High-sensitivity isoelectric focusing of biotinylated peptides: a new method

A novel technique to selectively analyze prelabeled peptides by isoelectric focusing (IEF) is presented. The conditions are described for biotinylation of peptides, their separation in polyacrylamide gels by IEF, and their fixation to the gel matrix with glutaraldehyde. The gels are developed by a color reaction catalyzed by an avidin-coupled enzyme. The technique is suitable for peptides with at least one free amino group or guanidino group after N-terminal biotinylation. The presence of other peptides or proteins does not interfere with the detection. The sensitivity is below 10 pmol, representing a 1000-fold improvement over existing techniques for analyzing low molecular weight peptides by IEF.     

A new method for pH determination in isoelectric focusing experiments

A rapid and reproducible method for the pH measurement in the effluent from density gradient electrofocusing is described. By this procedure, after preparative isoelectric focusing, the detection of protein zones and pH measurement can be accomplished simultaneously, by serially coupling a uv flow cell with a pH flow cell. This last one is connected to the recorder by a control unit, which allows the simultaneous printing of pH and uv absorption on the same chart.     

The zymogram method for detection of ribonucleases after isoelectric focusing: analysis of multiple forms of human, bovine, and microbial enzymes.

A zymogram method for detection of in situ ribonuclease (RNase) activity, combined with isoelectric focusing in a thin layer of polyacrylamide gel (IEF-PAGE), has been developed. After incubation with a dried agarose film containing substrate RNA, ethidium bromide, and an appropriate reaction buffer, which was placed tightly on the top of the focused gel, sharp and distinct dark bands corresponding to RNase isoenzymes on a fluorescent background appeared under uv light. Addition of urea to the IEF-PAGE gel at a final concentration of 4.8 M permitted optimal focusing of the RNases. This method had not only a high sensitivity of less than 0.1 ng purified RNase A, but also a high band resolution compared with the immunostaining method. It was also useful for analysis of purified enzymes, including bovine pancreatic RNases and two types of human urine RNase as mammalian enzymes, and RNases T1 and T2 as microbial enzymes, as well as for detection of RNases present in crude tissue extracts, resulting in more detailed elucidation of the multiplicity of these enzymes.     

Separation of two forms of rabbit metallothionein by isoelectric focusing

Rabbits were given repeated injections of cadmium chloride. Cadmium- and zinc-containing protein fractions were obtained from the livers of these animals by precipitation procedures and Sephadex G-75 chromatography. The protein thus obtained showed several characteristics similar to those of the earlier described protein metallothionein. Further separation by isoelectric focusing showed two main protein peaks with isoelectric points at 3.9 and 4.5 respectively. Amino acid analysis of these two forms showed similar content of most amino acids [residues per cent.: cysteine (28%), aspartate (8%), threonine (5–6%), serine (12%), glycine (7%), alanine (13%), methionine (2%), isoleucine (2%)] but with a small difference in content of lysine (12 and 13% respectively), proline (9 and 5% respectively) and glutamate (2 and 4% respectively). The two forms of the protein both contained cadmium, but only the one with pI4.5 contained also significant amounts of zinc.     

Albumin Paris 2: a new genetic variant distinguished by isoelectric focusing.

Until recently, the characterization of genetic variants of human serum albumin was performed by electrophoretic typing prior to the determination of their amino acid substitutions. We describe a procedure using isoelectric focusing in the presence of urea for the analysis of the genetic variation of albumin. This procedure allowed a clear distinction of a new variant, previously found to be identical with albumin Sondrio according to its relative electrophoretic mobilities at 3 pHs. This new variant, the third rare albumin allotype identified in the Ile-de-France region, was called albumin Paris 2.     

UniFrac: a new phylogenetic method for comparing microbial communities

We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such as chemistry and geography, to similarities between samples. We demonstrate the utility of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice. Our results reveal that (i) cultured isolates from ice, water, and sediment resemble each other and environmental clone sequences from sea ice, but not environmental clone sequences from sediment and water; (ii) the geographical location does not correlate strongly with bacterial community differences in ice and sediment from the Arctic and Antarctic; and (iii) bacterial communities differ between terrestrially impacted seawater (whether polar or temperate) and warm oligotrophic seawater, whereas those in individual seawater samples are not more similar to each other than to those in sediment or ice samples. These results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.     

Separation of membrane proteins in an undenatured form by isoelectric focusing

Conditions are described which allow good resolution of membrane proteins in an undenatured form by isoelectric focusing in thin polyacrylamide gels in Triton X-100. High voltages and deionization of the acrylamide are essential. Streaking is grossly reduced by sample application in Bio-Gel P-60, by deionization of the Triton, and dialysis of membrane samples against low ionic strength buffer at slightly alkaline pH. The latter step also greatly improves solubilization of the membrane components. Reproducible isoelectric focusing patterns of proteins from red cell, thyroid, and lymphocyte membrane are presented.     

pH-dependent binding analysis, a new and rapid method for isoelectric point estimation

Based upon the pH-dependent binding affinity of amphoteric molecules for an ion exchanger, and by taking advantage of batch procedures, a facile method was developed for estimating isoelectric points of these molecules. The new method allows pI measurements to be accomplished within 1 h. Moreover, any possible protein-ampholyte interaction or artifact formation, as may be introduced from the presence of carrier ampholytes when conventional focusing methods are employed, is eliminated by the method. In addition, because of the short processing time, isoelectric points of proteins can be measured at any desired temperature without much risk of protein denaturation. Seven proteins with well-defined isoelectric points were examined by the method. The measured pI values were within a range of 0.2 pH unit or less of the reported values. The precision of pI measurements by the method can be even further improved with the employment of a narrower pH gradient. Since the isoelectric point is an important parameter which governs much of the art of separating proteins, the advent of a simple and rapid method for its measurement would be of use for selecting the proper strategy for protein isolation and purification.     

Two-dimensional protein analysis by isoelectric focusing in a multi-cell plate system

A practical and low cost system for isoelectric protein focusing (IEF) was developed. The system uses a multi-cell glass plate compatible with a common vertical one-dimensional electrophoresis chamber, dispensing specific IEF apparatus. After focusing, the IEF gels are easily recovered. The resulting two-dimensional (2-D) gels have provided efficient protein separation for different concentrations and extracts.     

Purification of hirudin by the method of isoelectric focusing]

Crude hirudin preparation was purified by isoelectric focussing in pH gradient 3-5. The presence of at least two active isoforms with pI 3.8 and 3.9 was demonstrated. The component with pI value of 3.9 possessed the specific activity as high as 8200 NIH AT units/mg.     

Study of cystinaminopeptidase heterogeneity in animal sera by the isoelectric focusing method.

Study of the quantitative distribution of cystinaminopeptidase activity in the serum of pregnant and control animals (cow, sheep and rat) by the isoelectric focusing method showed heterogeneity of the cystinaminopeptidase activity of the animals' serum enzymatic system, which was well pronounced in the cow and rat and less pronounced in the sheep. The authors assume from their results that the principal difference between the pregnant and control animals is not the total increase in the level of activity of the enzyme in question, but the shift in its incidence, or the increase in activity at a given pH. It is possible that pregnancy, in man and animals, produces in the serum cystinaminopeptidase system (which is evidently heterogeneous even under normal, physiological conditions) given changes, i.e. the formation of new fractions with a different pI from the controls; other fractions disappear, or their activity diminishes.     

A new method for immobilizing microbial cells by crosslinking

A method for immobilization of microbial cells was developed designed. The method uses based on generation of reactive aldehyde groups on the cell wall surface under conditions of periodate oxidation. The linking of aldehyde groups by various bifunctional aromatic diamines and then by glutaraldehyde produced immobilized cells, which are promising for the use in biocatalysis with high-molecular-weight substrates of high molecular weight.     

Serial analysis of ribosomal sequence tags (SARST): a high-throughput method for profiling complex microbial communities

Two decades of culture-independent studies have confirmed that microbial communities represent the most complex and concentrated pool of phylogenetic diversity on the planet. There remains a need for innovative molecular tools that can further our knowledge of microbial diversity and its functional implications. We present the method and application of serial analysis of ribosomal sequence tags (SARST) as a novel tool for elucidating complex microbial communities, such as those found in soils and sediments. Serial analysis of ribosomal sequence tags uses a series of enzymatic reactions to amplify and ligate ribosomal sequence tags (RSTs) from bacterial small subunit rRNA gene (SSU rDNA) V1-regions into concatemers that are cloned and sequenced. This approach offers a significant increase in throughput over traditional SSU rDNA clone libraries, as up to 20 RSTs are obtained from each sequencing reaction. To test SARST and measure the bias associated with this approach, RST libraries were prepared from a defined mixture of pure cultures and from duplicate arctic soil DNA samples. The actual RST distribution reflected the theoretical composition of the original defined mixture. Data from duplicate soil libraries (1345 and 1217 RSTs, with 525 and 505 unique RSTs, respectively) indicated that replication provides a strongly correlated RST profile (r(2) = 0.80) and division-level distribution of RSTs (r(2) = 0.99). Using sequence data from abundant soil RSTs, we designed specific primers that successfully amplified a larger portion of the SSU rDNA for further phylogenetic analysis. These results suggest that SARST is a powerful approach for reproducible high-throughput profiling of microbial diversity amenable to medical, industrial or environmental microbiology applications.