A procedure for the separation and quantitation of tryptophan and amino sugars on the amino acid analyzer

Tryptophan, 5-methyl tryptophan, glucosamine, and galactosamine can be separated from each other and hydrolysis products including lysinoalanine by chromatography on a 6 × 260-mm column of W-3H resin. The column is developed at 70°C for 20 min with pH 3.95 (0.4 Na⁺) buffer, followed by pH 6.4 (1 Na⁺) buffer for 55 min using a Beckman 119 CL amino acid analyzer. The recovery of the internal standards, 5-methyl tryptophan and galactosamine, can then be used to correct for tryptophan and glucosamine losses, respectively. The procedure uses the column and buffers normally employed for protein hydrolysate analysis and does not require additional resin columns, special buffers, or flow rate changes.     

A suitable and efficient procedure for the removal of decontaminating antibiotics from tissue allografts

The presence of residual antibiotics in tissue allografts after decontamination with antibiotic cocktails may result in widely documented adverse effects in predisposed subjects. Moreover, antibiotic residues may mask contaminating microorganisms, resulting in falsely negative sterility tests, with potential risk of post-surgical infections. The objective of the present study was to define a rinsing procedure capable of eliminating antibiotic residues from cardiovascular, bone and skin tissues after decontamination with BASE.128. Different washing patterns, employing BASE medium, were applied. The presence of antibiotic residues in tissue homogenates was assessed by agar diffusion test at different stages of tissue processing. To test whether antibiotic residues can result in falsely negative microbiological analysis, we induced a superficial tissue contamination with known inoculum concentration. By employing four different porcine tissues, we here report direct evidence that the presence of even limited amounts of antibiotics in decontaminated tissues interferes with sterility testing. This has implications in terms of increased risk of infections in allograft recipients. To minimize this risk, we developed a procedure for extensive removal of antibiotics from allografts, allowing for subsequent detection of microbial contaminations that may occur during transportation, storage or processing prior to allograft transplantation. Our study emphasizes the importance of validating all processes and analytical methods in tissue banking, in order to warrant tissue safety. This will minimize the risks of post-surgical infections as well as antibiotic-induced anaphylaxis in predisposed patients.     

A method for hydrolyzing and determining the amino acid compositions of picomole quantities of proteins in less than 3 hours

A method is described for quantitatively hydrolyzing proteins in 45 min and for analyzing the hydrolysates by high-performance liquid chromatography in an additional 52 min. The α-amino acids were detected by the fluorescence of their o-phthaldialdehyde derivatives. Ten picomoles of each of the commonly occuring α-amino acids could be reliably determined. The method described yielded OPA-ethanethiolamino acid derivatives that were stable for $\text{1}\text{h}$ h and the HPLC method produced a better separation than previously published methods.     

Optimization of the hydrochloric acid concentration used for trifluoroacetate removal from synthetic peptides.

Trifluoroacetate (CF3COO-, or TFA) is almost always present in commercially synthesized peptides. Unfortunately, it has a strong infrared (IR) absorption band at 1673 cm-1, significantly overlapping or even completely obscuring the amide I band of a peptide. In such cases TFA must be removed from the solution in order to be able to use IR absorption spectroscopy for peptide secondary structure determination. The most convenient and widely used procedure involves peptide lyophilization from a 0.1 M HCl solution. In our studies of the tryptophan-rich antimicrobial peptide indolicidin, we have found that caution should be taken when using this HCl concentration. High HCl concentrations (>10 mM in unbuffered solutions and > 50 mM in buffered solutions) may modify the peptide structure and reduce its thermal stability, thereby interfering with subsequent structural investigations of the peptide. Our results indicate that HCl concentrations between 2 and 10 mM are adequate to remove essentially all TFA impurities without any modification of the peptide secondary structure.     

A robust curve-fitting procedure for the analysis of plasmid DNA strand break data from gel electrophoresis

A robust method for fitting to the results of gel electrophoresis assays of damage to plasmid DNA caused by radiation is presented. This method makes use of nonlinear regression to fit analytically derived dose-response curves to observations of the supercoiled, open circular and linear plasmid forms simultaneously, allowing for more accurate results than fitting to individual forms. Comparisons with a commonly used analysis method show that while there is a relatively small benefit between the methods for data sets with small errors, the parameters generated by this method remain much more closely distributed around the true value in the face of increasing measurement uncertainties. This allows for parameters to be specified with greater confidence, reflected in a reduction of errors on fitted parameters. On test data sets, fitted uncertainties were reduced by 30%, similar to the improvement that would be offered by moving from triplicate to fivefold repeats (assuming standard errors). This method has been implemented in a popular spreadsheet package and made available online to improve its accessibility.     

Efficient removal of detergents from proteins and peptides in a spin column format

Detergents are commonly used in protein–chemistry protocols and may be necessary for protein extraction, solubilization, and denaturation; however, their presence interferes with many downstream analysis techniques, including mass spectrometry (MS). To enable downstream analysis, it is critical to remove unbound detergents from protein and peptide samples. In this study, we describe a high-performance resin that offers exceptional detergent removal for proteins and peptides. When used in a spin column format, this resin dramatically improves protein and peptide MS results by more than 95% removal of 1–5% detergents, including sodium dodecyl sulfate (SDS), sodium deoxycholate, Chaps, Triton X-100, Triton X-114, NP-40, Brij-35, octyl glucoside, octyl thioglucoside, and lauryl maltoside, with high recovery of proteins and peptides. Postcolumn liquid chromatography–tandem MS (LC–MS/MS) analysis of trypsin digests of bovine serum albumin (BSA) and HeLa cell lysate revealed excellent sequence coverage, indicating successful removal of detergent from the peptides. Matrix-assisted laser desorption/ionization (MALDI)–MS analysis of unprocessed and processed samples further confirmed efficient removal of detergents. The advantages of this method include speed (<15 min), efficient detergent removal, and high recovery of proteins and peptides.     

A procedure for the purification of beta-lactoglobulin from bovine milk using gel filtration chromatography at low pH

A simple and rapid procedure for the purification of beta-lactoglobulin (β-LG) from bovine milk is described. The procedure exploits the major difference in molecular mass of β-LG and other whey components and the existence of the former in monomeric form at acidic pH. Gel filtration of whey was carried out using a Bio-Gel P10 column at pH 3.0. Residual caseins and other milk proteins were excluded from the gel and β-LG and alpha-lactalbumin (α-LA) emerged as two fully resolved peaks. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) suggested that β-LG was purified to apparent homogeneity, while absorption, fluorescence, and circular dichroism spectroscopy indicated the native-like conformation of the protein. Western blot analysis revealed that the antibodies raised against the purified β-LG in rabbits also readily react with the commercial bovine protein. This procedure requires only 4-5 hr for the purification of about 10 mg of β-LG from a single run while using a small column (2.3 cm x 83 cm) of Bio-Gel P10 and has the potential for scaling up.     

An improved procedure for the synthesis of dehydroamino acids and dehydropeptides from the carbonate derivatives of serine and threonine using tetrabutylammonium fluoride

Dehydroamino acids are important precursors for the synthesis of a number of unnatural amino acids and are structural components in many biologically active peptide derivatives. However, efficient synthetic procedures for their production in large amounts and without side reactions are limited. We report here an improved procedure for the synthesis of dehydroalanine and dehydroamino butyric acid from the carbonate derivatives of serine and threonine using TBAF. The antiselective E₂ elimination of the carbonate derivatives of serine and threonine using TBAF is milder and more efficient than other available procedures. The elimination reaction is completed in less than 10 min with various carbonate derivatives studied and the methodology is very efficient for the synthesis of dehydroamino acids and dehydropeptides. The procedure thus provides an easy access to key synthetic precursors and can be used to introduce interesting structural elements to designed peptides. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.     

Evaluation of gel filtration resins for the removal of PCR-inhibitory substances from soils and sediments

A variety of gel filtration resins (Sephadex G200 and G150; Sepharose 6B, 4B and 2B; Bio-Gel P100, P200; and Toyopearl HW 55, HW 65, and HW 75) were evaluated for their efficacy in removing PCR-inhibitory substances from feedlot soil DNA crude extracts using gravity-flow disposable columns. Sepharose resins demonstrated the best properties for DNA purification when compared to other gel filtration resins, and Sepharose 2B was the most efficient purification resin based upon flow rate and the elution of DNA and humic acids from the columns. A method for purifying large solution volumes of DNA extract economically was also developed using low-cost disposable Disposaflex columns. Crude DNA extracts of cattle feedlot soil and aquifer sediment impacted by animal and human wastes were easily purified using the Disposaflex column method regardless of whether a gentle chemical lysis or a bead mill homogenization DNA extraction method was employed.     

A procedure for the separation of glucosamine from glucosaminitol

A simple procedure is described for the preparation of glucosamine and glucosaminitol, employing column chromatography on Sephadex G-10, using a borate-phosphate buffer as elutrient.     

An improved procedure for the isolation of nuclear DNA from leaves of wild grapevine dried with silica gel

An efficient and convenient method is presented for the isolation of nuclear DNA from leaves of wildVitis species that have been dried with silica gel. The nuclear DNA obtained with this method is suitable for both PCR amplification and digestion with restriction endonucleases.     

A biocatalyst for the removal of sulfite from alcoholic beverages

The presence of sulfites in alcoholic beverages, particularly in wines, can cause allergic responses with symptoms ranging from mild gastrointestinal problems to life threatening anaphylactic shock in a substantial portion of the population. We have developed a simple and inexpensive biocatalytic method that employs wheatgrass (Triticum aestivum) chloroplasts for the efficient oxidation of sulfites in wines to innocuous sulfates. A sufficiently high rate of sulfite oxidation was obtained in the presence of ethanol at concentrations commonly found in most wines. Crude chloroplast preparations at a concentration as low as 5 mg/mL were capable of reducing sulfite in commercial white wines from 150 ppm to under 7.5 ppm within 3 hours. A 93% removal of sulfite in commercial red wines was observed with 1 mg/mL chloroplasts within 45 min. Optimal sulfite removal efficiency was observed at pH 8.5 and was promoted by illumination, indicating the participation of light-induced photosynthetic electron transport processes in sulfite oxidation. Overall, this work indicates that biocatalytic oxidation using wheatgrass chloroplasts can be employed to remove sulfites from beverages prior to consumption.     

A procedure for purification of the ryanodine receptor from skeletal muscle

In this paper, we describe a simple and reproducible method for purifying large quantities of ryanodine receptor from skeletal muscle membranes. The procedure involves the use of ion exchange chromatography and sucrose gradient centrifugation to purify the protein which has been identified as the calcium release protein of the sarcoplasmic reticulum (Imagawa, T., Smith, J., Coronado, R. and Campbell, K. (1987) J. Biol. Chem. 262:16,636-16,643). Addition of micromolar quantities of unlabeled ryanodine prior to solubilization and throughout the isolation procedure appears to stabilize the tetrameric structure of the ryanodine receptor. The purified receptor, consisting predominantly of a 400K polypeptide on SDS-PAGE, binds [3H]ryanodine with a binding affinity similar to that in membranes. Overall recovery of ryanodine binding activity was 21% of the initial activity with a 30-fold purification of the receptor.     

Gellan gel beads containing magnetic nanoparticles: An effective biosorbent for the removal of heavy metals from aqueous system

This study describes an efficient adsorbent consisting of magnetic Fe₃O₄ and gellan gum, which couples magnetic separation with ionic exchange for heavy metal removal. Adsorption kinetics analysis showed that the adsorption capacities were in an order of Pb²⁺ > Cr³⁺ > Mn²⁺. Different experimental parameters studies indicated that adsorbent dosage, initial metal concentration, temperature and initial pH played important roles in adsorption process. Additionally, the Freundlich model gave a better fit to the experimental data than the Langmuir model. Chemical analysis of calcium ions released into the bulk solutions demonstrated that carboxyl group is critical for binding Pb²⁺, Mn²⁺ and Cr³⁺. Furthermore, a high desorption efficiency was obtained by sodium citrate.     

A procedure for the automatic determination of hydrophobic cores in protein structures.

An algorithm is described for automatically detecting hydrophobic cores in proteins of known structure. Three pieces of information are considered in order to achieve this goal. These are: secondary structure, side-chain accessibility, and side-chain-side-chain contacts. Residues are considered to contribute to a core when they occur in regular secondary structure and have buried side chains that form predominantly nonpolar contacts with one another. This paper describes the algorithm's application to families of proteins with conserved topologies but low sequence similarities. The aim of this investigation is to determine the efficacy of the algorithm as well as to study the extent to which similar cores are identified within a common topology.     

A procedure for isolating vacuoles from leaves of the halophyte Suaeda maritima

Abstract. A method is described here for isolating protoplasts and vacuoles from leaves of the halophyte Suacda maritima. Integrity of the protoplasts and vacuoles was tested by staining and shown to be more than 75%, while use of biochemical markers, staining and light microscopy suggested a high degree of purity of the vacuoles. Phosphatase and NADH cytochrome- c -reductase were associated with vacuoles; phosphatase showed an eight-fold enrichment and NADH cytochrome- c -reductase a 3.5-fold enrichment relative to protoplasts. The vacuoles contained only 15% of the protein in protoplasts.