Journal of biochemical and biophysical methods最新文献

Chromatographic separation of enantiomers to assure or enhance chiral purity is of considerable importance and can be achieved by the use of selectors of great structural variety. Cyclodextrins are an important and frequently used class, and they are multimodal selectors since multiple chiral interactions are possible by very different mechanisms. Here, the results of a preliminary examination on the possible value of computational molecular modeling approaches for the predictability of cyclodextrin selector effects for compounds that possess both geometrical and optical isomerism are presented. Interactions between various cyclodextrins and pyrethroic acids are modeled, interpreted, and compared to experimental capillary electrophoresis data.

The alternating current (AC_t) polarographic behavior of lansoprazole (LNS) and omeprazole (OMP) was studied in Britton Robinson buffers (BRb) over the pH range 4.1–11.5. In BRb of pH 9.6 and 10.5, well-defined AC_t peaks were obtained for both LNS and OMP, respectively. The current–concentration plots were rectilinear over the ranges of 0.4–20 µg mL^− 1 and 0.2–10 µg mL^− 1 for LNS and OMP respectively. The minimum detection limits (S/N = 2) were 0.02 µg mL^− 1 (5.4 × 10^− 8 M) and 0.01 µg mL^− 1 (2.9 × 10^− 8 M) for LNS and OMP, respectively. The proposed method was successfully applied to the analysis of the two drugs in their commercial capsules. The average percent recoveries were favorably compared to those obtained by reference methods. Co-administered drugs such as naproxen and methotrexate did not interfere with the proposed method. The proposed method was further extended to the in-vitro determination of the lansoprazole in spiked plasma, the percentage recoveries was 98.47 ± 1.29 (n = 4). The pathway for the electrode reaction for both drugs involved reduction of the sulphonyl group into the corresponding thiol group at the Dropping Mercury Electrode. The advantages of the method were time saving and more sensitive than the other published voltammetric method. Yet The present study is the first report on the use of alterating current polarography (AC_t) in this respect.

Arginine-specific ADP-ribosylation is one of the posttranslational modifications of proteins by transferring one ADP-ribose moiety of NAD to arginine residues of target proteins. This modification, catalyzed by ADP-ribosyltransferase (Art), is reversed by ADP-ribosylarginine hydrolase (AAH).

In this study, we describe a new method combining an anti-ADP-ribosylarginine antibody (αADP-R-Arg Ab) and AAH for detection of the target protein of ADP-ribosylation. We have raised αADP-R-Arg Ab with ADP-ribosylated histone and examined the reactivity of the antibody with proteins treated by Art and/or AAH, as well as in situ ADP-ribosylation system with mouse T cells. Our results indicate that the detection of ADP-ribosylated protein with αADP-R-Arg Ab and AAH is a useful tool to explore the target proteins of ADP-ribosylation. We applied the method to search endogenously ADP-ribosylated protein in the rat, and detected possible target proteins in the skeletal muscle, which has high Art activity.

A one-of-a-kind high speed optical multichannel spectrometer was designed and built at NIH and described in this journal in 1997 [J.W. Cole, R.W. Hendler, P.D. Smith, H.A. Fredrickson, T.J. Pohida, W.S. Friauf. A high speed optical multichannel analyzer. J Biochem Biophys Methods 1997;35:16–174.]. The most unique aspect of this instrument was the ability to follow an entire time course from a single activation using a single sample. The instrument has been used to study rapid kinetic processes in the photon-driven bacteriorhodopsin photocycle and electron transport from cytochrome c to cytochrome aa₃ and from cytochrome aa₃ to oxygen. The present paper describes a second generation instrument with a number of important enhancements which significantly improve its capabilities for multichannel kinetic studies. An example application is presented in which the kinetics of photon-induced proton flow across the biological membrane is measured simultaneously with the individual steps of the photocycle determined optically. Matching the time constants for the two processes indicates which molecular transformations are associated with major proton movements.

Chitosan (CS) gel beads were prepared by using phase inversion and precipitation technique. The gel beads could bind copper (II), by which Cu (II) ion-immobilized chitosan gel beads (CS-Cu²⁺ gel beads) were prepared, and the amount of the immobilized Cu (II) was about 35 mg/g when the CS gel beads were incubated in 150 ppm cupric sulfate solution. The CS-Cu²⁺ gel beads could selectively adsorb histidine (His) from the mixed solution containing His and tryptophan (Trp); and the selective coefficient which was defined as the adsorbed amount ratio of His to Trp was about 8.0 at the pH value of 7.4. The effect of the pH value on the amino acid adsorption was also studied. In order to investigate the relationship of the amino acid adsorption and protein adsorption, the adsorbed amounts for IgG and albumin were determined; and the results indicated that the CS-Cu²⁺ gel beads could adsorb a larger amount of IgG than albumin due to the larger amount of the exposed residual His. The study provided a sorbent and a method to selectively remove His and IgG.

In this study we present the experimental and mathematical model for a precise assessment of isolated blood vessels dynamic response under a sudden change of blood pressure. Only the end points within the time interval of the considered dynamic response of the blood vessel, or so-called “alternate steady states” of the processes, were usually considered in various studies. These studies do not provide an insight how the process variables change between these alternate steady states. Isolated blood vessels (rat abdominal aorta) were used to determine how the process dynamics can be described in detailed quantitative terms by mathematical parameters. The experimental model and mathematical procedures presented in this study describe precisely (at a high sensitivity level) the time history of the pressure and the diameter change in between alternate steady states, when an abrupt change of blood pressure occurs at the vessel outlet. Also, the experimental model and mathematical procedures were used to determine changes in the stress–strain law, caused by the action of L-arginine. The presented experimental design and mathematical model can be used for assessment of isolated blood vessel dynamic responses under different stimuli, such as drug effects, electrostimulation etc.

We present a straightforward method to create spatial gradients of substrate bound protein for live cell studies using only mechanical parts. Protein concentration gradients on a micron scale can be fabricated in several minutes for a relatively low cost using a method that is generally applicable to any protein and substrate combination. We describe the details of the device construction, and provide examples of mammalian cells grown on substrates patterned with protein concentration gradients using this technique.

DNA molecular weight markers are routinely used in agarose gel electrophoresis. Here we report a method called PCR-synthesized marker (PSM) to generate DNA molecular rulers by PCR in the laboratory. This strategy can also be used to produce 100 bp RNA molecular weight markers by run-off transcription.

Fluorescence Recovery After Photobleaching (FRAP) using the confocal laser scanning microscope has become a standard method used to determine the diffusion coefficient and mobile fraction of cell surface proteins. A common experimental approach is to bleach a stripe on the cell surface and fit the ensuing FRAP curve to a 1D diffusion model. This model is derived from the time course of recovery to an infinitely long stripe bleached on an infinite flat plane. This choice of model dictates the use of a long bleach stripe. We demonstrate that, in the case of a long bleach stripe, the finite extent of the cell leads to significant errors in parameter estimation. We further show that these errors are reduced when a relatively small stripe is bleached. Unfortunately, diffusion to such a region is fundamentally two dimensional and therefore applying the 1D model of diffusion leads to significant errors. We derive an equation suitable for fitting to FRAP data acquired from small bleach regions and analyze its accuracy using simulated data. We propose that the use of a small bleach region along with a two dimensional diffusion model is the ideal protocol for cell surface FRAP.

The recent advent of microarray technology and RNA amplification allows us to compare the expression profiles of thousands of genes from small amounts of tissue or cells. We have compared and contrasted various methods of RNA preparation, RNA amplification, target labelling and array analysis in order to achieve a streamlined protocol for microarraying small samples. We have concluded that usage of the NIA 15K cDNA array set, in combination with RNA extraction using the Mini RNA Isolation kit (Zymo), amplification with the RiboAmp kit (Arcturus), followed by indirect labelling via the Atlas™ PowerScript™ Fluorescent Labelling kit (using a modified protocol), is optimal with a material derived from either very early stage mouse embryos or individually picked embryonic stem cell colonies. Normalisation using the analysis package Limma (Bioconductor) with data normalisation by print tip Loess, using the “normexp” function with an offset of 50 for background adjustment, and incorporating A-quantile between array normalisation was best with our results. Furthermore, RT-PCR confirmation of array results is achievable without amplification, thereby controlling for amplification bias. These methods will be of great utility in mapping the transcriptome of embryonic and other small samples.