Stoichiometry of the amido black reaction with proteins

Housekeeping Proteins in Meat Quality Research: Are They Reliable Markers for Internal Controls in Western Blot? A Mini Review

Advancements in technology and analytical methods enable researchers to explore the biochemical events that cause variation in meat quality. Among those, western blot techniques have been successfully used in identifying and quantifying the key proteins that have critical functions in the development of meat quality. Housekeeping proteins, like β-actin, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and tubulins are often used as internal controls in western blots to normalize the abundance of the protein of interest. However, there are increasing concerns about using housekeeping proteins for western blot normalization, as these proteins do not demonstrate any loading differences above the relatively small total protein loading amounts of 10μg. In addition, the interaction between these housekeeping proteins and programmed cell death processes highlights the concerns about using the housekeeping protein as the internal control in meat quality research. Moreover, recent proteomic research has indicated that the abundance of some housekeeping proteins, like β-actin, GAPDH, and tubulin, can be altered by preslaughter stress, dietary supplementation, sex, slaughter method, genotype, breed, aging period, muscle type, and muscle portion. Furthermore, these housekeeping proteins could have differential expression in meat with differing color stability, tenderness, and water holding capacity. Therefore, this review aims to examine the realities of using housekeeping proteins as the loading control in meat quality research and introduce some alternative methods that can be used for western blot normalization.

The use of error rates to predict and characterize the efficacy of presumptive field tests

From a forensic perspective, a presumptive test, one which indicates the presence or absence of a certain target material such as blood, is an invaluable tool. Among these tests, there are different specificities, sensitivities, and shelf lives. The accuracy of a test is an algebraic combination of the specificity and sensitivity of the test. Each test has limitations as given by its false positive and false negative rates. The aim of this study was to illustrate how the false positive and false negative rates are to be properly determined using a simulation study for the phenolphthalein test. New presumptive tests must be properly evaluated/validated through testing of commonly encountered household items and other potentially probative items usually found at crime scenes, however, the makeup of test sets must appropriately capture all error rates. In order to correctly use these results when the test is applied to an unknown sample recovered at a crime scene, the error rates cannot be applied directly to estimate whether or not the sample is actually the analyte of interest. In a validation study, the forensic scientist calculates the false positive rate as the p(Positive Reaction|Blood), whereas at the scene, the crime scene investigator wishes to determine the p(Blood|Positive Reaction). All crime scene investigators need to ensure that the conditional is not transposed when interpreting such results. Furthermore, this work provides a model for the assessment of a multiple test diagnostic system intended for investigators.

Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants

BACKGROUND

In biogas plants, complex microbial communities produce methane and carbon dioxide by anaerobic digestion of biomass. For the characterization of the microbial functional networks, samples of 11 reactors were analyzed using a high-resolution metaproteomics pipeline.

RESULTS

Examined methanogenesis archaeal communities were either mixotrophic or strictly hydrogenotrophic in syntrophy with bacterial acetate oxidizers. Mapping of identified metaproteins with process steps described by the Anaerobic Digestion Model 1 confirmed its main assumptions and also proposed some extensions such as syntrophic acetate oxidation or fermentation of alcohols. Results indicate that the microbial communities were shaped by syntrophy as well as competition and phage-host interactions causing cell lysis. For the families Bacillaceae, Enterobacteriaceae, and Clostridiaceae, the number of phages exceeded up to 20-fold the number of host cells.

CONCLUSION

Phage-induced cell lysis might slow down the conversion of substrates to biogas, though, it could support the growth of auxotrophic microbes by cycling of nutrients.

Tubulin or Not Tubulin: Heading Toward Total Protein Staining as Loading Control in Western Blots

Western blotting is an analytical method widely used for detecting and (semi-)quantifying specific proteins in given samples. Western blots are continuously applied and developed by the protein community. This review article focuses on a significant, but not yet well-established, improvement concerning the internal loading control as a prerequisite to accurately quantifying Western blots. Currently, housekeeping proteins (HKPs) like actin, tubulin, or GAPDH are often used to check for equal loading or to compensate potential loading differences. However, this loading control has multiple drawbacks. Staining of the total protein on the blotting membrane has emerged as a better loading control. Total protein staining (TPS) represents the actual loading amount more accurately than HKPs due to minor technical and biological variation. Further, the broad dynamic range of TPS solves the issue of HKPs that commonly fail to show loading differences above small loading amounts of 0.5-10 μg. Although these and further significant advantages have been demonstrated over the past 10 years, only a small percentage of laboratories take advantage of it. The objective of this review article is to collect and compare information about TPS options and to invite users to reconsider their applied loading control. Nine benefits of TPS are discussed and seven different variants are critically evaluated by comparing technical details. Consequently, this review article offers an orientation in selecting the appropriate staining type. I conclude that TPS should be the preferred loading control in future Western blot approaches.

Studies of the Escherichia coli Rsd-sigma70 complex

Escherichia coli Rsd protein was previously identified on the basis of its binding to the RNA polymerase sigma(70) subunit. The Rsd-sigma(70) complex has been studied using different methods. Our data show that Rsd associates with sigma(70) to form a complex with a stoichiometry of 1:1. Alanine scanning and deletion mutagenesis were used to locate regions of sigma(70) that are required for the formation of the Rsd-sigma(70) complex.

Reflective densitometry of Western blots to quantitate the developmentally regulated accumulation of myosin light chain 3

We have employed a monoclonal antibody to fast myosin alkali light chains to study the accumulation of myosin light chain 3 (MLC3f) in the breast and limb musculature of developing quail embryos using quantitative densitometry of Western blots. Our analyses reveal that MLC3f is first detected in the breast muscle of 11 day embryos and accumulates at a constant rate until hatching at day 16. This data suggests, by extrapolation, that MLC3f accumulation is initiated at day 10 in embryonic breast muscle. MLC3f is also first detected in the limb muscle of 11 day embryos, but does not accumulate rapidly until after day 13. These results demonstrate the effective use of reflective densitometry in the study of developmental problems and in the quantitation of Western blots in general.

Quantitation of protein by alkaline extraction of naphthol blue black-stained polypeptides in sodium dodecyl sulfate-polyacrylamide slab-gels

A sodium dodecyl sulfate-polyacrylamide slab-gel system was used to study the alkaline extraction of Naphthol Blue Black B-stained polypeptides. A simple, rapid, and reproducible method for quantitative assessment of 1- to 5-micrograms quantities of individual polypeptides in the molecular weight range of 14,000 to 120,000 is described. The working range of the assay may be extended to the 20-micrograms level at the expense of rapidity.

Increased fraction of acid-soluble proteins in 0.35 M NaCl extracts of nuclei from rat liver tumors

1. The fraction of proteins extracted from nuclei with 0.35 M NaCl and soluble in 2% trichloroacetic acid was examined in five Morris hepatomas and rat liver. 2. This fraction was a much greater percentage of the total 0.35 M NaCl soluble proteins in the tumors than in normal or regenerating liver. 3. In part, this difference was due to proteins with molecular weights greater than high mobility group proteins. 4. The conditions for precipitation of high mobility group proteins 1 and 2 with trichloroacetic acid were found to differ in hepatoma and liver fractions.

Characteristic protein fractions of cerebrospinal fluid disc electrophoretic analysis

The present work was undertaken to determine characteristic proteins of normal cerebrospinal fluid (CSF) by disc electrophoresis in polyacrylamide gel, and to evaluate their usefulness as indicators of blood-brain-CSF barrier disturbance. The technique has been applied to 1280 samples of unconcentrated CSF obtained from 27 reference subjects and 847 neurological patients, with a simultaneous analysis of 361 sera. The pre-albumin content (mean +/- S.D. as a percentage of total protein, 11.0 +/- 2.3%) was higher than formerly reported. One reason for this is that preliminary concentration was not necessary, and the second is related to the principle of protein resolution. The no. 5 protein band of the post-albumin group (3.9 +/- 1.1%) was characteristic, though it has not yet been identified. The no. 3 protein band of the post-transferrin group (5.2 +/- 1.7%) was highly specific to CSF; it was found to be closely related to transferrin, and may correspond to tau fraction obtained by other methods. Barrier dysfunction was easily recognizable by the appearance of polymers of haptoglobin 2-1 or 2-2, because only haptoglobin 1-1 was detected in normal CSF. The percentage of the main region of the G-zone (13.7 +/- 2.6%) was postulated as normal content of CSF immunoglobulins.

Oxidation of the sulfhydryl forms of insulin A-chain and B-chain

A modified procedure for the preparation of the S-sulfonates of the A- and B-chains of insulin and their conversion to the sulfhydryl forms by tri-n-butylphosphine is described. Air oxidation of the sulfhydryl forms of the A-chain in dilute solution (0.2 mg/ml) either in the presence or absence of urea at pH 9.0 yields primarily monomeric, intrachain disulfides. Similar treatment of the reduced B-chain yield monomeric, intrachain disulfide in 7 M urea but a large number of oligomeric, interchain disulfides in the absence of urea. Electrolytic reduction of insulin in 7 M urea of pH 8.5, followed by oxidation of the sulfhydryls in dilute solution in 7 M urea at pH 9.0 yields primarily a mixture of the monomeric, intrachain disulfides of the A-chain and of the B-chain which can be separated by chromatography on Sp-Sephadex in acidic urea. The rate of the oxidation of the sulfhydryls of the two separate chains was much slower and less complete than that reported for the two chains crosslinked by the carbonylbismethionyl residue.

The effect of various stains on quantitative agarose-gel electrophoresis: evaluation of the results with the aid of an analog computer

The effect of dyes of varying purity and with different binding mechanisms on quantitative electrophoresis was examined with the aid of agarose-gel electrophoresis, the phoretogram curves being evaluated with an analog computer. Concurrent quantitative results were obtained with the three dyes tested, viz. Amido Black 10 B, Ponceau Red S and Procion Brilliant Blue. It is concluded that no falsification of electrophoresis results will be caused by dyes with colour-producing secondary components.

The extraction of proteins from eukaryotic ribosomes and ribosomal subunits

Proteins were extracted from rat liver ribosomes and ribosomal subunits: with 67% acetic acid (in the presence of 3.3 mM, 33 mM, or 67 mM Mg) with 2 M LiCL in 4 M urea; with 0.25 N HCI; with 1% SDS; and after RNase digestion. The most efficient extraction and the best recovery were either with acetic acid in the presence of 33 mM or 67 mM Mg, or with LiCI-urea. Protein extracted with acetic acid, LiCi-urea, or with HCI had little or no contamination with RNA. The ribosomal proteins were analyzed by two-dimensional polyacrylamide gel electrophoresis: the proteins extracted with acetic acid were the most soluble in the sample gel solution; their electrophoretograms displayed the maximum number of spots and the smallest number of derivatives or altered proteins. Preparations of protein extracted with SDS or RNase were relatively insoluble in the sample gel solution, and proteins extracted with HCI showed a large number of derivatives. All things considered, the most satisfactory method for the extraction of protein from eukaryotic ribosomes is with 67% acetic acid in the presence of 33 mM MgCl2.