Exploring Dynamics of Molybdate in Living Animal Cells by a Genetically Encoded FRET Nanosensor

Molybdenum (Mo) is an essential trace element for almost all living organisms including animals. Mo is used as a catalytic center of molybdo-enzymes for oxidation/reduction reactions of carbon, nitrogen, and sulfur metabolism. Whilst living cells are known to import inorganic molybdate oxyanion from the surrounding environment, the in vivo dynamics of cytosolic molybdate remain poorly understood as no appropriate indicator is available for this trace anion. We here describe a genetically encoded Förester-resonance-energy-transfer (FRET)-based nanosensor composed of CFP, YFP and the bacterial molybdate-sensor protein ModE. The nanosensor MolyProbe containing an optimized peptide-linker responded to nanomolar-range molybdate selectively, and increased YFP:CFP fluorescence intensity ratio by up to 109%. By introduction of the nanosensor, we have been able to successfully demonstrate the real-time dynamics of molybdate in living animal cells. Furthermore, time course analyses of the dynamics suggest that novel oxalate-sensitive- and sulfate-resistant- transporter(s) uptake molybdate in a model culture cell.     

High-resolution Time-lapse Imaging and Automated Analysis of Microtubule Dynamics in Living Human Umbilical Vein Endothelial Cells

The physiological process by which new vasculature forms from existing vasculature requires specific signaling events that trigger morphological changes within individual endothelial cells (ECs). These processes are critical for homeostatic maintenance such as wound healing, and are also crucial in promoting tumor growth and metastasis. EC morphology is defined by the organization of the cytoskeleton, a tightly regulated system of actin and microtubule (MT) dynamics that is known to control EC branching, polarity and directional migration, essential components of angiogenesis. To study MT dynamics, we used high-resolution fluorescence microscopy coupled with computational image analysis of fluorescently-labeled MT plus-ends to investigate MT growth dynamics and the regulation of EC branching morphology and directional migration. Time-lapse imaging of living Human Umbilical Vein Endothelial Cells (HUVECs) was performed following transfection with fluorescently-labeled MT End Binding protein 3 (EB3) and Mitotic Centromere Associated Kinesin (MCAK)-specific cDNA constructs to evaluate effects on MT dynamics. PlusTipTracker software was used to track EB3-labeled MT plus ends in order to measure MT growth speeds and MT growth lifetimes in time-lapse images. This methodology allows for the study of MT dynamics and the identification of how localized regulation of MT dynamics within sub-cellular regions contributes to the angiogenic processes of EC branching and migration.     

Membrane Protein Dimerization in Cell-Derived Lipid Membranes Measured by FRET with MC Simulations

Many membrane proteins are thought to function as dimers or higher oligomers, but measuring membrane protein oligomerization in lipid membranes is particularly challenging. Förster resonance energy transfer (FRET) and fluorescence cross-correlation spectroscopy are noninvasive, optical methods of choice that have been applied to the analysis of dimerization of single-spanning membrane proteins. However, the effects inherent to such two-dimensional systems, such as the excluded volume of polytopic transmembrane proteins, proximity FRET, and rotational diffusion of fluorophore dipoles, complicate interpretation of FRET data and have not been typically accounted for. Here, using FRET and fluorescence cross-correlation spectroscopy, we introduce a method to measure surface protein density and to estimate the apparent Förster radius, and we use Monte Carlo simulations of the FRET data to account for the proximity FRET effect occurring in confined two-dimensional environments. We then use FRET to analyze the dimerization of human rhomboid protease RHBDL2 in giant plasma membrane vesicles. We find no evidence for stable oligomers of RHBDL2 in giant plasma membrane vesicles of human cells even at concentrations that highly exceed endogenous expression levels. This indicates that the rhomboid transmembrane core is intrinsically monomeric. Our findings will find use in the application of FRET and fluorescence correlation spectroscopy for the analysis of oligomerization of transmembrane proteins in cell-derived lipid membranes.     

RootAnalyzer: A Cross-Section Image Analysis Tool for Automated Characterization of Root Cells and Tissues

The morphology of plant root anatomical features is a key factor in effective water and nutrient uptake. Existing techniques for phenotyping root anatomical traits are often based on manual or semi-automatic segmentation and annotation of microscopic images of root cross sections. In this article, we propose a fully automated tool, hereinafter referred to as RootAnalyzer, for efficiently extracting and analyzing anatomical traits from root-cross section images. Using a range of image processing techniques such as local thresholding and nearest neighbor identification, RootAnalyzer segments the plant root from the image’s background, classifies and characterizes the cortex, stele, endodermis and epidermis, and subsequently produces statistics about the morphological properties of the root cells and tissues. We use RootAnalyzer to analyze 15 images of wheat plants and one maize plant image and evaluate its performance against manually-obtained ground truth data. The comparison shows that RootAnalyzer can fully characterize most root tissue regions with over 90% accuracy.     

Statistical Dynamics of Flowing Red Blood Cells by Morphological Image Processing

Blood is a dense suspension of soft non-Brownian cells of unique importance. Physiological blood flow involves complex interactions of blood cells with each other and with the environment due to the combined effects of varying cell concentration, cell morphology, cell rheology, and confinement. We analyze these interactions using computational morphological image analysis and machine learning algorithms to quantify the non-equilibrium fluctuations of cellular velocities in a minimal, quasi-two-dimensional microfluidic setting that enables high-resolution spatio-temporal measurements of blood cell flow. In particular, we measure the effective hydrodynamic diffusivity of blood cells and analyze its relationship to macroscopic properties such as bulk flow velocity and density. We also use the effective suspension temperature to distinguish the flow of normal red blood cells and pathological sickled red blood cells and suggest that this temperature may help to characterize the propensity for stasis in Virchow''s Triad of blood clotting and thrombosis.     

利用荧光共振能量转移技术监测高通量低能量激光诱导细胞凋亡过程中caspase-3活性的动态变化

荧光共振能量转移可用于对生物大分子之间的距离进行定性、定量检测。应用荧光共振能量转移技术对高通量低能量激光诱导肺腺癌细胞凋亡过程中caspase-3的激活过程进行实时动态监测。实验结果表明:高通量低能量激光可以诱导肺腺癌细胞(human lung adenocarcinoma cell,ASTC-a-1)凋亡。同时荧光共振能量转移技术是一个有效的监测caspase-3在凋亡过程中活性动态变化的方法。     

Quantification of Fungal Hyphae in Leaves of Deciduous Trees by Automated Image Analysis

An optical method to quantify the fungal hyphae within decomposing leaves of deciduous trees was developed. The plant matrix was partially destroyed under hydrolytic conditions, and fungal hyphae and cellulose residues within the leaves were stained with Calcofluor M2R. Cellulose residues were subsequently depolymerized by cellulase, and fungal hyphae were separated from the remaining plant matrix with a pressurized air-water mixture. An image analysis program to quantify the fungal hyphae was written. The program included the recognition of fungal hyphae, the elimination of stomata from the images, and the measuring of lengths of fungal hyphae. The optical method was verified by a chemical method relying on glucosamine as an indicator of fungal biomass. The fungal biomass in leaves of Fagus silvatica and Quercus petraea at early states of decomposition was 0.2 to 0.4% of the leaf weight. The biomass reached a maximum within 2 to 4 weeks (optical method, 0.5 to 0.7%; chemical method, 1 to 1.4% of the initial leaf weight) and decreased thereafter.     

Automated Quantification and Sizing of Unbranched Filamentous Cyanobacteria by Model-Based Object-Oriented Image Analysis

Quantification and sizing of filamentous cyanobacteria in environmental samples or cultures are time-consuming and are often performed by using manual or semiautomated microscopic analysis. Automation of conventional image analysis is difficult because filaments may exhibit great variations in length and patchy autofluorescence. Moreover, individual filaments frequently cross each other in microscopic preparations, as deduced by modeling. This paper describes a novel approach based on object-oriented image analysis to simultaneously determine (i) filament number, (ii) individual filament lengths, and (iii) the cumulative filament length of unbranched cyanobacterial morphotypes in fluorescent microscope images in a fully automated high-throughput manner. Special emphasis was placed on correct detection of overlapping objects by image analysis and on appropriate coverage of filament length distribution by using large composite images. The method was validated with a data set for Planktothrix rubescens from field samples and was compared with manual filament tracing, the line intercept method, and the Utermöhl counting approach. The computer program described allows batch processing of large images from any appropriate source and annotation of detected filaments. It requires no user interaction, is available free, and thus might be a useful tool for basic research and drinking water quality control.Automated quantification and sizing of single cells by microscopy and image analysis are routinely used to determine microbial biomass (2, 6, 18). In contrast, fully automated quantification and measurement of the length of filamentous organisms are considerably more difficult, and not all problems have been solved satisfactorily yet, even though there is a strong demand for such approaches both in microbial ecology and in drinking water quality control (5). The filamentous cyanobacterium Planktothrix rubescens is a prominent organism in this context. It produces a variety of potent toxins (3, 4, 11, 12, 14) that may threaten animal and human health. Its ability to form blooms in some freshwater habitats makes this organism highly relevant in terms of public health and drinking water control (8, 9, 13, 23). Moreover, P. rubescens has recently been reported to unexpectedly invade drinking water reservoirs (15). Not surprisingly, monitoring of filamentous cyanobacteria is a standard task in many laboratories. Cyanobacterial biomass is often used as a proxy for estimating toxin concentration, as determination of this biomass is less costly than chemical analysis. Determination of abundance and biomass is routinely performed by microscopy using either the Utermöhl sedimentation method (20) or collection of cells on filters (22). These methods involve manual microscopy and are thus labor-intensive and time-consuming.A major improvement in filament quantification occurred when charge-coupled device (CCD) cameras and image analysis software became available. Several automated or semiautomated methods have been proposed for measuring total filament length, either indirectly (e.g., the line-intercept method) (16, 17) or directly by filament detection via image analysis of either fluorescence (10, 22) or bright-field images (1). However, the filamentous nature of P. rubescens (i.e., its remarkable length-to-width ratio) poses problems for determination of the number and length of individual filaments by conventional image analysis. P. rubescens filaments are around 5 to 8 μm wide (7, 23), whereas their length ranges from less than 50 μm to more than 2,500 μm. If the length of individual filaments is measured, filaments have to be located entirely within a field of view (FOV), which means that large areas have to be imaged. Larger FOV areas may be viewed by using lower magnifications, but this comes at the cost of lower levels of fluorescence intensity and resolution, which are important for both efficient imaging and precise measurement. A second problem results from the fact that filamentous organisms often overlap in a microscopic preparation. Overlapping objects in a two-dimensional image, like the images generated by wide-field microscopy, cannot be correctly separated by conventional image analysis that is based on thresholding and binarization; two overlapping objects typically are merged into a single object. While the effect of this artifact on the automated determination of abundance is obvious, the corresponding error in the length measurements depends greatly on the method used. These problems have been discussed in great detail by Walsby and Avery (22), but no automated solution has been proposed yet.The aim of this work was to develop a computer program that (i) counts filaments, (ii) measures the length of individual filaments, and (iii) determines the cumulative lengths of filaments in large composite images generated by epifluorescence microscopy. The probability that a filament is located only partially in an FOV and thus cannot be measured and the probability of filament overlaps were assessed theoretically by using a Monte Carlo simulation approach. Here we specifically address the problem of overlapping filaments and describe a strategy to recognize and correctly count them. The performance of the algorithm was tested by using measurements for filaments in images obtained by the manual filament tracing, line-intercept (16), and Utermöhl methods.     

LPA-induced mutually exclusive subcellular localization of active RhoA and Arp2 mRNA revealed by sequential FRET and FISH

We previously demonstrated that mRNAs for the subunits of the Arp2/3 complex localize to protrusions in fibroblasts (Mingle et al. in J Cell Sci 118:2425–2433, 2005). However, the signaling pathway that regulates Arp2/3 complex mRNA localization remains unknown. In this study we have identified lysophosphatidic acid (LPA) as a potent inducer of Arp2 mRNA localization to protrusions in fibroblasts via the RhoA-ROCK pathway. As RhoA is known to be activated locally in the cells, we sought to understand how spatial activation of Rho affects Arp2 mRNA localization. By sequentially performing fluorescence resonance energy transfer (FRET) and fluorescence in situ hybridization (FISH), we have visualized active RhoA and Arp2 mRNA in the same cells. Upon LPA stimulation, approximately two times more cells than those in the serum-free medium showed mutually exclusive localization of active RhoA and Arp2 mRNA. These results demonstrate the importance of localized activation of Rho in Arp2 mRNA localization and provide new insights as to how Rho regulates Arp2/3 complex mRNA localization. To our best knowledge, this is the first report in which FRET and FISH are combined to detect localized protein activity and mRNA in the same cells. This method should be easily adopted for the detection of other fluorescence protein based biosensors and DNA/RNA in the same cells.     

Analysis of Magnetosome Chains in Magnetotactic Bacteria by Magnetic Measurements and Automated Image Analysis of Electron Micrographs

Magnetotactic bacteria (MTB) align along the Earth''s magnetic field by the activity of intracellular magnetosomes, which are membrane-enveloped magnetite or greigite particles that are assembled into well-ordered chains. Formation of magnetosome chains was found to be controlled by a set of specific proteins in Magnetospirillum gryphiswaldense and other MTB. However, the contribution of abiotic factors on magnetosome chain assembly has not been fully explored. Here, we first analyzed the effect of growth conditions on magnetosome chain formation in M. gryphiswaldense by electron microscopy. Whereas higher temperatures (30 to 35°C) and high oxygen concentrations caused increasingly disordered chains and smaller magnetite crystals, growth at 20°C and anoxic conditions resulted in long chains with mature cuboctahedron-shaped crystals. In order to analyze the magnetosome chain in electron microscopy data sets in a more quantitative and unbiased manner, we developed a computerized image analysis algorithm. The collected data comprised the cell dimensions and particle size and number as well as the intracellular position and extension of the magnetosome chain. The chain analysis program (CHAP) was used to evaluate the effects of the genetic and growth conditions on magnetosome chain formation. This was compared and correlated to data obtained from bulk magnetic measurements of wild-type (WT) and mutant cells displaying different chain configurations. These techniques were used to differentiate mutants due to magnetosome chain defects on a bulk scale.     

RhoA在上皮性卵巢癌细胞中的表达与侵袭性的相关性

培养上皮性卵巢癌细胞H08910PM、H08910及正常卵巢上皮细胞HOSEA 3种细胞.对3种细胞分别采用免疫细胞化学法检测RhoA的表达、Transwell小室体外侵袭试验测定体外侵袭能力、与人脐静脉内皮细胞HUVEC建立细胞共培养系统测定血管形成能力.结果表明,RhoA在H08910PM细胞中表达最强,在H08910中次之,在HOSEA中最弱;3种细胞的侵袭能力以H08910PM最强,H08910较弱,HOSEA无侵袭能力;H08910PM的血管形成能力最强,H08910其次,HOSEA无血管形成能力(P<0.01).Pearson相关分析结果显示,RhoA表达水平分别与细胞侵袭能力及血管形成能力呈正相关(P<0.05).RhoA在上皮性卵巢癌细胞中表达水平越高,细胞体外侵袭及血管形成能力随之更强.RhoA可能作为重要因子参与上皮性卵巢癌的侵袭转移过程.     

Effect of Phosphorylation on EGFR Dimer Stability Probed by Single-Molecule Dynamics and FRET/FLIM

Deregulation of epidermal growth factor receptor (EGFR) signaling has been correlated with the development of a variety of human carcinomas. EGF-induced receptor dimerization and consequent trans- auto-phosphorylation are among the earliest events in signal transduction. Binding of EGF is thought to induce a conformational change that consequently unfolds an ectodomain loop required for dimerization indirectly. It may also induce important allosteric changes in the cytoplasmic domain. Despite extensive knowledge on the physiological activation of EGFR, the effect of targeted therapies on receptor conformation is not known and this particular aspect of receptor function, which can potentially be influenced by drug treatment, may in part explain the heterogeneous clinical response among cancer patients. Here, we used Förster resonance energy transfer/fluorescence lifetime imaging microscopy (FRET/FLIM) combined with two-color single-molecule tracking to study the effect of ATP-competitive small molecule tyrosine kinase inhibitors (TKIs) and phosphatase-based manipulation of EGFR phosphorylation on live cells. The distribution of dimer on-times was fitted to a monoexponential to extract dimer off-rates (k_off). Our data show that pretreatment with gefitinib (active conformation binder) stabilizes the EGFR ligand-bound homodimer. Overexpression of EGFR-specific DEP-1 phosphatase was also found to have a stabilizing effect on the homodimer. No significant difference in the k_off of the dimer could be detected when an anti-EGFR antibody (425 Snap single-chain variable fragment) that allows for dimerization of ligand-bound receptors, but not phosphorylation, was used. These results suggest that both the conformation of the extracellular domain and phosphorylation status of the receptor are involved in modulating the stability of the dimer. The relative fractions of these two EGFR subpopulations (interacting versus free) were obtained by a fractional-intensity analysis of ensemble FRET/FLIM images. Our combined imaging approach showed that both the fraction and affinity (surrogate of conformation at a single-molecule level) increased after gefitinib pretreatment or DEP-1 phosphatase overexpression. Using an EGFR mutation (I706Q, V948R) that perturbs the ability of EGFR to dimerize intracellularly, we showed that a modest drug-induced increase in the fraction/stability of the EGFR homodimer may have a significant biological impact on the tumor cell’s proliferation potential.     

High-Throughput Method for Automated Colony and Cell Counting by Digital Image Analysis Based on Edge Detection

Counting cells and colonies is an integral part of high-throughput screens and quantitative cellular assays. Due to its subjective and time-intensive nature, manual counting has hindered the adoption of cellular assays such as tumor spheroid formation in high-throughput screens. The objective of this study was to develop an automated method for quick and reliable counting of cells and colonies from digital images. For this purpose, I developed an ImageJ macro Cell Colony Edge and a CellProfiler Pipeline Cell Colony Counting, and compared them to other open-source digital methods and manual counts. The ImageJ macro Cell Colony Edge is valuable in counting cells and colonies, and measuring their area, volume, morphology, and intensity. In this study, I demonstrate that Cell Colony Edge is superior to other open-source methods, in speed, accuracy and applicability to diverse cellular assays. It can fulfill the need to automate colony/cell counting in high-throughput screens, colony forming assays, and cellular assays.     

利用FRET技术实时研究顺铂诱导的Caspase-9活化

该研究旨在在活细胞内研究顺铂诱导Caspase-9活化的动态过程.实验样品经顺铂处理后,应用基于FRET原理设计的荧光探针pSCAT-9来检测Capase-9活化的动态过程.结果表明:在顺铂诱导细胞凋亡的后期,可以明显检测到Caspase-9的活化,且其进程快,约30 min即可完成.研究表明,应用FRET技术,可以在活细胞内实时、直观、可视地研究顺铂诱导的Capase-9活化,从而客观地反映Caspase-9在该凋亡信号通路中的动态行为及时空传递特性.     

Quantification of Dynamic Morphological Drug Responses in 3D Organotypic Cell Cultures by Automated Image Analysis

Glandular epithelial cells differentiate into complex multicellular or acinar structures, when embedded in three-dimensional (3D) extracellular matrix. The spectrum of different multicellular morphologies formed in 3D is a sensitive indicator for the differentiation potential of normal, non-transformed cells compared to different stages of malignant progression. In addition, single cells or cell aggregates may actively invade the matrix, utilizing epithelial, mesenchymal or mixed modes of motility. Dynamic phenotypic changes involved in 3D tumor cell invasion are sensitive to specific small-molecule inhibitors that target the actin cytoskeleton. We have used a panel of inhibitors to demonstrate the power of automated image analysis as a phenotypic or morphometric readout in cell-based assays. We introduce a streamlined stand-alone software solution that supports large-scale high-content screens, based on complex and organotypic cultures. AMIDA (Automated Morphometric Image Data Analysis) allows quantitative measurements of large numbers of images and structures, with a multitude of different spheroid shapes, sizes, and textures. AMIDA supports an automated workflow, and can be combined with quality control and statistical tools for data interpretation and visualization. We have used a representative panel of 12 prostate and breast cancer lines that display a broad spectrum of different spheroid morphologies and modes of invasion, challenged by a library of 19 direct or indirect modulators of the actin cytoskeleton which induce systematic changes in spheroid morphology and differentiation versus invasion. These results were independently validated by 2D proliferation, apoptosis and cell motility assays. We identified three drugs that primarily attenuated the invasion and formation of invasive processes in 3D, without affecting proliferation or apoptosis. Two of these compounds block Rac signalling, one affects cellular cAMP/cGMP accumulation. Our approach supports the growing needs for user-friendly, straightforward solutions that facilitate large-scale, cell-based 3D assays in basic research, drug discovery, and target validation.     

Subcellular Localization of RhoA and Ezrin at Membrane Ruffles of Human Endothelial Cells: Differential Role of Collagen and Fibronectin

Endothelial cells and the regulation of their migration are of prime importance in many physiological and pathological processes such as angiogenesis. RhoA, an important Rho family member known to trigger actin reorganization, has been shown to mediate the formation of focal adhesions and stress fibers in quiescent fibroblasts. However, recent studies have emphasized its functional diversity and its implication in migration or metastatic processes in different cell types other than fibroblasts. Its role in endothelial cells is little known. In this study, we were interested by analyzing in human endothelial cells the subcellular redistribution of endogenous RhoA and the reorganization of cytoskeletal actin induced by two important extracellular matrix proteins, collagen and fibronectin. This paper shows a translocation of RhoA and its association with cortical actin in focal contact domains at membrane ruffles and at lamellipodia of spread or migrating endothelial cells, in the absence of any soluble mitogen stimulation. Furthermore, RhoA was found colocalized with ezrin, a member of the ERM family proteins newly described as important membrane-actin cytoskeleton linkers, at early membrane ruffles of endothelial cells spread on collagen but not on fibronectin. The present study points out that extracellular matrix, depending on the nature of its components, may promote distinct assemblies of focal contact constitutive proteins and strongly suggests that endothelial RhoA, like Rac1, may be an important mediator of matrix signaling pathway regulating endothelial cell adhesiveness and motility, independently of growth factor stimulation.     

一种高效自动化的转录组差异性表达分析方法

差异性表达分析是转录组研究的核心目标之一,对于揭示基因功能和调控规律具有重要意义。但该分析属于多步迭代且耗时较长的计算密集型过程,软件之间具有复杂的数据依赖关系,输入输出格式不尽相同。传统方式下,软件安装与使用复杂、繁琐的手动操作、分析环境的不易迁移以及无法按需集成都是有待解决的关键问题。针对上述问题,文中首次将云开源项目Docker容器技术应用于生物信息领域,提出一种高效自动化的转录组差异性表达分析方法。首先将最佳实践流程在Docker容器中内置与集成,其次多脚本联动与Web服务相结合,最后形成一个轻量级、易迁移、高效自动化的转录组差异性表达分析"黑匣子"。实验结果表明,与传统方式相比,该方法的分析时间缩短约72%,效率提升2倍多,为研究人员提供了更高效的技术支持。     

Changes in Cytoplasmic pH Measured by 31P-NMR in Cells of Nitellopsis obtusa

The cytoplasmic pH of Nitellopsis obtusa measured by the ³¹P-nuclearmagnetic resonance method was about 7.3. Since normal cell havea large vacuole, a long period of time is needed to accumulatesignals for cytoplasmic phosphate. To measure the cytoplasmicpH in a shorter period, cytoplasm-rich cells were prepared bycentrifugation. The cytoplasmic pH of these cells was also about7.3. Illumination reversibly increased the cytoplasmic pH from7.3 to 7.8. When the cytoplasm-rich cell was illuminated, themembrane potential hyperpolarized concomitant with the alkalificationof the cytoplasm. (Received December 5, 1983; Accepted May 12, 1984)