Total cellular RNA content: correlation between flow cytometry and ultraviolet spectroscopy

Total RNA content in Chinese hamster ovary and HeLa-S3 cells determined by ultraviolet spectroscopy is compared with the red fluorescence distribution of acridine orange-stained cells observed by flow cytometry. A correlation coefficient of 0.93 is obtained when these methods of estimating RNA content are compared after various RNAse treatments. These data suggest that acridine orange staining effectively quantitates total cellular RNA content when analyzed by flow cytometry, although DNA is also shown to contribute a low but significant background of red fluorescence.     

Imaging large-scale neural activity with cellular resolution in awake, mobile mice

We report a technique for two-photon fluorescence imaging with cellular resolution in awake, behaving mice with minimal motion artifact. The apparatus combines an upright, table-mounted two-photon microscope with a spherical treadmill consisting of a large, air-supported Styrofoam ball. Mice, with implanted cranial windows, are head restrained under the objective while their limbs rest on the ball's upper surface. Following adaptation to head restraint, mice maneuver on the spherical treadmill as their heads remain motionless. Image sequences demonstrate that running-associated brain motion is limited to approximately 2-5 microm. In addition, motion is predominantly in the focal plane, with little out-of-plane motion, making the application of a custom-designed Hidden-Markov-Model-based motion correction algorithm useful for postprocessing. Behaviorally correlated calcium transients from large neuronal and astrocytic populations were routinely measured, with an estimated motion-induced false positive error rate of <5%.     

A single-fractal analysis of cellular analyte-receptor binding kinetics utilizing biosensors

A fractal analysis of a confirmative nature only is presented for cellular analyte-receptor binding kinetics utilizing biosensors. Data taken from the literature can be modeled by using a single-fractal analysis. Relationships are presented for the binding rate coefficient as a function of the fractal dimension and for the analyte concentration in solution. In general, the binding rate coefficient is rather sensitive to the degree of heterogeneity that exists on the biosensor surface. It is of interest to note that examples are presented where the binding coefficient, k exhibits an increase as the fractal dimension (D(f)) or the degree of heterogeneity increases on the surface. The predictive relationships presented provide further physical insights into the binding reactions occurring on the surface. These should assist in understanding the cellular binding reaction occurring on surfaces, even though the analysis presented is for the cases where the cellular "receptor" is actually immobilized on a biosensor or other surface. The analysis suggests possible modulations of cell surfaces in desired directions to help manipulate the binding rate coefficient (or affinity). In general, the technique presented is applicable for the most part to other reactions occurring on different types of biosensor or other surfaces.     

Robust optimization of total joint replacements incorporating environmental variables.

Direct search techniques for the optimal design of biomechanical devices are computationally intensive requiring many iterations before converging to a global solution. This, along with the incorporation of environmental variables such as multiple loading conditions and bone properties, makes direct search techniques infeasible. In this study, we introduced new methods that are based on the statistical design and analysis of computer experiments to account efficiently for environmental variables. Using data collected at a relatively small set of training sites, the method employs a computationally inexpensive predictor of the structural response that is statistically motivated. By using this predictor in place of the simulator (e.g., finite element model), a sufficient number of iterations can be performed to facilitate the optimization of the complex system. The applicability of these methods was demonstrated through the design of a femoral component for total hip arthroplasty incorporating variations in joint force orientation and cancellous bone properties. Beams on elastic foundation (BOEF) finite element models were developed to simulate the structural response. These simple models were chosen for their short computation time. This allowed us to represent the actual structural response surface by an exhaustive enumeration of the design and environmental variable space, and provided a means by which to validate the statistical predictor. We were able to predict the structural response and the optimal design accurately using only 16 runs of the computer code. The general trends predicted by the BOEF models were in agreement with previous three-dimensional finite element computer simulations, and experimental and clinical results, which demonstrated that the important features of intramedullary fixation systems were captured. These results indicate that the statistically based optimization methods are appropriate for optimization studies using computationally demanding models.     

Determining the number of specific proteins in cellular compartments by quantitative microscopy

This protocol describes a method for determining both the average number and variance of proteins, in the few to tens of copies, in isolated cellular compartments such as organelles and protein complexes. Other currently available protein quantification techniques either provide an average number, but lack information on the variance, or they are not suitable for reliably counting proteins present in the few to tens of copies. This protocol entails labeling of the cellular compartment with fluorescent primary-secondary antibody complexes, total internal reflection fluorescence microscopic imaging of the cellular compartment, digital image analysis and deconvolution of the fluorescence intensity data. A minimum of 2.5 d is required to complete the labeling, imaging and analysis of a set of samples. As an illustrative example, we describe in detail the procedure used to determine the copy number of proteins in synaptic vesicles. The same procedure can be applied to other organelles or signaling complexes.     

Technical report: application of the Metafer2 fluorescence scanning system for the analysis of radiation-induced chromosome aberrations measured by FISH-chromosome painting

The Metafer2 fluorescence scanning system was used for routine analysis of radiation-induced exchange aberrations measured by fluorescence in situ hybridisation (FISH) chromosome painting in human peripheral lymphocytes. The system enables a rapid and unbiased fully-automated finding and image acquisition of fluorescently stained metaphase spreads. The chromosome aberration analysis is performed interactively from stored digitised processed gallery images, presented on a screen. Appropriate software image filters are available to further improve these pictures by background correction, noise reduction and fluorescence signal enhancement.Data sets generated by computer-assisted and manual scoring of radiation-induced reciprocal translocations (2B) and total 2B (2B+related 'one-way' types) or complete dicentrics (2A) and total 2A (2A+related 'one-ways') involving painted target chromosomes 2, 3 or 4 were compared and no significant differences were found.A linear-quadratic dose-response curve for total translocations (2B+'one-ways'+complex-derived types) based on computer-assisted analysis of 27,741 metaphases with chromosome 4 painting was compared to a curve obtained earlier for manually scored translocations in a set of target chromosomes 1, 4 and 12. After extrapolation to the whole genome, no significant difference between both curves was found.From our results it can be derived that computer-assisted aberration analysis using the Metafer2 system is a reliable alternative to manual analysis. Since time saving for computer-assisted translocation analysis is about 50% compared to manual scoring, this system is highly promising for a practical application in retrospective biodosimetry of human radiation exposure.     

Relative ligand binding to small or large aggregates measured by scanning correlation spectroscopy.

Cell surface receptors transduce signals, required to produce cellular activity, that may be mediated by ligand-induced receptor aggregation. Several receptor systems exhibit both low and high ligand affinities and some models of receptor activation associate receptor clusters with high or low ligand binding affinity. In the present work succinyl concanavalin A, which binds with both high and low affinity to receptors, was studied on 3T3 Swiss mouse fibroblasts, where preaggregation of receptors has been postulated. Scanning fluorescence correlation spectroscopy measurements were used to determine the relationship between the degree of ligand binding and the state of receptor aggregation. Correlation analysis of fluorescence fluctuations across the cell surface reveal that the variance of the fluctuations (quantitated by g[0]) increased when the ligand concentration was varied from 0.33 to 67 mg/L. The g(0) values reached a plateau at concentrations greater than approximately 10 mg/L. These data are incompatible with homogeneous receptor distributions or equal affinity receptor binding but are compatible with a partly aggregated receptor system with high affinity binding to small aggregates, and low affinity binding to large aggregates. Computer simulated scanning fluorescence correlation spectroscopy experiments confirm that background fluorescence from the cell does not account for the experimentally observed effects.     

不同方法检测鸡蛋表面菌落总数的相关性研究

研究了ATP生物荧光检测法与国标法《GB4789.2-2010食品卫生微生物学检验菌落总数测定》检测鸡蛋壳表面细菌总数的相关性。采用ATP生物荧光检测法和国标法对40个混合样品表面细菌总数进行检测,以log CFU/个蛋壳为横坐标(x),以logRLU/个蛋壳为纵坐标(y),分别进行线性、对数、乘幂、指数拟合。结果表明,ATP荧光检测法与国标法检测结果 Pearson相关系数为0.912,线性模型y=0.7306x-1.0041(R2=0.8322)拟合度较高。该试验结果为ATP荧光检测法在鸡蛋壳表面细菌总数快速检测中应用的可行性提供了依据。     

Changes in rRNA levels during stress invalidates results from mRNA blotting: fluorescence in situ rRNA hybridization permits renormalization for estimation of cellular mRNA levels

Regulation of gene expression can be analyzed by a number of different techniques. Some techniques monitor the level of specific mRNA directly, and others monitor indirectly by determining the level of enzymes encoded by the mRNA. Each method has its own inherent way of normalization. When results obtained by these techniques are compared between experiments in which differences in growth rates, strains, or stress treatments occur, the normalization procedure may have a significant impact on the results. In this report we present a solution to the normalization problem in RNA slot blotting experiments, in which mRNA levels routinely are normalized to a fixed amount of extracted total RNA. The cellular levels of specific mRNA species were estimated using a renormalization with the total RNA content per cell. By a combination of fluorescence in situ rRNA hybridization, which estimates the relative level of rRNA per cell, and slot blotting to rRNA probes, which estimates the level of rRNA per extracted total RNA, the amount of RNA per cell was calculated in a series of heat shock experiments with the gram-positive bacterium Lactococcus lactis. It was found that the level of rRNA per cell decreased to 30% in the course of the heat shock. This lowered ribosome level led to a decrease in the total RNA content, resulting in a gradually increasing overestimation of the mRNA levels throughout the experiment. Using renormalized cellular mRNA levels, the HrcA-mediated regulation of the genes in the hrcA-grpE-dnaK operon was analyzed. The hybridization data suggested a complex heat shock regulation indicating that the mRNA levels continued to rise after 30 min, but after renormalization the calculated average cellular levels exhibited a much simpler induction pattern, eventually attaining a moderately increased value.     

Effects of cargo molecules on the cellular uptake of arginine-rich cell-penetrating peptides

The identification of cell-penetrating peptides (CPPs) as vectors for the intracellular delivery of conjugated molecules such as peptides, proteins, and oligonucleotides has emerged as a significant tool to modulate biological activities inside cells. The mechanism of CPP uptake by the cells is still unclear, and appears to be both endocytotic and non-endocytotic, depending on the CPP and cell type. Moreover, it is also unknown whether cargo sequences have an effect on the uptake and cellular distribution properties of CPP sequences. Here, we combine results from quantitative fluorescence microscopy and binding to lipid membrane models to determine the effect of cargo peptide molecules on the cellular uptake and distribution of the arginine-rich CPPs, R7, and R7W, in live cells. Image analysis algorithms that quantify fluorescence were used to measure the relative amount of peptide taken up by the cell, as well as the extent to which the uptake was endocytotic in nature. The results presented here indicate that fusion of arginine-rich CPPs to peptide sequences reduces the efficiency of uptake, and dramatically changes the cellular distribution of the CPP from a diffuse pattern to one in which the peptides are mostly retained in endosomal compartments.     

Effects of cargo molecules on the cellular uptake of arginine-rich cell-penetrating peptides

The identification of cell-penetrating peptides (CPPs) as vectors for the intracellular delivery of conjugated molecules such as peptides, proteins, and oligonucleotides has emerged as a significant tool to modulate biological activities inside cells. The mechanism of CPP uptake by the cells is still unclear, and appears to be both endocytotic and non-endocytotic, depending on the CPP and cell type. Moreover, it is also unknown whether cargo sequences have an effect on the uptake and cellular distribution properties of CPP sequences. Here, we combine results from quantitative fluorescence microscopy and binding to lipid membrane models to determine the effect of cargo peptide molecules on the cellular uptake and distribution of the arginine-rich CPPs, R₇, and R₇W, in live cells. Image analysis algorithms that quantify fluorescence were used to measure the relative amount of peptide taken up by the cell, as well as the extent to which the uptake was endocytotic in nature. The results presented here indicate that fusion of arginine-rich CPPs to peptide sequences reduces the efficiency of uptake, and dramatically changes the cellular distribution of the CPP from a diffuse pattern to one in which the peptides are mostly retained in endosomal compartments.     

Pyrene binary probes for unambiguous detection of mRNA using time-resolved fluorescence spectroscopy

We report here the design, synthesis and application of pyrene binary oligonucleotide probes for selective detection of cellular mRNA. The detection strategy is based on the formation of a fluorescent excimer when two pyrene groups are brought into close proximity upon hybridization of the probes with the target mRNA. The pyrene excimer has a long fluorescence lifetime (>40 ns) compared with that of cellular extracts (~7 ns), allowing selective detection of the excimer using time-resolved emission spectra (TRES). Optimized probes were used to target a specific region of sensorin mRNA yielding a strong excimer emission peak at 485 nm in the presence of the target and no excimer emission in the absence of the target in buffer solution. While direct fluorescence measurement of neuronal extracts showed a strong fluorescent background, obscuring the detection of the excimer signal, time-resolved emission measurements indicated that the emission decay of the cellular extracts is ~8 times faster than that of the pyrene excimer probes. Thus, using TRES of the pyrene probes, we are able to selectively detect mRNA in the presence of cellular extracts, demonstrating the potential for application of pyrene excimer probes for imaging mRNAs in cellular environments that have background fluorescence.     

A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays

Analysing pooled DNA on microarrays is an efficient way to genotype hundreds of individuals for thousands of markers for genome-wide association. Although direct comparison of case and control fluorescence scores is possible, correction for differential hybridization of alleles is important, particularly for rare single nucleotide polymorphisms. Such correction relies on heterozygous fluorescence scores and requires the genotyping of hundreds of individuals to obtain sufficient estimates of the correction factor, completely negating any benefit gained by pooling samples. We explore the effect of differential hybridization on test statistics and provide a solution to this problem in the form of a central resource for the accumulation of heterozygous fluorescence scores, allowing accurate allele frequency estimation at no extra cost.     

Mapping of cellular compartments based on ultrastructural immunogold labeling

Ultrastructural identification of subcellular morphologically inconspicuous compartments is based on detection of specific molecules or by a presence of specific functions. Such compartments are detected using antibodies with attached label, usually gold particles. However, the gold particles have a point pattern, while a compartment is a coherent area. In addition, some background labeling is always present that complicates identification of the labeled compartments. The aim of this study was therefore to develop a stereological method that would enable us to define cellular compartments based on delineating the borders of gold particle clusters, and to test the practical use of the method using biological experimental data. New computer program plug-ins were developed to facilitate the practical use of the stereological method. The kernel estimation method was successfully tested by detection of ribosomal rRNA over morphologically recognizable nucleoli. In a next step, we successfully detected individual chromosomal domains-nuclear compartments that cannot be distinguished in cell nuclei morphologically. The results show that the new stereological/image analysis method is well able to discriminate cellular compartments based on density of immunogold particles. The plug-ins were made available to scientific community at http://nucleus.biomed.cas.cz/gold.     

Total internal reflection with fluorescence correlation spectroscopy: nonfluorescent competitors

Total internal reflection with fluorescence correlation spectroscopy is a method for measuring the surface association/dissociation rate constants and absolute densities of fluorescent molecules at the interface of a planar substrate and solution. This method can also report the apparent diffusion coefficient and absolute concentration of fluorescent molecules very close to the surface. Theoretical expressions for the fluorescence fluctuation autocorrelation function when both surface association/dissociation kinetics and diffusion through the evanescent wave, in solution, contribute to the fluorescence fluctuations have been published previously. In the work described here, the nature of the autocorrelation function when both surface association/dissociation kinetics and diffusion through the evanescent wave contribute to the fluorescence fluctuations, and when fluorescent and nonfluorescent molecules compete for surface binding sites, is described. The autocorrelation function depends in general on the kinetic association and dissociation rate constants of the fluorescent and nonfluorescent molecules, the surface site density, the concentrations of fluorescent and nonfluorescent molecules in solution, the solution diffusion coefficients of the two chemical species, the depth of the evanescent field, and the size of the observed area on the surface. Both general and approximate expressions are presented.     

Re-absorption of chlorophyll fluorescence in leaves revisited. A comparison of correction models.

The application of correction methods to account for re-absorption of chlorophyll fluorescence emission in leaves is subject to a number of controversies in the literature. These uncertainties lead to high discrepancies in the corrected spectral distribution of fluorescence and consequently in the interpretation of related physiological features of plants, according to the chosen method used in the process of correction. In this research, three correction methods, based on transmittance and/or reflectance measurements on leaves, were analysed comparatively. One method gave high values for the corrected fluorescence ratio between 685 nm and 737 nm (F685/F737 approximately 7 to 20 according to the different species of leaves). The two other methods were found to give similar results with corrected fluorescence ratios around a value of two (F685/F737 approximately 2). While the first method was developed in the light of empirical considerations, the latter two models are based upon defined physical approaches depicting interaction between light and matter. The theoretical basis of these methods, the validation methodologies used to support them and the similarity in the spectra corrected by light re-absorption for both models, all showed that they should be treated as confident and suitable approximations to solve the problem of light re-absorption in leaves.     

An iron-dependent and transferrin-mediated cellular uptake pathway for plutonium

Plutonium is a toxic synthetic element with no natural biological function, but it is strongly retained by humans when ingested. Using small-angle X-ray scattering, receptor binding assays and synchrotron X-ray fluorescence microscopy, we find that rat adrenal gland (PC12) cells can acquire plutonium in vitro through the major iron acquisition pathway--receptor-mediated endocytosis of the iron transport protein serum transferrin; however, only one form of the plutonium-transferrin complex is active. Low-resolution solution models of plutonium-loaded transferrins derived from small-angle scattering show that only transferrin with plutonium bound in the protein's C-terminal lobe (C-lobe) and iron bound in the N-terminal lobe (N-lobe) (Pu(C)Fe(N)Tf) adopts the proper conformation for recognition by the transferrin receptor protein. Although the metal-binding site in each lobe contains the same donors in the same configuration and both lobes are similar, the differences between transferrin's two lobes act to restrict, but not eliminate, cellular Pu uptake.     

细胞代谢复杂网络研究进展

复杂网络理论为细胞代谢网络研究提供了新的工具,基于复杂网络理论的细胞代谢网络研究可称细胞代谢复杂网络研究．先简要介绍了细胞代谢复杂网络的研究背景;随后详细总结和论述了细胞代谢复杂网络在建模、分析和控制三个方面的研究现状;再进一步指出了细胞代谢复杂网络在建模、分析和控制这三个方面研究中所存在的一些问题．为细胞代谢复杂网络领域的研究指出了一些有意义的方向,具有一定的参考价值。     

Compliance and cost control for cryopreservation of cellular starting materials: An industry perspective

Over the last decade, cancer immunotherapy has progressed from an academically interesting field to one of the most promising forms of new treatments in which not the cancer but the immune system is treated. In particular, genetic modification for purposeful redirection of autologous T cells is providing hope to many treatment-resistant patients. This personalized form of medicine is radically different from more traditional oncologic drugs. With these evolving medical advancements and more cellular therapies becoming available, some regulatory agencies have created new regulatory requirements to manage the production of these types of products. The regulations are specifically suited for the manufacture of gene and cell therapy products, as they use a risk-based approach towards product development and manufacturing, when there is limited characterization available. The correct interpretation of how and when requirements apply is crucial, since theoretical approaches to implementing GMP can easily lead to disproportionate and unwarranted restrictions that may not address the specific risks that regulators were intending to control. This is especially relevant for cell collection and biopreservation preceding the manufacturing process for products manufactured from autologous T cells. Both the fresh and cryopreserved apheresis materials can be filed as minimally manipulated starting materials to the authorities. The preservation of such cellular material can then routinely be managed using the available regulations for tissues and cells, allowing for a more fit-for-purpose approach to the control measures implemented.     

Image correlation spectroscopy. II. Optimization for ultrasensitive detection of preexisting platelet-derived growth factor-beta receptor oligomers on intact cells.

Previously we introduced image correlation spectroscopy (ICS) as an imaging analog of fluorescence correlation spectroscopy (FCS). Implementation of ICS with image collection via a standard fluorescence confocal microscope and computer-based autocorrelation analysis was shown to facilitate measurements of absolute number densities and determination of changes in aggregation state for fluorescently labeled macromolecules. In the present work we illustrate how to use ICS to quantify the aggregation state of immunolabeled plasma membrane receptors in an intact cellular milieu, taking into account background fluorescence. We introduce methods that enable us to completely remove white noise contributions from autocorrelation measurements for individual images and illustrate how to perform background corrections for autofluorescence and nonspecific fluorescence on cell population means obtained via ICS. The utilization of photon counting confocal imaging with ICS analysis in combination with the background correction techniques outlined enabled us to achieve very low detection limits with standard immunolabeling methods on normal, nontransformed human fibroblasts (AG1523) expressing relatively low numbers of platelet-derived growth factor-beta (PDGF-beta) receptors. Specifically, we determined that the PDGF-beta receptors were preaggregated as tetramers on average with a mean surface density of 2.3 clusters micrometer(-2) after immunolabeling at 4 degreesC. These measurements, which show preclustering of PDGF-beta receptors on the surface of normal human fibroblasts, contradict a fundamental assumption of the ligand-induced dimerization model for signal transduction and provide support for an alternative model that posits signal transduction from within preexisting receptor aggregates.