Electrophoretic Analysis Research Articles

Purification and characterization of a novel glutamate dehydrogenase from Geotrichum candidum with higher alcohol and amino acid activity

Crude enzyme from Geotrichum candidum S12 exhibited high activity towards hexanol at pH 4.0, distinguishing it from currently known enzymes. To identify the dominant enzyme contributing to this activity, the crude enzyme extract was separated into different fractions by ammonium sulfate precipitation, MonoQ anion-exchange chromatography, and Sephacryl S-200 gel filtration chromatography. Afraction with high activity towards hexanol at pH 4.0 was obtained, exhibiting 38-fold improved purity and a specific activity of 3802.7 U/mg. After electrophoretic analysis, the fraction showed a molecular weight of 223 kDa by Native-PAGE and 51.4 kDa by SDS-PAGE. The purified fraction was identified as a glutamate dehydrogenase (GDH) by peptide mass fingerprinting data. This fraction showed high activity towards glutamate, α-ketoglutarate, hexanol, and isoamyl alcohol with a Km value of 41.74, 4.01, 20.37, and 19.37 mM, respectively, but with no activity towards methanol, ethanol, 1-propanol, and isobutanol. As a comparison, the GDH from yeast had no activity towards hexanol and other alcohols. Kinetic analysis revealed that glutamate and hexanol served as competitive inhibitors to each other for the purified GDH. The GDH showed the highest activity towards hexanol at pH 4.0 and 30 °C, and was the most stable at pH 2.2–7.0 and ≤40 °C. The presence of ADP, Fe2+, K+, and Zn2+ increased the enzymatic activity towards hexanol and EDTA, Pb2+, Mn2+, ATP, and DTT decreased the activity. These novel characteristics expand the reported properties of GDH and suggest the newly characterized GDH has unique potential for practical application.

Antibacterial serine protease from Wrightia tinctoria: Purification and characterization

A serine protease was purified from the leaves of Wrightia tinctoria by sequential flow through method comprising screening, optimization, ammonium sulfate precipitation, gel filtration and ion exchange column chromatography. The yield and purification fold obtained were 11.58% and 9.56 respectively. A single band of serine protease was visualized on SDS-PAGE and 2-D gel electrophoretic analyses were revealed with the molecular mass of 38.5 kDa. Serine protease had an optimum pH of 8.0 and was stable at 45°C with high relative protease activity. The addition of metal ions such as Mg2+ and Mn2+ exhibits a high relative activity. Serine protease had a potent antibacterial activity against both Gram-positive and Gram-negative bacteria. A 10 μg/ml of serine protease was tested against S. aureus, M. luteus, P. aeruginosa and K. pneumoniae which had 21, 20, 18 and 17 mm of zone of inhibition respectively. Serine protease from W. tinctoria degrades the peptidoglycan layer of bacteria which was visualized by transmission electron microscopic analysis.

Interaction of DDP with bovine serum albumin facilitates formation of the protein dimers

Interaction of bovine serum albumin (BSA) with cis- and trans- isomers of diamminedichloroplatinum(II) (DDP) was studied using electrophoretic analysis and Fourier transformed infrared spectroscopy (FTIR). The application of FTIR spectroscopy allowed us to study the DDP/BSA complexes in D2O solutions using protein concentrations close to the physiological level (30 mg/ml) with platinum to BSA molar ratios in the range of 1:1 to 150:1. Under these conditions we have observed formation of relatively weak non-covalent intermolecular protein complexes, which dominated over the BSA-Pt-BSA crosslinks. Analysis of the IR spectra in the region of amide I′ band revealed that the fraction of the α-helical regions in the protein decreases from ∼65% to approximately 55% and 48% in the complexes with cis- and trans-DDP respectively, while the amount of extended β-structures increases from ∼15 to 20% in BSA to 20–30% in its complexes with cis-DDP and up to 35–40% in trans-DDP/BSA complexes. Based on the data obtained we conclude that multiple intermolecular interactions take place in the solution facilitated by the changes in the BSA secondary structure, induced by DDP binding.

Using Electrophoretic Immunoassay to Monitor Hormone Secretion.

It has been demonstrated that microfluidic systems allow integration of sampling, reagent mixing, and rapid electrophoretic analysis. They have also proven useful for culturing cells wherein control over the environment allows novel and automated experiments. Here, we describe a microchip-based electrophoresis assay that allows cell culture and hormone monitoring. An online gradient generator can control cell culture condition precisely. This system has been applied for Pancreas islets' glucose sensitivity studies.

Biochemical Characterization of Prions.

Prion disease or transmissible spongiform encephalopathies are characterized by the presence of the abnormal form of the prion protein (PrPSc). The pathological and transmissible properties of PrPSc are enciphered in its secondary and tertiary structures. Since it's well established that different strains of prions are linked to different conformations of PrPSc, biochemical characterization of prions seems a preliminary but reliable approach to detect, analyze, and compare prion strains. Experimental biochemical procedures might be helpful in distinguishing PrPSc physicochemical properties and include resistance to proteinase K (PK) digestion, insolubility in nonionic detergents, PK-resistance under denaturing conditions and sedimentation properties in sucrose gradients. This biochemical approach has been extensively applied in human prion disorders and subsequently expanded for PrPSc characterization in animals. In particular, in sporadic Creutzfedlt-Jakob disease (sCJD) PrPSc is characterized by two main glycotypes conventionally named Type 1 and Type 2, based on the apparent gel migration at 21 and 19kDa of the PrPSc PK-resistant fragment. An additional PrPSc type was identified in sCJD characterized by an unglycosylated dominant glycoform pattern and in 2010 a variably protease-sensitive prionopathy (VPSPr) was reported showing a PrPSc with an electrophoretic ladder like pattern. Additionally, the presence of PrPSc truncated fragments completes the electrophoretic characterization of different prion strains. By two-dimensional (2D) electrophoretic analysis additional PrPSc pattern was identified, since this procedure provides information about the isoelectric point and the different peptides length related to PK cleavage, as well as to glycosylation extent or GPI anchor presence. We here provide and extensive review on PrPSc biochemical analysis in human and animal prion disorders. Further, we show that PrPSc glycotypes observed in CJD share similarities with PrPSc in bovine spongiform encephalopathy forms (BSE).

Correlation between Pathological Characteristics and Young's Modulus Value of Spastic Gastrocnemius in a Spinal Cord Injury Rat Model.

The goal of the present study were (1) to investigate the pathological characteristics of gastrocnemius muscle (GM) and quantitatively assess GM tissue stiffness in rat models with spinal cord injury (SCI) and (2) to explore the correlation between pathological characteristics changes and Young's modulus value of GM. 24 Sprague Dawley male rats were allocated into normal control groups and SCI model subgroups, respectively. GM stiffness was assessed with shear wave sonoelastography technology. All GMs were further analyzed by pathological examinations. GM weights were decreased, the ratio of type I fibers was decreased, and the ratio of type II fibers was increased in the GM in the model group. MyHC-I was decreased, while MyHC-II was increased according to the electrophoretic analysis in model subgroups. The elastic modulus value of GM was increased in the model group. A significant negative correlation was found between Young's modulus value of GM and the ratio of type I fibers of GM in model subgroup. Our studies showed that the stiffness of GM is correlated with pathological characteristics during the initial stages of SCI in rats. We also identified shear wave sonoelastography technology as a useful tool to assess GM stiffness in SCI rat models.

Probable secondary transmission of antimicrobial-resistant Escherichia coli between people living with and without pets.

Companion animals are considered as one of the reservoirs of antimicrobial-resistant (AR) bacteria that can be cross-transmitted to humans. However, limited information is available on the possibility of AR bacteria originating from companion animals being transmitted secondarily from owners to non-owners sharing the same space. To address this issue, the present study investigated clonal relatedness among AR E. coli isolated from dog owners and non-owners in the same college classroom or household. Anal samples (n=48) were obtained from 14 owners and 34 non-owners; 31 E. coli isolates were collected (nine from owners and 22 from non-owners). Of 31 E. coli, 20 isolates (64.5%) were resistant to at least one antimicrobial, and 16 isolates (51.6%) were determined as multi-drug resistant E. coli. Six isolates (19.4%) harbored integrase genes (five harbored class I integrase gene and one harbored class 2 integrase gene, respectively). Pulsed-field gel electrophoretic analysis identified three different E. coli clonal sets among isolates, indicating that cross-transmission of AR E. coli can easily occur between owners and non-owners. The findings emphasize a potential risk of spread of AR bacteria originating from pets within human communities, once they are transferred to humans. Further studies are needed to evaluate the exact risk and identify the risk factors of secondarily transmission by investigating larger numbers of isolates from pets, their owners and non-owners in a community.

Gel electrophoretic analysis of taxonomic correlation between Solanum nigrum and Solanum surattense

Gel electrophoretic analysis of taxonomic correlation between <i>Solanum nigrum</i> and <i>Solanum surattense</i>

Nanomaterials for sample pretreatment prior to capillary electrophoretic analysis.

Nanomaterials are, in analytical science, used for a broad range of purposes, covering the area of sample pretreatment as well as separation, detection and identification of target molecules. This review covers the application of nanomaterials for sample pretreatment in capillary electrophoresis. It targets the utilization of nanomaterials for sample purification, preconcentration and/or extraction coupled both off-line and on-line with capillary electrophoretic analysis. Especially due to their large surface area, nanoparticles and nanomaterials are exceptionally helpful in making up for the limited concentration detection limits provided by capillary electrophoresis. This method possesses excellent separation power; however, its sensitivity may be problematic in some cases. Therefore, this review is focused on utilization of nanomaterials as a powerful tool for sample preconcentration, which is so often required prior to capillary electrophoretic analysis.

ADVERSE PREGNANCY OUTCOMES AND CORRELATION OF \r\nPREGNANCY GINGIVITIS WITH SUSPECTED \r\nPERIODONTOPATHOGENS

Ponte Academic JournalNov 2017, Volume 73, Issue 11 ADVERSE PREGNANCY OUTCOMES AND CORRELATION OF \r\nPREGNANCY GINGIVITIS WITH SUSPECTED \r\nPERIODONTOPATHOGENSAuthor(s): Gülden Ereş ,Esra Zor, Cengiz Han AçıkelJ. Ponte - Nov 2017 - Volume 73 - Issue 11 doi: 10.21506/j.ponte.2017.11.9 Abstract:Background/Aim: To investigate the presence of Aggregatibacter actinomycetemcomitans and Prevotella intermedia and their correlation with the adverse pregnancy outcomes in pregnancy gingivitis.\r\nMaterials and methods: Sixtysix pregnant women participated voluntarily in this study. Subgingival plaque samples were obtained from sites showing signs of gingivitis as well as from healthy sites by inserting paper points into the pockets for 30 seconds. Aggregatibacter actinomycetemcomitans and Prevotella intermedia were detected by using a method of agarose gel electrophoretic analysis of DNA extracted from plaque samples and amplified by PCR.\r\nResults: Our results showed that the rate of preterm labor was higher in P. intermedia negative healthy sites than in P. intermedia positive healthy sites (p < 0.05) and it was found that absence of P. intermedia increased the risk of preterm labor 10 times.\r\nConclusion: This preliminary study indicates that the oral cavity can be a good source of data for the studies investigating the manifestations of adverse pregnancy outcomes Download full text:Check if you have access through your login credentials or your institution Username Password

Amino Acid Composition, Protein Fractions and Electrophoretic Analysis of Seed Storage Proteins in Lupins

Amino Acid Composition, Protein Fractions and Electrophoretic Analysis of Seed Storage Proteins in Lupins

A Method for Isolation of Extracellular Vesicles and Characterization of Exosomes from Brain Extracellular Space.

Extracellular vesicles (EV), including exosomes, secreted vesicles of endocytic origin, and microvesicles derived from the plasma membrane, have been widely isolated and characterized from conditioned culture media and bodily fluids. The difficulty in isolating EV from tissues, however, has hindered their study in vivo. Here, we describe a novel method designed to isolate EV and characterize exosomes from the extracellular space of brain tissues. The purification of EV is achieved by gentle dissociation of the tissue to free the brain extracellular space, followed by sequential low-speed centrifugations, filtration, and ultracentrifugations. To further purify EV from other extracellular components, they are separated on a sucrose step gradient. Characterization of the sucrose step gradient fractions by electron microscopy demonstrates that this method yields pure EV preparations free of large vesicles, subcellular organelles, or debris. The level of EV secretion and content are determined by assays for acetylcholinesterase activity and total protein estimation, and exosomal identification and protein content are analyzed by Western blot and immuno-electron microscopy. Additionally, we present here a method to delipidate EV in order to improve the resolution of downstream electrophoretic analysis of EV proteins.

203 SINGLE-STEP GENE EDITING OF 3 XENOANTIGENS IN PORCINE FIBROBLASTS USING PROGRAMMABLE NUCLEASES

Programmable nucleases (ZFN, Tal Effector Nucleases, and CRISPR) opened a new era for mammal genome editing, in particular for the pigs used for xenotransplantation. Multiple gene editing events are required both for knockout (KO) of xenoantigens and for targeted integration of human protective genes (Perota et al. 2016 J. Genet. Genomics 43, 233–23). The objective of the present work was to edit selected pig lines to KO the enzymes coding for the most relevant xenoantigens (i.e. GGTA1, CMAH, and B4GalNT2), combining Talens and CRISPR/Cas9 technologies to magnetic beads selection (Li et al. 2013 Xenotransplantation 22, 20–31). Primary porcine adult fibroblasts were transfected using Nucleofector (V-024 program). In a single reaction 2 × 106 fibroblasts were co-transfected using 2 different sets of TALENS (4 μg/set) specific for CMAH (Conchon et al., 2013) and GGTA1 (Perota et al., 2015) genes together with B4GalNT2-specific CRISPR/Cas9 expression vector (2 μg; pX330-B4GalNT2; Estrada et al., 2015). Eight days post-transfection (DPT), Gal–/– cells were selected initially using biotin-conjugated IB4 lectin (Sigma, St. Louis, MO, USA) and magnetic beads (Dynabeads M-280, Thermo Fisher Scientific, Waltham, MA, USA). The selected cells were then plated on 150-mm Petri dishes (200 cells/dish) and cultured for 10 days. Selected colonies were expanded for PCR analysis and cryopreserved for somatic cell nuclear transfer (SCNT). All colonies were analysed by PCR for CMAH gene and their resulting products were digested with HindIII (HindIII-RFLP). Colonies that lost wild-type HindIII as a consequence of Talens effected deletion were PCR characterised for GGTA1, selecting those that had detectable Indels after gel electrophoresis and finally analysed by PCR for B4GalNT2. All PCR products were validated by sequencing for all the 3 genes of interest (TopoTA, Thermo Fisher Scientific). Selected colonies were used as nuclear donors for SCNT (Lagutina et al., 2006). Eight DPT we obtained 3.45 ×106 cells. About 6.0 × 103 Gal-negative cells (0.17%) were collected from the supernatant after magnetic beads separation. Eighteen DPT, 120 colonies were picked up and their HindIII-RFLP analyses on CMAH gene revealed that 22 colonies (18.3%) were KO for both CMAH alleles. Of these 22 colonies following electrophoretic analyses of GGTA1-PCR products, 13 colonies had detectable Indels. These 13 colonies were finally PCR analysed and sequenced for B4GalNT2 and sequenced. Final sequencing results confirmed that 2 colonies (1.6%) resulted in KO for the 3 genes. Three different zona-free SCNT experiments were done and 579 reconstructed embryos were obtained. On Day 7, 322 morulae or blastocysts (56%) were transferred in 3 synchronised sows and 2 (66%) became pregnant. In conclusion, after gene editing with programmable nucleases, combining beads-mediated selection with well-designed molecular analyses, we developed a multistep assay that can be used efficiently to detect desired gene edited events in cell colonies suitable for the SCNT. Embryos generated after SCNT were able to establish pregnancies at a high rate. This work is supported by European FP7 grants Translink (n° 603049) and Xenoislet (n° 601827).

Comparative Evaluation of Genomic and Laboratory Approaches for Determination of Shiga Toxin Subtypes in Escherichia coli

The determination of Shiga toxin (ST) subtypes can be an important element in the risk characterization of foodborne ST-producing Escherichia coli (STEC) isolates for making risk management decisions. ST subtyping methods include PCR techniques based on electrophoretic or pyrosequencing analysis of amplicons and in silico techniques based on whole genome sequence analysis using algorithms that can be readily incorporated into bioinformatics analysis pipelines for characterization of isolates by their genetic composition. The choice of technique will depend on the performance characteristics of the method and an individual laboratory's access to specialized equipment or personnel. We developed two whole genome sequence-based ST subtyping tools: (i) an in silico PCR algorithm requiring genome assembly to replicate a reference PCR-based method developed by the Statens Serum Institut (SSI) and (ii) an assembly-independent routine in which raw sequencing results are mapped to a database of known ST subtype sequence variants (V-Typer). These tools were evaluated alongside the SSI reference PCR method and a recently described PCR-based pyrosequencing technique. The V-Typer method results corresponded closely with the reference method in the analysis of 67 STEC cultures obtained from a World Health Organization National Reference Laboratory. In contrast, the in silico PCR method failed to detect ST subtypes in several cases, a result which we attribute to assembly-induced errors typically encountered with repetitive gene sequences. The V-Typer can be readily integrated into bioinformatics protocols used in the identification and characterization of foodborne STEC isolates.

Methods for Proteome Analysis of Campylobacter jejuni Using 2-D Electrophoresis.

This chapter describes protocols used for two-dimensional electrophoretic analysis of the proteome or subproteome of Campylobacter jejuni, a major human food-borne pathogen. The following protocols, adapted to Campylobacter strains, include all the steps from cultivation to gel-support protein separation.

Using of purified platelets for investigation of “cell-efector” model in hemostasis system

Gel filtration on a column of Sepharose 4B was tested as method for separating platelet fraction. The results of cytological and electrophoretic analysis showed absence of other blood cells and plasma proteins in the content of the resulting cell fraction. Obtained platelets were proved to keep morphological stability and retain the ability to aggregate in response to ADP – one of the main physiological inductors

Capillary electrochromatography of proteins and peptides (2006-2015).

This review summarizes the development and the applications of capillary electrochromatographic techniques pertinent to the analysis of proteins and peptides, which took place over the last 10 years (2006-mid-2016). This "hybrid" technique is useful for the analysis of a broad spectrum of proteins and peptides and is an approach that is complementary to the liquid chromatographic and the capillary electrophoretic analysis. All modes of capillary electrochromatography are described here, which includes particle-packed columns, monolithic stationary phases, and open-tubular capillary electrochromatography.

Target Amplicon Sequencing for Genotyping Genome-Wide Single Nucleotide Polymorphisms Identified by Whole-Genome Resequencing in Peanut.

Genome-wide genotyping data regarding breeding materials are essential resources for improving breeding efficiency, especially in plants with complex genomes with a high degree of polyploidy. Several current breeding efforts in cultivated peanut ( L.), which has a tetraploid genome, are devoted to developing high oleic acid cultivars. Genetic maps for such breeding programs have been developed using simple-sequence repeat (SSR) markers, the use of which requires time-consuming electrophoretic analyses. Next-generation sequencing (NGS) technology can overcome this technical hurdle. Initially, we attempted double-digest restriction site-associated DNA sequencing on peanut breeding materials used to develop high oleic acid cultivars. However, this method was not effective because few single nucleotide polymorphism (SNPs) were available because of low genetic diversity of the lines. The genome sequences of the probable diploid ancestors of cultivated peanut, Krapov. & W. C. Greg. and Krapov. & W. C. Greg., are available. Therefore, we next employed whole-genome resequencing analysis to obtain genome-wide SNP data. In this analysis, we observed large biases in the numbers and genomic positions of interspecific and intraspecific SNPs. For genome-wide genotyping, we selected a subset of SNPs covering the peanut genome as the targets of amplicon sequencing analysis. Using this technique, genome-wide genotypes of the breeding materials were easily and rapidly determined. The SNP information and analytic methods developed in this study should accelerate genetics, genomics, and breeding in peanut.

Characterization of Bombyx mori and Antheraea pernyi silk fibroins and their blends as potential biomaterials.

Fibroin proteins isolated from the cocoons of certain silk-producing insects have been widely investigated as biomaterials for tissue engineering applications. In this study, fibroins were isolated from cocoons of domesticated Bombyx mori (BM) and wild Antheraea pernyi (AP) silkworms following a degumming process. The object of this study was to obtain an assessment on certain properties of these fibroins in order that a concept might be had regarding the feasibility of using their blends as biomaterials. Membranes, 10–20 μm thick, which are water-insoluble, flexible and transparent, were prepared from pure fibroins and from their blends, and subjected to water vapor annealing in vacuum, with the aim of providing materials sufficiently strong for manipulation. The resulting materials were characterized by electrophoretic analysis and infrared spectrometry. The tensile properties of the membranes were measured and correlated with the results of infrared analysis. At low concentrations of any of the two fibroins, the mechanical characteristics of the membranes appeared to be adequate for surgical manipulation, as the modulus and strength surpassed those of BM silk fibroin alone. It was noticed that high concentrations of AP silk fibroin led to a significant reduction in the elasticity of membranes.

Tamoxifen inhibits mitochondrial oxidative stress damage induced by copper orthophenanthroline.

In this work, we studied the effect of tamoxifen and cyclosporin A on mitochondrial permeability transition caused by addition of the thiol-oxidizing pair Cu2+ -orthophenanthroline. The findings indicate that tamoxifen and cyclosporin A circumvent the oxidative membrane damage manifested by matrix Ca2+ release, mitochondrial swelling, and transmembrane electrical gradient collapse. Furthermore, it was found that tamoxifen and cyclosporin A prevent the generation of TBARs promoted by Cu2+ -orthophenanthroline, as well as the inactivation of the mitochondrial enzyme aconitase and disruption of mDNA. Electrophoretic analysis was unable to demonstrate a cross-linking reaction between membrane proteins. Yet, it was found that Cu2+ -orthophenanthroline induced the generation of reactive oxygen species. It is thus plausible that membrane leakiness is due to an oxidative stress injury.