Measurement of protein concentration by quantitative electron microscopy

The method of quantitative electron microscopy was applied to the measurement of protein concentration in thin sections. The human erythrocyte was selected as a model because of its apparently uniform protein concentration. Phosphotungstic acid (PTA) in aqueous solution was used as a reversible stain for protein, and PTA-stained Dowex resin spheres were embedded along with the red cells as standards for measurement of section thickness. The mass of stain removed from a given area of sectioned red cell by buffer (pH 7.4) was measured by quantitative electron microscopy. From the stoichiometry of the reaction between PTA and red cell protein established in this study, the amount of protein present in the measured area was calculated. From this amount of protein and the measured thickness, the concentration of protein was calculated and expressed as g/100 ml, for comparison with the clinical laboratory value for hemoglobin. Groups of red cells from the same sample were measured on 3 different days and their mean values (g/100 ml ± SD) were 29 ± 3.9, 30 ± 2.7, and 33 ± 4.6, compared to the clinical laboratory value of 32.1 g/100 ml packed cells, after correction for volume change and protein loss during fixation.     

Cytochemistry of kinetochores under electron microscopy

A cytochemical analysis has been performed on kinetochores of mouse, Allium and grasshopper under the electron microscope. The study was carried out using serial sections and cytochemical methods. Alcoholic PTA was used for basic protein staining and the EDTA method for preferential staining of ribonucleoproteins. In mouse and Allium chromosomes the kinetochore appears positively stained after PTA and EDTA. In grasshopper chromosomes, kinetochores appear as a fibrillar and less dense region and are positively stained after EDTA. Blocks from mouse treated with HCl prior to PTA stain show lower contrast in the kinetochore. When Allium cepa anthers were treated with RNase and perchloric acid (PCA) there was no positive effect after EDTA stain in the kinetochore region. It is suggested that non-DNA material takes part in the constitution of the kinetochore. This material would be made up, at least in part, of basic proteins and ribonucleoproteins.     

Double modification of cytidine residues in DNA]

The reaction of O-beta-diethylaminoethylhydroxylamine (O-beta-HA) with cytidine was studied and its mechanism was shown to be analogous to that of the reaction of hydroxylamine of O-methylhydroxylamine with cytidine. In experiments involving reaction of denatured DNA with O-beta-HA., Sephadex G-15 columns were used for the quantitative separation of normal and modified nucleosides after enzymatic hydrolysis of modified DNA by exonuclease A5 followed by alkaline phosphatase treatment. DNA cytidine residues of free cytidine with O-beta-HA. Modified cytidines can form complex with phosphotungstic acid (PTA). It was shown that one mole of PTA was bound per one mole of modified cytidine either in DNA or in free state. Electron microscopic examination of denatured DNA molecules modified by O-beta-HA and reacted with PTA revealed linear arrays of electron-scattering spots which presumably correspond to PTA molecules complexed with modified cytidine in DNA chains.     

Glycation changes the charge distribution of type I collagen fibrils

In aging and diabetes, glycation of collagen molecules leads to the formation of cross-links that could alter the surface charge on collagen fibrils, and hence affect the properties and correct functioning of a number of tissues. The electron-optical stain phosphotungstic acid (PTA) binds to positively charged amino acid side-chains and leads to the characteristic banding pattern of collagen seen in the electron microscope; any change in the charge on these side-chains brought about by glycation will affect the uptake of PTA. We found that, upon glycation, a decrease in stain uptake was observed at up to five regions along the collagen D-period; the greatest decrease in stain uptake was apparent at the c1 band. This reduction in PTA uptake indicates that the binding of fructose leads to an alteration in the surface charge at several sites along the D-period. Not all lysine and arginine residues are involved; there appear to be specific residues that suffer a loss of positive charge.     

Staining of the elastic fibers in insect connective tissue after tannic acid/glutaraldehyde fixation.

Locust neural lamella and Calpodes connective tissue fixed in glutaraldehyde have a fibrous component which stains after reaction with DAB and osmication and after staining sections with PTA. The fibers also stain when fixed in glutaraldehyde with tannic acid followed by osmication and section staining with lead citrate.     

MEASUREMENT OF THICKNESS WITHIN SECTIONS BY QUANTITATIVE ELECTRON MICROSCOPY

To apply the method of quantitative electron microscopy to the measurement of mass in thin sections, the thickness of the section at or very near the structure to be studied must be known. Dowex anion exchange resin AG 1 x 2, stained with phosphotungstic acid (PTA) at pH 6.4, was used as a thickness standard which could be embedded and sectioned. The sectioned PTA-Dowex appeared uniformly stained and exhibited suitable electron opacity. The stoichiometry of the reaction between PTA and the Dowex resin was measured by three independent methods based on gravimetric, colorimetric, and nitrogen determinations whose results showed close agreement. From the PTA uptake, the density of the stained spheres was calculated. Mass of a defined area of PTA-Dowex was measured by quantitative electron microscopy, and from this mass and density, the volume and then the thickness were calculated. The values for thickness were compared to those obtained by interference microscopy on the embedding medium alone in the same sections.     

侵染半夏的两种病毒的分离纯化和初步鉴定

用自然感染的半夏（Ｐｉｎｅｌｌｉａｔｅｒｎａｔａ）为材料,经粗提纯后检查到一种线状病毒和一种球状病毒,用两种方法对担提纯样品中的病毒粒子进行了分离纯化。１０％－７０％连续甘油梯度８００００ｇ离心１５０分钟获得两条病毒带,经紫外吸收测定均为强的核蛋白吸收峰,病毒粒子检查分别为球状和线状病毒粒子,线状病毒经浓缩收集为均一成份．与芋花叶病毒（Ｄａｓｈｅｅｍｍｏｓａｉｃｖｉｒｕｓ,ＤＭＶ）抗体有强的阳性反应。粗提纯样品经０．８％琼脂糖凝胶电脉分离为一条蛋白带,该条带回收后经紫外吸收测定为核蛋白吸收峰,电镜下检查为均一的球状病毒,以ＴＭＶ为对照、醋酸铀（ＵＡＣ）负染后测得该球状病毒（ｐｉｎｅｌｌｉａｓｐｈｅｒｉｃａｌｖｉｒｕｓ１．ＰｓＶ－１）的大小为３１．７ｎｍ;戊二醛固定后磷钨酸（ＰＴＡ）负染测得ＰｓＶ—１的大小为３４．０ｎｍ。各组分经ＳＤＳ－聚丙烯酸胺凝焦电泳分析测得线状病毒和球状病毒的外壳蛋白分子量分别为２０ＫＤ和２８ＫＤ。初步确定线状病毒为ＤＭＶ．球状病毒ＰｓＶ—１为侵梁天南星科半夏的一种新病毒。     

A search for protein cores in chromosomes: Is the scaffold an artifact?

A protein chromosome scaffold structure has been proposed that acts as a structural framework for attachment of chromosomal DNA. There are several troubling aspects of this concept: (1) such structures have not been seen in many previous thin-section and whole-mount electron microscopy studies of metaphase chromosomes, while they are readily seen in leptotene and zygotene chromosomes; (2) such a structure poses problems for sister chromatid exchanges; and (3) the published photographs show a marked variation in the amount of scaffold in different whole-mount preparations. An alternative explanation is that the scaffold in whole-mount preparations represents incomplete dispersion of the high concentration of chromatin in the center of chromosomes, and when the histones are removed and the DNA dispersed, the remaining nonhistone proteins (NHPs) aggregate to form a chromosome-shaped structure. Two studies were done to determine if the scaffold is real or an artifact: (1) Chinese hamster mitotic cells and isolated chromosomes were examined using two protein stains -EDTA-regressive staining and phosphotungstic acid (PTA) stain. The EDTA-regressive stain showed ribonucleoprotein particles at the periphery of the chromosomes but nothing at the center of the chromosomes. The PTA stain showed the kinetochore plates but no central structures; and (2) isolated chromosomes were partially dispersed to decrease the high concentration of chromatin in the center of the chromosome, then treated with 4 M ammonium acetate or 2 M NaCl to dehistonize them and disperse the DNA. Under these circumstances, no chromosome scaffold was seen. We conclude that the scaffold structure is an artifact resulting from incomplete dispersion of central chromatin and aggregation of NHPs in dehistonized chromosomes.     

Observations on the Kinetics of Uranyl Acetate and Phosphotungstic Acid Staining of Chromatin in thin Sections for Electron Microscopy

When thin sections of spermatogenic chromatin are fixed with either glutaraldehyde alone or postfixed with osmium tetroxide (OsO₄) and stained with uranyl acetate (UAc) for increasing times, even after as little as 1 min, stain uptake is proportional to section thickness. Greater UAc uptake is observed in chromatin fixed with gutaraldehyde only, but stain uptake is reduced following a long wash with distilled water to a level similar to that seen with postfixed chromatin. Lead citrate poststaining of chromatin fixed with either glutaraldehyde or postfixed with OsO₄ increases UAc uptake by a factor of about 3.

The staining of thin sections of spermatogenic chromatin with ethanolic phosphotungstic acid (PTA) shows a region where stain uptake is proportional to section thickness followed by a plateau. This staining pattern is seen in chromatin fixed with glutaraldehyde alone or postfixed with OsO₄; similar levels for final PTA uptake are also observed.

An increase in the resin content of embedded chromatin postfixed with OsO₄ is proposed to explain the decrease and increase in the rate of migration of UAc and ethanolic PTA staining solutions, respectively.     

Copper iodide staining of protein blots on nitrocellulose membranes

Copper iodide staining which can detect protein levels as low as 100-150 pg/mm2 on nitrocellulose membranes is described. The staining is quantitative as measured by densitometry. Staining is complete within 5 min and may be removed by washing the membrane for 15 min without loss of immunoreactivity. The stain utilizes a reddish-brown precipitate of copper iodide in highly alkaline conditions. Because of its high sensitivity, convenience, and low cost, this stain may be more practical than amido black or gold- and silver-based stains for most laboratory purposes.     

Observations on the kinetics of uranyl acetate and phosphotungstic acid staining of chromatin in thin sections for electron microscopy

When thin sections of spermatogenic chromatin are fixed with either glutaraldehyde alone or postfixed with osmium tetroxide (OsO4) and stained with uranyl acetate (UAc) for increasing times, even after as little as 1 min, stain uptake is proportional to section thickness. Greater UAc uptake is observed in chromatin fixed with glutaraldehyde only, but seen with postfixed chromatin. Lead citrate poststaining of chromatin fixed with either glutaraldehyde or postfixed with OsO4 increases UAc uptake by a factor of about 3. The staining of thin sections of spermatogenic chromatin with ethanolic phosphotungstic acid (PTA) shows a region where stain uptake is proportional to section thickness followed by a plateau. This staining pattern is seen in chromatin fixed with glutaraldehyde alone or postfixed with OsO4; similar levels for final PTA uptake are also observed. An increase in the resin content of embedded chromatin postfixed with OsO4 is proposed to explain the decrease and increase in the rate of migration of UAc and ethanolic PTA staining solutions, respectively.     

Electron microscopy of interphase chromosomes in situ; binding of permanganate to chicken erythrocytes.

From quantitative electron-microscope observations on the binding of permanganate to regions of erythrocytes and reticulocytes of known chemical composition, it is concluded that KMnO4, like phosphotungstic acid (PTA), binds preferentially to sites on proteins. Compared with PTA, KMnO4 binding exhibits less anomalous behaviour. The data support the hypothesis previously put forward that the 2 regions, or phases, in condensed chromatin differ in both molecular composition and concentration. The increase in binding to protein which occurs during nuclear haemolysis is interpreted in terms of protein-protein interaction in the chromatin of the intact cell.     

An evaluation of Coomassie Brilliant Blue as a stain for quantitative microdensitometry of protein in section.

The specificity and stoichiometry of the binding of Coomassie Brilliant Blue (CBB) to protein in section has been examined using both frozen protein matrices and plant material. The maximum adsorbance of the stain, bound and in solution, was found to be 620 nm although variation in the results at this wavelength necessitated measurements to be made at 600 nm. After enzyme treatments of sectioned plant material embedded in resin, all CBB-binding biological material was shown to be sensitive to non-specific protease. The relationship between optical density at 600 nm and section thickness was tested statistically against the Lambert-Beer law, using microdensitometry of cryostat-sectioned, frozen genatine solution. The analyses showed conclusively that, under these conditions, CBB adheres strongly to the Lambert-Beer relationship. CBB may thus be considered as a very specific protein stain, eminently suited both to cytological observation and quantitative microdensitometry.     

Standard specimens for stain calibration: application to Romanowsky-Giemsa staining.

Standardized specimens with reproducible staining properties were fabricated from extracts of biological objects (bovine liver, nucleoprotamine and defatted muscle). The standard specimens were stained with two formulations of the Romanowsky-Giemsa stain (RG), using the same azure B and eosin Y. One formulation used methanol and Sorensen's buffer and the other DMSO and Hepes buffer as solvents. The standard specimens were stained either in the composite stain or in the individual dyes dissolved in the same solvents and at the same concentration as the composite stain. Solution spectroscopy demonstrated different spectra for the two formulations with some wavelength regions varying by more than an order of magnitude. The RG spectra were also very different from those of the individual dyes dissolved at the RG concentration in the respective solvents. The stained standard specimens were analyzed by microspectrophotometry and were found to have spectra similar to those of cell smears. Furthermore, the standard specimens were shown to be a repeatable substrate for stain uptake. The transmitted light intensity from random fields of the same standardized specimen varied +/- 5%. When specimens were stained at the same time, the specimen-to-specimen variation depended on preparation conditions and the measurement wavelength, but was as good as +/- 5% for some conditions. The quantitative stain performance of both formulations was studied and compared. The standardized specimens provide a tool for the quantitative study of staining processes and specimen preparation procedures and for stain calibration.     

Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis

The combination of isotope coded affinity tag (ICAT) reagents and tandem mass spectrometry constitutes a new method for quantitative proteomics. It involves the site-specific, covalent labeling of proteins with isotopically normal or heavy ICAT reagents, proteolysis of the combined, labeled protein mixture, followed by the isolation and mass spectrometric analysis of the labeled peptides. The method critically depends on labeling protocols that are specific, quantitative, general, robust, and reproducible. Here we describe the systematic evaluation of important parameters of the labeling protocol and describe optimized labeling conditions. The tested factors include the ICAT reagent concentration, the influence of the protein, SDS, and urea concentrations on the labeling reaction, and the reaction time. We demonstrate that using the optimized conditions specific and quantitative labeling was achieved on standard proteins as well as in complex protein mixtures such as a yeast cell lysate.     

EFFECTS OF PHOSPHOTUNGSTATE NEGATIVE STAINING ON THE MORPHOLOGY OF THE ISOLATED GOLGI APPARATUS

Isolated Golgi complexes can be recognized in phosphotungstate (PTA) negative stain as stacks of membranous plates surrounded by a complex anastomosing network of tubules and vesicles. The extent of this tubular network is, however, much greater than can be observed in thin sections of whole cells. To determine which of the steps leading to the final negatively stained image may produce the observed changes, we have monitored each of the steps by other electron microscope and biochemical methods. The first damage to the membranes seems to occur during the initial isolation procedure as judged by the appearance of smooth patches on the freeze-fractured membrane faces that are normally covered with particles. Subsequent suspension of the Golgi fraction in water, to dilute the sucrose for negative staining, leads to the disappearnce of the stacking, to some tubulation and some vesiculation of the membranes as judged by thin section and freeze-cleave microscopy. The latter technique also reveals an increase in smooth-cleaving membrane faces. Application of the negative stain to the water-washed Golgi fraction, finally, produces extensive tubular arrays and a simultaneous decrease in the remaining large membranous vesicles. The freeze-cleaved tubular membranes appear essentially smooth except for small patches of aggregated particles. Parallel gel electrophoresis studies of the membranes and of the water and negative stain wash extracts indicate that protein extraction is involved in these morphological changes. PTA seems to be a particularly effective solvent for certain membrane proteins that are not removed by the water wash. These observations suggest that removal of membrane proteins alters structural restraints on the membrane lipids so that they behave semiautonomously like myelinics and form new artificial structures. This does not eliminate the possibility, however, that some tubules also exist in the Golgi apparatus in vivo.     

A postembedding staining method of intensifying alcian blue reactions of acidic glycoconjugates with phosphotungstic acid in electron microscopy

For the effective visualization of acidic glycoconjugates in electron microscopy, a post-embedding staining method has been devised for intensifying their alcian blue (AB) reactions by means of phosphotungstic acid (PTA). Tissue samples were prepared by glutaraldehyde-paraformaldehyde fixation of pieces of the trachea, aorta, and colon from adult rats. LR-White resin-embedded ultrathin sections were stained first with AB (pH = 1.0 or 2.5) and then reacted for PTA. In the tissues examined, the AB reaction of acidic glycoconjugates involved was effectively intensified by subsequent PTA staining in nearly all of the ultrastructures known to contain such carbohydrates. The majority of these ultrastructures failed to show any pronounced densities, if stained singly with PTA under the identical staining conditions. In all the ultrastructures, a series of selective methods such as active methylation and digestion with testicular hyaluronidase or neuraminidase have substantiated the selectivity of the PTA intensified AB reactions for acidic glycoconjugates involved. The present PTA intensified AB method resulted virtually in no contaminations of the backgrounds and can be regarded as a reliable and useful technique for the effective visualization of both intra- and extracellular acidic glycoconjugates in electron microscopy.     

Standard Specimens for Stain Calibration: Application to Romanowsky-Giemsa Staining

Standardized specimens with reprodcible staining properties were fabricated from extracts of biological objects (bovine liver, nucleoprotamine and defatted muscle). The standard specimens were stained with two formulations of the Romanowsky-Giemsa stain (RG), using the same azure B and eosin Y. One formulation used methanol and Sorensen's buffer and the other DMSO and Hepes buffer as solvents. The standard specimens were stained either in the composite stain or in the individual dyes dissolved in the same solvents and at the same concentration as the composite stain. Solution spectroscopy demonstrated different spectra for the two formulations with some wavelength regions varying by more than an order of magnitude. The RG spectra were also very different from those of the individual dyes dissolved at the RG concentration in the respective solvents. The stained standard specimens were analyzed by microspectrophotometry and were found to have spectra similar to those of cell smears. Furthermore, the standard specimens were shown to be a repeatable substrate for stain uptake. The transmitted light intensity from random fields of the same standardized specimen varied ±5%. When specimens were stained at the same time, the specimen-to-specimen variation depended on preparation conditions and the measurement wavelength, but was as good as ±5% for some conditions. The quantitative stain performance of both formulations was studied and compared. The standardized specimens provide a tool for the quantitative study of staining processes and specimen preparation procedures and for stain calibration.     

Utility of a direct dual-mode development analysis on blotted protein mixtures

Classic blotting methods remain a commonly applied approach to specific protein identification in gel electrophoresis of complex mixtures despite the inherent difficulty in band or spot matching due to significant variability of protein migration or localization in replicate blotting experiments. A direct application of both protein stain and protein blotting on a single membrane significantly reduces the complexity of the experiment and provides increased confidence of signal matching. Digital alignment of images acquired from both total protein stain and blotting development modes on a single membrane allows unambiguous spot or band assignments in these experiments as well as retention of quantitative information acquired from both modes of signal generation. A direct and simple method applying a fluorescent protein stain that is compatible with subsequent detection by antibody or lectin recognition factors along with common image adjustment software is examined. The utility of this blot dual-mode development method for direct protein recognition and quantification in one- and two-dimensional electrophoresis is demonstrated for bioanalytical objectives where replicate experiments are challenged by sample complexity.