Spectrally resolved time-correlated single photon counting: a novel approach for characterization of endogenous fluorescence in isolated cardiac myocytes

A new setup for time-resolved fluorescence micro-spectroscopy of cells, based on multi-dimensional time-correlated single photon counting, was designed and tested. Here we demonstrate that the spectrometer allows fast and reproducible measurements of endogenous flavin fluorescence measured directly in living cardiac cells after excitation with visible picosecond laser diodes. Two complementary approaches for the analysis of spectrally- and time-resolved autofluorescence data are presented, comprising the fluorescence decay fitting by exponential series and the time-resolved emission spectroscopy analysis. In isolated cardiac myocytes, we observed three distinct lifetime pools with characteristic lifetime values spanning from picosecond to nanosecond range and the time-dependent red shift of the autofluorescence emission spectra. We compared obtained results to in vitro recordings of free flavin adenine dinucleotide (FAD) and FAD in lipoamide dehydrogenase (LipDH). The developed setup combines the strength of both spectral and fluorescence lifetime analysis and provides a solid base for the study of complex systems with intrinsic fluorescence, such as identification of the individual flavinoprotein components in living cardiac cells. This approach therefore constitutes an important instrumental advancement towards redox fluorimetry of living cardiomyocytes, with the perspective of its applications in the investigation of oxidative metabolic state under pathophysiological conditions, such as ischemia and/or metabolic disorders.     

Rapid quantitative analysis using a single molecule counting approach

Single molecule detection of target molecules specifically bound by paired fluorescently labeled probes has shown great potential for sensitive quantitation of biomolecules. To date, no reports have rigorously evaluated the analytical capabilities of a single molecule detection platform employing this dual-probe approach or the performance of its data analysis methodology. In this paper, we describe a rapid, automated, and sensitive multicolor single molecule detection apparatus and a novel extension of coincident event counting based on detection of fluorescent probes. The approach estimates the number of dual-labeled molecules of interest from the total number of coincident fluorescent events observed by correcting for unbound probes that randomly pass through the interrogation zone simultaneously. Event counting was evaluated on three combinations of distinct fluorescence channels and was demonstrated to outperform conventional spatial cross-correlation in generating a wider linear dynamic response to target molecules. Furthermore, this approach succeeded in detecting subpicomolar concentrations of a model RNA target to which fluorescently labeled oligonucleotide probes were hybridized in a complex background of RNA. These results illustrate that the fluorescent event counting approach described represents a general tool for rapid sensitive quantitative analysis of any sample analyte, including nucleic acids and proteins, for which pairs of specific probes can be developed.     

Exploration of phylogenetic data using a global sequence analysis method

Background  

Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets.     

Thermal stability of a flavoprotein assessed from associative analysis of polarized time-resolved fluorescence spectroscopy

Upon gradually heating a particular mutant of the flavoprotein NADH peroxidase, it was found from the peculiar time-resolved fluorescence anisotropy pattern of the flavin prosthetic group (FAD) that, at elevated temperature, FAD is released from the tetrameric enzyme. Since in this case a mixture of free and enzyme-bound FAD contributes to the time-dependent fluorescence anisotropy, its analysis can only be accomplished by an associative fitting model, in which specific fluorescence lifetimes of both species are linked to specific correlation times. In this letter the general approach to the associative polarized fluorescence decay analysis is described. The procedure can be used for other flavoproteins to determine the temperature at which the onset of thermal denaturation will start, leading to release of the flavin prosthetic group. Received: 20 November 1998 / Revised version: 6 April 1999 / Accepted: 8 April 1999     

尼泊尔生态系统质量评估与时空格局变化——基于参照条件的评估方法

良好的生态系统质量是维持人类社会供给需求和可持续发展目标实现的重要保障。针对尼泊尔自然地理环境复杂多样,区域间气候差异明显的特点,结合基于参照条件的评估方法可以得到生态系统质量的相对水平值,其结果能够反映出不同的变化信息。植被是区域生态系统质量变化的重要指示器,利用尼泊尔五大地理区以及四种主要植被生态系统类型划分出20个生态评估区,从表征植被生态系统的水平结构、生产功能和垂直结构3个方面计算生态参数相对密度指标（RVI）,结合主成分分析法构建植被生态系统质量指数（VEQI）,并以其国家自然保护区为参照,构建基于参照条件的生态系统质量评估模型,计算了尼泊尔2016和2020年基于参照条件的植被生态系统质量指数（VEQI''）并分析其生态系统质量的时空格局变化。结果表明：（1）2016至2020年,尼泊尔生态系统质量现实值VEQI的平均值增加了3.49%,总体上,在参照生态系统质量（VEQI_ref）提高（约1.41%）的背景下,生态系统质量相对水平值VEQI''增加了1.42%;（2）对于尼泊尔地区,评估区89%分位数的VEQI与其对应的国家自然保护区的参照值具有很强的相关性,总体差异较小,可以代替作为参照值;（3）从空间格局变化趋势来看,尼泊尔生态系统质量变好、基本稳定和变差的面积分别占植被生态系统总面积的74.16%、14.25%和11.59%。与数量不足、较难收集利用的野外观测台站数据相比,国家自然保护区更接近理想参照生态系统的假设,通过有限的自然保护区确定生态评估区的参照值,实现生态系统质量的快速评估,其结果具有更好的时空可比性,可以为区域生态质量变化评估及量化分析等方面提供参考。     

Fluorescence as a method to reveal structures and membrane-interactions of amyloidogenic proteins

Amyloidogenesis is a characteristic feature of the 40 or so known protein deposition diseases, and accumulating evidence strongly suggests that self-association of misfolded proteins into either fibrils, protofibrils, or soluble oligomeric species is cytotoxic. The most likely mechanism for toxicity is through perturbation of membrane structure, leading to increased membrane permeability and eventual cell death. There have been a rather limited number of investigations of the interactions of amyloidogenic polypeptides and their aggregated states with membranes; these are briefly reviewed here. Amyloidogenic proteins discussed include A-beta from Alzheimer's disease, the prion protein, α-synuclein from Parkinson's disease, transthyretin (FAP, SSA amyloidosis), immunoglobulin light chains (primary (AL) amyloidosis), serum amyloid A (secondary (AA) amyloidosis), amylin or IAPP (Type 2 diabetes) and apolipoproteins. This review highlights the significant role played by fluorescence techniques in unraveling the nature of amyloid fibrils and their interactions and effects on membranes. Fluorescence spectroscopy is a valuable and versatile method for studying the complex mechanisms of protein aggregation, amyloid fibril formation and the interactions of amyloidogenic proteins with membranes. Commonly used fluorescent techniques include intrinsic and extrinsic fluorophores, fluorescent probes incorporated in the membrane, steady-state and lifetime measurements of fluorescence emission, fluorescence correlation spectroscopy, fluorescence anisotropy and polarization, fluorescence resonance energy transfer (FRET), fluorescence quenching, and fluorescence microscopy.     

参照点位法下的参照状态在草原生态系统损害基线判定中的应用分析

生态环境损害基线的判定是环境损害鉴定与评估的基础与前提。参照点位法作为目前损害基线判定中使用最为广泛的方法之一,有效弥补了历史数据不完善的问题。在基线判断的过程中,参照点位选择的不同,会导致判定基线的参照状态不同,进而影响对人类干扰程度的判定和损害基线的基准值的设定。但目前缺乏统一的对草原生态系统参照状态的讨论与分析。提出了草原生态系统参照点位法的评价指标体系,对文献资料中的样点进行分类和筛选,形成4种参照状态,选择最优的参照状态对损害基线进行判定,并以内蒙古锡林郭勒盟锡林浩特典型草原区为案例进行实例分析。结果表明:对于自然保护区、草原实验站宜采用极小干扰状态和历史状态作为基线标准。对于实施了人为正向干扰的地区宜采用最佳可获得状态作为基线标准。对于草原的其他大部分地区,宜采用最低干扰状态作为基线标准。     

Standard reference materials and data quality assurance in the biomedical analysis of trace elements

Accurate and precise analytical data of the concentrations of bioanalytes in bioclinical studies are of fundamental importance. Quality assurance procedures should always be performed to check the overall analytical work. This can be conveniently performed if appropriate standard reference materials with known concentrations of the analyte object of study are available. This paper underlines the key points related to the production and use of biological standard materials for trace element analysis. In particular, the present situation in the field of trace element determination in human biological fluids and the related problems are illustrated. The considerations given in this work may contribute to the preparation of the new biomarker standard materials.     

Measurement of green fluorescent protein concentration in single cells by image analysis

The gene encoding the green fluorescent protein (GFP) has been widely used in studies of gene expression. The GFP can be detected nondestructively in living cells or tissues by the green fluorescence of the protein under blue light. Solutions of enhanced GFP (EGFP) of known concentration were filled in glass capillaries and used to calibrate a method for quantitative determination of EGFP or GFP-S65T in plant cells. Images captured by a digital camera were analyzed to determine the linear range for measurement of EGFP expression. The value of the method was illustrated by analysis of the relative levels of GFP expression under control of different promoters in aleurone cells of barley.     

Combined thermodynamic and kinetic analysis of GroEL interacting with CXCR4 transmembrane peptides

GroEL along with ATP and its co-chaperonin GroES has been demonstrated to significantly enhance the folding of newly translated G-protein-coupled receptors (GPCRs). This work extends the previous studies to explore the guest capture and release processes in GroEL-assisted folding of GPCRs, by the reduced approach of employing CXCR4 transmembrane peptides as model substrates. Each of the CXCR4-derived peptides exhibited high affinity for GroEL with a binding stoichiometry near seven. It is found that the peptides interact with the paired α helices in the apical domain of the chaperonin which are similar with the binding sites of SBP (strongly binding peptide: SWMTTPWGFLHP). Complementary binding study with a single-ring version of GroEL indicates that each of the two chaperonin rings is competent for accommodating all the seven CXCR4 peptides bound to GroEL under saturation condition. Meanwhile, the binding kinetics of CXCR4 peptides with GroEL was also examined; ATP alone, or in combination of GroES evidently promoted the release of the peptide substrates from the chaperonin. The results obtained would be beneficial to understand the thermodynamic and kinetic nature of GroEL-GPCRs interaction which is the central molecular event in the assisted folding process.     

Instrumental neutron activation analysis of rib bone samples and of bone reference materials

The instrumental neutron activation analysis method was used for the determination of trace elements in rib bone samples taken from autopsies of accident victims. The elements Br, Ca, Cl, Cr, Fe, Mg, Mn, Na, P, Sr, Rb, and Zn were determined in cortical tissues by using short and long irradiations with thermal neutron flux of the IEA-R1m nuclear reactor. The reference materials NIST SRM 1400 Bone Ash and NIST SRM 1486 Bone Meal were also analyzed in order to evaluate the precision and the accuracy of the results. It was verified that lyophilization is the most convenient process for drying bone samples because it does not cause any element losses. Comparisons were made between the results obtained for rib samples and the literature values as well as between the results obtained for different ribs from a single individual and for bones from different individuals.     

The measurement of subnanosecond fluorescence decay of flavins using time-correlated photon counting and a mode-locked Ar ion laser.

A system is described consisting of a mode-locked Ar ion laser and time-resolved photon-counting electronics. The system is capable of measuring fluorescence lifetimes in the subnanosecond time domain. The Ar ion laser is suitable for the excitation of flavins, since the available laser wavelengths encompass the first absorption band of the yellow chromophore. Due to the high radiation density and the short pulse, both the time and wavelength resolution of the fluorescence of very weakly emitting compounds can be measured. Experiments have been described for flavin models exhibiting single and multiple modes of decay. In these examples lifetimes were determined both from deconvolved decay curves and from direct analysis of the tail of the curve, where no interference of the exciting pulse is encountered. Both determinations showed very good agreement. Due to the highly polarized laser light the decay of the emission anisotropy could be measured directly after the exciting pulse. In principle, fast rotational motions might be detected. An anisotropy measurement conducted with a flavoprotein with a noncovalently attached FAD is presented.     

Global analysis of fluorescence fluctuation data

Over the last decade the number of applications of fluorescence correlation spectroscopy (FCS) has grown rapidly. Here we describe the development and application of a software package, FCS Data Processor, to analyse the acquired correlation curves. The algorithms combine strong analytical power with flexibility in use. It is possible to generate initial guesses, link and constrain fit parameters to improve the accuracy and speed of analysis. A global analysis approach, which is most effective in analysing autocorrelation curves determined from fluorescence fluctuations of complex biophysical systems, can also be implemented. The software contains a library of frequently used models that can be easily extended to include user-defined models. The use of the software is illustrated by analysis of different experimental fluorescence fluctuation data sets obtained with Rhodamine Green in aqueous solution and enhanced green fluorescent protein in vitro and in vivo.An erratum to this article can be found at Victor V. Skakun, Mark A. Hink and Anatoli V. Digris contributed equally to this work.     

An evaluation of thermal and epithermal neutron activation analysis compton suppression methods for biological reference materials

For neutron activation analysis (NAA), the usual matrix problems of sodium, chlorine, and bromine are well known to give rise to high backgrounds that inhibit the determination of several trace elements for short-lived or medium-lived NAA. For long counting times in long-lived NAA, very low backgrounds are required to achieve good sensitivities. We have investigated the use of thermal and epithermal NAA in conjunction with Compton suppression to determine several elements such as arsenic, antimony, cadmium, and mercury, at the level of a few nanograms. The values of these techniques are discussed in contrast to the standard radiochemical methods.     

Chemical strategies for the global analysis of protein function

As the human genome project nears completion, biological research is entering a new era in which experimental focus will shift from identifying novel genes to determining the function of gene products. Rising to this challenge, several technologies have emerged that aim to characterise genes and/or proteins collectively rather than individually. Of particular interest is a new breed of strategies that employs synthetic chemistry to enrich our understanding of protein function on a global scale.     

A first global analysis of plasmid encoded proteins in the ACLAME database

Many plasmids are mobile genetic elements (MGEs) and, as other members of that group of DNA entities, their genomes display a mosaic and combinatorial structure, making their classification extremely difficult. As other MGEs, plasmids play a major role in horizontal transfer of genetic materials and genome reorganization. Yet, the full impact of such phenomenon on major properties of the host cell, such as pathogenicity, the ability to use new carbon sources or resistance to antibiotics, remains to be fully assessed. More and more complete plasmid genome sequences are available. However, in the absence of standards for storing plasmid sequence data and annotating genes and gene products on sequenced plasmid genomes, the resulting information remains rather limited. Using 503 sequenced plasmids organized in the ACLAME database, we discuss how, by structuring information on the genomes, their host and the proteins they code for, one can gain access to either global or more detailed analysis of the plasmid sequence information, as illustrated by a network representation of the relationships between plasmids.     

Classification and counting of fluorescent pollen using an image analysis system

Pollen viability is commonly assessed by fluorochromatic reaction (FCR) because of the high correlation between positive fluorescence of the pollen grains and their ability to germinate. One of the advantages of this method is its simplicity. An experiment to test FCR analysis for reproducibility, however, showed that results are affected by subjectivity. There is little consistency between analysts, and assessment by the same analyst may differ for the same pollen sample image examined at different times. These problems were solved by a computerized image analysis system that provides a method for classifying positive and negative fluorescent pollen and automatic counting of the grains in each class. The computerized image analysis system does not change the biochemistry of the FCR test, but avoids some experimental errors owing to the subjectivity of the analyst. Microscope images of the pollen after FCR were digitized and later analyzed by specially designed software, "Plant Meter." This software deletes the dark background of the image to isolate the grains, and subsequently counts positive and negative fluorescent pollen grains. An experiment was carried out to validate software output and it showed reliable results. Moreover, the software is user friendly and very little training is necessary for analysts to achieve reliable results.     

GPIomics: global analysis of glycosylphosphatidylinositol‐anchored molecules of Trypanosoma cruzi

Glycosylphosphatidylinositol (GPI) anchoring is a common, relevant posttranslational modification of eukaryotic surface proteins. Here, we developed a fast, simple, and highly sensitive (high attomole‐low femtomole range) method that uses liquid chromatography‐tandem mass spectrometry (LC‐MSⁿ) for the first large‐scale analysis of GPI‐anchored molecules (i.e., the GPIome) of a eukaryote, Trypanosoma cruzi, the etiologic agent of Chagas disease. Our genome‐wise prediction analysis revealed that approximately 12% of T. cruzi genes possibly encode GPI‐anchored proteins. By analyzing the GPIome of T. cruzi insect‐dwelling epimastigote stage using LC‐MSⁿ, we identified 90 GPI species, of which 79 were novel. Moreover, we determined that mucins coded by the T. cruzi small mucin‐like gene (TcSMUG S) family are the major GPI‐anchored proteins expressed on the epimastigote cell surface. TcSMUG S mucin mature sequences are short (56–85 amino acids) and highly O‐glycosylated, and contain few proteolytic sites, therefore, less likely susceptible to proteases of the midgut of the insect vector. We propose that our approach could be used for the high throughput GPIomic analysis of other lower and higher eukaryotes.