Analysis of Time-Varying Biological Data Using Rainflow Cycle Counting

A wide range of biological investigations lead to time-history data. The characterization of such data can be difficult particularly in the presence of signal noise or superimposed signals. Several methods are described which can be brought to bear including FFT, thresholding, peak counting, and range counting. However, each of these approaches has significant disadvantages. In this paper we describe a novel method, known as rainflow cycle counting, for characterizing time varying biological time-history data in terms of spiking or oscillation amplitude and frequency. Rainflow counting is a straightforward algorithm for identifying complete cycles in the data and determining their amplitudes. The approach is simple, reliable, easily lends itself to automation, and robust even in the presence of superimposed signals or background noise. After describing the method, its use and behavior are demonstrated on three sample histories of intracellular calcium concentration in chondrocytes exposed to fluid shear stress. The method is also applied to a more challenging data set that has had an artificial random error included. The results demonstrate that the rainflow counting algorithm identifies signal oscillations and appropriately determines their amplitudes even when superimposed or distorted by background noise. These attractive properties make rainflow counting a powerful approach for quantifying and characterizing biological time histories.     

Primary culture of gustatory receptor neurons from the blowfly, Phormia regina

Flies provide a powerful model system for exploring signaling systems in gustatory receptor neurons (GRNs). To elucidate the cellular and molecular bases of these signaling systems, we sought to develop techniques to dissociate GRNs. We developed a primary culture of GRNs isolated from the labella of the blowfly, Phormia regina, 4-5 days after pupation. Dissected labella were treated with papain in a low Ca2+ saline solution and shaken in Leibovitz's L-15 medium supplemented with 20-hydroxyecdysone, L-ascorbic acid, and trehalose with a test tube mixer. Released cells were plated and kept at 29 degrees C in a medium containing fetal bovine serum. After a minimum of 2 days in culture, we observed survival or growth of bipolar cells with the characteristic morphology of GRNs. We also examined taste responsiveness by monitoring intracellular Ca2+ with a Ca2+-sensitive fluorescent dye, fluo-3. For some bipolar cells, application of sucrose, NaCl, or LiCl for 5-20 s transiently increased the intracellular Ca2+ levels in cell bodies for 20-30 s. The primary cell culture described here is useful for functional analysis of GRNs.     

生物实验数据的两因素方差分析

结合实例详细地叙述了生物实验数据的两因素方差分析计算方法,具有较强的实用意义。并介绍了如何分析计算结果。     

基因芯片数据分析过程:从原始数据到生物学意义

基因芯片实验要得到可靠的生物学结论,必须基于优化的实验设计和科学的数据分析。讨论了与基因芯片数据分析方法相关的实验设计方面的几个问题,简述了差异表达分析、聚类分析及功能富集分析等分析方法及其进展,并介绍了部分软件及应用。     

Expression of mutant SOD1 in astrocytes induces functional deficits in motoneuron mitochondria

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by motoneuron degeneration resulting in paralysis and eventual death. ALS is regarded as a motoneuron-specific disorder but increasing evidence indicates non-neuronal cells play a significant role in disease pathogenesis. Although the precise aetiology of ALS remains unclear, mutations in the superoxide dismutase (SOD1) gene are known to account for approximately 20% of familial ALS. We examined the influence of SOD1(G93A) expression in astrocytes on mitochondrial homeostasis in motoneurons in a primary astrocyte : motoneuron co-culture model. SOD1(G93A) expression in astrocytes induced changes in mitochondrial function of both SOD1(G93A) and wild-type motoneurons. In the presence of SOD1(G93A) astrocytes, mitochondrial redox state of both wild-type and SOD1(G93A) motoneurons was more reduced and mitochondrial membrane potential decreased. While intra-mitochondrial calcium levels [Ca(2+)](m) were elevated in SOD1(G93A) motoneurons, changes in mitochondrial function did not correlate with [Ca(2+)](m). Thus, expression of SOD1(G93A) in astrocytes directly alters mitochondrial function even in embryonic motoneurons, irrespective of genotype. These early deficits in mitochondrial function induced by surrounding astrocytes may increase the vulnerability of motoneurons to other neurotoxic mechanisms involved in ALS pathogenesis.     

Exploratory Data Analysis of the Multilevel Anthropogenic Zinc Cycle

A comprehensive multilevel contemporary cycle for stocks and flows of zinc is analyzed by the tools of exploratory data analysis. The analysis is performed at three discrete organizational levels—country (53 countries and 1 country group that together comprise essentially all anthropogenic stocks and flows of zinc), world region (9 world regions), and the planet as a whole. The results demonstrate the following: (1) Exploratory data analysis provides valuable and otherwise unobtainable information about material flows, especially those across multiple spatial levels. (2) All distributions of countrylevel zinc stock and flow data are highly skewed, a few countries having large magnitudes, many having small magnitudes. Rates of fabrication of zinc-containing products for the countries are poorly correlated with rates of extraction, reflecting the fact that many countries that extract zinc do not fabricate products from zinc to any significant degree, and vice versa. (4) Virtually all countries are adding zinc to stock in the use phase (in galvanizing applications, zinc castings, etc.). These rates of addition are highly correlated with rates of zinc entering use in all regions, and are higher in regions under vigorous development. (5) With weak confidence, the rate of zinc landfilling by countries appears to be highly correlated with the rate of discard. (6) The statistical distributions of regional-level zinc cycle parameters are approximately log normal. (7) The extremes of normalized statistical distributions of zinc flow values are broader at lower spatial levels (country versus region, for example), but regional interquartile ranges for zinc entering use and zinc discards are higher at regional level then at country level.     

Radial spread of aequorin Ca2+ signal in single frog skeletal muscle fibers

The Ca²⁺-sensitive photoprotein aequorin was injected into single frog skeletal muscle fibers, and the intracellular aequorin light intensity during muscle activation with different maneuvers was mapped with digital imaging microscopy. During 50 Hz electrical activation (tetanus), the aequorin light intensity from different locations in the muscle fiber rose with very similar time course. Caffeine (10 mM) application, on the other hand, caused aequorin light signals to show significantly different time courses, with an earlier increase in Ca²⁺ concentration near the surface of the fiber than near the core. The non-uniform rise of intracellular Ca²⁺ concentration with caffeine treatment is consistent with the slow inward diffusion of caffeine and subsequent Ca²⁺ release from sarcoplasmic reticulum.     

Facilitated intracellular transport of TrkA by an interaction with nerve growth factor

Intracellular transport of neurotrophin receptors together with neurotrophins is one of the key events of neurotrophin signaling for the growth and the survival of neurons. However, the involvement of neurotrophin signaling in the regulation of intracellular transport of neurotrophin receptors has been remained unclear. We visualized the behavior of TrkA, a receptor of nerve growth factor (NGF), by labeling with GFP in PC12 cells. We found remarkable changes of the behavior of TrkA-GFP upon the application of NGF. Before the application, only ~37% of the fluorescent dots of TrkA showed translocations along neurites of PC12 cells. After the application, number of the dots showing the directional movement increased to ~65%. The averaged velocities of the directional movement of TrkA-GFP dots became higher after the application of NGF. We tested the idea whether NGF binding accelerated the translocations of TrkA by simultaneously observing TrkA-GFP and fluorescently labeled NGF, Cy3.5-NGF. The velocity of TrkA-GFP dots associated with Cy3.5-NGF was remarkably higher than that of TrkA-GFP dots without Cy3.5-NGF. On the basis of these observations, we hypothesize that there is a signaling mechanism within a single vesicle that facilitates the intracellular transport of each vesicle containing the activated TrkA.     

In Vivo image Analysis Using iRFP Transgenic Mice

Fluorescent proteins with light wavelengths within the optical window are one of the improvements in in vivo imaging techniques. Near-infrared (NIR) fluorescent protein (iRFP) is a stable, nontoxic protein that emits fluorescence within the NIR optical window without the addition of exogenous substrate. However, studies utilizing an in vivo iRFP model have not yet been published. Here, we report the generation of transgenic iRFP mice with ubiquitous NIR fluorescence expression. iRFP expression was observed in approximately 50% of the offspring from a matings between iRFP transgenic and WT mice. The serum and blood cell indices and body weights of iRFP mice were similar to those of WT mice. Red fluorescence with an excitation wavelength of 690 nm and an emission wavelength of 713 nm was detected in both newborn and adult iRFP mice. We also detected fluorescence emission in whole organs of the iRFP mice, including the brain, heart, liver, kidney, spleen, lung, pancreas, bone, testis, thymus, and adipose tissue. Therefore, iRFP transgenic mice may therefore be a useful tool for various types of in vivo imaging.     

Intracellular pH change does not appear as a prerequisite for triggering activation of Barnea candida (Mollusca,Pelecypoda) oocytes

Barnea Candida oocytes, exposed to excess KCl, ammonia, or digitonin, exhibit germinal vesicle breakdown (GVBD) and reinitiate meiosis, at least up to first polar body extrusion. While we confirm that KCl—but not ammonia-induced activation requires external calcium, our findings that digitonin is effective at any pH from 6 to 8, in the presence of calcium, while the phorbol ester TPA and diacylglycerol fail to reinitiate meiosis, strongly suggests calcium as the main trigger for this process. Preliminary experiments using the fluorescent probes fluorescein diacetate and Quin 2/AM show, moreover, that KCl and ammonia produce both an intracellular calcium surge (30 nM) and a slight alkalinization of the intracellular cytoplasm from 7.84 to 8.05.     

Using a Genetically Encoded Sensor to Identify Inhibitors of Toxoplasma gondii Ca2+ Signaling

The life cycles of apicomplexan parasites progress in accordance with fluxes in cytosolic Ca²⁺. Such fluxes are necessary for events like motility and egress from host cells. We used genetically encoded Ca²⁺ indicators (GCaMPs) to develop a cell-based phenotypic screen for compounds that modulate Ca²⁺ signaling in the model apicomplexan Toxoplasma gondii. In doing so, we took advantage of the phosphodiesterase inhibitor zaprinast, which we show acts in part through cGMP-dependent protein kinase (protein kinase G; PKG) to raise levels of cytosolic Ca²⁺. We define the pool of Ca²⁺ regulated by PKG to be a neutral store distinct from the endoplasmic reticulum. Screening a library of 823 ATP mimetics, we identify both inhibitors and enhancers of Ca²⁺ signaling. Two such compounds constitute novel PKG inhibitors and prevent zaprinast from increasing cytosolic Ca²⁺. The enhancers identified are capable of releasing intracellular Ca²⁺ stores independently of zaprinast or PKG. One of these enhancers blocks parasite egress and invasion and shows strong antiparasitic activity against T. gondii. The same compound inhibits invasion of the most lethal malaria parasite, Plasmodium falciparum. Inhibition of Ca²⁺-related phenotypes in these two apicomplexan parasites suggests that depletion of intracellular Ca²⁺ stores by the enhancer may be an effective antiparasitic strategy. These results establish a powerful new strategy for identifying compounds that modulate the essential parasite signaling pathways regulated by Ca²⁺, underscoring the importance of these pathways and the therapeutic potential of their inhibition.     

Calcium wave propagation in pancreatic acinar cells: functional interaction of inositol 1,4,5-trisphosphate receptors, ryanodine receptors, and mitochondria

In pancreatic acinar cells, inositol 1,4,5-trisphosphate (InsP(3))-dependent cytosolic calcium ([Ca(2+)](i)) increases resulting from agonist stimulation are initiated in an apical "trigger zone," where the vast majority of InsP(3) receptors (InsP(3)R) are localized. At threshold stimulation, [Ca(2+)](i) signals are confined to this region, whereas at concentrations of agonists that optimally evoke secretion, a global Ca(2+) wave results. Simple diffusion of Ca(2+) from the trigger zone is unlikely to account for a global [Ca(2+)](i) elevation. Furthermore, mitochondrial import has been reported to limit Ca(2+) diffusion from the trigger zone. As such, there is no consensus as to how local [Ca(2+)](i) signals become global responses. This study therefore investigated the mechanism responsible for these events. Agonist-evoked [Ca(2+)](i) oscillations were converted to sustained [Ca(2+)](i) increases after inhibition of mitochondrial Ca(2+) import. These [Ca(2+)](i) increases were dependent on Ca(2+) release from the endoplasmic reticulum and were blocked by 100 microM ryanodine. Similarly, "uncaging" of physiological [Ca(2+)](i) levels in whole-cell patch-clamped cells resulted in rapid activation of a Ca(2+)-activated current, the recovery of which was prolonged by inhibition of mitochondrial import. This effect was also abolished by ryanodine receptor (RyR) blockade. Photolysis of d-myo InsP(3) P(4(5))-1-(2-nitrophenyl)-ethyl ester (caged InsP(3)) produced either apically localized or global [Ca(2+)](i) increases in a dose-dependent manner, as visualized by digital imaging. Mitochondrial inhibition permitted apically localized increases to propagate throughout the cell as a wave, but this propagation was inhibited by ryanodine and was not seen for minimal control responses resembling [Ca(2+)](i) puffs. Global [Ca(2+)](i) rises initiated by InsP(3) were also reduced by ryanodine, limiting the increase to a region slightly larger than the trigger zone. These data suggest that, while Ca(2+) release is initially triggered through InsP(3)R, release by RyRs is the dominant mechanism for propagating global waves. In addition, mitochondrial Ca(2+) import controls the spread of Ca(2+) throughout acinar cells by modulating RyR activation.     

综述——新型纳米生物材料的研发：稀土上转换荧光纳米材料的制备与生物应用

近几年,稀土上转换荧光纳米材料作为新型的荧光探针受到研究者的广泛关注,其优势在于光化学稳定性好、发射谱带窄、荧光寿命长、Stokes位移大等．同时,它利用近红外激光器作为激发光源,组织穿透能力好、对生物组织的损伤小、几乎没有背景荧光,使其应用于生物活体荧光成像成为可能．本文主要综述了最近稀土上转换荧光纳米材料在制备与生物应用方面的研究进展．     

Using Median Lines in Robust Bivariate Data Analysis

Methods for robust comparison of bivariate errors-in-variables are considered. The concept of median lines is introduced for the robust estimation of principal components. Median lines separate the bivariate sample space into two equally sized parts. Statistical properties of the model parameters are derived. Robust residual analysis assesses linear relationships as well as goodness of fit and allows for the detection of potential outliers. Special emphasis is laid on graphical methods. A bivariate box-plot is proposed for exploratory data analysis. The median lines procedure is illustrated by a real example.     

基于独立元分析和非线性指数分析的脑电信号中伪迹分量的自动去除

脑电(electroencephalography,EEG)信号中不可避免地存在着眼动、心跳、肌电信号以及线性噪声等伪迹干扰,这些伪迹的存在极大地影响了脑电信号分析的准确性,因此在进行脑电信号分析前需要去除伪迹干扰。为了有效地去除伪迹,结合独立元分析和非线性指数分析,提出一种自动识别并去除脑电信号中伪迹分量的方法。该方法还可同时用于提取脑电信号中的基本节律如!波等。相应的模拟与实际脑电数据的实验结果表明所提议的方法具有很好的识别和去除脑电信号伪迹分量的性能。     

Intracellular calcium activity in isolated bovine adrenal chromaffin cells in the presence and absence of 60 Hz magnetic fields

This study examined whether 60 Hz magnetic field (MF) exposure alters intracellular calcium levels ([Ca(2+)](i)) in isolated bovine adrenal chromaffin cells, a classic model of neural responses. [Ca(2+)](i) was monitored by fluorescence video imaging of cells loaded with the calcium indicator fluo-4 during exposures to magnetic flux densities of 0.01, 0.1, 1.0, 1.4, or 2.0 mT. MFs generated by Helmholtz coils constructed from bifilar wire allowed both 60 Hz field and sham exposures. Following a 5 min monitoring period to establish baseline patterns, cells were subjected for 10 min to a 60 Hz MF, sham field or no field. Reference calcium responses and assessment of cell excitability were obtained by the sequential addition of the nicotinic cholinergic receptor agonist dimethylphenylpiperazinium (DMPP) and a depolarizing concentration of KCl. Throughout an 8 day culture period, cells exhibited spontaneous fluctuations in [Ca(2+)](i). Comparisons of the number of cells exhibiting transients, the number and types of calcium transients, as well as the time during monitoring when transients occurred showed no significant differences between MF exposed cells and either sham exposed or nonexposed cells. With respect to the percentage of cells responding to DMPP, differences between 1 and 2 mT exposed cells and both nonexposed and sham exposed cells reached statistical significance during the first day in culture. No statistically significant differences were observed for responses to KCl. In summary, our data indicate that [Ca(2+)](i) in chromaffin cells is unaffected by the specific 60 Hz MF intensities used in this study. On the other hand, plasma membrane nicotinic receptors may be affected in a manner that is important for ligand-receptor interactions.     

Distribution and Function of Cardiac Ryanodine Receptor Clusters in Live Ventricular Myocytes

The cardiac Ca²⁺ release channel (ryanodine receptor, RyR2) plays an essential role in excitation-contraction coupling in cardiac muscle cells. Effective and stable excitation-contraction coupling critically depends not only on the expression of RyR2, but also on its distribution. Despite its importance, little is known about the distribution and organization of RyR2 in living cells. To study the distribution of RyR2 in living cardiomyocytes, we generated a knock-in mouse model expressing a GFP-tagged RyR2 (GFP-RyR2). Confocal imaging of live ventricular myocytes isolated from the GFP-RyR2 mouse heart revealed clusters of GFP-RyR2 organized in rows with a striated pattern. Similar organization of GFP-RyR2 clusters was observed in fixed ventricular myocytes. Immunofluorescence staining with the anti-α-actinin antibody (a z-line marker) showed that nearly all GFP-RyR2 clusters were localized in the z-line zone. There were small regions with dislocated GFP-RyR2 clusters. Interestingly, these same regions also displayed dislocated z-lines. Staining with di-8-ANEPPS revealed that nearly all GFP-RyR2 clusters were co-localized with transverse but not longitudinal tubules, whereas staining with MitoTracker Red showed that GFP-RyR2 clusters were not co-localized with mitochondria in live ventricular myocytes. We also found GFP-RyR2 clusters interspersed between z-lines only at the periphery of live ventricular myocytes. Simultaneous detection of GFP-RyR2 clusters and Ca²⁺ sparks showed that Ca²⁺ sparks originated exclusively from RyR2 clusters. Ca²⁺ sparks from RyR2 clusters induced no detectable changes in mitochondrial Ca²⁺ level. These results reveal, for the first time, the distribution of RyR2 clusters and its functional correlation in living ventricular myocytes.     

More Accurate Dose-Response Estimation Using Monte-Carlo Uncertainty Analysis: The Data Cube Approach

The traditional q₁ ^* methodology for constructing upper confidence limits (UCLs) for the low-dose slopes of quantal dose-response functions has two limitations: (i) it is based on an asymptotic statistical result that has been shown via Monte Carlo simulation not to hold in practice for small, real bioassay experiments (Portier and Hoel, 1983); and (ii) it assumes that the multistage model (which represents cumulative hazard as a polynomial function of dose) is correct. This paper presents an uncertainty analysis approach for fitting dose-response functions to data that does not require specific parametric assumptions or depend on asymptotic results. It has the advantage that the resulting estimates of the dose-response function (and uncertainties about it) no longer depend on the validity of an assumed parametric family nor on the accuracy of the asymptotic approximation. The method derives posterior densities for the true response rates in the dose groups, rather than deriving posterior densities for model parameters, as in other Bayesian approaches (Sielken, 1991), or resampling the observed data points, as in the bootstrap and other resampling methods. It does so by conditioning constrained maximum-entropy priors on the observed data. Monte Carlo sampling of the posterior (constrained, conditioned) probability distributions generate values of response probabilities that might be observed if the experiment were repeated with very large sample sizes. A dose-response curve is fit to each such simulated dataset. If no parametric model has been specified, then a generalized representation (e.g., a power-series or orthonormal polynomial expansion) of the unknown dose-response function is fit to each simulated dataset using “model-free” methods. The simulation-based frequency distribution of all the dose-response curves fit to the simulated datasets yields a posterior distribution function for the low-dose slope of the dose-response curve. An upper confidence limit on the low-dose slope is obtained directly from this posterior distribution. This “Data Cube” procedure is illustrated with a real dataset for benzene, and is seen to produce more policy-relevant insights than does the traditional q₁ ^* methodology. For example, it shows how far apart are the 90%, 95%, and 99% limits and reveals how uncertainty about total and incremental risk vary with dose level (typically being dominated at low doses by uncertainty about the response of the control group, and being dominated at high doses by sampling variability). Strengths and limitations of the Data Cube approach are summarized, and potential decision-analytic applications to making better informed risk management decisions are briefly discussed.