Polyacrylamide Slab Gel Research Articles

Variation in oxidative defense system and physiological traits in Maize under drought stress

The study included the role of key metabolites involved in oxidative defense, and osmotic adjustment under water stress is still undiscovered. We have evaluated whether antioxidant potential could be nominated as a potential marker of drought resistance in three maize hybrids (SC01, SC703, and SC720). Underwater deficiency in all maize hybrids decreased significantly compared to control samples in grain yield, photosynthetic pigments, and phenolic compounds. In contrast, proline and glycine betaine (GB) significantly increased. In contrast, a significant increase (p<?0.05) was detected in the lipid peroxidation indicator of malondialdehyde (MDA). The hydrogen peroxide (H2O2) and total soluble proteins remained unaffected under drought stress in the three maize hybrids. Electrophoretic investigations attributed three, two, and one isoforms, respectively, to peroxidase (POX), superoxide dismutase (SOD), and catalase (CAT). In the studied maize hybrids, SOD isoforms, including Fe-SOD, Cu/Zn-SOD, and Mn-SOD, appeared on the 8% slab polyacrylamide gels. The water stress decreases Mn-SOD, Cu/Zn-SOD, and Fe-SOD activities in all three hybrids. Further, POX1, POX2, and CAT activities decreased in SC01 and SC703, while they increased in SC720 under water deficit stress. In all maize hybrids, oxidative stress from water limitation leads to significant changes in the enzymatic/non-enzymatic antioxidants and main organic osmolytes. Based on the current study's findings, we believe that Cu/Zn-SOD activity, proline, and photosynthetic pigments might be used as biochemical indicators of water stress tolerance.

Sensitivity and applications of the PCR Single-Strand Conformation Polymorphism method.

PCR Single-Strand Conformation Polymorphism is a method used to identify and detect mutations and is now well known for its many applications on living beings. This paper will discuss the experimental details, limitations and sensitivity of the PCR Single-Strand Conformation Polymorphism method in relation to all existing literature available to us until today. Genomic DNA extraction, PCR amplification and Single-Strand Conformation Polymorphism conditions (concentration of polyacrylamide slab gel electrophoresis, dissociation treatment of double- stranded DNA) and comparison with PCR Restriction Fragment Length Polymorphism are presented. Since its discovery in 1989, there have been many variations, innovations, and modifications of the method, which makes it very easy, safe, fast and for this reason widely applied in clinical diagnostic, forensic medicine, biochemical, veterinary, microbiological, food and environmental laboratories. One of the possible applications of the method is the diagnosis and identification of mutations in new strains of coronaviruses, because science needs more tools to tackle the problem of this pandemic. The PCR Single-Strand Conformation Polymorphism method can be applied in many cases provided that control samples are available and the required conditions of the method are achieved.

A simple method of drying polyacrylamide slab gels that eliminates cracking.

The polyacrylamide slab gel is the most common gel format for analyzing protein samples by electrophoresis. Drying these gels is useful in many biological applications; for example, autoradiography, in which radiolabeled proteins are separated to enable their detection and identification. Dried protein gels can also serve as an ideal method of preserving the gel itself for permanent record-keeping and allowing densitometry at a convenient time. Here I describe a simple and highly reproducible gel-drying method that results in dried gels without the cracks that are frequently encountered with many existing gel-drying methods.

Protein diffusion from microwells with contrasting hydrogel domains.

Understanding and controlling molecular transport in hydrogel materials is important for biomedical tools, including engineered tissues and drug delivery, as well as life sciences tools for single-cell analysis. Here, we scrutinize the ability of microwells—micromolded in hydrogel slabs—to compartmentalize lysate from single cells. We consider both (i) microwells that are “open” to a large fluid (i.e., liquid) reservoir and (ii) microwells that are “closed,” having been capped with either a slab of high-density polyacrylamide gel or an impermeable glass slide. We use numerical modeling to gain insight into the sensitivity of time-dependent protein concentration distributions on hydrogel partition and protein diffusion coefficients and open and closed microwell configurations. We are primarily concerned with diffusion-driven protein loss from the microwell cavity. Even for closed microwells, confocal fluorescence microscopy reports that a fluid (i.e., liquid) film forms between the hydrogel slabs (median thickness of 1.7 μm). Proteins diffuse from the microwells and into the fluid (i.e., liquid) layer, yet concentration distributions are sensitive to the lid layer partition coefficients and the protein diffusion coefficient. The application of a glass lid or a dense hydrogel retains protein in the microwell, increasing the protein solute concentration in the microwell by ∼7-fold for the first 15 s. Using triggered release of Protein G from microparticles, we validate our simulations by characterizing protein diffusion in a microwell capped with a high-density polyacrylamide gel lid (p > 0.05, Kolmogorov-Smirnov test). Here, we establish and validate a numerical model useful for understanding protein transport in and losses from a hydrogel microwell across a range of boundary conditions.

Electrophoretic system for express analysis of whey protein fractions

Fractional specificity of biological action and ability to form bioactive peptides, which have a positive effect on different physiological systems of the body in the processes of proteolysis and digestion, are characteristic for whey proteins. Prospects for the production and application of whey protein fractions are related to the necessity of their composition control. The comparative analysis of the electrophoretic systems previously used for the milk protein analysis was carried out for the creation of an express analysis method of whey protein fractions. These are the anode disc electrophoresis system in the presence of sodium dodecyl sulfate, the Davis disc electrophoresis system for acidic proteins in native conditions, the system in a homogeneous polyacrylamide gel with urea. The Davis disc electrophoresis system for acidic proteins was chosen as the basis. For the adaptation of this system to the requirements of express analysis, the stacking polyacrylamide gel was removed from its composition and the concentration of the separating gel was reduced. The difference in the composition of electrode buffer and gel buffer ions was used to provide the high separation efficiency of protein fractions. This allows saving the effect of protein concentration in the whey sample on the first stages of electrophoresis. The position of the basic whey protein fractions on electrophoregrams was established with the help of homogeneous marker proteins (β-lactoglobulin and whey albumin). Аn accessible electrophoresis system in the slabs of a homogeneous polyacrylamide gel for serial express analysis of the fractional composition of whey proteins has been proposed as a result of researches. The system allows reliable identification of four protein fractions (α-LA, β-LG, BSA and IG). Close average values and standard deviations of the content of these fractions in 15 whey samples of one milk batch, obtained by the densitometry of three electrophoregrams: β-LG (37.3±4.2, 36.5±2.8; 38.3±2.7), α-LA (15.8±1.5, 15.8±1.3, 16.4±1.1), BSA (8.2±1.1, 8.0±1.0, 9.4±1.1), IG (17.6±1.9, 17.4±1.5, 16.8±1.5) testify about good reproducibility of the method. The proposed method may be useful for the express identification of the basic whey protein fractions, which are precursors of biologically active peptides.

Identification of Carboxylesterase, Butyrylcholinesterase, Acetylcholinesterase, Paraoxonase, and Albumin Pseudoesterase in Guinea Pig Plasma through Nondenaturing Gel Electrophoresis.

Drugs to protect against nerve agent toxicity are tested in animals. The current preferred small animal model is guinea pigs because their plasma bioscavenging capacity resembles that of NHP. We stained nondenaturing polyacrylamide slab gels with a variety of substrates, inhibitors, and antibodies to identify the esterases in heparinized guinea pig plasma. An intense band of carboxylesterase activity migrated behind albumin. Minor carboxylesterase bands were revealed after background activity from paraoxonase was inhibited by using EDTA. The major butyrylcholinesterase band was a disulfide-linked dimer. Incubation with the antihuman butyrylcholinesterase antibody B2 18-5 shifted the butyrylcholinesterase dimer band to slower migrating complexes. Carboxylesterases were distinguished from butyrylcholinesterase by their sensitivity to inhibition by bis-p-nitrophenyl phosphate. Acetylcholinesterase tetramers formed a complex with the antihuman acetylcholinesterase antibody HR2. Organophosphorus toxicants including cresyl saligenin phosphate, dichlorvos, and chlorpyrifos oxon irreversibly inhibited the serine esterases but not paraoxonase. Albumin pseudoesterase activity was seen in gels stained with α- or β-naphthyl acetate and fast blue RR. We conclude that guinea pig plasma has 2 types of carboxylesterase, butyrylcholinesterase dimers and 5 minor butyrylcholinesterase forms, a small amount of acetylcholinesterase tetramers, paraoxonase, and albumin pseudoesterase activity. A knockout mouse with no carboxylesterase activity in plasma is available and may prove to be a better model for studies of nerve agent toxicology than guinea pigs.

Multiple scattering of polarized light in birefringent slab media: experimental verifications and simulations.

The effective scattering Mueller matrices were measured for backward and forward scattering by applying a narrow polarized light on a polyacrylamide slab gel, which was strained vertically to generate birefringence inside. Monte Carlo simulations were performed in conditions that were the same as possible. The measured and simulated matrices were simplified to the reduced ones. They agreed well in both original and reduced forms. While they approximately take reciprocal forms for backward scattering, they approximately satisfy matrix forms that correspond to a reciprocal position of the mirror image for forward scattering. The reduced matrices were factorized by the Lu-Chipman polar decomposition to obtain the polarization parameters. The polarization parameters were in good agreement between the measurement and simulation and showed characteristic features of anisotropic slab media with a birefringence axis parallel to the slab surface.

SDS-PAGE procedure: Application for characterization of new entirely uncharged nucleic acids analogs.

SDS-PAGE is considered to be a universal method for size-based separation and analysis of proteins. In this study, we applied the principle of SDS-PAGE to the analysis of new entirely uncharged nucleic acid (NA) analogues, - phosphoryl guanidine oligonucleotides (PGOs). The procedure was also shown to be suitable for morpholino oligonucleotides (PMOs) and peptide nucleic acids (PNAs). It was demonstrated that SDS can establish hydrophobic interactions with these types of synthetic NAs, giving them a net negative charge and thus making these molecules mobile in polyacrylamide slab gels under the influence of an electric field.

Top-down/Bottom-up Mass Spectrometry Workflow Using Dissolvable Polyacrylamide Gels.

Biologists' preeminent toolbox for separating, analyzing, and visualizing proteins is SDS-PAGE, yet recovering the proteins embedded in these polyacrylamide media as intact species is a long-standing challenge for mass spectrometry. In conventional workflows, protein mixtures from crude biological samples are electrophoretically separated at high-resolution within N,N'-methylene-bis-acrylamide cross-linked polyacrylamide gels to reduce sample complexity and facilitate sensitive characterization. However, low protein recoveries, especially for high molecular weight proteins, often hinder characterization by mass spectrometry. We describe a workflow for top-down/bottom-up mass spectrometric analyses of proteins in polyacrylamide slab gels using dissolvable, bis-acryloylcystamine-cross-linked polyacrylamide, enabling high-resolution protein separations while recovering intact proteins over a broad size range efficiently. The inferior electrophoretic resolution long associated with reducible gels has been overcome, as demonstrated by SDS-PAGE of crude tissue extracts. This workflow elutes intact proteins efficiently, supporting MS and MS/MS from proteins resolved on biologists' preferred separation platform.

Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis.

The pioneering work by Patrick H. O’Farrell established two-dimensional gel electrophoresis as one of the most important high-resolution protein separation techniques of modern biochemistry (Journal of Biological Chemistry 1975, 250, 4007–4021). The application of two-dimensional gel electrophoresis has played a key role in the systematic identification and detailed characterization of the protein constituents of skeletal muscles. Protein changes during myogenesis, muscle maturation, fibre type specification, physiological muscle adaptations and natural muscle aging were studied in depth by the original O’Farrell method or slightly modified gel electrophoretic techniques. Over the last 40 years, the combined usage of isoelectric focusing in the first dimension and sodium dodecyl sulfate polyacrylamide slab gel electrophoresis in the second dimension has been successfully employed in several hundred published studies on gel-based skeletal muscle biochemistry. This review focuses on normal and physiologically challenged skeletal muscle tissues and outlines key findings from mass spectrometry-based muscle proteomics, which was instrumental in the identification of several thousand individual protein isoforms following gel electrophoretic separation. These muscle-associated protein species belong to the diverse group of regulatory and contractile proteins of the acto-myosin apparatus that forms the sarcomere, cytoskeletal proteins, metabolic enzymes and transporters, signaling proteins, ion-handling proteins, molecular chaperones and extracellular matrix proteins.

Allozyme variation of the endemic and vulnerable Dyera lowii Hook.f. in Central Kalimantan: Implications for genetic resources conservation

Dyera lowii is an endemic and vulnerable tree species of commercial value as chewing gum found inpeat swamp forests, scatteredly distributed in Sumatra, Kalimantan, and Peninsular Malaysia. Their existenceis now under severe threat due to habitat conversion. This study is aimed to assess genetic diversity withinfour natural populations (Hampangen, Parahangan, Sebangau, Selat Nusa ) and one plantation in CentralKalimantan based on allozyme variation. Electrophoresis procedures were conducted with an isoelectricfocusing polyacrylamide slab gel system. The result showed high genetic diversity (HE=0.52) and gene fl ow(3.402) seemed to be effective. A total of 14 alleles were found among all the analysed population. Meannumber of alleles per locus (Aa) was 3.206, and the effective number of alleles per locus (Ae) was 2.21. Geneticdifferentiation between populations (FST) was signifi cant at the moderately level (0.0685). Most allozymevariation was found within population (93.2%). Special attention is essential to conserve a private allele ofGot-1-e (9%) at Selat Nusa population. Sebangau population missed the alleles of Est-2-b and Got-1-a, as foundin other populations. Selat Nusa population is expected to enhance the effective management for geneticresources conservation of this vulnerable species in the future.

Response of antioxidant enzyme activity and pigment content in common bean (Phaseolus vulgaris L.) seedlings under salt stress

Abstract. In order to evaluate the effects of osmotic stress on fresh weight, pigment content and responses of antioxidant enzymes including superoxide dismutase (SOD), peroxidase (POX) and catalase (CAT), a factorial experiment was carried out under laboratory conditions with five common bean genotypes and two salt stress levels induced by NaCl (control and 400 mM). Electrophoretic analyses were performed for three antioxidant enzymes SOD, POX and CAT in leafs of common bean genotype seedlings using 8% slab polyacrylamide gels. For SOD, POX and CAT, three, three and one isozymes were observed, respectively. Salinity was decreased fresh weight and chlorophyll content. Anthocyanins and carotenoids concentration was increased in common bean genotypes. Statistical analysis showed that salinity stress has a significant effect on fresh weight, pigment content and enzymatic activities in common bean seedlings. SOD, POX and CAT activities were increased significantly in the salt stress compared with control condition about 40, 21 and 30.5 percent, respectively. These results seem to indicate that 41218 genotype of common bean tolerance to salt stress is associated with enhance activity of antioxidant enzymes.

Spatiotemporal fractionation of two DNA fragments by microfluidic devices

Microfluidics exhibit great promise as an alternative to conventional polyacrylamide slab gels to improve separation performance and decrease cross-contamination in the fractionation of selected DNA fragments from a complex mixture. This article provides a method to enable the spatial and temporal fractionation of multiple DNA fragments. We incorporate ten parallel extraction channels to increase the sampling range to cover multiple DNA fragments. Two neighboring fragments of 36, and 39 bases were first separated and simultaneously collected within 8 min. The ten recovered fractions were then analyzed by polymerase chain reaction amplification and capillary electrophoresis analysis. Six recovered DNA samples from the ten channels exhibited purities greater than 90 %, and two exhibited purities higher than 99 %. In contrast to a single extraction channel, this method also provides a better technical solution to high-throughput problems perceived to be more fundamental.

Evidence for the presence of lipid-free monomolecular apolipoprotein A-1 in plasma

The first step in reverse cholesterol transport is a process by which lipid-free or lipid-poor apoA-1 removes cholesterol from cells through the action of ATP binding cassette transporter A1 at the plasma membrane. However the structure and composition of lipid-free or -poor apoA-1 in plasma remains obscure. We previously obtained a monoclonal antibody (MAb) that specifically recognizes apoA-1 in preβ1-HDL, the smallest apoA-1-containing particle in plasma, which we used to establish a preβ1-HDL ELISA. Here, we purified preβ1-HDL from fresh normal plasma using said antibody, and analyzed the composition and structure. ApoA-1 was detected, but neither phospholipid nor cholesterol were detected in the purified preβ1-HDL. Only globular, not discoidal, particles were observed by electron microscopy. In nondenaturing PAGE, no difference in the mobility was observed between the purified preβ1-HDL and original plasma preβ1-HDL, or between the preβ1-HDL and lipid-free apoA-1 prepared by delipidating HDL. In sandwich ELISA using two anti-preβ1-HDL MAbs, reactivity with intact plasma preβ1-HDL was observed in ELISA using two MAbs with distinct epitopes but no reactivity was observed in ELISA using a single MAb, and the same phenomenon was observed with monomolecular lipid-free apoA-1. These results suggest that plasma preβ1-HDL is lipid-free monomolecular apoA-1.

Purification and Characterization of Peroxidase From Anthracnose Disease Infected Papaya (Carica papaya L.)

Peroxidase enzyme was isolated and purified from the pulp of disease infected ripen papaya of local variety by 90% ammonium sulphate precipitation, chromatography on DEAEcellulose followed by hydrophobic chromatography on Phenyl Sepharose CL-4B and the purifications achieved was about 7.2 fold with 2.5% recovery. The purified enzyme was homogeneous as judged by polyacrylamide slab gel electrophoresis. The purified enzyme had a Mr of about 55,000 and 50 000 as determined by gel filtration on Sephadex G-100 and SDS-PAGE, respectively. The molecular mass of the enzyme was found to be very similar under both reducing and non-reducing conditions indicating that the enzyme contains no subunit. The enzyme has the following characteristics: pH optima at 6.0, temperature optima around 38°C, enzyme activity was found to be strongly inhibited in the presence of potassium cyanide and Fe+2 while the activity was found to be remarkably increased in the presence of ammonium sulphate. The Km value for the peroxidase obtained with pyrogallol as substrate was 0.027 mM. DOI: http://dx.doi.org/10.3329/bjmb.v6i2.17643 Bangladesh J Med Biochem 2013; 6(2): 49-57

Structural Determinants of Tau Aggregation Inhibitor Potency

Small-molecule Tau aggregation inhibitors are under investigation as potential therapeutic agents against Alzheimer disease. Many such inhibitors have been identified in vitro, but their potency-driving features, and their molecular targets in the Tau aggregation pathway, have resisted identification. Previously we proposed ligand polarizability, a measure of electron delocalization, as a candidate descriptor of inhibitor potency. Here we tested this hypothesis by correlating the ground state polarizabilities of cyanine, phenothiazine, and arylmethine derivatives calculated using ab initio quantum methods with inhibitory potency values determined in the presence of octadecyl sulfate inducer under reducing conditions. A series of rhodanine analogs was analyzed as well using potency values disclosed in the literature. Results showed that polarizability and inhibitory potency directly correlated within all four series. To identify putative binding targets, representative members of the four chemotypes were added to aggregation reactions, where they were found to stabilize soluble, but SDS-resistant Tau species at the expense of filamentous aggregates. Using SDS resistance as a secondary assay, and a library of Tau deletion and missense mutants as targets, interaction with cyanine was localized to the microtubule binding repeat region. Moreover, the SDS-resistant phenotype was completely dependent on the presence of octadecyl sulfate inducer, but not intact PHF6/PH6* hexapeptide motifs, indicating that cyanine interacted with a species in the aggregation pathway prior to nucleus formation. Together the data suggest that flat, highly polarizable ligands inhibit Tau aggregation by interacting with folded species in the aggregation pathway and driving their assembly into soluble but highly stable Tau oligomers.

Novel moving reaction boundary-induced stacking and separation of human hemoglobins in slab polyacrylamide gel electrophoresis

We developed a novel polyacrylamide gel electrophoresis (PAGE) method to stack and separate human hemoglobins (Hbs) based on the concept of moving reaction boundary (MRB). This differs from the classic isotachophoresis (ITP)-based stacking PAGE in the aspect of buffer composition, including the electrode buffer (pH 8.62 Tris-Gly), sample buffer (pH 6.78 Tris-Gly), and separation buffer (pH 8.52 Tris-Gly). In the MRB-PAGE system, a transient MRB was formed between alkaline electrode buffer and acidic sample buffer, being designed to move toward the anode. Hbs carried partial positive charges in the sample buffer due to its pH below pI values of Hbs, resulting in electromigrating to the cathode. Hbs would carry negative charges quickly when migrated into the alkaline electrode buffer and be transported to the anode until meeting the sample buffer again. Thus, Hbs were stacked within a MRB until the transient MRB reached the separation buffer and then separated by zone electrophoresis with molecular sieve effect of the gel. The experimental results demonstrated that there were three clear and sharp protein zones of Hbs (HbA1c, HbA0, and HbA2) in MRB-PAGE, in contrast to only one protein zone (HbA0) in ITP-PAGE for large-volume loading (≥15 μl), indicating high stacking efficiency, separation resolution, and good sensitivity of MRB-PAGE. In addition, MRB-PAGE was performed in a conventional slab PAGE device, requiring no special device. Thus, it could be widely used in separation and analysis of diluted protein in a standard laboratory.

Repetitive use of polyacrylamide gels for the analysis and purification of oligonucleotides

The repetitive use of polyacrylamide slab gels for the analysis of oligonucleotides by ultraviolet (UV) shadowing across the complete electrophoresis cassette is addressed. Visualization of the samples is possible by preparing the gel between a quartz plate and a highly sensitive glass fluorescent plate whose preparation is described here. Within a working day, gels can be reloaded up to five times with no detriment to the resolution of the oligonucleotide bands. Taking advantage of this detection approach, we also devised a strategy to reuse gels in the purification of oligonucleotides, combining electroelution and subsequent concentration of the samples using centrifugal filter units.

A novel method that improves sensitivity of protein detection in PAGE and Western blot.

We have developed a simple and inexpensive method that improves sensitivity of protein and antigen detection in standard PAGE procedures. Our technique uses a sample microloader device with a funnel-like structure, filled with a 4% stacking gel. When attach to the top of a polyacrylamide slab gel, the proteins in a sample are concentrated by electrophoresis into a small volume as they emerge from the device's narrow outlet. Our microloader has several advantages over previous devices, including simple assembly, high versatility, and absence of cross-contamination between lanes. Addition of this device to a slab gel results in a fivefold increase in the sensitivity of antigen detection in a Western blot. As a result, less protein is required for loading and signal detection. Our protocol is a straightforward modification of a standard experimental technique, and is especially useful when only limited sample quantities are available.

On-Membrane Digestion Technology for Muscle Proteomics

High-resolution two-dimensional gel electrophoresis and in-gel digestion are routinely used for large-scale protein separation and peptide generation in mass spectrometry-based proteomics, respectively. However, the combination of isoelectric focusing in the first dimension and polyacrylamide slab gel electrophoresis in the second dimension is not suitable for the proper separation of integral proteins and high-molecular-mass proteins. In addition, in-gel trypsination may not result in a high degree of efficient digestion levels for the production of large numbers of peptides in the case of certain protein species. The application of gradient one-dimensional gel electrophoresis and on-membrane digestion can overcome these technical problems and be extremely helpful for the comprehensive identification of proteins that are underrepresented in routine two-dimensional gel electrophoretic approaches. This review critically examines the general application of on-membrane digestion techniques in proteomics and its recent application for the identification of very large integral membrane proteins from skeletal muscle by mass spectrometry. This includes the discussion of proteomic studies that have focused on the proteomic characterization of the membrane cytoskeletal protein dystrophin from sarcolemma vesicles and the ryanodine receptor calcium release channel of the sarcoplasmic reticulum from skeletal muscle.