Data Cubes and Matrix Formulae for Convenient Handling of Physical Flow Data

If the technosphere and the biosphere are divided into cells, the presence and turnover of a substance in a study area can be summarized in a vector of stocks and a matrix of flows between different pairs of cells. Likewise the stocks and flows of several substances or materials in one or more time periods can be summarized in multidimensional data cubes. In this article, we provide a theoretical framework for handling physical flow data, and we demonstrate how a set of matrix operations can facilitate exploratory analysis and quality assessment of such data regardless of the number of substances, materials, and time periods considered. In particular, we show how matrices and cubes of flow data can be recalculated when the collection of cells is modified by joining cells, and also what information is required to recalculate flows when cells are split. Furthermore, we illustrate how and under what circumstances substance-flow data originating from different studies with different collections of cells can be compared or merged. The generic character of the given formulae facilitates the development of software for physical flow data.     

Alterations in intermediate filament proteins in rat kidney proximal tubule epithelial cells

Changes in the intermediate filament composition of rat kidney proximal tubule cells in culture have been investigated. The data suggest that differentiated tubular epithelial cells do not express vimentin, but vimentin expression is induced when the cells begin to proliferate in culture. The cultured cells are positive for both cytokeratins and vimentin by immunofluorescence microscopy. The data support the concept that the intermediate filament composition of proximal tubule epithelial cells can be altered during proliferation induced by nephrotoxic chemicals or by neoplastic transformation.     

Adaptive features of natural killer cells,lymphocytes of innate immunity

Natural killer cells (NK cells) are traditionally attributed to the innate immune system. It is considered that previously received stimuli have little effect on the functioning of these immune cells. Indeed, NK cells even without prior sensitization provide a rapid effector response against tumor, virus-infected, or otherwise damaged cells. They have a limited repertoire of receptors, the expression of which does not require somatic recombination. However, recent data indicate that NK cells may acquire the properties specific to adaptive immune cells. In particular, NK cells have been shown to possess the features of immunological memory, namely, the ability to more quickly and effectively respond to a repeated stimulus. The mechanisms of memory acquisition in NK cells differ from those implemented in T and B lymphocytes and are still rather vague. Presumably, some of these mechanisms underlie the significant phenotypic and functional NK cell diversity emerging during their differentiation. The recent data accumulated in this area considerably change the existing immunology paradigm, which postulates a clear delineation of the adaptive and innate immune cells. The published data on phenotypic and functional characteristics of NK cells and particular changes in these characteristics during NK cell differentiation and generation of memory-like NK cells are reviewed.     

Radiation sensitivity of human and murine peripheral blood lymphocytes,stem and progenitor cells

Immunodeficiency is a severe side effect of radiation therapy, notably at high radiation doses. It may also impact healthy individuals exposed to environmental ionizing radiation. Although it is believed to result from cytotoxicity of bone marrow cells and of immunocompetent cells in the peripheral blood, the response of distinct bone marrow and blood cell subpopulations following exposure to ionizing radiation is not yet fully explored. In this review, we aim to compile the knowledge on radiation sensitivity of immunocompetent cells and to summarize data from bone marrow and peripheral blood cells derived from mouse and human origin. In addition, we address the radiation response of blood stem and progenitor cells. The data indicate that stem cells, T helper cells, cytotoxic T cells, monocytes, neutrophils and, at a high degree, B cells display a radiation sensitive phenotype while regulatory T cells, macrophages, dendritic cells and natural killer cells appear to be more radioresistant. No conclusive data are available for basophil and eosinophil granulocytes. Erythrocytes and thrombocytes, but not their precursors, seem to be highly radioresistant. Overall, the data indicate considerable differences in radiosensitivity of bone marrow and blood normal and malignant cell populations, which are discussed in the light of differential radiation responses resulting in hematotoxicity and related clinical implications.     

Cell volume measurement as an estimation of mammalian cell biomass

Measurements of volume distributions and dry weight are made on hybridoma cells in culture. The volume of viable hybridoma cells is significantly larger than that of nonviable cells. During exponential growth, the volume of the viable hybridoma cells is found to be significantly larger than that during other stages of batch culture. Proportionality is found between the volume of the cells and their dry weight, indicating that the volume data can be used in conjunction with cell concentration data as a practical technique for indirect measurement of the biomass concentration present in a culture. Comparison of dry weight concentrations in continuous culture to predictions from the volume data shows very good agreement.     

Importance of observation interval in two-dimensional video analysis of individual diatom cells

The effect of the observation interval on two-dimensional trajectory analysis of motility of individual diatom cells of Navicula sp. was studied by comparing thinned-out observation data. The trajectory of cell movement was visualized accurately even after thinning the data interval. However, the analysis of velocity fluctuations of individual cells was found to be significantly affected by the data interval. Reproducibility of the results was guaranteed by analyzing many independent cells. In addition, comparison between automatic and manual determination of cell positions proved that automatic determination was a reliable process. Our data indicated that two-dimensional trajectory analysis using a computer can be a powerful technique to study diatom locomotion.     

Direct mobilization of retinol from hepatic perisinusoidal stellate cells to plasma.

We have studied the mechanism for mobilization of retinol from stellate cells. Our data show that perisinusoidal stellate cells isolated from liver contained retinol-binding protein (RBP) mRNA. By Western blot analysis we found that cultivated liver stellate cells secreted RBP into the medium. Cultivated stellate cells loaded in vitro with [3H]retinyl ester mobilized radioactive retinol as a complex with RBP. Furthermore, exogenous RBP added to the medium of cultured stellate cells increased the secretion of retinol to the medium. These data suggest that liver stellate cells in vivo mobilize retinol directly to the blood and that a transfer to parenchymal cells for secretion as holo-RBP is not required. The direct mobilization of retinol from liver stellate cells as retinol-RBP to blood is indirectly supported by the demonstration of RBP mRNA production and RBP secretion by lung stellate cells. The data suggest that the same mechanism for retinol mobilization may exist in hepatic and extrahepatic stellate cells. This is, vitamin A-storing stellate cells in liver, lungs, and probably also in other organs may synthesize their own RBP (or alternatively use exogenous RBP) and mobilize holo-RBP directly to the blood.     

High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics

The importance of single-cell level data is increasingly appreciated, and significant advances in this direction have been made in recent years. Common to these technologies is the need to physically segregate individual cells into containers, such as wells or chambers of a micro-fluidics chip. High-throughput Single-Cell Labeling (Hi-SCL) in drops is a novel method that uses drop-based libraries of oligonucleotide barcodes to index individual cells in a population. The use of drops as containers, and a microfluidics platform to manipulate them en-masse, yields a highly scalable methodological framework. Once tagged, labeled molecules from different cells may be mixed without losing the cell-of-origin information. Here we demonstrate an application of the method for generating RNA-sequencing data for multiple individual cells within a population. Barcoded oligonucleotides are used to prime cDNA synthesis within drops. Barcoded cDNAs are then combined and subjected to second generation sequencing. The data are deconvoluted based on the barcodes, yielding single-cell mRNA expression data. In a proof-of-concept set of experiments we show that this method yields data comparable to other existing methods, but with unique potential for assaying very large numbers of cells.     

Exogenous reference RNA for normalization of real-time quantitative PCR

We have utilized an in vitro transcribed 3' mRNA fragment of the plant gene ribulose bisphosphate carboxylase (RuBisCO) as an exogenous standard for normalization of quantitative PCR data. Both K562 cells and primary erythroid CD34+ progenitor cells were treated with sodium butyrate and changes in gamma-globin mRNA levels were assayed using a previously published TaqMan probe and primer set, while RuBisCO levels were assayed by a SYBR Green detection assay. The data presented show that a correction to measured gamma-globin induction was necessary with both cell types. The correction for the CD34+ progenitor cells was a striking 95% increase, while that for the K562 cells was 44%. The use of an exogenous reference such as in vitro transcribed mRNA for the RuBisCO plant gene provides a robust and sample-independent method for the normalization of quantitative PCR data in bacterial and animal cells.     

The copper-dependent accumulation of magnesium in Escherichia coli

Cu2(+)-induced accumulation of Mg ions by E. coli cells has been studied. The accumulation was demonstrated to take place only when the cell had endogenous energetic resources. The data obtained and their correlation with the data on Cu2+ binding by bacterial cells and Cu2(+)-dependent streptomycin accumulation allowed to conclude that copper induced nonspecific potential-dependent influx of cations into cells.     

Vesicle fusion and fission in plants and yeast

Measurements of the membrane capacitance on animal cells has provided an excellent technique for monitoring of exo- and endocytotic activity in intact living cells. Here we review recent data in which the same technique was applied to plant cells and cells of the budding yeast Saccharomyces cerevisiae. The data show that unitary exo- and endocytotic events can also be measured with the same technique after removing the cell wall from these cells. The resulting protoplasts execute the same type of transient and permanent fusion/fission that is known from animal cells. Also the size of the vesicles, which are fusing or budding, are of the same order of magnitude as those recorded in animal cells. Together these data support the view of an evolutionary conserved mechanism for unitary exo- and endocytosis events in eukaryotes. The successful recordings of exo- and endocytotic activity in Saccharomyces cerevisiae by capacitance measurements now pave the way for correlating the abundant information on the molecular machinery of exo- and endocytosis in this model organism with distinct functional properties.     

Use of cryopreserved cells for enabling greater flexibility in compound profiling

Measurement of intracellular calcium release following agonist challenge within cells expressing the relevant membrane protein is a commonly used format to derive structure-activity relationship (SAR) data within a compound profiling assay. The Fluorometric Imaging Plate Reader (FLIPR) has become the gold standard for this purpose. FLIPR traditionally uses cells that are maintained in continuous culture for compound profiling of iterative chemistry campaigns. This supply dictates that assays can only be run on 4 of 5 weekdays, or alternative cell culture machinery is required such that plating can occur remotely at the weekend. The data reported here demonstrate that high-quality compound profiling data can be generated from the use of cryopreserved cells and that these cells can also be plated at various densities to generate equivalent data between 24 and 72 h post-plating. Hence, the authors report a method that allows data generation throughout the week and without the requirement of highly automated cell culture or continuous culture.     

Some theoretical and practical considerations for multivariate statistical cell classification useful in autologous stem cell transplantation and tumor cell purging.

BACKGROUND: As flow cytometric data becomes more complex, it becomes increasingly difficult to classify cells using conventional flow cytometry data techniques based on visual classification of the data by user-drawn regions. This paper shows some simple applications of multivariate statistical classification to classify flow cytometric data. METHODS: Discriminant Function Analysis (DFA) and Logistic Regression (LR) analysis techniques were evaluated with respect to their potential utility in the problem of detecting human breast cancer cells within normal bone marrow cells. Data sets having defined properties were employed to evaluate the potential utility of these statistical classification techniques whose performance was measured by ROC analysis. RESULTS: Two extreme but reasonable situations are presented: (1) data where the separation of cells was obvious by visual inspection and (2) data where major overlaps in the values of the individual FCM parameters made intuitive classification improbable. Both DFA and LR analysis were able to classify the cells of each type with acceptable accuracy and yield.CONCLUSIONS: The excellent empirical performance of both DFA and LR techniques, suggests that they offer promising approaches for classifying multiparameter FCM data using objective rules that may represent an improvement over commonly employed ad hoc approaches.     

细胞支架研究进展

目前细胞培养通常采用二维平面培养技术,但由于在培养板和培养瓶二维细胞培养并不能完全模拟体内细胞的三维生长环境,因此所得的试验数据与在体情况有偏差。然而细胞支架材料却能为细胞提供一个良好的三维生长环境,更利于细胞粘附、生长和增殖。目前可用于细胞支架材料的来源有天然和人工两大类,现将细胞支架研究进展综述如下。     

Regulation by adherent cells of macromolecular synthesis in lymphocyte populations.

The role of adherent cells in the regulation of lymphocyte DNA, RNA, and protein synthesis was investigated. Splenic adherent cells suppressed DNA synthesis of spleen cells. The reverse was true of lymph node adherent cells, i.e., DNA synthesis was less in the absence of adherent cells. Histocompatibility was not required for interaction between adherent and nonadherent cells. The regulatory adherent cell in either case was not θ positive. Removal of splenic adherent cells decreased RNA and protein synthesis of nonadherent spleen cells. RNA synthesis by lymph node cells increased when adherent cells were removed, but protein synthesis was lower. Autoradiographic analysis revealed that removal of adherent spleen cells allowed a greater number of nonadherent cells to respond to the presence of mitogen. Adherent cells were observed to regulate DNA synthesis of B lymphocytes also. Lymph node adherent cells amplified DNA synthesis in both nonadherent spleen and lymph node cells, while splenic adherent cells suppressed splenic nonadherent cells but stimulated nonadherent lymph node cells. We feel the data are compatible with the idea that at least two functionally distinct adherent cell populations exist. A mechanism is suggested to explain the data.     

Detection of suppressor T lymphocytes and estimation of their frequency in limiting dilution assays by generalized linear regression modeling

The estimate of the frequency of suppressor T lymphocytes in unfractionated cell populations remains challenging, mainly because these regulatory cells do not display specific immunophenotypic markers. In this paper, we describe a novel theoretical approach for quantifying the frequency of suppressor cells. This method is based on limiting dilution data modeling, and allows the simultaneous estimation of the frequencies of both proliferating and suppressor cells. We used previously published biological data, characterizing the inhibiting activity of suppressor T cell clones. Starting from these data, we propose a mathematical model describing the interaction between suppressor and proliferating T cells, and applied to a Poisson process. Limiting dilution data corresponding to this non-single-hit, suppressor two-target Poisson model were artificially generated, then modeled according to a generalized linear regression procedure. Deviation from the single-hit Poisson model was revealed by a statistical slope test, and a stepwise analysis of the regression appeared to be an efficient method that strongly argued in favor of the presence of suppressor cells. By using the frequency of proliferating T cells calculated in the first step of the regression, we demonstrated the possibility to provide a reasonable estimate of the frequency of suppressor T cells. Based on these findings, a practical decision-making procedure is given to perform standard analyses of limiting dilution data.     

Histochemical study of carbonic anhydrase and HCO3(-)-stimulated adenosine triphosphatase in the rat stomach during hydrochloric acid secretion]

By means of histochemical methods it was established that carboanhydrase of the parietal cells of fundal glands and HCO-3 stimulated ATP-ase of the rat's gastric mucosa capillaries disposed next to the parietal cells were activated by food and histamine. The obtained data confirm the idea of the multicellular functional essembly sustaining HCL secretion (R. I. Salganik, 1974). Should gastrin induce the formation of histamine in endocrinous cells and the histamine activate carboanhydrase in parietal cells, our data confirm the supposition that HCO-3-ions stimulate ATP-ase sustaining the exchange between HCO-3-cells and C1- of blood to form HCl in the endothelial cells of blood capillaries adjacent to the parietal cells.     

Bismuth uptake in rat testicular macrophages: a follow-up observation suggesting that bismuth alters interactions between testicular macrophages and Leydig cells.

Recent studies suggest that bismuth accumulates in Leydig cells. In addition, a reduced level of serum testosterone and a statistically significant reduction of Leydig cells have been observed. It was therefore hypothesized that Bi has a direct toxic effect on rat Leydig cells. We have now developed a method for double labeling of bismuth and ED-2 (a marker for testicular macrophages). The present data demonstrate that the heavily bismuth-loaded cells in rat testis, originally interpreted as being Leydig cells, are bismuth-loaded macrophages. Consequently, our data suggest a modified hypothesis regarding bismuth-induced interactions between testicular macrophages and Leydig cells.     

Perfusion of charophyte cells: a critical analysis of the method

The data obtained by different types of intracellular perfusionwere compared. As the ligated cells cannot be space-clamped,the efficiency of compartment-clamping was evaluated, showingthat the difference I/V (current-voltage) profile between space-clampedand compartment-clamped data could be approximated by a straightline. The time-dependence of the clamp currents was not affectedby the clamp technique. The comparison of different sets of data was quantified by fittingthe I/V curves with a mathematical model (Beilby and Walker,1996). The I/V curves of ligated cells perfused with 1 mM ATPshowed the closest similarity to intact cells with resting potentialsof –22010 mV (7 cells) and similar model parameter values.The cells under open-end perfusion with ATP showed less hyperpolarizedresting p.d.s (potential differences): –17512 mV (4 cells).For both preparations the —ATP data were similar withresting p.d.s at –80 12 mV (5 ligated cells, 7 open-endcells). The excited state was more pronounced in open-end cells(resting level: –5912 mV, 5 cells) than in ligated cells(resting level: –6512 mV, 7 cells). In open-end cellsthe pump responded faster to changes of ATP concentration thanthe excitation channels. The cells stabilized with Pb(NO₃)₂were strongly depolarized both with ATP: –8010 mV (6cells) and without: 010 mV (6 cells). Most model parametersdiffered from those in the intact cells. The excited state wasabolished. Key words: Intracellular perfusion, current-voltage characteristics, Chara, stabilization with Pb(NO₃)₂, ATP effects, voltage clamp techniques     

Study on Ultrastructure and Localization of Acid Phosphatase of Gastrodia elata Cortical Cells in Their Digestive Process of Armillaria mellea

In order to study the mechanism of the digestive process of Armillaria mellea in Castrodia data, electron microscopy and cytochemical method for determination of acid phosphatase activity was employed. The provacuoles were formed by means of expanded or convoluted ER under the stimulation of cortical cells and large cells of Gastrodia data by Armillaria mellea. A product of acid phosphatase (lead phosphate deposits) occured on the tonoplast. The papillae were produced in the cell wall of cortex in Gastrodia data when Armillaria mellea penetrated into its cortex. Our results showed that the enzyme was not released from cell of Armillaria mellea. A number of small vacuoles in the cortical cells disappeared. At the same time, lead phosphate deposits on the Armillaria mellea hyphae wall were observed and than Armillaria mellea hyphae wall was going to be digested, and the hyphae lost their structure. The activity of Armillaria mellea hyphae was not observed in the large cell of Gastrodia data. A great deal of small vacuoles and mitochondria were produced, at the same time the renewable nuclei and nuclolar vacuoles etc. appeared in the large cells of Gastrodia data under the stimulation of Armillaria mellea.