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Quantitative proteome analysis in benign thyroid nodular disease using the fluorescent ruthenium II tris(bathophenanthroline disulfonate) stain.

Thyroid tumorigenesis involves qualitative and quantitative changes in protein expression, which can be comprehensively studied by proteome analysis. However, one of the technical bottlenecks of proteomics remains a reliable, sensitive and inexpensive method for quantification of differentially expressed proteins. This is due to the limited linear range of most available protein stains, i.e. silver and Coomassie blue, and high costs of commercially available fluorescent stains. In this paper we describe our experience with a lab-made ruthenium based fluorescent stain (ruthenium II tris(bathophenanthroline disulfonate) (RuBPs)) to perform proteome analysis of nodular thyroid disease. We first compared the properties of RuBPs with two highly sensitive protein stains: (1) silver staining and (2) the commercially available fluorescent dye Sypro Ruby. We show that in addition to its highly sensitive staining capabilities similar to Sypro Ruby and silver (2 ng), RuBPs offers several advantages such as a broad dynamic range (similar to Sypro Ruby and 500 times broader than the dynamic range of silver stain), low costs ( 0.03 per gel) and excellent compatibility with mass spectrometry. We then applied the inexpensive RuBPs stain to 2D gels (pH 4-7) of four benign thyroid nodules and normal thyroid tissue. We were able to detect approximately 1800 protein spots/gel in our thyroid samples. Quantitative changes in protein expression levels of at least 20-42 proteins were noted in the benign nodules compared with the normal thyroid tissue of the same patient. Differentially expressed spots were further characterised by nano-LC-FTICR and MALDI-TOF mass spectrometry. In summary we demonstrate, that the novel fluorescent ruthenium II tris(bathophenanthroline disulfonate) stain is a highly sensitive, reliable and inexpensive tool for quantitative proteome analysis in thyroid nodular disease.

Dextrans↗

Evaluation of Papanicolaou stain for studying micronuclei in buccal cells under field conditions.

OBJECTIVE: To compare Papanicolaou (Pap) and May-Grünwald Giemsa (MGG) stain as 2 techniques for staining for buccal mucosal cells to detect micronuclei (MN) infield studies. STUDY DESIGN: Eighty cytologic smears (2 per individual) were taken from the buccal mucosa of 40 cigarette smokers recruited at a rural village in Egypt. Forty smears were stained with Pap stain and 40 with MGG stain. All were assessed for cellularity and scored for MN. RESULTS: Pap stain was faster and easier to process and transport in the field study than was MGG stain. Regarding MGG smears, bacteria and cell debris masked the MN as compared to Pap smears, in which the fixative destroyed the bacteria and made the cell boundaries clearly demarcated. Using Pap stain, MN were seen easily in transparent cytoplasm. CONCLUSION: Pap stain is the preferred method infield studies for scoring and detecting MN in cells of buccal mucosa.

Azure Stains↗

Improved stability of methanolic wright's stain with additive reagents.

Additive reagents have been investigated to improve the stability of methanolic Wright's stain. The addition of ammonium halides, monoalkylamine hydrochlorides, dialkylamine hydrochlorides or trialkylamine hydrochlorides to methanolic Wright's stain was found to enhance the stability of stain components in methanol. No change in performance is observed with these additives present. Random precipitation in the stain solution was still observed with the addition of ammonium halides and monoalkylamine hydrochlorides. No precipitation was found in stain solutions containing hydrochlorides of most dialkylamines and trialkylamines. Of the compounds evaluated, 0.6% diethylamine hydrochloride added to methanolic stain solutions produced the most desirable overall results. Mechanisms of stabilization and precipitation in these stain solutions are proposed. Essentially, separation of the thiazine-eosinate ion pair through interaction with an appropriate additive increases stain stability. The solubilities of thiazine-eosinate or additive cation-eosinate ion pairs in methanol determine the formation of precipitate in such stain solutions.

Amines↗

Staining of DNA-phosphate groups with a mixture of azure A and acridine yellow.

This paper deals with staining of DNA-phosphate groups with a mixture of an equal parts of aqueous solution of azure A and acridine yellow in a 1:1 proportion and also embodies a study of the absorption properties of the stained nuclei. It also embodies results of sequential staining of nuclei stained first with azure A followed by staining with acridine yellow and vice versa, after extraction of RNA with cold phosphoric acid. The results indicate that the absorption peaks of nuclei differ from those of nuclei stained for DNA-aldehyde molecules with azure A-SO2 or acridine yellow-SO2. The in vitro absorption characteristics of an aqueous solution of azure A and those of an aqueous solution of acridine yellow are also presented herein. The conclusion obtained from this study is that all the phosphate groups of DNA do not take part in the staining process when staining is carried out with azure A or acridine yellow alone after after RNA has been extracted. This is because the nuclei stained with these dyes sequentially show the presence of acridine yellow-DNA and azure A-DNA complex.

Acridines↗

An improved formulation of SYPRO Ruby protein gel stain: comparison with the original formulation and with a ruthenium II tris (bathophenanthroline disulfonate) formulation.

SYPRO Ruby protein gel stain is compatible with a variety of imaging platforms since it absorbs maximally in the ultraviolet (280 nm) and visible (470 nm) regions of the spectrum. Dye localization is achieved by noncovalent, electrostatic and hydrophobic binding to proteins, with signal being detected at 610 nm. Since proteins are not covalently modified by the dye, compatibility with downstream proteomics techniques such as matrix-assisted laser desorption/ionisation-time of flight mass spectrometry is assured. The principal limitation of the original formulation of SYPRO Ruby protein gel stain, is that it was only compatible with a limited number of gel fixation procedures. Too aggressive a fixation protocol led to diminished signal intensity and poor detection sensitivity. This is particularly apparent when post-staining gels subjected to labeling with other fluorophores such as Schiff's base staining of glycoproteins with fluorescent hydrazides. Consequently, we have developed an improved formulation of SYPRO Ruby protein gel stain that is fully compatible with commonly implemented protein fixation procedures and is suitable for post-staining gels after detection of glycoproteins using the green fluorescent Pro-Q Emerald 300 glycoprotein stain or detection of beta-glucuronidase using the green fluorescent ELF 97 beta-D-glucuronide. The new stain formulation is brighter, making it easier to manually excise spots for peptide mass profiling. An additional benefit of the improved formulation is that it permits staining of proteins in isoelectric focusing gels, without the requirement for caustic acids.

Animals↗

How the fixation-embedding protocol affects the specificity and efficiency of immunocytochemical stains for gonadotropin subunits.

This report describes a study designed to test factors that may affect the efficiency and specificity of stains for gonadotropins. These include chemical or freeze-fixation and dehydration, heat polymerization of the plastic embedding compound, dehydration in organic solvents, and etching. Specifically, postembedding stains for LH or FSH subunits were applied to 1-micron sections of 1) Araldite-embedded pituitaries that were either chemically fixed and dehydrated or freeze-fixed and freeze-dried; 2) Aldehyde-fixed pituitaries that were dehydrated in water-soluble glycol methacrylate (GMA) and embedded in GMA at 4 degrees C; and 3) p-formaldehyde-fixed pituitaries that were embedded in paraffin. A fourth group of pituitaries was dispersed and grown in monolayers for 1-3 days. These were stained following glutaraldehyde fixation. The optimal dilution of the primary antisera varied with the protocol; however, the percentage of cells staining for beta subunits did not change. In contrast, postembedding stains showed that alpha subunit reactivity is masked or destroyed in pituitaries that are fixed in glutaraldehyde and embedded in Araldite. Alpha chain reactivity was detected (in 14% of cells) either after freeze-fixation and freeze-drying followed by Araldite embedding, or after 4% paraformaldehyde fixation and GMA embedding (in 17% of cells). Staining in paraffin-embedded pituitaries was seen in only 10% of the cells. Preembedding stains for alpha chains were strikingly sensitive, however, and immunoreactivity was seen in 18-26% of the population of monolayer cells. Thus, whereas the percentages of cells staining for beta subunits do not change following the use of most of the fixation and embedding protocols, alpha chain reactivity is destroyed by all but the mildest. These findings show that one can control or improve the specificity of the stains for LH and FSH by the fixation-embedding protocol.

Animals↗

Banding patterns in rat incisor enamel stained by histochemical complexing methods for calcium.

A characteristic banding pattern can be visualized at the surface of the rat incisor in the maturation zone of amelogenesis by staining with glyoxal bis(2-hydroxyanil) (GBHA). Other banding patterns can be obtained with certain histological and fluorochrome stains and by radioautography following 45Ca injection. In this study, several histochemical reagents known to complex with different states of calcium were used to stain the surface of enamel. Rat incisors were quickly dissected and immediately immersed in solutions containing the following calcium-binding reagents: arsenazo III, calmagite, murexide, N,N-naphthaloylhydroxylamine, and calcein. Routinely, one contralateral lower incisor from each pair was counterstained with GBHA in order to relate each of the staining patterns to the banded distribution of maturation ameloblasts that is reflected by the characteristic GBHA staining pattern in the enamel. Each of the reagents used in this study demonstrated a staining pattern consisting of a series of broad bands running transversely and obliquely across the enamel. In all cases, the dyes stained predominantly that enamel associated with ruffle-ended ameloblasts, i.e. enamel left unstained by GBHA. Some of the reagents also stained enamel in the secretion zone. The appearance and distribution of the staining patterns reflect the banded distribution of maturation ameloblasts and appear to be controlled on a time scale related to the rapid modulation of these cells.

Animals↗

Trauma-induced Golgi-like staining of neurons: a new approach to neuronal organization and response to injury.

A new esterification-silver approach to the directed staining of the dendritic trees of traumatized neurons is described. Stained neurons compare favorably to those labeled with silver chromate Golgi impregnations in the visualization of dendritic arbors. Cells in all parts of the brain, including the hypothalamus, hippocampus, cerebral cortex, cerebellum, striatum, spinal cord, thalamus, and olfactory bulb, can be detected after focal trauma to that region. Selection of neurons to be stained is made by increasing their affinity for silver with many different types of directed neuronal trauma, including micropipette wounds, pressure, surgical incision, chemical cytotoxicity, and impact trauma. Trauma to one area of the brain results in dendritic arbors staining only in the injured area; other areas of the brain are free of dendritic staining. Injury can be produced either in vivo or in vitro. In vitro injury to neurons allows a high degree of localization and facilitates the analysis of neuronal response to trauma in the absence of complicating factors such as blood flow and secondary injury. The selective affinity for silver staining in this approach is increased very rapidly, allowing detection of traumatized cells fixed minutes after injury. Brains of all mammals used appear to stain similarly, including the rat, mouse, pig, and human. Axons, although labeled less frequently than dendritic arbors, are induced to stain just as rapidly as dendrites. The ability to visualize a large part of the dendritic tree after trauma allows the segregation of neuronal subtypes on the basis of their differential response to injury. Subpopulations of cells in the same area of the brain appear to respond differently to trauma. Differential response of neurons to trauma can easily be detected. For instance, slight variations in trauma can be used to label selectively the major subpopulations of neurons in the hippocampus, including pyramidal cells, interneurons near the pyramidal cell layer, or granule cells. Similarly, neurons of the hypothalamic paraventricular and arcuate nuclei respond to compression trauma much more dramatically than other cell types in the same region of the hypothalamus. Hypothalamic neurons were studied extensively, particularly in regions that are difficult to routinely stain with Golgi impregnations, including the arcuate, paraventricular, supraoptic, and suprachiasmatic nuclei. Trauma to these areas was made in vitro after removal of the brain from the skull, allowing easy access to the ventral surface of the brain.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

Acetylcholinesterase staining differentiates functionally distinct auditory pathways in the barn owl.

The aim of this study was to examine how the functional specialization of the barn owl's auditory brainstem might correlate with histochemical compartmentalization. The barn owl uses interaural intensity and time differences to encode, respectively, the vertical and azimuthal positions of sound sources in space. These two auditory cues are processed in parallel ascending pathways that separate from each other at the level of the cochlear nuclei. Sections through the auditory brainstem were stained for acetylcholinesterase (AChE) to examine whether nuclei that process different auditory cues stain differentially for this enzyme. Of the two cochlear nuclei, angularis showed more intense staining than nucleus magnocellularis. Nucleus angularis projects to all of the nuclei and subdivisions of nuclei that belong to the intensity processing pathway. Acetylcholinesterase stained all regions that contain terminal fields of nucleus angularis and thus provided discrimination between the time and intensity pathways. Moreover, staining patterns with acetylcholinesterase were complementary to those previously reported with an anti-calbindin antibody, which stains terminal fields of nucleus laminaris, and thus stains all the nuclei and subdivisions of nuclei that belong to the time pathway. Some of the gross staining patterns observed with AChE were similar to those reported with antibodies to glutamate decarboxylase. However, AChE is a more convenient and definitive marker in discriminating between these pathways than is calbindin or glutamate decarboxylase. Acetylcholinesterase staining of the intensity pathway in the owl may be related to encoding of sound intensity by spike rate over large dynamic ranges.

Acetylcholinesterase↗

A gentle fixation and permeabilization method for combined cell surface and intracellular staining with improved precision in DNA quantification.

A method was developed for gentle fixation of mammalian cells and permeabilization of their membranes. The method is useful for staining of intracellular antigens or quantification of DNA content simultaneously with cell surface staining. Cells are treated for 1 h at 4 degrees C with 0.25% buffered paraformaldehyde then for 15 min at 37 degrees C with 0.2% Tween 20 detergent in PBS. The procedure permits excellent staining of intracellular proteins, very low coefficients of variation (CV) on the G0G1-peak of DNA distributions, and preservation of the integrity of cell surface antigens. The low vs. 90 degrees angle light scatter profile of cell clusters is maintained thereby allowing discrimination of different cell populations including human peripheral blood lymphocytes and monocytes for gating and analytic purposes. The method was successfully used on a variety of other cell types, including human thymocytes, murine thymocytes and spleen cells, and several leukemic cell lines. Dual-color surface antigen staining combined with DNA staining with 7-amino-actinomycin D (7-AAD) on peripheral blood mononuclear cells (PBMC) cultured with tetanus toxoid allowed the determination of the cell subset that was preferentially stimulated. Staining for internal antigens was done on CCRF-CEM for expression of CD3 epsilon and on NALM-6 for expression of mu. The technique we developed gave bright and specific staining of internal antigens in the examples presented here. It is particularly suited for correlations of internal antigen staining with DNA staining and/or surface immunofluorescence.

Antigens↗

Highly sensitive, specific, and stable new fluorescent DNA stains for confocal laser microscopy and image processing of normal paraffin sections.

The area, volume, shape, DNA content, and chromatin pattern of nuclei can be important for the diagnosis and prognosis of cancers. Confocal laser scan microscopy can be useful to obtain such information by optical slicing and three-dimensional (3-D) reconstruction of nuclei in thick paraffin sections. To retrieve individual quantitative features from the section, highly sensitive, specific, and stable fluorescent stains are required. Two new nuclei acids stains (TOTO-1 iodide and YOYO-1 iodide) can detect picogram amounts of nucleic acids in gels. Despite their high sensitivity to detect DNA, they have not been used to stain nuclei in paraffin embedded tissue sections (as routinely applied in surgical cancer pathology). We have developed a technique to stain nuclei in 4% buffered formaldehyde fixed paraffin tissue sections using TOTO-1 iodide and YOYO-1 iodide. The technique developed gives bright specific staining of the nuclei (with nearly zero background intensity, much less than with acriflavine). Moreover, TOTO-1 iodide and YOYO-1 iodide stains both give fluorescent signals only when they interact with DNA. Thus washing off the excess stain left on the stained specimen is not necessary (washing of excessive stain is necessary with acriflavine). Care has to be taken that the deparaffinizing liquids (xylol etc.) are not polluted with eosin (a frequently used counterstain in surgical pathology specimens), as this gives undesired fluorescence of cytoplasm and connective tissue at the same wavelength as TOTO-1 iodide and YOYO-1 iodide. Contrary to acriflavine, bleaching of TOTO-1 iodide and YOYO-1 iodide fluorescence is minimal, even after 30 min continuous laser light excitation.(ABSTRACT TRUNCATED AT 250 WORDS)

Acriflavine↗

Cytologic detection of Pneumocystis carinii: a comparison of Papanicolaou and other histochemical stains.

Pneumocystis carinii, a common pathogen among immunocompromised patients, has been investigated in cytologic specimens using both the histochemical stains and ultraviolet (UV) fluorescence following Papanicolaou staining. We reviewed 57 pulmonary cytologic specimens obtained from 23 patients and compared the results of specific histochemical stains and Papanicolaou-stained preparations under UV excitation. Specific Pneumocystis fluorescence was observed in 26 of 49 Papanicolaou-stained specimens. Thirty-seven specimens were examined using both histochemical staining and after Papanicolaou UV staining. A comparison of the two techniques showed the Papanicolaou UV technique to have 89% sensitivity and 95% specificity. Cellulosic filters were the most valuable Papanicolaou-stained preparation for Pneumocystis diagnosis. The authors conclude that UV fluorescence of Papanicolaou-stained specimens obtained by noninvasive procedures is a rapid, accurate, and economical method for diagnosing pulmonary Pneumocystis carinii infections.

Biopsy↗

Diagnosis of Pneumocystis carinii pneumonia by cytologic evaluation of Papanicolaou-stained bronchial specimens.

To evaluate the sensitivity and specificity of diagnosing Pneumocystis carinii pneumonia (PCP) by Papanicolaou-stained bronchial brushing and wash/lavage specimens obtained by fiberoptic bronchoscopy, the cytologic preparations and clinical records from 58 immunocompromised patients were reviewed. Bronchial brushings and wash/lavage specimens were examined using methenamine silver (Grocott) and Papanicolaou stains. Pneumocystis carinii pneumonia was recognized with Papanicolaou stain by identifying distinctive alveolar casts, which frequently contained collections of encysted sporozoites. Thirty cases of PCP were identified, and Grocott-stained bronchial wash/lavage specimens were positive in 29 instances (97%). Grocott staining of the transbronchial biopsy was positive for PCP in 18 of 22 specimens (82%). Bronchial brushings were insensitive, yielding a positive specimen in only 30% of cases of PCP. Alveolar casts of PCP were identified by Papanicolaou-stained slides of wash/lavage specimens in 83% of cases of Pneumocystis pneumonia. These proteinaceous alveolar casts were not seen in other pulmonary disorders. Encysted sporozoites were found in 56% of cases in which Papanicolaou-stained alveolar casts were identified. We conclude that the diagnosis of PCP can be made rapidly and reliably on the Papanicolaou-stained bronchial wash/lavage or bronchial brush specimens by detecting the characteristic alveolar casts, which contain P. carinii-encysted sporozoites. The presence of encysted sporozoites within alveolar casts is pathognomonic for PCP, and methenamine silver stains can be eliminated in those cases in which encysted sporozoites are identified.

Bronchoalveolar Lavage Fluid↗

Differentiation of proteins in polyacrylamide gels by a modification of silver staining for the PhastSystem and a laser densitometer.

Nonspecific background staining of the gel matrix is the limiting factor in the differentiation of proteins using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. It is caused by nonspecific binding of silver ions in the gel matrix, either to nonprotein compounds or through the chemistry of the polyacrylamide gel itself. The resulting stain of the gel produces a stain baseline, making differentiation of protein bands with a laser densitometer difficult. We have therefore developed a modified silver staining method for the PhastSystem to reduce such nonspecific background staining. Apart from slowing the development program by lowering the temperature to 15 degrees C and shortening the incubation time to 4 min, the essential step in the modification is the combined use of an EDTA and Tris-acetate buffer solution which stops the reduction of silver ions. The reduced background staining leads to an improved detection of protein bands and virtually identical zero lines for the laser densitograms and the stain baselines. The total staining time is 91 min. All steps in the program are fully automated and continuous, employing the PhastSystem staining unit.

Densitometry↗

Optimized conditions for diluting and reusing a fluorescent protein gel stain.

This study elucidates the optimum conditions at the minimum cost for using SYPRO Ruby protein gel stain. It deals with the effects of gel fixation and staining times, as well as dilution and reuse of SYPRO Ruby protein gel stain in one-dimensional (1-D) gels. Signal strength and dynamic range were highest in gels that were fixed thoroughly before staining, followed by overnight staining. Using the optimized protocol, dilution or reuse of the stain reduces the dynamic range and signal intensity. Sensitivity remains high if the stain is reused up to two times, but signal intensity is reduced up to 2.5-fold in twice used stain. Sensitivity also remains high if the stain is diluted 1:2 in water, but signal intensity is reduced up to 6-fold. Of the two options, reuse or dilution, reuse better retains signal intensity and dynamic range.

Electrophoresis, Polyacrylamide Gel↗

Functional characterization of two-dimensional gel-separated proteins using sequential staining.

Proteins separated by two-dimensional (2-D) gel electrophoresis can be visualized using various protein staining methods. This is followed by downstream procedures, such as image analysis, gel spot cutting, protein digestion, and mass spectrometry (MS), to characterize protein expression profiles within cells, tissues, organisms, or body fluids. Characterizing specific post-translational modifications on proteins using MS of peptide fragments is difficult and labor-intensive. Recently, specific staining methods have been developed and merged into the 2-D gel platform so that not only general protein patterns but also patterns of phosphorylated and glycosylated proteins can be obtained. We used the new Pro-Q Diamond phosphoprotein dye technology for the fluorescent detection of phosphoproteins directly in 2-D gels of mouse leukocyte proteins, and Pro-Q Emerald 488 glycoprotein dye to detect glycoproteins. These two fluorescent stains are compatible with general protein stains, such as SYPRO Ruby stain. We devised a sequential procedure using Pro-Q Diamond (phosphoprotein), followed by Pro-Q Emerald 488 (glycoprotein), followed by SYPRO Ruby stain (general protein stain), and finally silver stain for total protein profile. This multiple staining of the proteins in a single gel provided parallel determination of protein expression and preliminary characterization of post-translational modifications of proteins in individual spots on 2-D gels. Although this method does not provide the same degree of certainty as traditional MS methods of characterizing post-translational modifications, it is much simpler, faster, and does not require sophisticated equipment and expertise in MS.

Animals↗

Rapid and easy protein staining for SDS-PAGE using an intramolecular charge transfer-based fluorescent reagent.

High-performance staining for 1-D and 2-D SDS-PAGE was carried out using a novel protein-binding fluorophore (Dye 1), which noncovalently interacts with proteins and provides a fluorescence emission response to proteins by intramolecular charge transfer. In order to achieve the high-throughput analysis of proteins for SDS-PAGE, the general protocols for in-gel protein staining (SDS-PAGE, fixation, staining, washing, and detection) were simplified to produce an easy and rapid protocol (SDS-PAGE together with staining, washing, and detection). This method was performed by preparation of an electrophoresis buffer containing Dye 1 under optimum conditions, and by the binding of Dye 1 to proteins in the gel during the SDS-PAGE. As a result, this study required only 15 min for protein staining as a minimum time. On the other hand, it takes several hours for the general protein staining method, such as SYPRO Ruby staining (18 h) and CBB staining (105 min). Moreover, the protein-to-protein variation was low, and the detection limit was 7.0 ng/band of BSA (S/N = 3.0) in this method, which was as sensitive as the short-protocol silver staining methods. On the basis of these results, this rapid and easy protocol for SDS-PAGE using Dye 1 may be widely applicable and convenient for users in the various scientific and medical fields.

Animals↗

Section staining for electron microscopy using tannic acid as a mordant: a simple method for visualization of glycogen and collagen.

The possibility that tannic acid and other classical mordants can be used in the electron microscopical section staining technique has been tested. A mordant can be defined as a chemical that combines with both a certain specific tissue component and the staining substance and thereby permits a staining reaction that otherwise will not be obtained. The following features were found to characterize section staining of tannic acid mordanted sections. Tannic acid apparently blocks those sites that normally would be contrasted by uranyl acetate or some other staining compounds. Ribosomes remain unstained. Glycogen particles, on the other hand, were stained, whereas they are not in non-mordanted sections. In fact, glycogen was the only cytoplasmic component to be contrasted by the uranyl acetate, and collagen the only extracellular component. Several different section staining solutions gave the same staining patterns of examined cells and tissues. Specificity of the reaction thus seems to depend on the mordant rather than on the heavy atom section stain. Some other tested mordants, which have also been used in the light microscopical technique, did not give any useful new information.

Animals↗