Construction of a sensitive pyrogen-testing cell model by site-specific knock-in of multiple genes

A pyrogen test is crucial for evaluating the safety of drugs and medical equipment, especially those involved in injections. As existing pyrogen tests, including the rabbit pyrogen test, the limulus amoebocyte lysate (LAL) test and the monocyte activation test have limitations, development of new models for pyrogen testing is necessary. Here we develop a sensitive cell model for pyrogen test based on the lipopolysaccharides (LPS) signal pathway. TLR4, MD2, and CD14 play key roles in the LPS-mediated pyrogen reaction. We established a new TLR4/MD2/CD14-specific overexpressing knock-in cell model using the CRISPR/CAS9 technology and homologous recombination to detect LPS. Stimulation of our TLR4/CD14/MD2 knock-in cell line model with LPS leads to the release of the cytokines IL-6 and TNF-alpha, with a detection limit of 0.005 EU/ml, which is greatly lower than the lower limit of 0.015 EU/ml detected by the Tachypleus amebocyte lysate (TAL) assay.     

Growth of a single cell

A theory of growth of a cell which takes up nutrients by diffusion or active transport is discussed. The main conclusion is that the volume should grow at least as fast as the third power of the time. Existing experimental evidence is not a conclusive test of the theory, and further experiments to test it are proposed.     

Fluorometric test of cell membrane integrity

A fluorometric test for assessing cell membrane integrity of bone marrow, based on the use of fluorescein diacetate (FDA), is described. It is demonstrated that the amount of fluorescein extracted from the labeled cells is directly proportional to the number of intact cells and that this relationship is not affected by the presence of the dead cells. The experimental conditions required for the accuracy of this test are as follows: (1) During the incubation with FDA the number of cells should not exceed ca. 3 × 10⁶ cells/ml. (2) With the fluorescein concentration of 2 μg/ml, the incubation temperature should be within the range of 20 to 30 °C for a period of 10 to 20 min. (3) To prevent the loss of fluorescein by labeled cells during washing, the cells must be maintained at a temperature near 0 °C. (4) If the cells are contaminated by hemoglobin, an appropriate correction of the fluorescein readings must be made. Provided that the controls are appropriately adjusted, the accuracy of the test should not be affected by the presence of serum and/or of DMSO in the reaction medium. Other potential sources of error may be the enhanced loss of fluorescein due to the presence of albumin or platelet-absorbed serum and the possible activation of esterases before the FDA treatment. It is concluded that the results of this test should be interpreted in terms of relative changes of the collective cell membrane integrity rather than in terms of cell viability, and that these results may be more meaningful than those based on the visual assessment of either the FDA-labeled cells or of the cells subjected to the dye exclusion test.     

Metabolism-mediated neurotoxicity: the significance of genetically engineered cell lines and new three-dimensional cell cultures

Until now, no in vitro methods for determining neurotoxic effects, on Phase I and Phase II biotransformation-driven metabolite formation or for the evaluation of the metabolism-mediated hazard of a chemical, have been validated. The current test guidelines are based on studies in vivo, involving animals exposed to the test substance. Novel in vitro testing instead of animal testing is required by Directive 86/609/EEC. In the EU White Paper on a Strategy for a Future Chemicals Policy, which may result in up to 20,000 chemicals being screened for toxicity, the use of non-animal test methods is seen as essential and is encouraged. The aim of the present work was to demonstrate the significance of novel technologies, including the use of genetically engineered cell lines and three-dimensional cell culture techniques for direct application in the regulatory hazard-assessment process. Furthermore, attempts were made to make in vitro toxicity tests for specific applications more-readily available for inclusion in the chemical hazard-assessment process, by exploiting advances made in the life sciences.     

Evaluation of PREDISAFE,a cell kit for predicting eye irritancy of cosmetic raw materials and formulations

A cell kit named PREDISAFE based on the use of confluent rabbit fibroblastic cells has been designed to predict eye irritancy of cosmetic raw materials and formulations. The kit can be stored for a few days and/or shipped at room temperature. Cytotoxicity was estimated after 1 min or 15 min contact with test compounds using the neutral red release assay. For the 84 products tested, IC₅₀ values gave intervals similar to classes defined from the Draize test, i.e., mild, moderate, severe and extreme irritancy.Abbreviations IC₅₀ inhibiting concentration 50%     

Evaluation of cell membrane electropermeabilization by means of a nonpermeant cytotoxic agent

For the evaluation of cell membrane electropermeabilization, cells are usually exposed to electric pulses in the presence of propidium iodide, a fluorescent dye activated by binding to cellular DNA. The fraction of permeabilized cells is then determined using a flow cytometer. This widely established method has several drawbacks: (i) an arbitrary choice of minimum fluorescence intensity for characterization of permeabilized cells; (ii) the inability to detect cells disintegrated because of intense electropermeabilization; and (iii) false detection of cellular ghosts devoid of fluorescence because of leakage of DNA caused by electropermeabilization. Here, we present a simple and inexpensive method that eliminates these drawbacks. The method is based on the use of a cytotoxic agent that cannot permeate through an intact plasma membrane and thus leads to selective death of the electropermeabilized cells. The amount of nonpermeabilized cells is then determined by a suitable viability test. Bleomycin at a 5-nM concentration causes no statistically significant effect on cell survival in the absence of electric pulses, yet this concentration is sufficient for lethal toxicity in electropermeabilized cells. The amount of cells surviving the exposure relative to the control gives a reliable value of the fraction of nonpermeabilized cells.     

A model of cell cycle behavior dominated by kinetics of a pathway stimulated by growth factors

A modified version of a previously developed mathematical model [Obeyesekere et al., Cell Prolif. (1997)] of the G1-phase of the cell cycle is presented. This model describes the regulation of the G1-phase that includes the interactions of the nuclear proteins, RB, cyclin E, cyclin D, cdk2, cdk4 and E2F. The effects of the growth factors on cyclin D synthesis under saturated or unsaturated growth factor conditions are investigated based on this model. The solutions to this model (a system of nonlinear ordinary differential equations) are discussed with respect to existing experiments. Predictions based on mathematical analysis of this model are presented. In particular, results are presented on the existence of two stablesolutions, i. e., bistability within the G1-phase. It is shown that this bistability exists under unsaturated growth factor concentration levels. This phenomenon is very noticeable if the efficiency of the signal transduction, initiated by the growth factors leading to cyclin D synthesis, is low. The biological significance of this result as well as possible experimental designs to test these predictions are presented.     

A nonparametric approach to the discrimination of two cell populations

An approach to the statistical testing of differences between two cell populations the elements of which are characterized by multivariate data is described. The approach is based on the Fisher discriminant and the Kruskal-Wallis test. The method, which is sufficient but not necessary, makes no assumptions about the normality of the data or about the equality of the covariance matrices for each population.     

Strategy for selecting disposable bags for cell culture media applications based on a root‐cause investigation

The use of disposable bags for cell culture media storage has grown significantly in the past decade. Some of the key advantages of using disposable bags relative to non‐disposable containers include increased product throughput, decreased cleaning validation costs, reduced risk of cross contamination and lower facility costs. As the scope of use of disposable bags for cell culture applications increases, problematic bags and scenarios should be identified and addressed to continue improving disposables technologies and meet the biotech industry's needs. In this article, we examine a cell culture application wherein media stored in disposable bags is warmed at 37°C before use for cell culture operations. A problematic bag film was identified through a prospective and retrospective cell culture investigation. The investigation provided information on the scope and variation of the issue with respect to different Chinese hamster ovary (CHO) cell lines, cell culture media, and application‐specific parameters. It also led to the development of application‐specific test methods and enabled a strategy for disposable bag film testing. The strategy was implemented for qualifying an alternative bag film for use in our processes. In this test strategy, multiple lots of 13 bag film types, encompassing eight vendors were evaluated using a three round, cell culture‐based test strategy. The test strategy resulted in the determination of four viable bag film options based on the technical data. The results of this evaluation were used to conclude that a volatile or air‐quenched compound, likely generated by gamma irradiation of the problematic bag film, negatively impacted cell culture performance. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:1535–1549, 2013     

Identification of a prognostic alternative splicing signature in oral squamous cell carcinoma

Alternative splicing (AS) is critically associated with tumorigenesis and patient's prognosis. Here, we systematically analyzed survival-associated AS signatures in oral squamous cell carcinoma (OSCC) and evaluated their prognostic predictive values. Survival-related AS events were identified by univariate and multivariate Cox regression analyses using OSCC data from the TCGA head neck squamous cell carcinoma data set. The Percent Spliced In calculated by SpliceSeq from 0 to 1 was used to quantify seven types of AS events. A predictive model based on AS events was constructed by least absolute shrinkage and selection operator Cox regression assay and further validated using a training-testing cohort design. Patient survival was estimated using the Kaplan–Meier method and compared with Log-rank test. The receiver operating characteristics curve area under the curves was used to evaluate the predictive abilities of these predictive models. Furthermore, gene–gene interaction networks and the splicing factors (SFs)-AS regulatory network was generated by Cytoscape. A total of 825 survival-related AS events within 719 genes were identified in OSCC samples. The integrative predictive model was better at predicting outcomes of patients as compared to those models built with the individual AS event. The predictive model based on three AS-related genes also effectively predicted patients’ survival. Moreover, seven survival-related SFs were detected in OSCC including RBM4, HNRNPD, and HNRNPC, which have been linked to tumorigenesis. The SF-AS network revealed a significant correlation between survival-related AS genes and these SFs. Our findings revealed a systemic portrait of survival-associated AS events and the splicing network in OSCC, suggesting that AS events might serve as novel prognostic biomarkers and therapeutic targets for OSCC.     

Chemotaxis: a feedback-based computational model robustly predicts multiple aspects of real cell behaviour

The mechanism of eukaryotic chemotaxis remains unclear despite intensive study. The most frequently described mechanism acts through attractants causing actin polymerization, in turn leading to pseudopod formation and cell movement. We recently proposed an alternative mechanism, supported by several lines of data, in which pseudopods are made by a self-generated cycle. If chemoattractants are present, they modulate the cycle rather than directly causing actin polymerization. The aim of this work is to test the explanatory and predictive powers of such pseudopod-based models to predict the complex behaviour of cells in chemotaxis. We have now tested the effectiveness of this mechanism using a computational model of cell movement and chemotaxis based on pseudopod autocatalysis. The model reproduces a surprisingly wide range of existing data about cell movement and chemotaxis. It simulates cell polarization and persistence without stimuli and selection of accurate pseudopods when chemoattractant gradients are present. It predicts both bias of pseudopod position in low chemoattractant gradients and--unexpectedly--lateral pseudopod initiation in high gradients. To test the predictive ability of the model, we looked for untested and novel predictions. One prediction from the model is that the angle between successive pseudopods at the front of the cell will increase in proportion to the difference between the cell's direction and the direction of the gradient. We measured the angles between pseudopods in chemotaxing Dictyostelium cells under different conditions and found the results agreed with the model extremely well. Our model and data together suggest that in rapidly moving cells like Dictyostelium and neutrophils an intrinsic pseudopod cycle lies at the heart of cell motility. This implies that the mechanism behind chemotaxis relies on modification of intrinsic pseudopod behaviour, more than generation of new pseudopods or actin polymerization by chemoattractants.     

Tumor markers in the detection of recurrent transitional cell carcinoma of the bladder: a brief review

OBJECTIVE: To determine the status of the most promising tumor markers of bladder cancer, including comparison with cytology, technical complexity and utility in patient management. STUDY DESIGN: An extensive literature search was performed, and multiple markers were evaluated. The markers with the greatest potential for use as an adjunct to cytology were reviewed to determine the value of clinical implementation. Markers with a paucity of clinical research and poor results in clinical trials were omitted from review, as were genetic and cytologic prognostic determinants. RESULTS: NMP22, bladder tumor antigen, fibrin/fibrinogen degradation products, telomerase and QUANTICYT image analysis cytometry produced the most favorable and reproducible results. Each test obtained favorable sensitivities in comparison with cytology, especially in the detection of low grade lesions. Many also retrospectively placed patients in high- and low-risk groups based on the test results, allowing increased follow-up time between cystoscopies. However, inability to detect some high grade lesions reduces their utility. CONCLUSION: Continued clinical trials using these and other predictors of bladder cancer will eventually find a test that is suitable, in sensitivity and specificity, for use in urology clinics. Until that time, these tests may be useful in conjunction with cytology to prolong the interval between cystoscopies.     

Quantifying immunogold localization on electron microscopic thin sections: a compendium of new approaches for plant cell biologists

A review is presented of recently developed methods for quantifying electron microscopical thin sections on which colloidal gold-labelled markers are used to identify and localize interesting molecules. These efficient methods rely on sound principles of random sampling, event counting, and statistical evaluation. Distributions of immunogold particles across cellular compartments can be compared within and between experimental groups. They can also be used to test for co-localization in multilabelling studies involving two or more sizes of gold particle. To test for preferential labelling of compartments, observed and expected gold particle distributions are compared by χ(2) analysis. Efficient estimators of gold labelling intensity [labelling density (LD) and/or relative labelling index (RLI)] are used to analyse volume-occupying compartments (e.g. Golgi vesicles) and/or surface-occupying compartments (e.g. cell membranes). Compartment size is estimated by counting chance events after randomly superimposing test lattices of points and/or line probes. RLI=1 when there is random labelling and RLI >1 when there is preferential labelling. Between-group comparisons do not require information about compartment size but, instead, raw gold particle counts in different groups are compared by combining χ(2) and contingency table analyses. These tests may also be used to assess co-distribution of different sized gold particles in compartments. Testing for co-labelling involves identifying sets of compartmental profiles that are unlabelled and labelled for one or both of two gold marker sizes. Numbers of profiles in each labelling set are compared by contingency table analysis and χ(2) analysis or Fisher's exact probability test. The various methods are illustrated with worked examples based on empirical and synthetic data and will be of practical benefit to those applying single or multiple immunogold labelling in their research.     

Real-time monitoring of cell viability and cell density on the basis of a three dimensional optical reflectance method (3D-ORM): investigation of the effect of sub-lethal and lethal injuries

Cell density and cell viability have been followed on-line by using a three-dimensional optical reflectance method (3D-ORM) probe. This method has allowed to highlight the differences between a well-mixed and a scale-down bioreactor configured in order to reproduce mixing deficiencies during a fed-batch culture of Escherichia coli. These differences have been observed both for the obscuration factor (OBF) and the coincidence probability delivered by the probe. These parameters are correlated to flow cytometry measurement based on the PI-uptake test and cell density based on optical density measurement. This first set of results has pointed out the fact that the 3D-ORM probe is sensitive to sub-lethal injuries encountered by microbial cells in process-related conditions. The effect of lethal injuries has been further investigated on the basis of additional experiments involving heat stress and a sharp increase of the OBF has been observed indicating that cells are effectively injured by the increase of temperature. However, further improvement of the probe are needed in order to give access to single-cell measurements.     

Flow cytometric assessment of cell viability: a multifaceted analysis

Flow cytometry offers the possibility to simultaneously analyze, on a cell by cell basis, different parameters related to cell viability i.e. cell size, morphology and incorporation of dyes. Different types of analysis: light absorption of unstained/stained cells, forward angle light scattering (FALS), right angle light scattering (RALS) or both, cell fluorescence based on dye retention or dye exclusion (due to erythrosin B, ethidium bromide, fluorescein diacetate, rhodamine 123) were tested and compared, with the classical Trypan blue exclusion test, for their effectiveness in the determination of cell viability. Two types of cells in monolayer cultures (L929, SIRC) and a freshly isolated suspension of mouse splenocytes were used. For each dye, the optimal dose, incubation time and conditions for analysis were determined. Viability indications by different techniques for the three type of cell line and their reliability as compared with Trypan blue were analyzed.     

Effect of cell culture on 18S rRNA gene sequences in the cultural course of Taxus chinensis cells

Cell culture is an effective technology for taxol production. This paper discusses the effect of Taxus cell cultures on the 18S rRNA gene sequences based on the phylogenetic analysis of cultured T. chinensis cells and related species. The phylogenetic tree is reconstructed using the maximum parsimony method and the relative rate test to test the hypothesis of a molecular clock. The phylogenetic analysis indicates that cell culture changes the phylogenetic position of cultured T. chinensis cells. More than that, the 18S rRNA gene of cultured T chinensis cells has a faster rate of substitution than that of T. chinensis. With T. media as reference, the divergence time of the cultured T. chinensis cells is 7 Ma (million years) more than that of the T. chinensis cells based on the 18S rRNA gene sequences.     

Testing substitution models within a phylogenetic tree

Phylogenetic tree reconstruction frequently assumes the homogeneity of the substitution process over the whole tree. To test this assumption statistically, we propose a test based on the sample covariance matrix of the set of substitution rate matrices estimated from pairwise sequence comparison. The sample covariance matrix is condensed into a one-dimensional test statistic Delta = sum ln(1 + delta(i)), where delta(i) are the eigenvalues of the sample covariance matrix. The test does not assume a specific mutational model. It analyses the variation in the estimated rate matrices. The distribution of this test statistic is determined by simulations based on the phylogeny estimated from the data. We study the power of the test under various scenarios and apply the test to X chromosome and mtDNA primate sequence data. Finally, we demonstrate how to include rate variation in the test.     

CD8 T cell immunome analysis of Listeria monocytogenes

The identification of T cell epitopes is crucial for the understanding of the host response during infections with pathogenic microorganisms. Generally, the identification of relevant T cell responses is based on the analysis of T cell lines propagated in vitro. We used an ex vivo approach for the analysis of the CD8 T cell response against Listeria monocytogenes that is based upon the fractionation of naturally processed antigenic peptides and subsequent analysis with T cells in an enzyme-linked immunospot (ELISPOT) assay. Our data indicate that the direct ex vivo ELISPOT analysis of peptides extracted from infected tissues represents a versatile and potent test system for the analysis of the CD8 T cell immunome of microorganisms that furthermore requires neither the knowledge of the microbial genome nor of the specificity of responding T cells.     

Ramifications of a redox switch within a normal cell: its absence in a cancer cell

A previously described model for cellular proliferation, based on the relationship of the cell cycle to redox parameters, is explored here to account for the origin of the cancerous cell and some of its key abnormal characteristics, such as the Warburg effect, apoptosis, aneuploidy, and uncontrolled proliferation. We describe how the redox switch that characterizes normal cells and its absence in cancer cells is responsible for the origin and characteristics of cancer cells. Metabolic and chromosomal changes resulting from the lack of such a redox switch in cancer cells are described. The effects of a well-known carcinogen, cigarette smoking, are also applied to the model. This report emphasizes the role of the threshold intracellular redox potential in regulating cells.