Showing papers on "Gel electrophoresis published in 2018"

Two-Dimensional Gel Electrophoresis and 2D-DIGE.

Abstract: Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) continues to be one of the most versatile and widely used techniques to study the proteome of a biological system. In particular, a modified version of 2D-PAGE, two-dimensional difference gel electrophoresis (2D-DIGE), which uses differential labeling of protein samples with up to three fluorescent tags, offers greater sensitivity and reproducibility over conventional 2D-PAGE gels for differential quantitative analysis of protein expression between experimental groups. Both these methods have distinct advantages in the separation and identification of thousands of individual proteins species including protein isoforms and post-translational modifications. This review will discuss the principles of 2D-PAGE and 2D-DIGE including limitations to the methods. 2D-PAGE and 2D-DIGE continue to be popular methods in bioprocessing-related research (particularly on recombinant Chinese hamster ovary cells), which will also be discussed in the review chapter.

How many proteins can be identified in a 2DE gel spot within an analysis of a complex human cancer tissue proteome

Abstract: Two-dimensional gel electrophoresis (2DE) in proteomics is traditionally assumed to contain only one or two proteins in each 2DE spot. However, 2DE resolution is being complemented by the rapid development of high sensitivity mass spectrometers. Here we compared MALDI-MS, LC-Q-TOF MS and LC-Orbitrap Velos MS for the identification of proteins within one spot. With LC-Orbitrap Velos MS each Coomassie Blue-stained 2DE spot contained an average of at least 42 and 63 proteins/spot in an analysis of a human glioblastoma proteome and a human pituitary adenoma proteome, respectively, if a single gel spot was analyzed. If a pool of three matched gel spots was analyzed this number further increased up to an average of 230 and 118 proteins/spot for glioblastoma and pituitary adenoma proteome, respectively. Multiple proteins per spot confirm the necessity of isotopic labeling in large-scale quantification of different protein species in a proteome. Furthermore, a protein abundance analysis revealed that most of the identified proteins in each analyzed 2DE spot were low-abundance proteins. Many proteins were present in several of the analyzed spots showing the ability of 2DE-MS to separate at the protein species level. Therefore, 2DE coupled with high-sensitivity LC-MS has a clearly higher sensitivity as expected until now to detect, identify and quantify low abundance proteins in a complex human proteome with an estimated resolution of about 500 000 protein species. This clearly exceeds the resolution power of bottom-up LC-MS investigations.

DNA-Functionalized, Bivalent Proteins.

Abstract: Bivalent DNA conjugates of β-galactosidase (βGal), having pairs of oligonucleotides positioned closely on opposing faces of the protein, have been synthesized and characterized. These structures, due to their directional bonding characteristics, allow for the programmable access of one-dimensional protein materials. When conjugates functionalized with complementary oligonucleotides are combined under conditions that support DNA hybridization, periodic wire-type superstructures consisting of aligned proteins form. These structures have been characterized by gel electrophoresis, cryo-transmission electron microscopy, and negative-stain transmission electron microscopy. Significantly, melting experiments of complementary building blocks display narrowed and elevated melting transitions compared to the free duplex DNA, further supporting the formation of the designed binding mode, and unambiguously characterizing their association as DNA-mediated. These novel structures illustrate, for the first time, that di...

An Outbreak of NDM-1-Producing Klebsiella pneumoniae, Associated with OmpK35 and OmpK36 Porin Loss in Tunisia

Abstract: Objectives: To describe clinical and molecular characteristics of an outbreak due to metallo-β-lactamases (MBLs) producing Klebsiella pneumoniae collected at Charles Nicolle Hospital of Tunis and to analyze the impact of outer membrane porin (OMP) loss on carbapenem resistance levels. Methods: Between 2010 and 2015, 178 carbapenem-resistant Enterobacteriaceae were isolated. Screening for MBL production was performed using combined disk diffusion method, with imipenem and ethylene diamine tetraacetic acid (EDTA) as inhibitors. Resistance genes and virulence factors were identified by polymerase chain reaction (PCR) and sequencing. Genotyping was performed by pulsed-field gel electrophoresis and multilocus sequence typing. Genetic environment of carbapenemase genes was determined by PCR mapping. Conjugation assays were performed, and plasmids were assigned to incompatibility groups by PCR-based replicon typing. OMPs were profiled by sodium dodecyl sulfate-polyacrilamide gel electrophoresis, and porin genes ...

Optimization of Chemoenzymatic Mass Tagging by Strain-Promoted Cycloaddition (SPAAC) for the Determination of O-GlcNAc Stoichiometry by Western Blotting

Abstract: The dynamic modification of intracellular proteins by O-linked β-N-acetylglucosamine (O-GlcNAcylation) plays critical roles in many cellular processes. Although various methods have been developed for O-GlcNAc detection, there are few techniques for monitoring glycosylation stoichiometry and state (i.e., mono-, di-, etc., O-GlcNAcylated). Measuring the levels of O-GlcNAcylation on a given substrate protein is important for understanding the biology of this critical modification and for prioritizing substrates for functional studies. One powerful solution to this limitation involves the chemoenzymatic installation of polyethylene glycol polymers of defined molecular mass onto O-GlcNAcylated proteins. These “mass tags” produce shifts in protein migration during sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) that can be detected by Western blotting. Broad adoption of this method by the scientific community has been limited, however, by a lack of commercially available reagents and well-...

Identification and Antithrombotic Activity of Peptides from Blue Mussel (Mytilus edulis) Protein

Abstract: The blue mussel (Mytilus edulis) reportedly contains many bioactive components of nutritional value. Water-, salt- and acid-soluble M. edulis protein fractions were obtained and the proteins were trypsinized. The resultant peptides were analyzed by ultra-performance liquid chromatography quadrupole time of flight tandem mass spectrometry (UPLC-Q-TOF-MS/MS). 387 unique peptides were identified that matched 81 precursor proteins. Molecular mass distributions of the proteins and peptides were analyzed by sodium dodecyl sulfate-polyacryl amide gel electrophoresis (SDS-PAGE). The differences between the three protein samples were studied by Venn diagram of peptide and protein compositions. Toxicity, allergic and antithrombotic activity of peptides was predicted using database website and molecular docking respectively. The antithrombotic activity of enzymatic hydrolysate from water-, salt- and acid-soluble M. edulis protein were 40.17%, 85.74%, 82.00% at 5 mg/mL, respectively. Active mechanism of antithrombotic peptide (ELEDSLDSER) was also research about amino acid binding sites and interaction, simultaneously.

Difference Gel Electrophoresis

Abstract: The aim of this new edition of Difference Gel Electrophoresis is to provide a comprehensive update of this key method of gel-based proteomics. Two-dimensional gel electrophoresis is one of the most frequently used protein separation techniques in modern biochemistry and proteomics. Difference Gel Electrophoresis employs the direct labeling of proteomes with fluorescent dyes prior to large-scale gel electrophoretic separation enabling highthroughput comparative analyses.

A New Salt-Tolerant Thermostable Cellulase from a Marine Bacillus sp. Strain.

Abstract: A salt-tolerant cellulase secreted by a marine Bacillus sp. SR22 strain with wide resistance to temperature and pH was purified and characterized. Its approximate mass was 37 kDa. The endoglucanase, named as Bc22Cel, was purified by ammonium sulfate precipitation, gel filtration chromatography, and extraction from the gel after non-reducing sodium dodecyl sufate-polyacrylamide gel electrophoresis. The optimal pH value and temperature of Bc22Cel were 6.5 and 60°C, respectively. The purified Bc22Cel showed a considerable halophilic property, being able to maintain more than 70% of residual activity even when pre-incubated with 1.5 M NaCl for 1 h. Kinetic analysis of the purified enzyme showed the Km and Vmax to be 0.704 mg/ml and 29.85 μmol·ml-1·min-1, respectively. Taken together, the present data indicate Bc22Cel as a potential and useful candidate for industrial applications, such as the bioconversion of sugarcane bagasse to its derivatives.

Revealing the Amylase Interactome in Whole Saliva Using Proteomic Approaches.

Abstract: Understanding proteins present in saliva and their function when isolated is not enough to describe their real role in the mouth. Due to protein-protein interactions, structural changes may occur in macromolecules leading to functional modulation or modification. Besides amylase’s function in carbohydrate breakdown, amylase can delay proteolytic degradation of protein partners (e.g., histatin 1) when complexed. Due to its biochemical characteristics and high abundance in saliva, amylase probably interacts with several proteins acting as a biological carrier. This study focused on identifying interactions between amylase and other proteins found in whole saliva (WS) using proteomic approaches. Affinity chromatography was used, followed by gel electrophoresis methods, sodium dodecyl sulfate and native, tryptic in-solution and in-gel digestion, and mass spectrometry. We identified 66 proteins that interact with amylase in WS. Characterization of the identified proteins suggests that acidic (pI < 6.8) and low molecular weight (MW < 56 kDa) proteins have preference during amylase complex formation. Most of the identified proteins present biological functions related to host protection. A new protein-amylase network was constructed using the STRING database. Further studies are necessary to investigate individualities of the identified amylase interactors. These observations open avenues for more comprehensive studies on not yet fully characterized biological function of amylase.

An RGD-Containing Peptide Derived from Wild Silkworm Silk Fibroin Promotes Cell Adhesion and Spreading.

Abstract: Arginine-Glycine-Aspartate (RGD) tripeptide can promote cell adhesion when present in the amino acid of proteins such as fibronectin. In order to demonstrate the bioactivity of an RGD-containing silk protein, a gene encoding the RGD motif-containing peptide GSGAGGRGDGGYGSGSS (–RGD–) derived from nonmulberry silk was designed and cloned, then multimerised and inserted into a commercial pGEX expression vector for recombinant expression of (–RGD–)n peptides. Herein, we focus on two glutathione-S-transferase (GST)-tagged fusion proteins, GST–(–RGD–)4 and GST–(–RGD–)8, which were expressed in Escherichia coli BL21, purified by GST affinity chromatography, and analyzed with sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and mass spectrometry (MS). Target peptides (–RGD–)4 and (–RGD–)8 (6.03 and 11.5 kDa) were cleaved from the GST-tag by thrombin digestion, as verified with MS and SDS-PAGE. Isoelectric point analysis confirmed that target peptides were expressed and released in accordance with the original design. Target peptides self-assembled into a mainly α-helical structure, as determined by circular dichroism spectroscopy. Furthermore, (–RGD–)4 and (–RGD–)8 modified mulberry silk fibroin films were more effective for rapid cell adhesion, spreading and proliferative activity of L929 cells than some chemically synthesized RGD peptides modified and mulberry silk lacking the RGD motif.

Transketolase Is Identified as a Target of Herbicidal Substance α-Terthienyl by Proteomics.

Abstract: α-terthienyl is a natural phytotoxin isolated originally from Flaveria bidentis (L.) Kuntze. The bioassay presented here shows the strong herbicidal activity of α-terthienyl on Digitaria sanguinalis, Arabidopsis thaliana and Chlamydomonas reinhardtii. The α-terthienyl-induced response of A. thaliana at the protein level was analyzed at different times. Changes in the protein expression profiles were analyzed by two-dimensional gel electrophoresis and liquid chromatography tandem mass spectrometry (LC-MS/MS) mass spectrometry. Sixteen protein spots were identified that showed reproducible changes in the expression of at least 2-fold when compared to the control. Among these 16 spots, three were up-regulated and 13 were down-regulated. The decreased expression of several proteins associated with energy production and carbon metabolism suggested that these processes were affected by α-terthienyl. To search for the candidate proteins in this screen, A. thaliana T-DNA mutants of the candidate proteins were used to test their susceptibility to α-terthienyl. Amongst the others, attkl1, a mutant of transketolase, exhibited a significantly lower sensitivity to α-terthienyl when hit compared with Col-0. Based on the identification of the proteins associated with the response to α-terthienyl by proteomics, a candidate target protein transketolase was identified.

The proteome of neurofilament-containing protein aggregates in blood

Abstract: Protein aggregation in biofluids is a poorly understood phenomenon. Under normal physiological conditions, fluid-borne aggregates may contain plasma or cell proteins prone to aggregation. Recent observations suggest that neurofilaments (Nf), the building blocks of neurons and a biomarker of neurodegeneration, are included in high molecular weight complexes in circulation. The composition of these Nf-containing hetero-aggregates (NCH) may change in systemic or organ-specific pathologies, providing the basis to develop novel disease biomarkers. We have tested ultracentrifugation (UC) and a commercially available protein aggregate binder, Seprion PAD-Beads (SEP), for the enrichment of NCH from plasma of healthy individuals, and then characterised the Nf content of the aggregate fractions using gel electrophoresis and their proteome by mass spectrometry (MS). Western blot analysis of fractions obtained by UC showed that among Nf isoforms, neurofilament heavy chain (NfH) was found within SDS-stable high molecular weight aggregates. Shotgun proteomics of aggregates obtained with both extraction techniques identified mostly cell structural and to a lesser extent extra-cellular matrix proteins, while functional analysis revealed pathways involved in inflammatory response, phagosome and prion-like protein behaviour. UC aggregates were specifically enriched with proteins involved in endocrine, metabolic and cell-signalling regulation. We describe the proteome of neurofilament-containing aggregates isolated from healthy individuals biofluids using different extraction methods.

Comparative Study on Antibiotic Resistance and DNA Profiles of Salmonella enterica Serovar Typhimurium Isolated from Humans, Retail Foods, and the Environment in Shanghai, China.

Abstract: We characterized antibiotic resistance profiles, antibiotic resistance-associated genes, and pulsed-field gel electrophoresis (PFGE) patterns of 145 Salmonella enterica serotype Typhimuriu...

Two-dimensional Gel Electrophoresis Coupled with Mass Spectrometry Methods for an Analysis of Human Pituitary Adenoma Tissue Proteome.

Abstract: Human pituitary adenoma (PA) is a common tumor that occurs in the human pituitary gland in the hypothalamus-pituitary-targeted organ axis systems, and may be classified as either clinically functional or nonfunctional PA (FPA and NFPA). NFPA is difficult for early stage diagnosis and therapy due to barely elevating hormones in the blood compared to FPA. Our long-term goal is to use proteomics methods to discover reliable biomarkers for clarification of PA molecular mechanisms and recognition of effective diagnostic, prognostic markers and therapeutic targets. Effective two-dimensional gel electrophoresis (2DE) coupled with mass spectrometry (MS) methods were presented here to analyze human PA proteomes, including preparation of samples, 2D gel electrophoresis, protein visualization, image analysis, in-gel trypsin digestion, peptide mass fingerprint (PMF), and tandem mass spectrometry (MS/MS). 2-Dimensional gel electrophoresis matrix-assisted laser desorption/ionization mass spectrometry PMF (2DE-MALDI MS PMF), 2DE-MALDI MS/MS, and 2DE-liquid chromatography (LC) MS/MS procedures have been successfully applied in an analysis of NFPA proteome. With the use of a high-sensitivity mass spectrometer, many proteins were identified with the 2DE-LC-MS/MS method in each 2D gel spot in an analysis of complex PA tissue to maximize the coverage of human PA proteome.

Quantitative Proteomic Approach Targeted to Fibrinogen β Chain in Tissue Gastric Carcinoma.

Abstract: Elevated plasma fibrinogen levels and tumor progression in patients with gastric cancer (GC) have been largely reported. However, distinct fibrinogen chains and domains have different effects on coagulation, inflammation, and angiogenesis. The aim of this study was to characterize fibrinogen β chain (FGB) in GC tissues. Retrospectively we analyzed the data of matched pairs of normal (N) and malignant tissues (T) of 28 consecutive patients with GC at diagnosis by combining one- and two-dimensional electrophoresis (1DE and 2DE) with immunoblotting and mass spectrometry together with two-dimensional difference in gel electrophoresis (2D-DIGE). 1DE showed bands of the intact FGB at 50 kDa and the cleaved forms containing the fragment D at ~37-40 kDa, which corresponded to 19 spots in 2DE. In particular, spot 402 at ~50 kDa and spots 526 and 548 at ~37 kDa were of interest by showing an increased expression in tumor tissues. A higher content of spot 402 was associated with stomach antrum, while spots 526 and 548 amounts correlated with corpus and high platelet count (>208 × 10⁸/L). The quantification of FGB and cleaved products may help to further characterize the interconnections between GC and platelet/coagulation pathways.

Influence of glycation and pepsin hydrolysis on immunoreactivity of albumin/globulin fraction of herbicide resistant wheat line

Abstract: Nagy A., Marciniak-Darmochwa l K., Krawczuk S., Mierzejewska D., Kostyra H., Gelencser E .(2009): Influence of glycation and pepsin hydrolysis on immunoreactivity of albumin/globulin fraction of herbicide resistant wheat line. Czech J. Food Sci., 27: 320–329. The aim of this study was to investigate the influence of non-enzymatic glycosylation on the immunogenic proper ties of soluble wheat proteins. Albumin/globulin fractions of herbicide resistant wheat line were non-enzymatically glycosylated using glucose for seven days at 37°C. The changes in their structures and immunoreactivity were then determined. The protein fractions were also hydrolysed with pepsin to determine the resistance to digestion. Albu min/globulin fractions before and after non-enzymatic glycosylation were analysed using o -phthaldialdehyde method and sodium dodecyl sulphate-polyacrylamide gel electrophoresis. The immunoreactivity of the protein fractions was determined using enzyme-linked immunosorbent assay methods, as well as affinity chromatography. The soluble wheat proteins showed smaller amounts of available α-amino groups after non-enzymatic glycosylation, and were stronger immunogens after glycation, but their antigenicity was not been affected significantly. However, pepsin hydrolysis of wheat proteins decreased their immunoreactivity.

Miniaturized gel electrophoresis system for fast separation of nucleic acids

Abstract: Slab gel electrophoresis (SGE) is very common tool for DNA, RNA and protein analysis, but it is tedious, labor-intensive, skill-dependent, and relatively slow. Herein, we developed a biochip based SGE system, which can resolve the DNA fragments and record their separation process. By electrophoresis of 50 bp DNA ladder, we found that the 16 DNA fragments were effectively resolved within 14 min. In order to validate its feasibility and practicability, we take periodontal pathogens (e.g., Porphyromonas gingivalis (P.g), Tannerela forsythia (T.f), and Treponema denticola (T.d) ) as an example by separating their polymerase chain reaction products. Experiments demonstrated that P.g , T.d and T.f were diagnosed within 12 min, and the electrophoresis of P.g showed that the detection limit of this system was about 6.4 ng/μl. Such a low cost system is easy to operate, and can effectively improve SGE in the biological experiment, especially for the labs in the third world countries.

Enrichment of Bacterial Lipoproteins and Preparation of N-terminal Lipopeptides for Structural Determination by Mass Spectrometry.

Abstract: Lipoproteins are important constituents of the bacterial cell envelope and potent activators of the mammalian innate immune response. Despite their significance to both cell physiology and immunology, much remains to be discovered about novel lipoprotein forms, how they are synthesized, and the effect of the various forms on host immunity. To enable thorough studies on lipoproteins, this protocol describes a method for bacterial lipoprotein enrichment and preparation of N-terminal tryptic lipopeptides for structural determination by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Expanding on an established Triton X-114 phase partitioning method for lipoprotein extraction and enrichment from the bacterial cell membrane, the protocol includes additional steps to remove non-lipoprotein contaminants, increasing lipoprotein yield and purity. Since lipoproteins are commonly used in Toll-like receptor (TLR) assays, it is critical to first characterize the N-terminal structure by MALDI-TOF MS. Herein, a method is presented to isolate concentrated hydrophobic peptides enriched in N-terminal lipopeptides suitable for direct analysis by MALDI-TOF MS/MS. Lipoproteins that have been separated by Sodium Dodecyl Sulfate Poly-Acrylamide Gel Electrophoresis (SDS-PAGE) are transferred to a nitrocellulose membrane, digested in situ with trypsin, sequentially washed to remove polar tryptic peptides, and finally eluted with chloroform-methanol. When coupled with MS of the more polar trypsinized peptides from wash solutions, this method provides the ability to both identify the lipoprotein and characterize its N-terminus in a single experiment. Intentional sodium adduct formation can also be employed as a tool to promote more structurally informative fragmentation spectra. Ultimately, enrichment of lipoproteins and determination of their N-terminal structures will permit more extensive studies on this ubiquitous class of bacterial proteins.

Principle and Method of Silver Staining of Proteins Separated by Sodium Dodecyl Sulfate–Polyacrylamide Gel Electrophoresis

Abstract: Silver staining is an excellent technique for detecting proteins which are separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis due to its efficiency of detecting proteins present in nanograms. The technique is based on the simple principle that selective reduction of silver into metallic silver occurs at the initiation site in the close proximity of protein molecules. The staining process sequentially consists of protein fixation, sensitization, washing, silver impregnation, and finally development of image. Depending upon the amount of silver incorporated into the protein bands, different color of gel is produced on silver staining. Though different protocols of silver staining exist, the method described here is easy, cheap, reliable, and very sensitive.

A comprehensive model of DNA fragmentation for the preservation of High Molecular Weight DNA

Abstract: During DNA extraction the DNA molecule undergoes physical and chemical shearing, causing the DNA to fragment into shorter and shorter pieces. Under common laboratory conditions this fragmentation yields DNA fragments of 5-35 kilobases (kb) in length. This fragment length is more than sufficient for DNA sequencing using short-read technologies which generate reads 50-600 bp in length, but insufficient for long-read sequencing and linked reads where fragment lengths of more than 40 kb may be desirable. This study provides a theoretical framework for quality management to ensure access to high molecular weight DNA in samples. Shearing can be divided into physical and chemical shearing which generate different patterns of fragmentation. Exposure to physical shearing creates a characteristic fragment length where DNA fragments are cut in half by shear stress. This characteristic length can be measured using gel electrophoresis or instruments for DNA fragment analysis. Chemical shearing generates randomly distributed fragment lengths visible as a smear of DNA below the peak fragment length. By measuring the peak of DNA fragment length and the proportion of very short DNA fragments both sources of shearing can be measured using commonly used laboratory techniques, providing a suitable quantification of DNA integrity of DNA for sequencing with long-read technologies.

Antioxidant and antidiabetic activities of vanadium binding proteins purified from the sea squirt Halocynthia roretzi.

Abstract: Sea squirts accumulate vanadium compounds with potent antidiabetic activity, which are involved in immune defense. In this study, vanadium concentrations of fresh blood plasma, intestine, and muscle of the sea squirt Halocynthia roretzi were 6.3, 3.7 and 2.1 mg/kg respectively. Two vanadium binding proteins (VBPs) from blood plasma and intestine were purified through (NH4)2SO4 precipitation, and DEAE-Sepharose ion exchange and Sephacryl S-200 HR gel filtration chromatography, in that order. The purity and yield of the intestine and blood plasma vanadium binding proteins, VBPintestine and VBPblood plasma, were 13.4 folds and 7.1%, and 20.9 folds and 6.8%, respectively. There were two protein bands on the sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) with molecular weights of 24.3 and 68.8 kDa and one with 96.7 kDa on the native-PAGE of VBPblood plasma, whereas only one protein band of VBPintestine on the SDS-PAGE with 26.5 kDa. Antioxidant activities of VBPs were lower than that of ascorbic acid. Both VBPs exerted strong inhibitory activity against Saccharomyces cerevisiae and mild against Bacillus stearothermophilus and rat intestinal α-glucosidase. IC50 values of VBPintestine and VBPblood plasma against S. cerevisiae α‐glucosidase were 28.34 and 12.60 μg/ml, respectively. The K m , V max , k cat , and k cat /K m values of VBPintestine and VBPblood plasma were 4.29, 0.036, 6.58 and 1.53 × 103, and 7.63 mM, 0.057 mM/min, 10.41 s−1 and 1.36 × 103 (M sec)−1, respectively. There was a synergistic interaction between VBPblood plasma and VBPintestine on rat intestinal α-glucosidase inhibitory activity.