore and an isotype-matched negative control antibody labeled with another fluorophore. By taking a pixel-by-pixel calibrated ratio between the signals from each fluorescent image channel, accurate quantification of specific versus nonspecific binding affinity is achieved with cultured cells, yielding data that are in agreement with analyses via flow cytometry. We also demonstrate quantitative 3D microscopic imaging of biomarker expression in tissue models and in thick human biopsy samples of normal, HER2-negative, and HER2-positive breast tumors. This strategy enables rapid, quantitative, and unambiguous volumetric microscopy of biomarker expression in thick tissues, including whole biopsies, and will enable real-time optical assessment of disease markers in the living body.     

Ratiometric Imaging of Extracellular pH in Bacterial Biofilms with C-SNARF-4

pH in the extracellular matrix of bacterial biofilms is of central importance for microbial metabolism. Biofilms possess a complex three-dimensional architecture characterized by chemically different microenvironments in close proximity. For decades, pH measurements in biofilms have been limited to monitoring bulk pH with electrodes. Although pH microelectrodes with a better spatial resolution have been developed, they do not permit the monitoring of horizontal pH gradients in biofilms in real time. Quantitative fluorescence microscopy can overcome these problems, but none of the hitherto employed methods differentiated accurately between extracellular and intracellular microbial pH and visualized extracellular pH in all areas of the biofilms. Here, we developed a method to reliably monitor extracellular biofilm pH microscopically with the ratiometric pH-sensitive dye C-SNARF-4, choosing dental biofilms as an example. Fluorescent emissions of C-SNARF-4 can be used to calculate extracellular pH irrespective of the dye concentration. We showed that at pH values of <6, C-SNARF-4 stained 15 bacterial species frequently isolated from dental biofilm and visualized the entire bacterial biomass in in vivo-grown dental biofilms with unknown species composition. We then employed digital image analysis to remove the bacterial biomass from the microscopic images and adequately calculate extracellular pH values. As a proof of concept, we monitored the extracellular pH drop in in vivo-grown dental biofilms fermenting glucose. The combination of pH ratiometry with C-SNARF-4 and digital image analysis allows the accurate monitoring of extracellular pH in bacterial biofilms in three dimensions in real time and represents a significant improvement to previously employed methods of biofilm pH measurement.     

Ratiometric pH measurements using LysoSensor DND-192

A method for the ratiometric pH sensing using LysoSensor DND-192 is presented in this paper. It works in the physiological pH range. It is based on the use of two fluorophores which differ significantly in their lifetimes. As the discrimination of their emissions is performed through two different frequencies, this method can allow significant overlap of the emission spectra. A simple long-pass filter, or a combination of long- and short-pass filters, was used instead of narrow-bandpass devices. Importantly, the measurements were carried out under strong ambient light. The method could be used in a wide variety of applications, such as intracellular measurements, microscopy, bioprocess monitoring, etc.     

Staining Bacteria and Yeasts with Acid Dyes

Various acid dyes prove satisfactory for the routine staining of bacteria. Those used are acid fuchsin, anilin blue w. s., fast acid blue R, fast green FCF, light green, orseilline BB, erythrosin, phloxine and rose bengal. Acid fuchsin, fast green, anilin blue, and orseilline are especially recommended. Phenolic solutions of the dyes, acidified with acetic acid, with the addition of ferric chloride to those containing acid fuchsin, anilin blue, fast green or light green, are used. Procedures are given in detail for staining or demonstrating vegetative cells, resting and germinating spores, capsules, sheaths and glycogen in bacteria; germinating and conjugating spores of yeast; and for counterstaining after acid fast or Gram staining. The principal advantages of using acid dyes are better differentiation, and less tendency for slime amd debris to take the dye.     

Vital Staining with Two Dis-Azo Textile Dyes

Subcutaneous injections of 0.25% saline solutions of two dis-azo textile dyes, calcodur pink 2BL, C. I. 353, also known as benzo fast pink 2BL and amidine fast rose 2BL, and a blue dye, dianil blue G, C. I. 508, were made on alternate days on albino rats for one week. The blue dye is closely similar to Niagara blue 4B, C. I. 520, and dianil blue R, C. I. 465. Staining reactions were much like those of other vital blue disazo dyes. Although the pink dye exhibited a similar staining pattern, there were notable differences. The tissues of most glands were stained pink or red. Nuclei of the tubular epithelial cells of the kidney contained red granules as did the cytoplasm of the Kupfer cells. Most unusual was the bright red staining of the elastica interna of medium and large sized arteries.     

Fluorescence Lifetime Imaging of Membrane Lipid Order with a Ratiometric Fluorescent Probe

To monitor the lateral segregation of lipids into liquid-ordered (Lo) and -disordered (Ld) phases in lipid membranes, environment-sensitive dyes that partition in both phases but stain them differently have been developed. Of particular interest is the dual-color F2N12S probe, which can discriminate the two phases through the ratio of its two emission bands. These bands are associated with the normal (N^∗) and tautomer (T^∗) excited-state species that result from an excited-state intramolecular proton transfer. In this work, we investigated the potency of the time-resolved fluorescence parameters of F2N12S to discriminate lipid phases in model and cell membranes. Both the long and mean lifetime values of the T^∗ form of F2N12S were found to differ by twofold between Ld and Lo phases as a result of the restriction in the relative motions of the two aromatic moieties of F2N12S imposed by the highly packed Lo phase. This differed from the changes in the ratio of the two emission bands between the two phases, which mainly resulted from the decreased hydration of the N^∗ form in the Lo phase. Importantly, the strong difference in lifetimes between the two phases was preserved when cholesterol was added to the Ld phase. The two phases could be imaged with high contrast by fluorescence lifetime imaging microscopy (FLIM) on giant unilamellar vesicles. FLIM images of F2N12S-labeled live HeLa cells confirmed that the plasma membrane was mainly in the Lo-like phase. Furthermore, the two phases were found to be homogeneously distributed all over the plasma membrane, indicating that they are highly mixed at the spatiotemporal resolution of the FLIM setup. Finally, FLIM could also be used to sensitively monitor the change in lipid phase upon cholesterol depletion and apoptosis.     

Measuring Phagosome pH by Ratiometric Fluorescence Microscopy

Phagocytosis is a fundamental process through which innate immune cells engulf bacteria, apoptotic cells or other foreign particles in order to kill or neutralize the ingested material, or to present it as antigens and initiate adaptive immune responses. The pH of phagosomes is a critical parameter regulating fission or fusion with endomembranes and activation of proteolytic enzymes, events that allow the phagocytic vacuole to mature into a degradative organelle. In addition, translocation of H⁺ is required for the production of high levels of reactive oxygen species (ROS), which are essential for efficient killing and signaling to other host tissues. Many intracellular pathogens subvert phagocytic killing by limiting phagosomal acidification, highlighting the importance of pH in phagosome biology. Here we describe a ratiometric method for measuring phagosomal pH in neutrophils using fluorescein isothiocyanate (FITC)-labeled zymosan as phagocytic targets, and live-cell imaging. The assay is based on the fluorescence properties of FITC, which is quenched by acidic pH when excited at 490 nm but not when excited at 440 nm, allowing quantification of a pH-dependent ratio, rather than absolute fluorescence, of a single dye. A detailed protocol for performing in situ dye calibration and conversion of ratio to real pH values is also provided. Single-dye ratiometric methods are generally considered superior to single wavelength or dual-dye pseudo-ratiometric protocols, as they are less sensitive to perturbations such as bleaching, focus changes, laser variations, and uneven labeling, which distort the measured signal. This method can be easily modified to measure pH in other phagocytic cell types, and zymosan can be replaced by any other amine-containing particle, from inert beads to living microorganisms. Finally, this method can be adapted to make use of other fluorescent probes sensitive to different pH ranges or other phagosomal activities, making it a generalized protocol for the functional imaging of phagosomes.     

Metabolite profiling of CHO cells with different growth characteristics

Mammalian cell cultures are the predominant system for the production of recombinant proteins requiring post-translational modifications. As protein yields are a function of growth performance (among others), and performance varies greatly between culture medium (e.g., different growth rates and peak cell densities), an understanding of the biological mechanisms underpinning this variability would facilitate rational medium and process optimization, increasing product yields, and reducing costs. We employed a metabolomics approach to analyze differences in metabolite concentrations of CHO cells cultivated in three different media exhibiting different growth rates and maximum viable cell densities. Analysis of intra- and extracellular metabolite concentrations over the course of the cultures using a combination of HPLC and GC-MS, readily detected medium specific and time dependent changes. Using multivariate data analysis, we identified a range of metabolites correlating with growth rate, illustrating how metabolomics can be used to relate gross phenotypic changes to the fine details of cellular metabolism.     

The Mechanism of Stain Action with Basic Dyes

The chemical theory of staining is discussed in the light of recent discoveries respecting the mechanism of the reaction of basic dyes with substances of an acid character. It is pointed out that staining may result through the formation of addition products as well as through the formation of dye salts.     

The Mechanism of Stain Action with Basic Dyes

The chemical theory of staining is discussed in the light of recent discoveries respecting the mechanism of the reaction of basic dyes with substances of an acid character. It is pointed out that staining may result through the formation of addition products as well as through the formation of dye salts.     

Compatibility of Photoactive Dyes with Insect Biocontrol Agents

Integrated pest management (IPM) programmes often look for more specific ways to control pests. Biological control agents, such as the bacterium, Bacillus thuringiensis Berliner, and the fungus, Beauveria bassiana (Balsamo) Vuillemin, can control insects with minimal disturbance to the environment because of their host specificity and short half-lives. Often these agents alone cannot prevent yield loss or are too expensive. This study looked at the in vitro combination of these agents and photoactive dyes, especially phloxine B (red dye D&C 28), a Food and Drug Administration approved dye, with the intent to provide better insect control. Photoactive dyes are being tested for the control of many pest insects. Phloxine B and related xanthene dyes, eosin y, fluorescein and rose bengal inhibited the growth of both B. thuringiensis and B. bassiana . Phloxine B was the most inhibitory and fluorescein the least inhibitory dye for both microbes. The magnitude of inhibition increased with increasing concentration of dye and light intensity. Therefore, an adverse effect on the field performance of these biological control agents in combination with xanthene dyes would be expected.     

Metabolite changes associated with heat shocked avian fibroblast mitochondira

A previous report from our laboratory (Collier et al 1993) showed that the elongated tubules of mitochondria in the cytoplasm of cultured chicken embryo fibroblasts collpased to irregularly shaped structures surrounding the nuclear membrane after a 1 h heat shock treatment. The normal mitochondiral morphology reappeared upon removal of then thermal stress. We have now determined that several changes occured in mitochondrial-related metabolites under these same heat shock and recovery conditions. Among these were significant decreases in the levels of fumarate and malate and increases in the amounts of aspartate and glutamate. In contrast, other intermediates of the tri-carboxylic acid cycle were unaltered as were levels of ATP and phosphocreatine. The changes observed might result from heat shock-induced changes in enzyme activities of the mitochondria or from alterations in the membrane-embedded specialized carrier proteins that transport metabolites between cytosol and mitochondria, from a disorganization of the electron-transport system normally coupled to oxidative metabolism. The rapid recovery, however, suggested that these changes were transient and readily reversible.     

Novel Precursors of Fluorescent Dyes. 1. Interaction of the Dyes with Model Phospholipid in Monolayers

Photoactivated (“caged”) fluorescent dyes are modern tools for structure and function studies of cell membranes and subcellular organelles. Recently synthesized precursors of rhodamine fluorescent dyes (abbreviations PFD813 and PFD814) important for microscopic probing of biological objects have been studied in solution. In order to characterize the behavior at interfaces, monolayers of PFD813 and PFD814 on water have been formed and investigated. The interactions of these precursors with the biomembrane component dimyristoylphosphatidylethanolamine in monolayers at the air–water interface and after transfer to glass plates have been studied by measuring monolayer parameters and spectroscopic properties before and after photo-chemical formation of the fluorescent rhodamine dyes Rho813 and Rho814, respectively.     

The Detection of Tension Wood with Fluorescent Dyes

Sections of a thickness of 15 β cut from unfixed material by means of a freezing microtome were treated for 1 hr with 0.2% aqueous solutions of a number of fluorochromes. Under normal microscopical conditions no uniform staining pattern could be observed. With the aid of an ultraviolet microscope, however, one type of fluorescence pattern became apparent. In all cases observed the thickened gelatinous secondary cell walls of tension wood showed a remarkable lack of fluorescence; this in marked contrast with a very distinct fluorescence exhibited by the primary cell wall and by both primary and secondary cell walls of normal wood.