Two-color Fluorescence Labeling in Acrolein-fixed Brain Tissue

Acrolein is a potent fixative that provides both excellent preservation of ultrastructural morphology and retention of antigenicity, thus it is frequently used for immunocytochemical detection of antigens at the electron microscopic level. However, acrolein is not commonly used for fluorescence microscopy because of concerns about possible autofluorescence and destruction of the luminosity of fluorescent dyes. Here we describe a simple protocol that allows fine visualization of two fluorescent markers in 40-μm sections from acrolein-perfused rat brain. Autofluorescence was removed by pretreatment with 1% sodium borohydride for 30 min, and subsequent incubation in a 50% ethanol solution containing 0.3% hydrogen peroxide enhanced fluorescence labeling. Thus, fluorescence labeling can be used for high-quality detection of markers in tissue perfused with acrolein. Furthermore, adjacent acrolein-fixed sections from a single experiment can be processed to produce high-quality results for electron microscopy or fluorescence labeling. (J Histochem Cytochem 58:359–368, 2010)     

藻胆蛋白荧光探针及其标记

藻胆蛋白是一系列新型的荧光标记探针,具有优良的荧光特性,以藻胆蛋白荧光探针标记抗体还可用于血清可溶性抗原（或抗体）的荧光免疫检测,其标记方法可分为直接法和间接法。结合藻胆蛋白的特点,研究藻胆蛋白的标记方法有助于提高荧光免疫检测的灵敏度。     

d-Amino Acid Probes for Penicillin Binding Protein-based Bacterial Surface Labeling

Peptidoglycan is an essential and highly conserved mesh structure that surrounds bacterial cells. It plays a critical role in retaining a defined cell shape, and, in the case of pathogenic Gram-positive bacteria, it lies at the interface between bacterial cells and the host organism. Intriguingly, bacteria can metabolically incorporate unnatural d-amino acids into the peptidoglycan stem peptide directly from the surrounding medium, a process mediated by penicillin binding proteins (PBPs). Metabolic peptidoglycan remodeling via unnatural d-amino acids has provided unique insights into peptidoglycan biosynthesis of live bacteria and has also served as the basis of a synthetic immunology strategy with potential therapeutic implications. A striking feature of this process is the vast promiscuity displayed by PBPs in tolerating entirely unnatural side chains. However, the chemical space and physical features of this side chain promiscuity have not been determined systematically. In this report, we designed and synthesized a library of variants displaying diverse side chains to comprehensively establish the tolerability of unnatural d-amino acids by PBPs in both Gram-positive and Gram-negative organisms. In addition, nine Bacillus subtilis PBP-null mutants were evaluated with the goal of identifying a potential primary PBP responsible for unnatural d-amino acid incorporation and gaining insights into the temporal control of PBP activity. We empirically established the scope of physical parameters that govern the metabolic incorporation of unnatural d-amino acids into bacterial peptidoglycan.     

Label-Free Bacterial Imaging with Deep-UV-Laser-Induced Native Fluorescence

We introduce a near-real-time optical imaging method that works via the detection of the intrinsic fluorescence of life forms upon excitation by deep-UV (DUV) illumination. A DUV (<250-nm) source enables the detection of microbes in their native state on natural materials, avoiding background autofluorescence and without the need for fluorescent dyes or tags. We demonstrate that DUV-laser-induced native fluorescence can detect bacteria on opaque surfaces at spatial scales ranging from tens of centimeters to micrometers and from communities to single cells. Given exposure times of 100 μs and low excitation intensities, this technique enables rapid imaging of bacterial communities and cells without irreversible sample alteration or destruction. We also demonstrate the first noninvasive detection of bacteria on in situ-incubated environmental experimental samples from the deep ocean (Lo''ihi Seamount), showing the use of DUV native fluorescence for in situ detection in the deep biosphere and other nutrient-limited environments.Bacteria are widely recognized for living in extreme environments and as integral players in processes as varied as weathering, corrosion, environmental remediation, pathogenesis, and symbiosis (3, 4, 26). In most of these cases, surface-bound bacteria play key roles (1, 7, 19) and pose a particular challenge for researchers: the detection and imaging of life on reflective and/or fluorescent surfaces at the microbial (μm) scale (5, 12, 18). In environments ranging from the deep subsurface biosphere, dry deserts, and deep ice cores to hospitals and clean rooms, concentrations of bacteria, either as spores or active cells, can range from 10⁹ to less than 1,000 cells/gram (14, 22, 24, 25, 29, 34). Finding and quantifying these microbes when they are on surfaces usually involves epifluorescence techniques, using dyes that bind to DNA or proteins, and examining the fluorescence of those dyes under UV or visible illumination (6, 8, 9, 16, 23, 31).Current tagging methods offer a number of significant disadvantages. First, the mineral surfaces on which the microbes are found are often themselves highly fluorescent, making the microbes difficult or impossible to differentiate; second, the act of adding the fluorescent probe can alter the physical and chemical nature of the system; additionally, nonspecific binding can lead to overestimation of cell abundance (2, 18). Because of the problems associated with the fluorescence of minerals and staining to detect microbial cells, researchers typically resort to physically removing cells from surfaces and staining/counting them separately from their matrix (12). This is an inefficient process that involves both cell loss and the loss of information about the mineralogical context that may have an influence on the microbial ecology. More recently, cell staining of active cells with SYBR green 1 and a computer-assisted analysis method has demonstrated an ability to separate fluorescent cells from nonspecific binding (17). However, a label-free method to search for and quantify the distribution and abundance of bacteria on natural samples over multiple spatial scales has not been available.Label-free optical approaches using Raman scattering methods have been offered as a nondestructive imaging solution (13, 27). However, these systems utilize laser energies greater than 1 × 10⁹ joules/cm², exceeding the energies necessary for chemical damage to the cell (33), require relatively flat surfaces for optimal collection efficiency, and can suffer from background fluorescence of the target and the substrate it may reside on.In response to these challenges, we have developed an optical method that enables detection and imaging of single bacterial cells on natural and opaque surfaces and assessment of bacterial density and distribution of single cells to biofilms over spatial scales ranging from microns to centimeters. The method utilizes deep-UV (DUV) (<250-nm)-laser-induced native fluorescence of organic components intrinsic to the cell or spore while avoiding autofluorescence interference from the substrate. Here we show DUV native fluorescence as a near-real-time optical imaging method and demonstrate the first noninvasive detection of bacteria on in situ-incubated environmental experimental samples from the deep ocean (Lo''ihi Seamount) for which we correlate the bacterial biomass to distributions of the iron-oxide precipitates.     

板栗疫病菌绿色荧光与红色荧光蛋白共定位载体的构建

低毒病毒-板栗疫病菌组合是研究病毒与宿主相互作用的一个优秀的模式系统.我们构建了含绿色荧光蛋白基因gfp的载体pCPXHY2GFP与含红色荧光蛋白基因rfp的载体pCPXG418RFP,并用于转化野生型菌株EP155,获得了以潮霉素为筛选标记、表达绿色荧光蛋白的转化株pCPXHY2GFP/EP155和以G418为筛选标记、表达红色荧光蛋白的转化株pCPXG418RFP/EP155.将载体pCPXG418RFP转化pCPXHY2GFP/EP155,获得的转化株能观察到绿色荧光蛋白与红色荧光蛋白共定位的现象.板栗疫病菌绿色荧光与红色荧光共定位载体pCPXHY2GFP与pCPXG418RFP的构建,为深入研究病毒与宿主相互作用的分子机制提供了强有力的研究材料.     

SPEX, a System for the Expression of Recombinant Proteins from Gram-Positive Bacterial Vectors

Using a conserved pathway for surface protein extrusion, a system has been developed for the expression and secretion of proteins from gram-positive bacteria. As proof-of-concept, theStreptococcus gordoniiChallis strain has been engineered to express a series of recombinant proteins fused to the conserved region of the M6 protein ofStreptococcus pyogenes.In the prototype surface protein expression system, the recombinant M6 protein is anchored to the surface ofS. gordoniicells expressing it. In order to overexpress the protein and easily purify it away from the bacteria, the protein was modified to enable it to be secreted into the medium. To accomplish this, a stop codon was introduced into the gene just prior to the anchor region using site-directed mutagenesis. Using enzyme-linked immunosorbent assays, it was possible to quantitate the amount of protein expressed using this system. With little or no optimization, 3 mg of protein per liter of culture was expressed and secreted into the medium of a bacterial culture grown to an OD₆₀₀equal to 1.0. This system should be broadly applicable for the expression and secretion of a variety of proteins (antigens, hormones, and enzymes) directly into the medium.     

荧光标记寡核苷酸探针及其应用

寡核苷酸探针的标记非常重要。近年来 ,用荧光染料对探针进行非放射性标记受到很大重视 ,并取得了迅速发展 ,广泛应用于核酸序列测定、基因检测以及疾病诊断等。以下就寡核苷酸探针的荧光标记及其应用作一简要综述。     

A New Type of Fluorescence Labeling of Nucleosides,Nucleotides and Oligonucleotides

Abstract

Fluorescein has been coupled to the amino groups of the common nucleo-sides via a carbamoyl spacer to form a new type of conjugates. The corresponding phos-phoramidites have been prepared with Npe and Npeoc protecting groups for application in oligonucleotide synthesis. Hybridizations have been studied in dependence of the fluores-cing label as well as fluorescence quantum yields and fluorescence anisotropy effects.     

Pituitary Activation by Bacterial Endotoxins in the Rainbow Trout (Salmo gairdneri)

Endotoxins from Escherichia coli and Aeromonas salmonicida caused marked cortisol production in the rainbow trout (Salmo gairdneri).     

Examining the Conformational Dynamics of Membrane Proteins in situ with Site-directed Fluorescence Labeling

Two electrode voltage clamp electrophysiology (TEVC) is a powerful tool to investigate the mechanism of ion transport1 for a wide variety of membrane proteins including ion channels², ion pumps³, and transporters⁴. Recent developments have combined site-specific fluorophore labeling alongside TEVC to concurrently examine the conformational dynamics at specific residues and function of these proteins on the surface of single cells.We will describe a method to study the conformational dynamics of membrane proteins by simultaneously monitoring fluorescence and current changes using voltage-clamp fluorometry. This approach can be used to examine the molecular motion of membrane proteins site-specifically following cysteine replacement and site-directed fluorophore labeling^5,6. Furthermore, this method provides an approach to determine distance constraints between specific residues^7,8. This is achieved by selectively attaching donor and acceptor fluorophores to two mutated cysteine residues of interest.In brief, these experiments are performed following functional expression of the desired protein on the surface of Xenopus leavis oocytes. The large surface area of these oocytes enables facile functional measurements and a robust fluorescence signal⁵. It is also possible to readily change the extracellular conditions such as pH, ligand or cations/anions, which can provide further information on the mechanism of membrane proteins⁴. Finally, recent developments have also enabled the manipulation of select internal ions following co-expression with a second protein⁹.Our protocol is described in multiple parts. First, cysteine scanning mutagenesis proceeded by fluorophore labeling is completed at residues located at the interface of the transmembrane and extracellular domains. Subsequent experiments are designed to identify residues which demonstrate large changes in fluorescence intensity (<5%)³ upon a conformational change of the protein. Second, these changes in fluorescence intensity are compared to the kinetic parameters of the membrane protein in order to correlate the conformational dynamics to the function of the protein¹⁰. This enables a rigorous biophysical analysis of the molecular motion of the target protein. Lastly, two residues of the holoenzyme can be labeled with a donor and acceptor fluorophore in order to determine distance constraints using donor photodestruction methods. It is also possible to monitor the relative movement of protein subunits following labeling with a donor and acceptor fluorophore.     

大豆不同花叶病毒抗性品种胼胝质荧光标记初探

选用6个大豆品种与4个不同的大豆花叶病毒株系,分别组成抗病级别不同的组合,通过对接种叶片与上位叶症状观察、苯胺蓝染色辅以荧光显微镜观察和药物学试验,探讨了不同抗病级别组合中胼胝质(即β-l,3-葡聚糖)积累的特点及其在大豆抵抗大豆花叶病毒侵染过程中的作用。试验结果表明,大豆接种病毒后,在抗病级别分别为0～3的各个组合的叶肉细胞中,在侵染早期(接种后6、72 h)不同的组合在不同时间点分别观察到了胼胝质荧光,且胼胝质荧光出现的时间与抗病级别密切相关,即抗病性越强的组合在侵染点处观察到胼胝质的时间越早;而在抗病级别为5的组合中一直未能观察到胼胝质荧光。另外,在抗病级别为0级和1级的各组合中给叶片预注射2-DDG(2-deoxy-D-glucose,一种胼胝质合成抑制剂)再接种病毒,在上位叶能观察到坏死斑的出现并且通过RT-PCR能够检测到大豆花叶病毒外壳蛋白基因。以上结果表明,大豆被大豆花叶病毒侵染后,抗病性越强的品种就会在侵染点处越早地积累胼胝质,胼胝质的沉积与大豆抗病毒侵染密切相关。     

Genetically Modified Bacterial Strains and Novel Bacterial Artificial Chromosome Shuttle Vectors for Constructing Environmental Libraries and Detecting Heterologous Natural Products in Multiple Expression Hosts

The enormous diversity of uncultured microorganisms in soil and other environments provides a potentially rich source of novel natural products, which is critically important for drug discovery efforts. Our investigators reported previously on the creation and screening of an Escherichia coli library containing soil DNA cloned and expressed in a bacterial artificial chromosome (BAC) vector. In that initial study, our group identified novel enzyme activities and a family of antibacterial small molecules encoded by soil DNA cloned and expressed in E. coli. To continue our pilot study of the utility and feasibility of this approach to natural product drug discovery, we have expanded our technology to include Streptomyces lividans and Pseudomonas putida as additional hosts with different expression capabilities, and herein we describe the tools we developed for transferring environmental libraries into all three expression hosts and screening for novel activities. These tools include derivatives of S. lividans that contain complete and unmarked deletions of the act and red endogenous pigment gene clusters, a derivative of P. putida that can accept environmental DNA vectors and integrate the heterologous DNA into the chromosome, and new BAC shuttle vectors for transferring large fragments of environmental DNA from E. coli to both S. lividans and P. putida by high-throughput conjugation. Finally, we used these tools to confirm that the three hosts have different expression capabilities for some known gene clusters.     

Multicolor Whole-Cell Bacterial Sensing Using a Synchronous Fluorescence Spectroscopy-Based Approach

The wide collection of currently available fluorescent proteins (FPs) offers new possibilities for multicolor reporter gene-based studies of bacterial functions. However, the simultaneous use of multiple FPs is often limited by the bleed-through of their emission spectra. Here we introduce an original approach for detection and separation of multiple overlapping fluorescent signals from mixtures of bioreporters strains. The proposed method relies on the coupling of synchronous fluorescent spectroscopy (SFS) with blind spectral decomposition achieved by the Canonical Polyadic (CP) decomposition (also known as Candecomp/Parafac) of three-dimensional data arrays. Due to the substantial narrowing of FP emission spectra and sensitive detection of multiple FPs in a one-step scan, SFS reduced spectral overlap and improved the selectivity of the CP unmixing procedure. When tested on mixtures of labeled E. coli strains, the SFS/CP approach could easily extract the contribution of at least four overlapping FPs. Furthermore, it allowed to simultaneously monitor the expression of three iron responsive genes and pyoverdine production in P. aeruginosa. Implemented in a convenient microplate format, this multiplex fluorescent reporter method provides a useful tool to study complex processes with different variables in bacterial systems.     

MiL-FISH: Multilabeled Oligonucleotides for Fluorescence In Situ Hybridization Improve Visualization of Bacterial Cells

Fluorescence in situ hybridization (FISH) has become a vital tool for environmental and medical microbiology and is commonly used for the identification, localization, and isolation of defined microbial taxa. However, fluorescence signal strength is often a limiting factor for targeting all members in a microbial community. Here, we present the application of a multilabeled FISH approach (MiL-FISH) that (i) enables the simultaneous targeting of up to seven microbial groups using combinatorial labeling of a single oligonucleotide probe, (ii) is applicable for the isolation of unfixed environmental microorganisms via fluorescence-activated cell sorting (FACS), and (iii) improves signal and imaging quality of tissue sections in acrylic resin for precise localization of individual microbial cells. We show the ability of MiL-FISH to distinguish between seven microbial groups using a mock community of marine organisms and its applicability for the localization of bacteria associated with animal tissue and their isolation from host tissues using FACS. To further increase the number of potential target organisms, a streamlined combinatorial labeling and spectral imaging-FISH (CLASI-FISH) concept with MiL-FISH probes is presented here. Through the combination of increased probe signal, the possibility of targeting hard-to-detect taxa and isolating these from an environmental sample, the identification and precise localization of microbiota in host tissues, and the simultaneous multilabeling of up to seven microbial groups, we show here that MiL-FISH is a multifaceted alternative to standard monolabeled FISH that can be used for a wide range of biological and medical applications.     

Rapid Identification of Viable Bacterial Spores Using a Fluorescence Method

A method has been devised to differentiate viable and nonviable bacterial spores. “Germination-like” changes are initiated in spores with performic acid and lysozyme. The germinated spores are stained with aqueous acridine orange, a fluorescent dye. Nonviable spores fluoresce lemon-green and viable spores orange-red. It is proposed that with the use of a membrane filter resistant to performic acid and lysozyme, the method may be used for spore enumeration in foods in about 4 hr compared to conventional plating methods, which usually require up to 72 hr.     

NADH荧光法快速检测细菌总数

基于细菌胞内NADH的荧光特性及其在胞内含量稳定的特性, 建立一种快速检测细菌总数的新方法。该荧光法的NADH检测限为1 nmol/L, NADH含量在10 nmol/L~0.2 mmol/L间与荧光强度呈良好线性关系(R2 =0.9905)。经离心获得菌体细胞, 热Tris-HCl法提取胞内NADH, 以 342 nm为激发波长, 461 nm为发射波长测定提取液荧光强度, 1 h内可检测到样品1×104 CFU/mL菌数。结果表明该方法快速、灵敏、简便、重复性好, 可适用于食品卫生与安全、环境检测等领域活细菌数量的定量检测。     

Gateway-Based Destination Vectors for Functional Analyses of Bacterial ORFeomes: Application to the Min System in Brucella abortus

Twenty Gateway-compatible destination vectors were constructed. The vectors comprise fluorescent and epitope fusion tags, various drug markers, and replication origins that should make them useful for exploring existing microbial ORFeomes. In an attempt to validate several of these vectors, we observed polar and oscillating localization of MinD in Brucella abortus.     

Cloning Vectors for Rice

We developed various binary vectors that can be used for expressing a foreign gene in rice. Vectors pGA3426, pGA3436, and pGA3626 are intended for overexpression of a gene using the maize Ubiquitin promoter, whereas pGA3780 is for rather mild expression of a gene using the rice Actin1 promoter. Vector pGA3777 is for expressing two genes simultaneously. We also developed binary vectors for expressing a fusion protein with a tag. Four vectors (pGA3427, pGA3428, pGA3429, and pGA3438) are for protein tags with sGFP, HA, His, and Myc, respectively. Vector pGA3383 is for analyzing promoter activity using the GUS reporter. In this vector, multiple cloning sites in front of GUS can be utilized for accepting a promoter fragment. We also generated transient expression vectors for studying the subcellular localization of a protein. Vectors pGA3452, pGA3651, and pGA3652 are for GFP fusion; pGA3574 for RFP fusion; pGA3697 for Myc tag; and pGA3698 for HA tag. In addition, we generated pGA3506, pGA3516, pGA3592, and pGA3593 for facilitating the subcloning of full-length cDNA clones into our binary vectors.     

Use of 33P as an Indicator for 32P Pulse Labeling of Nucleic Acids in Bacterial Cultures

(33)P-phosphate can be used to follow bacterial phosphorus consumption before (32)P pulse labeling.