Discrimination of viable and non-viable cells using propidium iodide in two color immunofluorescence

The relative ease with which a flow cytometer can perform simultaneous two color immunofluorescence to examine subpopulations of lymphoid cells has been well documented. Thus, flow cytometers equipped with only a single argon laser can be used to delineate various cell types by exciting both fluorescein- and phycoerythrin-conjugated antibodies to cell surface antigens. One problem that remains, however, is the artifactual staining of dead cells and clumps, which cannot be distinguished from viable cells on the basis of cell surface staining characteristics. We describe a method for simultaneous two color analysis or sorting of viable leukocytes which requires only a single laser. The method utilizes propidium iodide, which stains dead cells and thereby excludes such cells from the analysis. Using this method, as many as four viable cell types have been simultaneously analyzed in a single sample.     

A comparison of TO-PRO-1 iodide and 5-CFDA-AM staining methods for assessing viability of planktonic algae with epifluorescence microscopy

Two fluorescent dyes, TO-PRO-1 iodide and 5-CFDA-AM, were evaluated for LIVE/DEAD assessment of unicellular marine algae Brachiomonas submarina and Tetraselmis suecica. Epifluorescence microscopy was used to estimate cell viability in predetermined mixtures of viable and non-viable algal cells and validated using microplate growth assay as reference measurements. On average, 5-CFDA-AM underestimated live cell abundance by ~25% compared with viability estimated by the growth assay, whereas TO-PRO-1 iodide provided accurate viability estimates. Furthermore, viability estimates based on staining with TO-PRO-1 iodide were not affected by a storage period of up to one month in -80°C, making the assay a good candidate for routine assessment of phytoplankton populations in field and laboratory studies.     

Improved mean estimation and its application to diagonal discriminant analysis

MOTIVATION: High-dimensional data such as microarrays have created new challenges to traditional statistical methods. One such example is on class prediction with high-dimension, low-sample size data. Due to the small sample size, the sample mean estimates are usually unreliable. As a consequence, the performance of the class prediction methods using the sample mean may also be unsatisfactory. To obtain more accurate estimation of parameters some statistical methods, such as regularizations through shrinkage, are often desired. RESULTS: In this article, we investigate the family of shrinkage estimators for the mean value under the quadratic loss function. The optimal shrinkage parameter is proposed under the scenario when the sample size is fixed and the dimension is large. We then construct a shrinkage-based diagonal discriminant rule by replacing the sample mean by the proposed shrinkage mean. Finally, we demonstrate via simulation studies and real data analysis that the proposed shrinkage-based rule outperforms its original competitor in a wide range of settings.     

Assessment of Sarcocystis neurona sporocyst viability and differentiation between viable and nonviable sporocysts using propidium iodide stain

Sarcocystis neurona has become recognized as the major causative agent of equine protozoal myeloencephalitis (EPM) in the Americas. At least 3 pathogenic species of Sarcocystis, including S. neurona, can be isolated from opossums. Methods are needed to ascertain whether these isolates are viable and capable of causing infections. In this study, the nuclear stain propidium iodide (PI) was used to differentiate between live (viable) and heat-killed (nonviable) S. neurona sporocysts. PI was excluded by live sporocysts but penetrated compromised sporocyst membrane and stained sporozoite nuclei of dead sporocysts. After live and dead sporocysts were mixed at various ratios, the number of unstained sporocysts detected after the staining procedure correlated significantly (r2 = 0.9978) with the expected numbers of live sporocysts. Sporocyst mixtures were also assayed for in vitro excystation and development in tissue cultures. The correlation between the percentage of plaques formed in tissue cultures and the percentage of expected infectious (live) sporocysts in each mixture was r2 = 0.6712. By analysis of variance, no statistically significant difference was measured between the percentage of viable sporocysts and the percentage of infectious sporocysts (P = 0.3902) in each mixture. In addition, there was evidence of a relation between PI impermeability of sporocysts and animal infectivity. These results suggest that the PI dye-exclusion technique can be a useful tool in identifying viability and potential infectivity of S. neurona sporocysts and in differentiating between viable and nonviable sporocysts.     

Effects of potassium iodide on the growth and metabolite accumulation of two planktonic diatoms

In this study the effects of potassium iodide on the growth and metabolite accumulation of Nitzschia closterium (Ehr.) W. Smith and Phaedactylum tricornutum Bolin were investigated to assess its possible application to the mass culture of the two diatoms in open environment, extensive systems. The results indicated that supplementation of potassium iodide at a concentration of 1000 mg L⁻¹ resulted in a reduction of the induction phase in cultures of N. closterium and P. tricornutum and led to an increase in the accumulation of biomass and extracellular polymeric substances. Conversely, the addition of potassium iodide, at all concentrations tested, showed no obvious effect on the fatty acid profiles of the two diatoms, particularly in the content of eicosapentaenoic and decosahexaenoic acid. Potassium iodide was also found to inhibit the growth of Dunaliella salina, Cryptomonas sp. and Chlorella sp. at minimum inhibitory concentrations of 356.8, 475.9 and 696.2 mg L⁻¹, respectively. It also inhibited bacteria, including species isolated from the two diatom cultures, at a minimum concentration of 400 mg L⁻¹. These results suggest that potassium iodide is an effective agent for inhibiting the proliferation of certain flagellate and non-flagellate algae, and bacteria, thus forming a favorable environment for diatoms to proliferate and consequently improving accumulation of biomass and EPS. These properties of potassium iodide provide a possible solution for preventing contamination from flagellate and non-flagellate algae in mass culture of the two diatoms without causing significant changes in their fatty acid composition.     

HPLC analysis of tetrahydrobiopterin and its pteridine derivatives using sequential electrochemical and fluorimetric detection: application to tetrahydrobiopterin autoxidation and chemical oxidation

Tetrahydrobiopterin (BH(4)) is an essential cofactor of endothelial nitric oxide (NO) synthase and when depleted, endothelial dysfunction results with decreased production of NO. BH(4) is also an anti-oxidant being a good "scavenger" of oxidative species. NADPH oxidase, xanthine oxidase, and mitochondrial enzymes producing reactive oxygen species (ROS) can induce elevated oxidant stress and cause BH(4) oxidation and subsequent decrease in NO production and bioavailability. In order to define the process of ROS-mediated BH(4) degradation, a sensitive method for monitoring pteridine redox-state changes is required. Considering that the conventional fluorescence method is an indirect method requiring conversion of all pteridines to oxidized forms, it would be beneficial to use a rapid quantitative assay for the individual detection of BH(4) and its related pteridine metabolites. To study, in detail, the BH(4) oxidative pathways, a rapid direct sensitive HPLC assay of BH(4) and its pteridine derivatives was adapted using sequential electrochemical and fluorimetric detection. We examined BH(4) autoxidation, hydrogen peroxide- and superoxide-driven oxidation, and Fenton reaction hydroxyl radical-driven BH(4) transformation. We demonstrate that the formation of the primary two-electron oxidation product, dihydrobiopterin (BH(2)), predominates with oxygen-induced BH(4) autoxidation and superoxide-catalyzed oxidation, while the irreversible metabolites, pterin and dihydroxanthopterin (XH(2)), are largely produced during hydroxyl radical-driven BH(4) oxidation.     

Stochastic compartmental modeling and parameter estimation with application to cancer treatment follow-up studies

In this paper we use marginal probabilities to derive expressions for the means, variances and covariances ofm-compartment systems. We also present an efficient algorithm for the estimation of the parameters of the system using time series data when measurements are available fromk of them compartments. An application of the analysis and parameter estimation procedure for a model representing the results of a cancer treatment follow-up study is given. Supported in part by NSF Grant Number DCR74-17282.     

Discrimination of viable and dead Vibrio vulnificus after refrigerated and frozen storage using EMA, sodium deoxycholate and real-time PCR

The effect of refrigerated and frozen storage on the viability of Vibrio vulnificus was evaluated using cell suspensions (1 × 10⁸ CFU/ml). Ethidium bromide monoazide (EMA) was utilized to selectively allow real-time (Rti) PCR amplification of target DNA from viable but not dead cells. Bacterial survivors from the EMA Rti-PCR were evaluated by comparison with the plate count assay following different temperature exposures (− 20 and 4 °C) every 24 h for 72 h. The log CFU values from the EMA Rti-PCR assays were erroneously higher than that from plate counts. DNA amplification was not completely suppressed by EMA treatment of low temperature destroyed cells suggesting that membrane damage was not sufficient to allow effective EMA penetration into the cells. The optimal concentration of sodium deoxycholate (SD) was also determined to enhance discrimination of viable and dead cells following exposure of cells to low temperatures. The use of 0.01% or less of SD did not inhibit the Rti-PCR amplification derived from viable bacterial cells. A rapid decrease of the log CFU was observed with cell suspensions subjected to frozen storage and a slow decline in the log CFU occurred at 4 °C. The combination of SD and EMA treatments applied to cells of V. vulnificus held at − 20 °C and 4 °C resulted in a high level of correlation between the log of CFU (plate counts) and the log of the number of viable cells determined from SD+EMA Rti-PCR.     

Relevance of Cryptosporidium parvum hsp70 mRNA amplification as a tool to discriminate between viable and dead oocysts

Two mRNA extraction methods were compared in this study to clarify the discrepancies found between authors regarding the presence of mRNA in inactivated Cryptosporidium parvum oocysts. Cryptosporidium parvum heat shock protein 70 (hsp70) mRNA extraction was performed by using oligo(dT)20-labeled magnetic beads or by incubating oocyst lysates with DNase I. Significant differences in mRNA recovery rates between these 2 techniques were observed when working on inactivated oocysts. We consistently detected hsp70 mRNA in oocysts heated at 60 C for 30 min and oocysts incubated in 10% formalin for 2 hr when using DNase I in the mRNA extraction procedure. In contrast, no mRNA was detected in such oocysts when magnetic beads were used for the mRNA extraction. The selective capture of long poly-A tail mRNA, when using oligo(dT)20-labeled magnetic beads, is proposed in this paper for explaining the discrepancies observed between the two mRNA extraction methods compared in this study. DNA decay in inactivated and aging oocysts makes quantitative polymerase chain reaction a potential alternative technique for assessing C. parvum oocyst viability status in environmental samples.     

Assessment of the degree of electrochemical treatment of sewage using biotesting

Studies were conducted on estimation of the toxicity levels in various oxygen-containing chlorine compounds formed during electrochemical treatment of sewage by using a culture isolated from activated sludge purifying antibiotic production waste. It was shown that the products formed during electrocatalytic treatment of solutions (concentration of NaCl 1.5-5 g/l, pH 2.0-12.0, volumetric current density up to 10 A/l) were not toxic and stimulated the growth of P. fluorescens.     

Fluorometric determination of amyloid fibrils in vitro using the fluorescent dye, thioflavin T1

We used a fluorometric method to examine amyloid fibrils, in vitro. These fibrils in the case of both murine senile and secondary amyloidosis were purified to apparent homogeneity from the water-suspended fraction of the liver of senescence-accelerated mouse, using sucrose density ultracentrifugation, and then the following assays were performed. In the absence of amyloid fibrils, thioflavine T fluoresced faintly at the excitation and emission maxima of 350 and 438 nm, respectively. In the presence of amyloid fibrils, thioflavine T fluoresced brightly at the excitation and emission maxima of 450 and 482 nm, respectively, and the fluorescence change was linear from 0 to 2.0 micrograms/ml amyloid fibrils. This fluorescence was maximal around pH 9.0. Fluorescence intensity in the presence of a constant amount of amyloid fibrils reached a plateau with increase in the thioflavine T concentration. Normal high density lipoproteins which contain apo A-II, the precursor of amyloid fibrils in murine senile amyloidosis, and acute phase high density lipoproteins which contain serum amyloid protein A, the precursor of amyloid fibrils in secondary amyloidosis, showed little fluorescence. The fluorescence was considerably diminished when structure of the amyloid fibrils was disrupted by guanidine-HCl treatment. This method will be useful for the determination of amyloid fibrils in vitro.     

A microassay for the determination of iodide and its application to the measurement of the iodination of proteins and the catalytic activities of iodo compounds

A microassay system based on the effect of the catalytic Sandell-Kolthoff reaction of iodide on the oxidation of arsenic(III) by cerium(IV) was developed to measure iodine-containing compounds. This rapid assay uses small quantities of reagents, is suitable for use with a photometric microplate reader, can test many samples simultaneously, and eliminates problems associated with the use of radiolabeled compounds to measure iodination. It can detect picogram quantities of iodide. We report the use of this assay to measure the conjugation of an iodine-containing hapten (iodinated Bolton-Hunter reagent, IBHR) to ovalbumin and human serum albumin. It has proven to be excellent for studying the relative molar catalytic activity of the iodine-containing compounds IBHR, thyroxine, 4-iodophenol, and lithium 3,4-diiodosalicylate. The interference by azide on the assay was investigated.     

A parameter estimation technique for stochastic self-assembly systems and its application to human papillomavirus self-assembly

Virus capsid assembly has been a key model system for studies of complex self-assembly but it does pose some significant challenges for modeling studies. One important limitation is the difficulty of determining accurate rate parameters. The large size and rapid assembly of typical viruses make it infeasible to directly measure coat protein binding rates or deduce them from the relatively indirect experimental measures available. In this work, we develop a computational strategy to deduce coat-coat binding rate parameters for viral capsid assembly systems by fitting stochastic simulation trajectories to experimental measures of assembly progress. Our method combines quadratic response surface and quasi-gradient descent approximations to deal with the high computational cost of simulations, stochastic noise in simulation trajectories and limitations of the available experimental data. The approach is demonstrated on a light scattering trajectory for a human papillomavirus (HPV) in vitro assembly system, showing that the method can provide rate parameters that produce accurate curve fits and are in good concordance with prior analysis of the data. These fits provide an insight into potential assembly mechanisms of the in vitro system and give a basis for exploring how these mechanisms might vary between in vitro and in vivo assembly conditions.