Electrophoresis Data Research Articles

Double-stranded DNA homology produces a physical signature

DNA is found in the cell largely as a negatively supercoiled molecule. This high-energy form of the genetic material can engender sequence-dependent structures, such as cruciforms, Z-DNA, or H-DNA, even though they are not favored by conventional conditions in relaxed DNA. A key feature of DNA in living systems is the presence of homology. We have sought homology-dependent structural phenomena based on topological relaxation. Using two-dimensional electrophoresis, we demonstrate a structural transition in supercoiled plasmid molecules containing homologous segments. Atomic force microscopy (AFM) reveals a dumbbell structure in molecules whose linking difference is beyond the transition point. The position of the dumbbell shaft is a function of the site of homology, and its extent is proportional to the linking difference. Second-site-reversion electrophoresis data support the notion that the shaft contains PX-DNA. Predicted cross-linking patterns generated in vivo suggest that homology-dependent structures can occur within the cell.

Interaction of E. coli DNA with diazine-bridged late first row transition metal complexes derived from hexadentate compartmental ligands: an approach to DNA cleavage/binding studies

A series of binuclear CoII, NiII, CuII and ZnII complexes having μ-1,2 diazine bridging have been prepared and characterized by various physico-chemical methods. The hexadentate ligands were synthesized by condensing 3,5-dichloroformyl-1H-pyrazole with 2-hydrazinobenzothiazole (L1H) or 4-aminoantipyrine (L2H) in 1:2 ratio. Gel electrophoresis data indicate cleavage of E. coli DNA to a minute extent by both [Co2L2(μ-Cl)Cl2(H2O)2]·H2O and [Ni2L2(μ-Cl)Cl2(H2O)2]. Conversely, the data for the remaining complexes indicated binding but not cleavage. These results were confirmed by viscosity measurements and absorption spectral studies. An intercalative binding mode is predicted when the title complexes interact with DNA.

Detection and mechanistic investigation of halogenated benzoquinone induced DNA damage by photoelectrochemical DNA sensor

Halogenated phenols are widely used as biocides and are considered to be possibly carcinogenic to humans. In this report, a previously developed photoelectrochemical DNA sensor was employed to investigate DNA damage induced by tetra-halogenated quinones, the in vivo metabolites of halogenated phenols. The sensor surface was composed of a double-stranded DNA film assembled on a SnO(2) semiconductor electrode. A DNA intercalator, Ru(bpy)(2)(dppz)(2+), was allowed to bind to the DNA film and produce photocurrent upon light irradiation. After the DNA film was exposed to 300 microM tetrafluoro-1,4-benzoquinone (TFBQ), the photocurrent dropped by 20%. In a mixture of 300 microM TFBQ and 2 mM H(2)O(2), the signal dropped by 40%. The signal reduction indicates less binding of Ru(bpy)(2)(dppz)(2+) due to structural damage of ds-DNA in the film. Similar results were obtained with tetra-1,4-chlorobenzoquinone (TCBQ), although the signal was not reduced as much as TFBQ. Fluorescence measurement showed that TFBQ/H(2)O(2) generated more hydroxyl radicals than TCBQ/H(2)O(2). Gel electrophoresis proved that the two benzoquinones produced DNA strand breaks together with H(2)O(2), but not by themselves. Using the photoelectrochemical sensor, it was also found that TCBQ covalently bound with DNA did not produce additional oxidative damage in the presence of H(2)O(2). The combined photoelectrochemistry, gel electrophoresis, and fluorescence data revealed distinctive differences between TFBQ and TCBQ in terms of DNA adduct formation and hydroxyl radical generation.

Molecular and Pathogenic Characterization ofSalmonella entericaSerovar Bovismorbificans Strains of Animal, Environmental, Food, and Human Origin in Hungary

In this study, we characterized 110 strains of Salmonella enterica serovar Bovismorbificans contaminating environment, animals, food of animal origin, and human, to assess their significance along the food chain in Hungary. Additionally, five strains from Germany were tested for comparative purposes. Characterization involved antibiotic susceptibility testing, class 1 integron detection by polymerase chain reaction, plasmid profiling, virulotyping (using virulence gene-specific polymerase chain reactions), and pulsed-field gel electrophoresis. Pathogenic potential of selected strains was tested in orally infected 1-day-old specific pathogen-free chicks. Eighty-two percent of the strains were susceptible to the 16 antibiotics tested, and none of them had class 1 integron. A multidrug-resistant human isolate harbored a bla(SHV5)-type extended-spectrum beta-lactamase gene, first reported in this serotype. All the strains possessed avrA, ssaQ, mgtC, spi4, and sopB genes indicating the presence of Salmonella pathogenicity islands 1-5, respectively, missed the phage-related genes sopE and gipA, but retained the phage-related gene sodC1. An approximately 90 kb large plasmid was characteristic to 80% of the strains, all of which carried the spvC gene. In vivo colonization testing of four selected strains in 1-day-old chicks resulted in significantly reduced liver and spleen colonization ability as compared with the Salmonella Enteritidis control strain, whereas their caecal colonization ability differed less from that of Salmonella Enteritidis. Pulsed-field gel electrophoresis data revealed the dominance of two pulsotypes (C2 and C5) without any specific temporal, geographical, and/or source-related linkages. The results show that Salmonella Bovismorbificans studied here are less invasive than Salmonella Enteritidis, but they may colonize and persist in several animal species and successfully contaminate meat products of different animal origin in Hungary.

Species status of two colour morphs of Eupelmus vesicularis (Hymenoptera: Eupelmidae) as revealed by allozyme electrophoresis, morphometric and host preference data

Eupelmus vesicularis (Retzius) is considered to be a widespread and polyphagous parasitoid recorded from more than 200 hosts. The aim of this study was to determine whether two colour forms of the putative species represent two different morphs of a single species or a pair of cryptic species. Three different methods – morphometric analysis, allozyme electrophoresis and evaluation of host preferences – were used to investigate the existence of two cryptic species. Bivariate and multivariate analyses clearly indicate two species that are also distinguishable electrophoretically at the Idh-2, G6pdh, Me, Pgm and Xdh loci. The evaluation of host preferences indicates some overlap in host range between the two species.

Development of a multi-locus sequence typing scheme for avian isolates of Pasteurella multocida

A total of 63 isolates of Pasteurella multocida from Australian poultry, all associated with fowl cholera outbreaks, and three international reference strains, representing the three subspecies within P. multocida were used to develop a multi-locus sequence typing scheme. Primers were designed for conserved regions of seven house-keeping enzymes – adk, est, gdh, mdh, pgi, pmi and zwf – and internal fragments of 570–784 bp were sequenced for all isolates and strains. The number of alleles at the different loci ranged from 11 to 20 and a total of 29 allelic profiles or sequence types were recognised amongst the 66 strains. There was a strong concordance between the MLST data and the existing multi-locus enzyme electrophoresis and ribotyping data. When used to study a sub-set of isolates with a known detailed epidemiological history, the MLST data matched the results given by restriction endonuclease analysis, pulsed-field gel electrophoresis, ribotyping and REP-PCR. The MLST scheme provides a high level of resolution and is an excellent tool for studying the population structure and epidemiology of P. multocida.

Proteomic analysis of time-dependent difference of protein expression profile changes during neuronal differentiation of mouse embryonic stem cells.

The study of ES cell-mediated neuronal differentiation allows elucidating the mechanism of neuronal development in spite of the complexity and the difficult accessibility. During the differentiation of embryonic stem cells into neuronal cell, the expression profiles in the level of protein were extensively investigated by proteomic analysis. These cells were analyzed for charges in proteome during the differentiation of ES cells by 2-dimensional electrophoresis (2-DE) and MALDI-TOF MS. Seven unique proteins were identified, some of which were differentially expressed at each stage. A complex system of neuronal differentiation can be activated in cultured embryonic stem cells and our two dimensional electrophoresis data should be useful for investigating some of the mechanism that regulates neuronal differentiation.

A comparison of imputation procedures and statistical tests for the analysis of two-dimensional electrophoresis data

BackgroundNumerous gel-based softwares exist to detect protein changes potentially associated with disease. The data, however, are abundant with technical and structural complexities, making statistical analysis a difficult task. A particularly important topic is how the various softwares handle missing data. To date, no one has extensively studied the impact that interpolating missing data has on subsequent analysis of protein spots.ResultsThis work highlights the existing algorithms for handling missing data in two-dimensional gel analysis and performs a thorough comparison of the various algorithms and statistical tests on simulated and real datasets. For imputation methods, the best results in terms of root mean squared error are obtained using the least squares method of imputation along with the expectation maximization (EM) algorithm approach to estimate missing values with an array covariance structure. The bootstrapped versions of the statistical tests offer the most liberal option for determining protein spot significance while the generalized family wise error rate (gFWER) should be considered for controlling the multiple testing error.ConclusionsIn summary, we advocate for a three-step statistical analysis of two-dimensional gel electrophoresis (2-DE) data with a data imputation step, choice of statistical test, and lastly an error control method in light of multiple testing. When determining the choice of statistical test, it is worth considering whether the protein spots will be subjected to mass spectrometry. If this is the case a more liberal test such as the percentile-based bootstrap t can be employed. For error control in electrophoresis experiments, we advocate that gFWER be controlled for multiple testing rather than the false discovery rate.

Determination of benzoate by paper chromatography with visualization due to its inhibitory activity in the reaction of the photosensitized autooxidation of pyrogallol A

The oxidation of 1,2,4-triacetoxybenzene (Pyrogallol A) and 3,3′,5,5′-tetramethylbenzydine by air oxygen in presence of tris-(2,2′-dipyridyl)ruthenium(II) as a photosensitizer is studied upon irradiation by visible light. The photooxidation of pyrogallol A was inhibited selectively by benzoate at pH 9–11. The rate of the reaction was not affected by other carboxylic acids but was influenced by short-chained aliphatic amines and transition metals. We developed a semiquantitative procedure for the determination of benzoate by paper chromatography. Therein, a common solution of pyrogallol A and a photosensitizer were used for the visualization followed by irradiation with an incandescent bulb. Benzoate was detected as a light spot with Rf ∼ 0.3 against a brown background. The measurement of reflectance intensity for the spot by reflectometry allowed the determination of 1 × 10−5–0.01 M benzoate within a precision of half-order of magnitude. The procedure was validated by comparison to the data of capillary electrophoresis and used to test beverages containing benzoate at levels of 10−4–10−3 M.

Magnetic resonance imaging to determine the incidence of brain ischaemia in patients with β-thalassaemia intermedia

One complication in patients with beta-thalassaemia who had prolonged survival is chronic hypercoagulable state, which results in thromboembolic events involving major organs including the brain. We determined the prevalence of microthrombosis in the brain in an asymptomatic subgroup of patients with b-thalassaemia intermedia (TI) who had undergone splenectomy. This retrospective review included 200 patients with TI diagnosed on the basis of blood count, haemoglobin (Hb) electrophoresis and clinical data. Their ages ranged from 18 to 34 years, 19 (63.3%) were women and 11 (36.7%) were men. We selected 30 patients at random who fulfilled the inclusion criteria: Hb concentration >7 g/dl), splenectomy and platelet count >500,000/ml. Their mean Hb concentration was 8.4 g/dl and their mean ferritin concentration was 519 ng/ml. Magnetic resonance imaging (MRI) was done in every patient, and the findings were interpreted by an expert neuroradiologist. Imaging studies showed pathological findings in 28% of the patients. Six had changes in the white matter suggestive of ischaemia and two had evidence of small infarctions. 1) In this small subset of patients diagnostic magnetic resonance imaging to monitor early asymptomatic or subclinical vascular damage in the brain can be considered when they reach the age of 20 years, and repeated every 3-5 years. 2) Treatment with antiplatelet aggregants is suggested in patients with documented asymptomatic brain ischaemia. 3) These results require confirmation in a larger group of similar patients with other types of thalassaemia who are multitransfused or have an intact spleen.

Bidirectional Correlation of NMR and Capillary Electrophoresis Fingerprints: A New Approach to Investigating Schistosoma mansoni Infection in a Mouse Model

We demonstrate the statistical integration of nuclear magnetic resonance (NMR) spectroscopy and capillary electrophoresis (CE) data in order to describe a pathological state caused by Schistosoma mansoni infection in a mouse model based on urinary metabolite profiles. Urine samples from mice 53 days post infection with S. mansoni and matched controls were analyzed via NMR spectroscopy and CE. The two sets of metabolic profiles were first processed and analyzed independently and were subsequently integrated using statistical correlation methods in order to facilitate cross assignment of metabolites. Using this approach, metabolites such as 3-ureidopropionate, p-cresol glucuronide, phenylacetylglycine, indoxyl sulfate, isocitrate, and trimethylamine were identified as differentiating between infected and control animals. These correlation analyses facilitated structural elucidation using the identification power of one technique to enhance and validate the other, but also highlighted the enhanced ability to detect functional correlations between metabolites, thereby providing potential for achieving deeper mechanistic insight into the biological process.

Effects of microbial transglutaminase and sodium alginate on cold-set gelation of porcine myofibrillar protein with various salt levels

The effects of microbial transglutaminase (TG) and sodium alginate (SA) systems on cold-set gelation of myofibrillar protein (MP) at various salt levels were investigated. The gelation kinetics data showed that both TG and SA had optimal but different salt levels to form an acceptable cold-set MP gel. Although their gelling characteristics were altered with different salt levels, the combination of TG and SA showed a rapid cold-set MP gel formation, regardless of salt levels. The effect of TG and SA on gel strength was reversed by increasing the salt level, while the cold-set MP gel strength of the TG and SA combination was not affected by salt levels. Furthermore, the SA system contributed to improved water-binding ability and cold-set MP gel formation, while the TG system enhanced the gel strength of the MP after cooking at low-salt levels. In addition, TG's effects on gel strength of MP increased at higher salt levels, the SA system prevented the moisture loss induced by the TG reaction. There was no evidence of any interaction between SA and MP in the thermogram and gel electrophoresis data. Results from this study suggested that a system combining TG with SA had the potential advantage of improving the water-binding ability and producing cold-set MP gelation at an even lower salt level than TG alone.

Effect of several cryoprotectants on the physicochemical and rheological properties of suwari gels from frozen squid surimi made by two methods

Functionality of squid surimi ( Dosidicus gigas) made by two methods (isoelectric precipitation A, and acid washing, B) and stored for 6 months at −15 °C, was analysed as a function of several cryoprotectants. The cryoprotectant effect was studied in terms of the ability to form suwari gels ( SA and SB) from the two kinds of surimi. Chemical analyses to detect protein aggregation, dynamic oscillatory tests at constant temperature (10 °C) and temperature sweep tests from 10 to 90 °C were performed. Frozen storage of surimi samples produced two different effects on the thermo-rheological properties of SA and SB suwari gels: in SB samples there were no significant differences over frozen storage. Of the SA samples, the ones with trehalose retained their initial viscoelastic properties best at 10 °C; moreover, trehalose significantly altered the pattern of the thermal gelation profile in SA samples, making it similar to SB samples. All these thermo-rheological results are consistent with protein solubility and electrophoresis (SDS–PAGE) data evidencing protein aggregation.

Sensitive Detection of KRAS Mutations in Archived Formalin-Fixed Paraffin-Embedded Tissue Using Mutant-Enriched PCR and Reverse-Hybridization

Recently, evidence has emerged indicating that assessment of KRAS mutations before anti-epidermal growth factor receptor therapy improves outcome in patients with metastatic colorectal cancer (CRC). We report here a novel reverse-hybridization (RH) assay to screen for KRAS mutations in formalin-fixed paraffin-embedded colorectal tissue samples. We combined mutant-enriched PCR based on peptide nucleic acid clamping and RH of amplification products to nitrocellulose test strips that contained a parallel array of oligonucleotide probes targeting 10 frequent mutations in codons 12 and 13 of the KRAS gene. DNA mixing experiments, which included eight different tumor cell lines with known KRAS mutations, were performed to examine the sensitivity of mutation detection. All KRAS mutations present in tumor cell lines were unambiguously identified by the RH assay with 1% of each cell line DNA diluted in normal DNA. RH was then used to screen for KRAS mutations in 74 colorectal tumor and 4 normal control samples. Twenty-six (35%) of the 74 tumor samples showed KRAS mutations. No mutation was found in the four samples of normal colorectal tissue. DNA sequencing without previous mutant enrichment, however, failed to detect four (15%) out of 26 KRAS-positive formalin-fixed paraffin-embedded samples (FFPE). This finding suggests that even after microdissection, mutant sequences in a given DNA isolate can be rare and more sensitive methods are needed for mutation analysis.

Homotaurine Metabolized to 3-Sulfopropanoate in Cupriavidus necator H16: Enzymes and Genes in a Patchwork Pathway

Homotaurine (3-aminopropanesulfonate), a natural product and an analogue of GABA (4-aminobutyrate), was found to be a sole source of nitrogen for Cupriavidus necator (Ralstonia eutropha) H16, whose genome sequence is known. Homotaurine nitrogen was assimilated into cell material, and the quantitative fate of the organosulfonate was sulfopropanoate, which was recovered in the growth medium. The first scalar reaction was shown to be inducible homotaurine:2-oxoglutarate aminotransferase, which released 3-sulfopropanal from homotaurine. This aminotransferase was purified to homogeneity and characterized. Peptide mass fingerprinting yielded locus tag H16_B0981, which was annotated gabT, for GABA transaminase (EC 2.6.1.19). Inducible, NAD(P)(+)-coupled 3-sulfopropanal dehydrogenase, which yielded 3-sulfopropanoate from 3-sulfopropanal, was also purified and characterized. Peptide mass fingerprinting yielded locus tag H16_B0982, which was annotated gabD1, for succinate-semialdehyde dehydrogenase (EC 1.2.1.16). GabT and GabD1 were each induced during growth with GABA, and cotranscription of gabTD was observed. In other organisms, regulator GabC or GabR is encoded contiguous with gabTD: candidate GabR' was found in strain H16 and in many other organisms. An orthologue of the GABA permease (GabP), established in Escherichia coli, is present at H16_B1890, and it was transcribed constitutively. We presume that GabR'PTD are responsible for the inducible metabolism of homotaurine to intracellular 3-sulfopropanoate. The nature of the exporter of this highly charged compound was unclear until we realized from the sodium dodecyl sulfate-polyacrylamide gel electrophoresis data that sulfoacetaldehyde acetyltransferase (EC 2.3.3.15; H16_B1872) was strongly induced during growth with homotaurine and inferred that the sulfite exporter encoded at the end of the gene cluster (H16_B1874) has a broad substrate range that includes 3-sulfopropanoate.

Glycoengineered Acid α-Glucosidase With Improved Efficacy at Correcting the Metabolic Aberrations and Motor Function Deficits in a Mouse Model of Pompe Disease

Improving the delivery of therapeutics to disease-affected tissues can increase their efficacy and safety. Here, we show that chemical conjugation of a synthetic oligosaccharide harboring mannose 6-phosphate (M6P) residues onto recombinant human acid alpha-glucosidase (rhGAA) via oxime chemistry significantly improved its affinity for the cation-independent mannose 6-phosphate receptor (CI-MPR) and subsequent uptake by muscle cells. Administration of the carbohydrate-remodeled enzyme (oxime-neo-rhGAA) into Pompe mice resulted in an approximately fivefold higher clearance of lysosomal glycogen in muscles when compared to the unmodified counterpart. Importantly, treatment of immunotolerized Pompe mice with oxime-neo-rhGAA translated to greater improvements in muscle function and strength. Treating older, symptomatic Pompe mice also reduced tissue glycogen levels but provided only modest improvements in motor function. Examination of the muscle pathology suggested that the poor response in the older animals might have been due to a reduced regenerative capacity of the skeletal muscles. These findings lend support to early therapeutic intervention with a targeted enzyme as important considerations in the management of Pompe disease.

Isolation and characterization of a new Cu–Fe protein from Desulfovibrio aminophilus DSM12254

The isolation and characterization of a new metalloprotein containing Cu and Fe atoms is reported. The as-isolated Cu-Fe protein shows an UV-visible spectrum with absorption bands at 320 nm, 409 nm and 615 nm. Molecular mass of the native protein along with denaturating electrophoresis and mass spectrometry data show that this protein is a multimer consisting of 14+/-1 subunits of 15254.3+/-7.6 Da. Mössbauer spectroscopy data of the as-isolated Cu-Fe protein is consistent with the presence of [2Fe-2S](2+) centers. Data interpretation of the dithionite reduced protein suggest that the metallic cluster could be constituted by two ferromagnetically coupled [2Fe-2S](+) spin delocalized pairs. The biochemical properties of the Cu-Fe protein are similar to the recently reported molybdenum resistance associated protein from Desulfovibrio, D. alaskensis. Furthermore, a BLAST search from the DNA deduced amino acid sequence shows that the Cu-Fe protein has homology with proteins annotated as zinc resistance associated proteins from Desulfovibrio, D. alaskensis, D. vulgaris Hildenborough, D. piger ATCC 29098. These facts suggest a possible role of the Cu-Fe protein in metal tolerance.

Effect of Electroosmotic Flow on the Electrophoresis of a Membrane-Coated Sphere along the Axis of a Cylindrical Pore

The electrophoresis of a membrane-coated spherical particle along the axis of a long, charged cylindrical pore was analyzed theoretically under the conditions of low surface potential and weak applied electrical field. The influences of the thickness of the double layer, the pore radius, the nature of the membrane layer, and the charged conditions of the particle and the pore on the electrophoretic behavior of the particle were investigated. The occurrence of the electroosmotic flow and the presence of the membrane layer were found to have a significant influence on the mobility of the particle. For instance, because the direction of electrophoresis does not depend solely on the applied electrical field and the nature of the charge carried by the particle, care must be taken in interpreting electrophoresis data. Furthermore, the magnitude of the electrophoretic mobility of a particle can show a local maximum as the concentration of electrolytes varies, which is of practical significance if electrophoresis is employed, for example, as a separation tool.

Synthesis of quadruplex‐forming tetra‐end‐linked oligonucleotides: Effects of the linker size on quadruplex topology and stability

G-quadruplexes are characteristic structural arrangements of guanine-rich DNA sequences that abound in regions with relevant biological significance. These structures are highly polymorphic differing in the number and polarity of the strands, loop composition, and conformation. Furthermore, the cation species present in solution strongly influence the topology of the G-quadruplexes. Recently, we reported the synthesis and structural studies of new G-quadruplex forming oligodeoxynucleotides (ODNs) in which the 3'- and/or the 5'-ends of four ODN strands are linked together by a non-nucleotidic tetra-end-linker (TEL). These TEL-ODN analogs having the sequence TGGGGT are able to form parallel G-quadruplexes characterized by a remarkable high thermal stability. We report here an investigation about the influence of the reduction of the TEL size on the molecularity, topology, and stability of the resulting TEL-G-quadruplexes using a combination of circular dichroism (CD), CD melting, (1)H NMR spectroscopy, gel electrophoresis, and molecular modeling data. We found that all TEL-(TGGGGT)(4) analogs, regardless the TEL size and the structural orientation of the ODN branches, formed parallel TEL-G-quadruplexes. The molecular modeling studies appear to be consistent with the experimental CD and NMR data revealing that the G-quadruplexes formed by TEL-ODNs having the longer TEL (L1-4) are more stable than the corresponding G-quadruplexes having the shorter TEL (S1-4). The relative stability of S1-4 was also reported. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 466-477, 2009.

The Charge on Beta-Lactoglobulin A and B under Self-associating Conditions

From electrophoretic and hydrodynamic measurements, the charge on monomeric proteins may be calculated accurately. It is not clear, though, how to analyze data from a self associating system. β-Lactoglobulin (β-LG) is a major whey protein abundant in cow milk. It has several genetic variants, is stable and self-associates under well characterized conditions. These factors make β-LG a good model to be used in the study of net charge and self-association. Both β-LG A and β-LG B were analyzed at pH 3, in a range of salt concentrations and protein concentrations. Under these conditions, self association is favored by higher salt concentrations. The mobility of β-LG was determined using capillary electrophoresis, with the Stokes radius determined using analytical ultracentrifugation. Self-association of β-LG A was characterized using sedimentation equilibrium. For both β-LG A and β-LG B, as ionic strength increased the mobility of the faster-moving peak decreased. With increased concentrations of β-LG A and β-LG B, the apparent mobility of this peak stayed the same. However, the boundary shapes observed in capillary electrophoresis were consistent with β-LG undergoing a mass-action association. It is difficult to interpret the capillary electrophoresis data quantitatively. Accordingly, membrane confined electrophoresis experiments are being used to determine the charge change on association.