Quantitation of phosphotyrosine signals in human prostate cell adhesion sites

A simple method is described for the quantitation of phosphotyrosine signaling in human prostate cell cultures. The phosphotyrosine signals are observed by standard immunohistochemistry techniques, and the resulting digital images are analyzed using the Scion image software program. The signals within the cell adhesion sites are quantitated using the density slice and particle analysis features of the software. The immunohistochemistry results are compared with detection of phosphotyrosine signals using a standard Western blotting procedure with whole cell lysates. The resulting data is converted into graphs using the Sigma Plot Program. This method is illustrated using damage-induced signaling within cell adhesion sites after a low dose of ionizing radiation.     

CORRELATED EVOLUTION OF GENOME SIZE AND CELL VOLUME IN DIATOMS (BACILLARIOPHYCEAE)1

A correlation between genome size and cell volume has been observed across diverse assemblages of eukaryotes. We examined this relationship in diatoms (Bacillariophyceae), a phylum in which cell volume is of critical ecological and biogeochemical importance. In addition to testing whether there is a predictive relationship across extant species, we tested whether evolutionary divergences in genome size were correlated with evolutionary divergences in cell size (using independent contrasts). We estimated total DNA content for 16 diatom species using a flow cytometer and estimated cell volumes using critical dimensions with scaling equations. Our independent contrast analyses indicated a significant correlated evolution between genome size and cell volume. We then explored the evolutionary and ecological implications of this evolutionary relationship. Diatom cell volume is an important component of the global carbon cycle; therefore, understanding the mechanisms that drive diatom genome evolution has both evolutionary and ecological importance.     

Estimating cell type composition using isoform expression one gene at a time

Human tissue samples are often mixtures of heterogeneous cell types, which can confound the analyses of gene expression data derived from such tissues. The cell type composition of a tissue sample may itself be of interest and is needed for proper analysis of differential gene expression. A variety of computational methods have been developed to estimate cell type proportions using gene-level expression data. However, RNA isoforms can also be differentially expressed across cell types, and isoform-level expression could be equally or more informative for determining cell type origin than gene-level expression. We propose a new computational method, IsoDeconvMM, which estimates cell type fractions using isoform-level gene expression data. A novel and useful feature of IsoDeconvMM is that it can estimate cell type proportions using only a single gene, though in practice we recommend aggregating estimates of a few dozen genes to obtain more accurate results. We demonstrate the performance of IsoDeconvMM using a unique data set with cell type–specific RNA-seq data across more than 135 individuals. This data set allows us to evaluate different methods given the biological variation of cell type–specific gene expression data across individuals. We further complement this analysis with additional simulations.     

Determining Cell Number During Cell Culture using the Scepter Cell Counter

Counting cells is often a necessary but tedious step for in vitro cell culture. Consistent cell concentrations ensure experimental reproducibility and accuracy. Cell counts are important for monitoring cell health and proliferation rate, assessing immortalization or transformation, seeding cells for subsequent experiments, transfection or infection, and preparing for cell-based assays. It is important that cell counts be accurate, consistent, and fast, particularly for quantitative measurements of cellular responses.Despite this need for speed and accuracy in cell counting, 71% of 400 researchers surveyed¹ who count cells using a hemocytometer. While hemocytometry is inexpensive, it is laborious and subject to user bias and misuse, which results in inaccurate counts. Hemocytometers are made of special optical glass on which cell suspensions are loaded in specified volumes and counted under a microscope. Sources of errors in hemocytometry include: uneven cell distribution in the sample, too many or too few cells in the sample, subjective decisions as to whether a given cell falls within the defined counting area, contamination of the hemocytometer, user-to-user variation, and variation of hemocytometer filling rate².To alleviate the tedium associated with manual counting, 29% of researchers count cells using automated cell counting devices; these include vision-based counters, systems that detect cells using the Coulter principle, or flow cytometry¹. For most researchers, the main barrier to using an automated system is the price associated with these large benchtop instruments¹.The Scepter cell counter is an automated handheld device that offers the automation and accuracy of Coulter counting at a relatively low cost. The system employs the Coulter principle of impedance-based particle detection³ in a miniaturized format using a combination of analog and digital hardware for sensing, signal processing, data storage, and graphical display. The disposable tip is engineered with a microfabricated, cell- sensing zone that enables discrimination by cell size and cell volume at sub-micron and sub-picoliter resolution. Enhanced with precision liquid-handling channels and electronics, the Scepter cell counter reports cell population statistics graphically displayed as a histogram.     

Freezing of cell sheets using a 3D freezer produces high cell viability after thawing

In cell therapy, transplanting an appropriate number of cells to the target site is crucial. One way to achieve this is to transplant cell sheets. Transplantation of cell sheets has already been utilized for various diseases in clinical practice. However, reducing the cost of cell sheet utilization is essential so as to facilitate the spread of regenerative medicine. Several ways to reduce costs are available, one of which is the use of allogenic cells. Another alternative is the use of cell sheets, which necessitates the development of methods for freezing cell sheets. This is the first study to report the use of a 3D Freezer for freezing cells. 3D Freezers have been used in the field of food processing and technology for a long time. The 3D Freezer freezes objects using cold air at a uniform temperature from all directions. In this study, we analyzed the cooling speed of human fibroblast sheets in 11 cell preservation solutions using a 3D Freezer and a Program Freezer. The cooling speed was ?2 °C per min in the 3D Freezer. Supercooling in 10 cell preservation solutions was lower in the 3D Freezer than in the Program Freezer. Cell viability after freeze–thaw of the cell sheets using 3D Freezer was more than 70% in five cell preservation solutions. The levels of hepatocyte growth factor and transforming growth factor-β1 were the same not only in the fibroblast sheets frozen using the five cell preservation solutions but also in the non-frozen fibroblast sheets. These results suggest that the 3D Freezer can freeze implantable cell sheets immediately after thawing.     

Monitoring of hormonal drug effect in a single breast cancer cell using an estrogen responsive GFP reporter vector delivered by a nanoneedle

In this study, we have evaluated a sensor system for a hormonal drug effect in a single cell level using a novel low invasive single cell DNA delivery technology using a nanoneedle. An estrogen responsive GFP reporter vector (pEREGFP9) was constructed and its estrogenic response activity was confirmed in breast cancer cells (MCF-7) using lipofection as the means of transferring the vector to the cells. The pEREGFP9 vector was delivered to a single MCF-7 using a nanoneedle and the effect of ICI 182,780, which is an antagonist of estrogen, was observed using the GFP expression level. By ICI 182,780 treatment, the fluorescence intensity of the GFP was decreased by 30-50% within 24h. This technology is the very first trial of single cell diagnosis and we are looking forward to applying it to precious single cell diagnosis in medical fields.     

The role of calmodulin in human renal cell carcinoma

Calmodulin is a ubiquitous intracellular calcium binding protein which has been shown to be associated with cell cycling. Previous studies using animal tumor models have suggested a positive correlation between tumor calmodulin content and rate of tumor growth. We studied the role of calmodulin in renal cell carcinoma (RCC) cell lines and compared this with short term normal fetal kidney cell lines. The effects of calmodulin inhibition was determined using the calmodulin inhibitor W13 (Naphthalene-sulfonamide) and its less active partner W12. Cell size, calmodulin content and inhibition studies using W13 did not reveal any simple correlations for the RCC cell lines, although the RCC lines did have a higher content than the fetal kidney cell lines. Calmodulin content determination of RCC and normal adult kidney tissue failed to show any difference. We conclude that, contrary to previous reports using animal models, there is no simple relationship between tumor growth rates and calmodulin content for human RCC.     

Using carboxyfluorescein diacetate succinimidyl ester to monitor human NK cell division: analysis of the effect of activating and inhibitory class I MHC receptors

Human NK cells labelled intracellularly with the fluorescent dye 5- and 6-carboxyfluorescein diacetate succinimidyl ester (CFSE) were used to assess the effect of ligating class I MHC receptors on NK cell division. The NK cell lines used in these studies expressed a selection of the killer immunoglobulin-like receptors CD158b and CD158a and the CD94/NKG2 family of C-type lectin receptors. The NK cells were cultured in medium containing recombinant (r)IL-2 and receptors were ligated using plastic bound mAb or using soluble murine IgG mAb and FcRII+ gamma-irradiated murine P815 cells. The results obtained show that ligating class I MHC-activating receptors in either culture system stimulates NK cells to divide. Quantitative analysis of cell division reveals that a substantial loss of NK progenitor cells occurs when NK cell-activating receptors are ligated using plastic bound mAb, consistent with concomitant activation-induced cell death. By contrast, progenitor cell loss is prevented when activating receptors are ligated using soluble mAb and P815 cells, suggesting a role for cellular costimulation in cell survival. When inhibitory receptors are coligated with activating receptors using soluble mAb and P815 cells, NK cell division is inhibited. These results demonstrate the potential importance of the activating and inhibitory class I MHC receptors in regulating NK cell proliferation.     

Identification of novel therapeutic targets in microdissected clear cell ovarian cancers

Clear cell ovarian cancer is an epithelial ovarian cancer histotype that is less responsive to chemotherapy and carries poorer prognosis than serous and endometrioid histotypes. Despite this, patients with these tumors are treated in a similar fashion as all other ovarian cancers. Previous genomic analysis has suggested that clear cell cancers represent a unique tumor subtype. Here we generated the first whole genomic expression profiling using epithelial component of clear cell ovarian cancers and normal ovarian surface specimens isolated by laser capture microdissection. All the arrays were analyzed using BRB ArrayTools and PathwayStudio software to identify the signaling pathways. Identified pathways validated using serous, clear cell cancer cell lines and RNAi technology. In vivo validations carried out using an orthotopic mouse model and liposomal encapsulated siRNA. Patient-derived clear cell and serous ovarian tumors were grafted under the renal capsule of NOD-SCID mice to evaluate the therapeutic potential of the identified pathway. We identified major activated pathways in clear cells involving in hypoxic cell growth, angiogenesis, and glucose metabolism not seen in other histotypes. Knockdown of key genes in these pathways sensitized clear cell ovarian cancer cell lines to hypoxia/glucose deprivation. In vivo experiments using patient derived tumors demonstrate that clear cell tumors are exquisitely sensitive to antiangiogenesis therapy (i.e. sunitinib) compared with serous tumors. We generated a histotype specific, gene signature associated with clear cell ovarian cancer which identifies important activated pathways critical for their clinicopathologic characteristics. These results provide a rational basis for a radically different treatment for ovarian clear cell patients.     

Cell poration and cell fusion using an oscillating electric field.

It has been shown in previous studies that cell poration (i.e., reversible permeabilization of cell membrane) and cell fusion can be induced by applying a pulse (or pulses) of high-intensity DC (direct current) electric field. Recently we suggested that such electro-poration or electro-fusion can also be accomplished by using an oscillating electric field. The DC field relies solely on the dielectric breakdown of the cell membrane to induce cell fusion. The oscillating field, on the other hand, can produce not only a dielectric breakdown, but also a sonicating motion in the membrane that could result in a structural fatigue. Thus, a combination of a DC field and an oscillating field is expected to enhance the efficiency of cell poration and cell fusion. This study is an experimental test of such an idea. Here, pulses of high-intensity, DC-shifted RF (radio frequency) electric field were used to induce cell poration and cell fusion. The fusion experiments were done on human red blood cells. The poration experiments were done on a fibroblast cell line using a molecular probe (which is a DNA plasmid containing the marker gene chloramphenicol acetyltransferase, CAT) and assayed by a gene transfection technique. It was found that the pulsed RF field is highly efficient in both cell fusion and cell poration. Also, in comparison with electro-poration using a DC field, the RF field results in a higher percentage of cells surviving the exposure to the electric field.     

Differential histone modification and protein expression associated with cell wall removal and regeneration in rice (Oryza sativa)

The cell wall is a critical extracellular structure that provides protection and structural support in plant cells. To study the biological function of the cell wall and the regulation of cell wall resynthesis, we examined cellular responses to enzymatic removal of the cell wall in rice (Oryza sativa) suspension cells using proteomic approaches. We find that removal of cell wall stimulates cell wall synthesis from multiple sites in protoplasts instead of from a single site as in cytokinesis. Nucleus DAPI stain and MNase digestion further show that removal of the cell wall is concomitant with substantial chromatin reorganization. Histone post-translational modification studies using both Western blots and isotope labeling assisted quantitative mass spectrometry analyses reveal that substantial histone modification changes, particularly H3K18(AC) and H3K23(AC), are associated with the removal and regeneration of the cell wall. Label-free quantitative proteome analyses further reveal that chromatin associated proteins undergo dramatic changes upon removal of the cell wall, along with cytoskeleton, cell wall metabolism, and stress-response proteins. This study demonstrates that cell wall removal is associated with substantial chromatin change and may lead to stimulation of cell wall synthesis using a novel mechanism.     

Stacked stem cell sheets enhance cell-matrix interactions

Cell sheet engineering has enabled the production of confluent cell sheets stacked together for use as a cardiac patch to increase cell survival rate and engraftment after transplantation, thereby providing a promising strategy for high density stem cell delivery for cardiac repair. One key challenge in using cell sheet technology is the difficulty of cell sheet handling due to its weak mechanical properties. A single-layer cell sheet is generally very fragile and tends to break or clump during harvest. Effective transfer and stacking methods are needed to move cell sheet technology into widespread clinical applications. In this study, we developed a simple and effective micropipette based method to aid cell sheet transfer and stacking. The cell viability after transfer was tested and multi-layer stem cell sheets were fabricated using the developed method. Furthermore, we examined the interactions between stacked stem cell sheets and fibrin matrix. Our results have shown that the preserved ECM associated with the detached cell sheet greatly facilitates its adherence to fibrin matrix and enhances the cell sheet-matrix interactions. Accelerated fibrin degradation caused by attached cell sheets was also observed.     

Noninvasive quality estimation of adherent mammalian cells for transplantation

The noninvasive quality estimation of adherent mammalian cells for transplantation is reviewed. The quality and heterogeneity of cells should be estimated before transplantation because cultured cells are not homogeneous but heterogeneous. The estimation of cell quality should be performed noninvasively because most protocols of regenerative medicine are autologous cell system. The differentiation level and contamination of other cell lineage could be estimated by two-dimensional cell morphology analysis and tracking using a conventional phase contrast microscope. The noninvasive determination of the laser phase shift of a cell using a phase-shifting laser microscope, which might be more noninvasive, and more useful than the atomic force microscope and digital holographic microscope, was carried out to determine the three-dimensional cell morphology, and the estimation of the cell cycle phase of each adhesive cell and the mean proliferation activity of a cell population. Chemical analysis of the culture supernatant by conventional analytical methods such as ELISA was also useful to estimate the differentiation level of a cell population. Chemical analysis of cell membrane and intracellular components using a probe beam, an infrared beam, and Raman spectroscopy was useful for diagnosing the viability, apoptosis, and differentiation of each adhesive cell.     

Loss of integrin α3 expression is associated with acquisition of invasive potential by ovarian clear cell adenocarcinoma cells

Among various types of surface epithelial ovarian carcinoma, clear cell adenocarcinoma often has a particularly poor prognosis even when diagnosed in stage I. It is resistant to existing anticancer drugs and appears to have different biological properties to other histological types of ovarian cancer. The present study was conducted using cell lines derived from ovarian clear cell adenocarcinoma in order to identify genes associated with the acquisition of malignant potential by this type of cancer. Two cell lines derived from ovarian clear cell adenocarcinoma (RMG-I and RMG-V), with different levels of invasive potential in an invasion assay, were used. DNA fragments were extracted from the band showing differences in the level of expression by RT-PCR with fluorescent differential display. A total of 56 different DNA base sequences were determined by direct sequencing. Primers were established using these base sequences and the level of expression in each cancer cell line was determined by real-time PCR. Integrin a3, the gene of which is present on chromosome 17q, was identified. It was also detected by a microarray analysis as one of the molecules showing a different level of expression between the two cell lines. Then the pattern of integrin a3 expression was investigated using immunocytochemical staining, and was found to differ between the two cell lines. The findings obtained using these cell lines derived from ovarian clear cell adenocarcinoma indicate that integrin alpha3 may associated with the acquisition of malignant potential by clear cell adenocarcinoma.     

A new methodology for plant cell viability assessment using intracellular esterase activity

 A plant cell suspension culture of Alfalfa (Medicago sativa L.) was grown in a bioreactor using a batch procedure. The cytoplasmic esterase activity (EC 3.1) was extracted from the cells and measured during cultivation using fluorescein diacetate as the fluorogenic substrate. This enzymatic activity was conclusively found to be correlated to cell viability assessed with the membrane integrity test using the trypan blue dye. This new viability determination method is convenient, simple and can be reproduced because: (1) the difficult step of counting the cells when using the trypan blue exclusion method is avoided and (2) the esterase activity level per viable cell constituted of numerous enzymes depends on cell viability but is independent of cellular metabolism. Received: 28 January 1999 / Accepted: 1 April 1999     

Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate

Selected or multiple reaction monitoring is a targeted mass spectrometry method (S/MRM-MS), in which many peptides are simultaneously and consistently analyzed during a single liquid chromatography-mass spectrometry (LC-S/MRM-MS) measurement. These capabilities make S/MRM-MS an attractive method to monitor a consistent set of proteins over various experimental conditions. To increase throughput for S/MRM-MS it is advantageous to use scheduled methods and unfractionated protein extracts. Here, we established the practically measurable dynamic range of proteins reliably detectable and quantifiable in an unfractionated protein extract from a human cell line using LC-S/MRM-MS. Initially, we analyzed S/MRM transition peak groups in terms of interfering signals and compared S/MRM transition peak groups to MS1-triggered MS2 spectra using dot-product analysis. Finally, using unfractionated protein extract from human cell lysate, we quantified the upper boundary of copies per cell to be 35 million copies per cell, while 7500 copies per cell represents a lower boundary using a single 35 min linear gradient LC-S/MRM-MS measurement on a current, standard commercial instrument.     

Stacked stem cell sheets enhance cell-matrix interactions

Cell sheet engineering has enabled the production of confluent cell sheets stacked together for use as a cardiac patch to increase cell survival rate and engraftment after transplantation, thereby providing a promising strategy for high density stem cell delivery for cardiac repair. One key challenge in using cell sheet technology is the difficulty of cell sheet handling due to its weak mechanical properties. A single-layer cell sheet is generally very fragile and tends to break or clump during harvest. Effective transfer and stacking methods are needed to move cell sheet technology into widespread clinical applications. In this study, we developed a simple and effective micropipette based method to aid cell sheet transfer and stacking. The cell viability after transfer was tested and multi-layer stem cell sheets were fabricated using the developed method. Furthermore, we examined the interactions between stacked stem cell sheets and fibrin matrix. Our results have shown that the preserved ECM associated with the detached cell sheet greatly facilitates its adherence to fibrin matrix and enhances the cell sheet-matrix interactions. Accelerated fibrin degradation caused by attached cell sheets was also observed.     

Cell cycle synchronization of tobacco BY-2 cells

Synchronization is a powerful technique for understanding cell cycle events. Here, we describe the procedure for synchronizing tobacco bright yellow 2 (BY-2) cell line, with which an exceptionally high level of synchrony can be achieved. It basically relies on an "arrest-and-release" strategy using aphidicolin, an inhibitor of DNA replication, and propyzamide, a plant-microtubule disruptant. In a single-step process using aphidicolin alone, a cell population with about 70% of the cells at mitosis can be achieved, whereas by a two-step method using the two inhibitors sequentially, the level of synchrony can reach over 90%. The method of choice depends not only on the peak mitotic cell proportion but also on the cell cycle stage that is targeted for analysis. Both procedures take about 1.5 days, and cell cycle progression can be observed from the S phase to the next G1 phase at about 12 h after a 24 h-period treatment with aphidicolin.     

溶葡球菌酶的比色测定及某些性质的研究

溶葡球菌酶是一种专一地溶解葡萄球菌的溶菌酶。和蛋清溶菌酶一样,通常采用比浊法进行测定,底物或为葡萄球菌、或为该菌的细胞壁、或为该菌细胞壁的肽聚糖。本文报道一种简便灵敏的溶葡球菌酶比色测定法,以偶联了KNR艳蓝染料的葡萄球菌(死)细胞或偶联了KNR艳蓝染料的该菌细胞壁肽聚糖为色源底物,根据酶作用后释放出的可溶性KNR生成物计算酶活性。本文采用该比色测定法检定了溶葡球菌酶的某些动力学性质。