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Sample records for reaction-denaturing gradient gel

  1. Detection of human DNA polymorphisms with a simplified denaturing gradient gel electrophoresis technique

    International Nuclear Information System (INIS)

    Noll, W.W.; Collins, M.

    1987-01-01

    Single base pair differences between otherwise identical DNA molecules can result in altered melting behavior detectable by denaturing gradient gel electrophoresis. The authors have developed a simplified procedure for using denaturing gradient gel electrophoresis to detect base pair changes in genomic DNA. Genomic DNA is digested with restriction enzymes and hybridized in solution to labeled single-stranded probe DNA. The excess probe is then hybridized to complementary phage M13 template DNA, and the reaction mixture is electrophoresed on a denaturing gradient gel. Only the genomic DNA probe hybrids migrate into the gel. Differences in hybrid mobility on the gel indicate base pair changes in the genomic DNA. They have used this technique to identify two polymorphic sites within a 1.2-kilobase region of human chromosome 20. This approach should greatly facilitate the identification of DNA polymorphisms useful for gene linkage studies and the diagnosis of genetic diseases

  2. Evaluation of denaturing gradient gel electrophoresis (DGGE) used ...

    African Journals Online (AJOL)

    Denaturing gradient gel electrophoresis (DGGE) is a powerful method used to study structure of bacterial communities, without cultivation, based on the diversity of the genes coding for ribosomal RNA. However, the results are strongly dependent on the respective target region of the used primer systems. Therefore, three ...

  3. Detection of human DNA polymorphisms with a simplified denaturing gradient gel electrophoresis technique.

    OpenAIRE

    Noll, W W; Collins, M

    1987-01-01

    Single base pair differences between otherwise identical DNA molecules can result in altered melting behavior detectable by denaturing gradient gel electrophoresis. We have developed a simplified procedure for using denaturing gradient gel electrophoresis to detect base pair changes in genomic DNA. Genomic DNA is digested with restriction enzymes and hybridized in solution to labeled single-stranded probe DNA. The excess probe is then hybridized to complementary phage M13 template DNA, and th...

  4. Bacterial analysis of combined periodontal-endodontic lesions by polymerase chain reaction-denaturing gradient gel electrophoresis.

    Science.gov (United States)

    Xia, Minghui; Qi, Qingguo

    2013-01-01

    We used denaturing gradient gel electrophoresis (DGGE) to compare bacterial profiles in periodontium and root canals of teeth with combined periodontal-endodontic lesions. Samples of dental plaque and necrotic pulp were collected from thirteen extracted teeth with advanced periodontitis. Genomic DNA was extracted for polymerase chain reaction (PCR) analysis using universal bacterial primers. The PCR products were then loaded onto DGGE gels to obtain fractionated bands. Characteristic DGGE bands were excised and DNA was cloned and sequenced. The number of bands, which indicates the number of bacterial species, was compared between dental plaques and necrotic pulp tissues from the same tooth. Although the difference was statistically significant (P bacteria species were present in both the periodontal pockets and root canals of the same tooth; however, periodontal bacteria did not always invade the root canals, and some bacteria in root canals were not present in periodontal pockets of the same tooth. In some teeth, unique bacteria in root canals had not passed from periodontal pockets. A basic local alignment search tool (BLAST) sequence search in Genbank indicated that new bacteria species were present in periodontal pockets and root canals. Their characteristics must thus be further analyzed.

  5. Denaturing gradient gel electrophoresis

    International Nuclear Information System (INIS)

    Kocherginskaya, S.A.; Cann, I.K.O.; Mackie, R.I.

    2005-01-01

    It is worthwhile considering that only some 30 species make up the bulk of the bacterial population in human faeces at any one time based on the classical cultivation-based approach. The situation in the rumen is similar. Thus, it is practical to focus on specific groups of interest within the complex community. These may be the predominant or the most active species, specific physiological groups or readily identifiable (genetic) clusters of phylogenetically related organisms. Several 16S rDNA fingerprinting techniques can be invaluable for selecting and monitoring sequences or phylogenetic groups of interest and are described below. Over the past few decades, considerable attention was focussed on the identification of pure cultures of microbes on the basis of genetic polymorphisms of DNA encoding rRNA such as ribotyping, amplified fragment length polymorphism and randomly amplified polymorphic DNA. However, many of these methods require prior cultivation and are less suitable for use in analysis of complex mixed populations although important in describing cultivated microbial diversity in molecular terms. Much less attention was given to molecular characterization of complex communities. In particular, research into diversity and community structure over time has been revolutionized by the advent of molecular fingerprinting techniques for complex communities. Denaturing or temperature gradient gel electrophoresis (DGGE/TGGE) methods have been successfully applied to the analysis of human, pig, cattle, dog and rodent intestinal populations

  6. Improvement of fragment and primer selection for mutation detection by denaturing gradient gel electrophoresis

    NARCIS (Netherlands)

    Wu, Y; Hayes, VM; Osinga, J; Mulder, IM; Looman, MWG; Buys, CHCM; Hofstra, RMW

    1998-01-01

    Denaturing gradient gel electrophoresis (DGGE) is one of the most powerful methods for mutation detection currently available. For successful application the appropriate selection of PCR fragments and PCR primers is crucial. The sequence of interest should always be within the domain with the lowest

  7. Denaturing gradient gel electrophoresis profiling of bacterial communities composition in Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, S.K.; Ramaiah, N.

    of Environmental Biology circleshadowdwnMay 2011circleshadowdwn Introduction The bacteria play a major role in carbon dynamics of marine ecosystems and, the importance of heterotrophic bacteria in marine ecosystem functioning is very well recognized (Azam et al..., 2008). Denaturing gradient gel-electrophoressis (DGGE) based fingerprinting helps estimate the numbers of dominant phylotype in a given sample (Muyzer et al., 1993). Very diverse bacterial assemblages such as those in the soils present many bands...

  8. Comparative analyses of amplicon migration behavior in differing denaturing gradient gel electrophoresis (DGGE) systems

    Science.gov (United States)

    Thornhill, D. J.; Kemp, D. W.; Sampayo, E. M.; Schmidt, G. W.

    2010-03-01

    Denaturing gradient gel electrophoresis (DGGE) is commonly utilized to identify and quantify microbial diversity, but the conditions required for different electrophoretic systems to yield equivalent results and optimal resolution have not been assessed. Herein, the influence of different DGGE system configuration parameters on microbial diversity estimates was tested using Symbiodinium, a group of marine eukaryotic microbes that are important constituents of coral reef ecosystems. To accomplish this, bacterial clone libraries were constructed and sequenced from cultured isolates of Symbiodinium for the ribosomal DNA internal transcribed spacer 2 (ITS2) region. From these, 15 clones were subjected to PCR with a GC clamped primer set for DGGE analyses. Migration behaviors of the resulting amplicons were analyzed using a range of conditions, including variation in the composition of the denaturing gradient, electrophoresis time, and applied voltage. All tests were conducted in parallel on two commercial DGGE systems, a C.B.S. Scientific DGGE-2001, and the Bio-Rad DCode system. In this context, identical nucleotide fragments exhibited differing migration behaviors depending on the model of apparatus utilized, with fragments denaturing at a lower gradient concentration and applied voltage on the Bio-Rad DCode system than on the C.B.S. Scientific DGGE-2001 system. Although equivalent PCR-DGGE profiles could be achieved with both brands of DGGE system, the composition of the denaturing gradient and application of electrophoresis time × voltage must be appropriately optimized to achieve congruent results across platforms.

  9. New comprehensive denaturing-gradient-gel-electrophoresis assay for KRAS mutation detection applied to paraffin-embedded tumours

    NARCIS (Netherlands)

    Hayes, VM; Westra, JL; Verlind, E; Bleeker, W; Plukker, JT; Hofstra, RMW; Buys, CHCM

    2000-01-01

    A comprehensive mutation detection assay is presented for the entire coding region and all splice site junctions of the KRAS oncogene. The assay is based on denaturing gradient gel electrophoresis and applicable to archival paraffin-embedded tumour material. All KRAS amplicons are analysed within

  10. Polymerase chain reaction-based denaturing gradient gel electrophoresis in the evaluation of oral microbiota.

    Science.gov (United States)

    Li, Y; Saxena, D; Barnes, V M; Trivedi, H M; Ge, Y; Xu, T

    2006-10-01

    Clinical evaluation of oral microbial reduction after a standard prophylactic treatment has traditionally been based on bacterial cultivation methods. However, not all microbes in saliva or dental plaque can be cultivated. Polymerase chain reaction-based denaturing gradient gel electrophoresis (PCR-DGGE) is a cultivation-independent molecular fingerprinting technique that allows the assessment of the predominant bacterial species present in the oral cavity. This study sought to evaluate the oral microbial changes that occurred after a standard prophylactic treatment with a conventional oral care product using PCR-DGGE. Twelve healthy adults participated in the study. Pooled plaque samples were collected at baseline, 24 h after prophylaxis (T1), and 4 days after toothbrushing with fluoride toothpaste (T4). The total microbial genomic DNA of the plaque was isolated. PCR was performed with a set of universal bacterial 16S rDNA primers. The PCR-amplified 16S rDNA fragments were separated by DGGE. The effects of the treatment and of dental brushing were assessed by comparing the PCR-DGGE fingerprinting profiles. The mean numbers of detected PCR amplicons were 22.3 +/- 6.1 for the baseline group, 13.0 +/- 3.1 for the T1 group, and 13.5 +/- 4.3 for the T4 group; the differences among the three groups were statistically significant (P < 0.01). The study also found a significant difference in the mean similarities of microbial profiles between the baseline and the treatment groups (P < 0.001). PCR-based DGGE has been shown to be an excellent means of rapidly and accurately assessing oral microbial changes in this clinical study.

  11. Screening for mutations in the uroporphyrinogen decarboxylase gene using denaturing gradient gel electrophoresis

    DEFF Research Database (Denmark)

    Christiansen, L; Ged, C; Hombrados, I

    1999-01-01

    to exon skipping, and a 2-bp deletion (415-416delTA) resulting in a frameshift and the introduction of a premature stop codon. Heterologous expression and enzymatic studies of the mutant proteins demonstrate that the three mutations leading to shortening or truncation of the UROD protein have no residual......, confirming the heterogeneity of the underlying genetic defects of these diseases. We have established a denaturing gradient gel electrophoresis (DGGE) assay for mutation detection in the UROD gene, enabling the simultaneous screening for known and unknown mutations. The established assay has proved able...

  12. Mutation screening of the TP53 gene by temporal temperature gradient gel electrophoresis.

    Science.gov (United States)

    Sørlie, Therese; Johnsen, Hilde; Vu, Phuong; Lind, Guro Elisabeth; Lothe, Ragnhild; Børresen-Dale, Anne-Lise

    2005-01-01

    A protocol for detection of mutations in the TP53 gene using temporal temperature gradient gel electrophoresis (TTGE) is described. TTGE is a mutation detection technique that separates DNA fragments differing by single base pairs according to their melting properties in a denaturing gel. It is based on constant denaturing conditions in the gel combined with a temperature gradient during the electrophoretic run. This method combines some of the advantages of the related techniques denaturing gradient gel electrophoresis (DGGE) and constant denaturant gel electrophoresis (CDGE) and eliminates some of the problems. The result is a rapid and sensitive screening technique that is robust and easily set up in smaller laboratory environments.

  13. Potential use of gradient denaturing gel electrophoresis in obtaining mutational spectra from human cells

    International Nuclear Information System (INIS)

    Thilly, W.G.

    1985-01-01

    A method is described to isolate mutations in DNA in human cells. When a double-stranded DNA migrates through an electric field on an electrophoretic gel, it is compact hydrodynamic structure relative to the same material in a melted form. Normally the solution in electrophoretic gels is uniform, but a way has been devised to set up a stable gradient of increasing solute concentration in the direction of DNA motion. Thus, as a double-stranded DNA molecule is drawn by the electric field into higher and higher concentrations of urea/formamide, it will eventually reach a point at which the concentration is high enough to melt the lower-melting-point region. The melting results in an essentially immobile structure within the gel so that the position at which the DNA molecule stops on the gradient gel is determined by its melting point, which is uniquely determined by its nucleotide sequence. A single base pair substitution within a low melting point sequence of some 100 base pairs changed the expected melting point by 0.4 0 C and resulted in about a 2-cm displacement under appropriate denaturing gel conditions. This expectation leads to the idea that if a mixture of DNA sequences derived from point mutations within the same restriction fragment were permitted to anneal with a complementary wild-type sequence, the melting point of each type of heteroduplex would differ depending on the kind and position of each mutation

  14. A novel polymerase chain reaction (PCR) - denaturing gradient gel electrophoresis (DGGE) for the identification of Micrococcaceae strains involved in meat fermentations. Its application to naturally fermented Italian sausages.

    Science.gov (United States)

    Cocolin, L; Manzano, M; Aggio, D; Cantoni, C; Comi, G

    2001-05-01

    A new molecular method consisting of polymerase chain reaction (PCR) amplification and denaturing gradient gel electrophoresis (DGGE) of a small fragment from the 16S rRNA gene identified the Micrococcaceae strains isolated from natural fermented Italian sausages. Lactic acid bacteria, total aerobic mesophilic flora, Enterobacteriaceae and faecal enterococci were also monitored. Micrococcaceaea control strains from international collections were used to optimise the method and 90 strains, isolated from fermented sausages, were identified by biochemical tests and PCR-DGGE. No differences were observed between the methods used. The results reported in this paper prove that Staphylococcus xylosus is the main bacterium involved in fermented sausage production, representing, from the tenth day of ripening, the only Micrococcaceaea species isolated.

  15. Behavior of variable V3 region from 16S rDNA of lactic acid bacteria in denaturing gradient gel electrophoresis.

    Science.gov (United States)

    Ercolini, D; Moschetti, G; Blaiotta, G; Coppola, S

    2001-03-01

    Separation of amplified V3 region from 16S rDNA by denaturing gradient gel electrophoresis (DGGE) was tested as a tool for differentiation of lactic acid bacteria commonly isolated from food. Variable V3 regions of 21 reference strains and 34 wild strains referred to species belonging to the genera Pediococcus, Enterococcus, Lactococcus, Lactobacillus, Leuconostoc, Weissella, and Streptococcus were analyzed. DGGE profiles obtained were species-specific for most of the cultures tested. Moreover, it was possible to group the remaining LAB reference strains according to the migration of their 16S V3 region in the denaturing gel. The results are discussed with reference to their potential in the analysis of LAB communities in food, besides shedding light on taxonomic aspects.

  16. Development and application of a selective pcr-denaturing gradient gel electrophoresis approach to detect a recently cultivated Bacillus group predominant in soil

    NARCIS (Netherlands)

    Tzeneva, V.A.; Li, Y.; Felske, A.; Vos, de W.M.; Akkermans, A.D.L.; Vaughan, E.E.; Smidt, H.

    2004-01-01

    The worldwide presence of a hitherto-nondescribed group of predominant soil microorganisms related to Bacillus benzoevorans was analyzed after development of two sets of selective primers targeting 16S rRNA genes in combination with denaturing gradient gel electrophoresis (DGGE). The high abundance

  17. Culture-based and denaturing gradient gel electrophoresis analysis of the bacterial community from Chungkookjang, a traditional Korean fermented soybean food.

    Science.gov (United States)

    Hong, Sung Wook; Choi, Jae Young; Chung, Kun Sub

    2012-10-01

    The bacterial community of Chungkookjang and raw rice-straw collected from various areas in South Korea was investigated using both culture-dependent and culture-independent methods. Pure cultures were isolated from Chungkookjang and raw rice-straw on tryptic soy agar plates with 72 to 121 colonies and identified by 16S rDNA gene sequence analysis, respectively. The traditional culture-based method and denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rDNA confirmed that Pantoea agglomerans and B. subtilis were identified as predominant in the raw rice-straw and Chungkookjang, respectively, from Iljuk district of Gyeonggi province, P. ananatis and B. licheniformis were identified as predominant in the raw rice-straw and Chungkookjang from Wonju district of Gangwon province, and Microbacterium sp. and B. licheniformis were identified as predominant in the raw rice-straw and Chungkookjang from Sunchang district of Jeolla province. Other strains, such as Bacillus, Enterococcus, Pseudomonas, Rhodococcus, and uncultured bacteria were also present in raw rice-straw and Chungkookjang. A comprehensive analysis of these microorganisms would provide a more detailed understanding of the biologically active components of Chungkookjang and help improve its quality. Polymerase chain reaction-denaturing gradient gel electrophoresis analysis can be successfully applied to a fermented food to detect unculturable or more species than the culture-dependent method. This technique is an effective and convenient culture-independent method for studying the bacterial community in Chungkookjang. In this study, the bacterial community of Chungkookjang collected from various areas in South Korea was investigated using both culture-dependent and culture-independent methods. © 2012 Institute of Food Technologists®

  18. Bacteria community study of combined periodontal-endodontic lesions using denaturing gradient gel electrophoresis and sequencing analysis.

    Science.gov (United States)

    Li, Hong; Guan, Rui; Sun, Jinghua; Hou, Benxiang

    2014-10-01

    The entire microbial population and predominant microflora of root canals (RCs) and adjacent periodontal pockets (PPs) from teeth with combined periodontal-endodontic lesions were determined and compared. Pooled RC and PP samples were collected from the molars of 20 patients diagnosed with combined periodontal-endodontic lesions. DNA was extracted for polymerase chain reaction-based denaturing gradient gel electrophoresis (PCR-DGGE), cloning, and sequence analysis. A coefficient of similarity (Cs) was used to determine the similarity of the bacterial profiles from RCs and PPs. Significantly fewer bands were produced by PCR-DGGE from RCs (5.9 ± 1.7) than from PPs (8.0 ± 1.8) (P bacteria in both the RC and PP samples were (in descending order) Filifactor alocis, Parvimonas micra, Porphyromonas gingivalis, and Tannerella forsythia. The high similarity in the sets of organisms present in both RC and PP samples in this study suggests that the pocket could be a source of RC infection. The data also demonstrate that combined periodontal-endodontic lesions consist of a diverse and complex microbial community.

  19. Detection by denaturing gradient gel electrophoresis of ammonia-oxidizing bacteria in microcosms of crude oil-contaminated mangrove sediments.

    Science.gov (United States)

    dos Santos, A C F; Marques, E L S; Gross, E; Souza, S S; Dias, J C T; Brendel, M; Rezende, R P

    2012-01-27

    Currently, the effect of crude oil on ammonia-oxidizing bacterium communities from mangrove sediments is little understood. We studied the diversity of ammonia-oxidizing bacteria in mangrove microcosm experiments using mangrove sediments contaminated with 0.1, 0.5, 1, 2, and 5% crude oil as well as non-contaminated control and landfarm soil from near an oil refinery in Camamu Bay in Bahia, Brazil. The evolution of CO(2) production in all crude oil-contaminated microcosms showed potential for mineralization. Cluster analysis of denaturing gradient gel electrophoresis-derived samples generated with primers for gene amoA, which encodes the functional enzyme ammonia monooxygenase, showed differences in the sample contaminated with 5% compared to the other samples. Principal component analysis showed divergence of the non-contaminated samples from the 5% crude oil-contaminated sediment. A Venn diagram generated from the banding pattern of PCR-denaturing gradient gel electrophoresis was used to look for operational taxonomic units (OTUs) in common. Eight OTUs were found in non-contaminated sediments and in samples contaminated with 0.5, 1, or 2% crude oil. A Jaccard similarity index of 50% was found for samples contaminated with 0.1, 0.5, 1, and 2% crude oil. This is the first study that focuses on the impact of crude oil on the ammonia-oxidizing bacterium community in mangrove sediments from Camamu Bay.

  20. Analysis of microbial diversity on deli slicers using polymerase chain reaction and denaturing gradient gel electrophoresis technologies.

    Science.gov (United States)

    Koo, O K; Mertz, A W; Akins, E L; Sirsat, S A; Neal, J A; Morawicki, R; Crandall, P G; Ricke, S C

    2013-02-01

    Cross-contamination of pathogenic and spoilage bacteria from food-contact surfaces to food products is a serious public health issue. Bacteria may survive and attach to food-contact surfaces by residual food components and/or background bacteria which may subsequently transfer to other food products. Deli slicers, generally used for slicing ready-to-eat products, can serve as potential sources for considerable bacterial transfer. The objective of this study was to assess the extent and distribution of microbial diversity of deli slicers by identification of pathogenic and background bacteria. Slicer-swab samples were collected from restaurants in Arkansas and Texas in the United States. Ten surface areas for each slicer were swabbed using sterile sponges. Denaturing gradient gel electrophoresis (DGGE) was applied to investigate the fingerprint of samples, and each band was further identified by sequence analysis. Pseudomonads were identified as the dominant bacteria followed by Enterobacteriaceae family, and lactic acid bacteria such as Lactococcus lactis and Streptococcus thermophilus were also found. Bacterial distribution was similar for all surface areas, while the blade guard exhibited the greatest diversity. This study provides a profile of the microbial ecology of slicers using DGGE to develop more specific sanitation practices and to reduce cross-contamination during slicing. © 2012 The Society for Applied Microbiology.

  1. Changes in the diversity of pig ileal lactobacilli around weaning determined by means of 16S rRNA gene amplification and denaturing gradient gel electrophoresis

    NARCIS (Netherlands)

    Janzcyk, P.; Pieper, R.; Smidt, H.; Souffrant, W.B.

    2007-01-01

    Our study aimed to provide a comprehensive characterization of changes in porcine intestinal Lactobacillus populations around the time of weaning based on 16S rRNA gene amplification and denaturing gradient gel electrophoresis (DGGE). DNA was extracted from the ileal contents of piglets at weaning

  2. Investigating the fermentation of cocoa by correlating denaturing gradient gel electrophoresis profiles and near infrared spectra

    DEFF Research Database (Denmark)

    Nielsen, Dennis Sandris; Snitkjær, Pia; van der Berg, Franciscus Winfried J

    2008-01-01

    demonstrating the microbial succession taking place during the fermentation. Subsequently the DGGE spectra were correlated to the NIR spectra using Partial Least Squares regression models (PLS2). Correlations of 0.87 (bacterial derived DGGE spectra) and 0.81 (yeast derived DGGE spectra) were obtained indicating......Raw cocoa has an astringent, unpleasant taste and flavour, and has to be fermented, dried and roasted in order to obtain the characteristic cocoa flavour and taste. During the fermentation microbial activity outside the cocoa beans induces biochemical and physical changes inside the beans...... of the beans and the chemical processes inside the beans have been carried out previously. Recently it has been shown that Denaturing Gradient Gel Electrophoresis (DGGE) offers an efficient tool for monitoring the microbiological changes taking place during the fermentation of cocoa. Near Infrared (NIR...

  3. A Comprehensive Quality Evaluation System for Complex Herbal Medicine Using PacBio Sequencing, PCR-Denaturing Gradient Gel Electrophoresis, and Several Chemical Approaches

    Directory of Open Access Journals (Sweden)

    Xiasheng Zheng

    2017-09-01

    Full Text Available Herbal medicine is a major component of complementary and alternative medicine, contributing significantly to the health of many people and communities. Quality control of herbal medicine is crucial to ensure that it is safe and sound for use. Here, we investigated a comprehensive quality evaluation system for a classic herbal medicine, Danggui Buxue Formula, by applying genetic-based and analytical chemistry approaches to authenticate and evaluate the quality of its samples. For authenticity, we successfully applied two novel technologies, third-generation sequencing and PCR-DGGE (denaturing gradient gel electrophoresis, to analyze the ingredient composition of the tested samples. For quality evaluation, we used high performance liquid chromatography assays to determine the content of chemical markers to help estimate the dosage relationship between its two raw materials, plant roots of Huangqi and Danggui. A series of surveys were then conducted against several exogenous contaminations, aiming to further access the efficacy and safety of the samples. In conclusion, the quality evaluation system demonstrated here can potentially address the authenticity, quality, and safety of herbal medicines, thus providing novel insight for enhancing their overall quality control.Highlight: We established a comprehensive quality evaluation system for herbal medicine, by combining two genetic-based approaches third-generation sequencing and DGGE (denaturing gradient gel electrophoresis with analytical chemistry approaches to achieve the authentication and quality connotation of the samples.

  4. A Comprehensive Quality Evaluation System for Complex Herbal Medicine Using PacBio Sequencing, PCR-Denaturing Gradient Gel Electrophoresis, and Several Chemical Approaches.

    Science.gov (United States)

    Zheng, Xiasheng; Zhang, Peng; Liao, Baosheng; Li, Jing; Liu, Xingyun; Shi, Yuhua; Cheng, Jinle; Lai, Zhitian; Xu, Jiang; Chen, Shilin

    2017-01-01

    Herbal medicine is a major component of complementary and alternative medicine, contributing significantly to the health of many people and communities. Quality control of herbal medicine is crucial to ensure that it is safe and sound for use. Here, we investigated a comprehensive quality evaluation system for a classic herbal medicine, Danggui Buxue Formula, by applying genetic-based and analytical chemistry approaches to authenticate and evaluate the quality of its samples. For authenticity, we successfully applied two novel technologies, third-generation sequencing and PCR-DGGE (denaturing gradient gel electrophoresis), to analyze the ingredient composition of the tested samples. For quality evaluation, we used high performance liquid chromatography assays to determine the content of chemical markers to help estimate the dosage relationship between its two raw materials, plant roots of Huangqi and Danggui. A series of surveys were then conducted against several exogenous contaminations, aiming to further access the efficacy and safety of the samples. In conclusion, the quality evaluation system demonstrated here can potentially address the authenticity, quality, and safety of herbal medicines, thus providing novel insight for enhancing their overall quality control. Highlight : We established a comprehensive quality evaluation system for herbal medicine, by combining two genetic-based approaches third-generation sequencing and DGGE (denaturing gradient gel electrophoresis) with analytical chemistry approaches to achieve the authentication and quality connotation of the samples.

  5. A Comprehensive Quality Evaluation System for Complex Herbal Medicine Using PacBio Sequencing, PCR-Denaturing Gradient Gel Electrophoresis, and Several Chemical Approaches

    Science.gov (United States)

    Zheng, Xiasheng; Zhang, Peng; Liao, Baosheng; Li, Jing; Liu, Xingyun; Shi, Yuhua; Cheng, Jinle; Lai, Zhitian; Xu, Jiang; Chen, Shilin

    2017-01-01

    Herbal medicine is a major component of complementary and alternative medicine, contributing significantly to the health of many people and communities. Quality control of herbal medicine is crucial to ensure that it is safe and sound for use. Here, we investigated a comprehensive quality evaluation system for a classic herbal medicine, Danggui Buxue Formula, by applying genetic-based and analytical chemistry approaches to authenticate and evaluate the quality of its samples. For authenticity, we successfully applied two novel technologies, third-generation sequencing and PCR-DGGE (denaturing gradient gel electrophoresis), to analyze the ingredient composition of the tested samples. For quality evaluation, we used high performance liquid chromatography assays to determine the content of chemical markers to help estimate the dosage relationship between its two raw materials, plant roots of Huangqi and Danggui. A series of surveys were then conducted against several exogenous contaminations, aiming to further access the efficacy and safety of the samples. In conclusion, the quality evaluation system demonstrated here can potentially address the authenticity, quality, and safety of herbal medicines, thus providing novel insight for enhancing their overall quality control. Highlight: We established a comprehensive quality evaluation system for herbal medicine, by combining two genetic-based approaches third-generation sequencing and DGGE (denaturing gradient gel electrophoresis) with analytical chemistry approaches to achieve the authentication and quality connotation of the samples. PMID:28955365

  6. An improved method for detecting genetic variation in DNA using denaturing gradient gel electrophoresis

    International Nuclear Information System (INIS)

    Takahashi, Norio; Hiyama, Keiko; Kodaira, Mieko; Satoh, Chiyoko.

    1990-05-01

    We have examined the feasibility of denaturing gradient gel electrophoresis (DGGE) of RNA:DNA duplexes to detect variations in genomic and cloned DNAs. The result has demonstrated that use of RNA:DNA duplexes makes DGGE much more practical for screening a large number of samples than use of DNA:DNA heteroduplexes, because preparation of RNA probes is easier than that of DNA probes. Three different 32 P-labeled RNA probes were produced. Genomic or cloned DNAs were digested with restriction enzymes and hybridized to labeled RNA probes, and resulting RNA:DNA duplexes were examined by DGGE. The presence of a mismatch(es) was detected as a difference in the mobility of bands on the gel. The experimental conditions were determined using DNA segments from cloned normal and three thalassemic human β-globin genes. The results from experiments on the cloned DNAs suggest that DGGE of RNA:DNA duplexes will detect nucleotide substitutions and deletions in DNA. In the course of these studies, a polymorphism due to a single-base substitution at position 666 of IVS2 (IVS2-666) of the human β-globin gene was directly identified using genomic DNA samples. A study of 59 unrelated Japanese from Hiroshima was undertaken in which the frequency of the allele with C at IVS2-666 was 0.48 and that of the allele with T was 0.52. This approach was found to be very effective for detecting heritable variation and should be a powerful tool for detecting fresh mutations in DNA, which occur outside the known restriction sites. (author)

  7. In vitro study of prebiotic properties of levan-type exopolysaccharides from Lactobacilli and non-digestible carbohydrates using denaturing gradient gel electrophoresis.

    Science.gov (United States)

    Bello, F D; Walter, J; Hertel, C; Hammes, W P

    2001-07-01

    Batch cultures inoculated with human faeces were used to study the prebiotic properties of levan-type exopolysaccharides (EPS) from Lactobacillus sanfranciscensis as well as levan, inulin, and fructooligosaccharide (FOS). Denaturing gradient gel electrophoresis of 16S rDNA fragments generated by PCR with universal primers was used to analyse the cultures. Characteristic changes were revealed in the composition of the gut bacteria during fermentation of the carbohydrates. An enrichment of Bifidobacterium spp. was found for the EPS and inulin but not for levan and FOS. The bifidogenic effect of the EPS was confirmed by culturing on selective medium. In addition, the use of EPS and FOS resulted in enhanced growth of Eubacterium biforme and Clostridium perfringens, respectively.

  8. The detection of Mycoplasma (formerly Eperythrozoon) wenyonii by 16S rDNA PCR and denaturing gradient gel electrophoresis.

    Science.gov (United States)

    McAuliffe, Laura; Lawes, Joanna; Bell, Suzanna; Barlow, Alex; Ayling, Roger; Nicholas, Robin

    2006-10-31

    Although the role of Mycoplasma wenyonii in disease is still subject to some debate, infections have been reported to result in parasitaemia, anaemia, scrotal and hind limb oedema, tachycardia, pyrexia, infertility, swollen teats, prefemoral lymphadenopathy and decreased milk production. Previously, diagnosis of M. wenyonii has been based on blood smears but is not specific for M. wenyonii and can be difficult to interpret. We have previously described the use of PCR and denaturing gradient gel electrophoresis (DGGE) for the detection and differentiation of Mycoplasma species. DGGE enables the rapid and specific identification of Mycoplasma species and is ideally suited to detecting both mixed infections and new and unusual species. In this study, we have used DGGE with universal primers to detect M. wenyonii DNA from blood samples. DGGE can be used on blood samples as a rapid and specific test for M. wenyonii and can also be used as a screening test for other blood borne pathogens.

  9. Variations among Japanese of the factor IX gene (F9) detected by PCR-denaturing gradient gel electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Satoh, Chiyoko; Takahashi, Norio; Asakawa, Junichi; Hiyama, Keiko; Kodaira, Meiko (Radiation Effects Research Foundation, Hiroshima (Japan))

    1993-01-01

    In the course of feasibility studies to examine the efficiencies and practicalities of various techniques for screening for genetic variations, the human coagulation factor IX (F9) genes of 63 Japanese families were examined by PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Four target sequences with lengths of 983-2,891 bp from the F9 genes of 126 unrelated individuals from Hiroshima and their 100 children were amplified by PCR, digested with restriction enzymes to approximately 500-bp fragments, and examined by DGGE - a total of 6,724 bp being examined per individual. GC-rich sequences (GC-clamps) of 40 bp were attached to both ends of the target sequences, as far as was feasible. Eleven types of new nucleotide substitutions were detected in the population, none of which produced RFLPs or caused hemophilia B. By examining two target sequences in a single lane, approximately 8,000 bp in a diploid individual could be examined. This approach is very effective for the detection of variations in DNA and is applicable to large-scale population studies. 46 refs., 3 figs., 1 tab.

  10. Use of denaturing gradient gel electrophoresis to detect Actinobacteria associated with the human faecal microbiota.

    Science.gov (United States)

    Hoyles, Lesley; Clear, Jessica A; McCartney, Anne L

    2013-08-01

    With the exceptions of the bifidobacteria, propionibacteria and coriobacteria, the Actinobacteria associated with the human gastrointestinal tract have received little attention. This has been due to the seeming absence of these bacteria from most clone libraries. In addition, many of these bacteria have fastidious growth and atmospheric requirements. A recent cultivation-based study has shown that the Actinobacteria of the human gut may be more diverse than previously thought. The aim of this study was to develop a denaturing gradient gel electrophoresis (DGGE) approach for characterizing Actinobacteria present in faecal samples. Amount of DNA added to the Actinobacteria-specific PCR used to generate strong PCR products of equal intensity from faecal samples of five infants, nine adults and eight elderly adults was anti-correlated with counts of bacteria obtained using fluorescence in situ hybridization probe HGC69A. A nested PCR using Actinobacteria-specific and universal PCR-DGGE primers was used to generate profiles for the Actinobacteria. Cloning of sequences from the DGGE bands confirmed the specificity of the Actinobacteria-specific primers. In addition to members of the genus Bifidobacterium, species belonging to the genera Propionibacterium, Microbacterium, Brevibacterium, Actinomyces and Corynebacterium were found to be part of the faecal microbiota of healthy humans. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Bacterial community structure in Apis florea larvae analyzed by denaturing gradient gel electrophoresis and 16S rRNA gene sequencing.

    Science.gov (United States)

    Saraithong, Prakaimuk; Li, Yihong; Saenphet, Kanokporn; Chen, Zhou; Chantawannakul, Panuwan

    2015-10-01

    This study characterizes the colonization and composition of bacterial flora in dwarf Asian honeybee (Apis florea) larvae and compares bacterial diversity and distribution among different sampling locations. A. florea larvae were collected from 3 locations in Chiang Mai province, Thailand. Bacterial DNA was extracted from each larva using the phenol-chloroform method. Denaturing gradient gel electrophoresis was performed, and the dominant bands were excised from the gels, cloned, and sequenced for bacterial species identification. The result revealed similarities of bacterial community profiles in each individual colony, but differences between colonies from the same and different locations. A. florea larvae harbor bacteria belonging to 2 phyla (Firmicutes and Proteobacteria), 5 classes (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacilli, and Clostridia), 6 genera (Clostridium, Gilliamella, Melissococcus, Lactobacillus, Saccharibacter, and Snodgrassella), and an unknown genus from uncultured bacterial species. The classes with the highest abundance of bacteria were Alphaproteobacteria (34%), Bacilli (25%), Betaproteobacteria (11%), Gammaproteobacteria (10%), and Clostridia (8%), respectively. Similarly, uncultured bacterial species were identified (12%). Environmental bacterial species, such as Saccharibacter floricola, were also found. This is the first study in which sequences closely related to Melissococcus plutonius, the causal pathogen responsible for European foulbrood, have been identified in Thai A. florea larvae. © 2014 Institute of Zoology, Chinese Academy of Sciences.

  12. Denaturing Gradient Gel Electrophoresis-Polymerase Chain Reaction Comparison of Chitosan Effects on Anaerobic Cultures of Broiler Cecal Bacteria and Salmonella Typhimurium.

    Science.gov (United States)

    Hume, Michael; Sohail, Muhammad Umar

    2018-04-01

    Enteropathogen colonization and product contamination are major poultry industry problems. The emergence of antibiotic resistance, and associated risks to human health, is limiting the use of antibiotics as first-line defense against enteropathogens in poultry. The chitin derivative, chitosan, has drawn substantial attention for its bactericidal properties. Different molecular weight (MW) chitosans can have varied effects against different bacteria in monoculture. In the current study, cecal contents from each of three market-age broilers and Salmonella Typhimurium, as indicator enteropathogen, were exposed to in vitro anaerobic culture to three chitosan preparations (0.08%, wt/vol), low (LMW), medium (MMW), and coarse (CMW). Effects of chitosan and the carrier solvent acetic acid, on cecal bacteria and Salmonella, were examined by denaturing gradient gel electrophoresis (DGGE) and Salmonella enumeration. Bacterial profiles for the three cecal contents were shown by DGGE to be very different. Each of the three cecal contents grown in the presence of 0.08% acetic acid was very different from the same contents grown without the chitosan solvent. Culturing cecal contents in the presence of chitosan altered the bacterial DGGE profiles from the control and acetic acid-only cultures. The DGGE chitosan-treated profiles for all three cecal sources were identical to each other regardless of the MW chitosan in the culture medium. Compared with Salmonella in monoculture, Salmonella decreased (p < 0.05) by about 1.5 log CFU/mL when grown in mixed culture with cecal contents. Salmonella monocultures in the presence of 0.08% of the chitosan solvent acetic acid decreased (p < 0.05) counts by almost 3.5 log CFU/mL. Combining acetic acid and cecal contents reduced (p < 0.05) Salmonella by 7 log CFU/mL. Adding the chitosan preparations to the mixtures reduced (p < 0.05) Salmonella by 8 log CFU/mL.

  13. Mutation screening of the TP53 gene by temporal temperature gel electrophoresis (TTGE).

    Science.gov (United States)

    Sørlie, Therese; Johnsen, Hilde; Vu, Phuong; Lind, Guro Elisabeth; Lothe, Ragnhild; Børresen-Dale, Anne-Lise

    2014-01-01

    A protocol for detection of mutations in the TP53 gene using temporal temperature gradient electrophoresis (TTGE) is described. TTGE is a mutation detection technique that separates DNA fragments differing by single base pairs according to their melting properties in a denaturing gel. It is based on constant denaturing conditions in the gel combined with a temperature gradient during the electrophoretic run. This method combines some of the advantages of the related techniques, denaturing gradient gel electrophoresis and constant denaturant gel electrophoresis, and eliminates some of the problems. The result is a rapid and sensitive screening technique which is robust and easily set up in smaller laboratory environments.

  14. Denaturing gradient gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples.

    Science.gov (United States)

    Pires, Ana C C; Cleary, Daniel F R; Almeida, Adelaide; Cunha, Angela; Dealtry, Simone; Mendonça-Hagler, Leda C S; Smalla, Kornelia; Gomes, Newton C M

    2012-08-01

    Mangroves are complex ecosystems that regulate nutrient and sediment fluxes to the open sea. The importance of bacteria and fungi in regulating nutrient cycles has led to an interest in their diversity and composition in mangroves. However, very few studies have assessed Archaea in mangroves, and virtually nothing is known about whether mangrove rhizospheres affect archaeal diversity and composition. Here, we studied the diversity and composition of Archaea in mangrove bulk sediment and the rhizospheres of two mangrove trees, Rhizophora mangle and Laguncularia racemosa, using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing of archaeal 16S rRNA genes with a nested-amplification approach. DGGE profiles revealed significant structural differences between bulk sediment and rhizosphere samples, suggesting that roots of both mangrove species influence the sediment archaeal community. Nearly all of the detected sequences obtained with pyrosequencing were identified as Archaea, but most were unclassified at the level of phylum or below. Archaeal richness was, furthermore, the highest in the L. racemosa rhizosphere, intermediate in bulk sediment, and the lowest in the R. mangle rhizosphere. This study shows that rhizosphere microhabitats of R. mangle and L. racemosa, common plants in subtropical mangroves located in Rio de Janeiro, Brazil, hosted distinct archaeal assemblages.

  15. Monitoring of the microbial communities involved in the soy sauce manufacturing process by PCR-denaturing gradient gel electrophoresis.

    Science.gov (United States)

    Tanaka, Yasushi; Watanabe, Jun; Mogi, Yoshinobu

    2012-08-01

    Soy sauce is a traditional seasoning produced through the fermentation of soybeans and wheat using microbes. In this study, the microbial communities involved in the soy sauce manufacturing process were analyzed by PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). The bacterial DGGE profile indicated that the bacterial microbes in the koji were Weissella cibaria (Weissella confusa, Weissella kimchii, Weissella salipiscis, Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus iners, or Streptococcus thermophilus), Staphylococcus gallinarum (or Staphylococcus xylosus), and Staphylococcus kloosii. In addition to these bacteria, Tetragenococcus halophilus was also detected in the mash during lactic acid fermentation. The fungal DGGE profile indicated that the fungal microbes in the koji were not only Aspergillus oryzae but also several yeasts. In the mash, Zygosaccharomyces rouxii appeared in the early fermentation stage, Candida etchellsii (or Candida nodaensis) and Candida versatilis were detected at the middle fermentation stage, and Candida etchellsii was detected at the mature fermentation stage. These results suggest that the microbial communities present during the soy sauce manufacturing process change drastically throughout its production. This is the first report to reveal the microbial communities involved in the soy sauce manufacturing process using a culture-independent method. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

  16. Detection in a Japanese population of a length polymorphism in the 5' flanking region of the human β-globin gene with denaturing gradient gel electrophoresis

    International Nuclear Information System (INIS)

    Takahashi, Noria; Hiyama, Keiko; Kodaira, Mieko; Satoh, Chiyoko

    1992-10-01

    An analysis of the ATTTT repeat polymorphism located approximately 1,400 base pairs upstream from the β-globin structural gene was carried out by denaturing gradient gel electrophoresis (DGGE) of RNA:DNA duplexes. Genomic or cloned DNAs were digested with restriction enzymes and hybridized with 32 P-labeled RNA probes, and resulting RNA:DNA duplexes were examined by DGGE. A difference in the number of repeat units was recognized by differences in duplex mobility on the DGGE gel. In this study of 81 unrelated Japanese from Hiroshima, a sequence heteromorphism was observed at this site. Alleles with 5 and 6 repeats of the ATTTT unit, which had already been reported, were found in polymorphic proportions. In addition, two unreported alleles, one having 7 repeats and the other having an A-to-G nucleotide substitution in the 5th repeat, were detected. Family study data showed that the segregation of these four types of variants is consistent with an autosomal codominant mode of inheritance. This study also demonstrated that DGGE of RNA:DNA duplexes is a sensitive tool for detecting variations in DNA. (author)

  17. Succession of bacterial and fungal communities during a traditional pot fermentation of rice vinegar assessed by PCR-mediated denaturing gradient gel electrophoresis.

    Science.gov (United States)

    Haruta, Shin; Ueno, Shintaro; Egawa, Isao; Hashiguchi, Kazunori; Fujii, Akira; Nagano, Masanobu; Ishii, Masaharu; Igarashi, Yasuo

    2006-05-25

    Denaturing gradient gel electrophoresis (DGGE) based on small subunit rRNA gene was applied to a traditional rice vinegar fermentation process in which the conversion of rice starch into acetic acid proceeded in a pot. The fungal DGGE profile indicated that the transition from Aspergillus oryzae to Saccharomyces sp. took place at the initial stage at which alcohol production was observed. The early stage was characterized by the coexistence of Saccharomyces sp. and lactic acid bacteria. Almost all of the bacterial DGGE bands related to lactic acid bacteria were replaced by bands derived from Lactobacillus acetotolerance and Acetobacter pasteurianus at the stage at which acetic acid started to accumulate. The microbial succession, tested in three different pots, was found to be essentially identical. Among the bacteria isolated at the early stage, some species differed from those detected by DGGE. This is the first report to reveal the microbial community succession that occurs during a unique vinegar fermentation process, as determined by a culture-independent method.

  18. Application of the denaturing gradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliate communities in soil.

    Science.gov (United States)

    Jousset, Alexandre; Lara, Enrique; Nikolausz, Marcell; Harms, Hauke; Chatzinotas, Antonis

    2010-02-01

    Ciliates (or Ciliophora) are ubiquitous organisms which can be widely used as bioindicators in ecosystems exposed to anthropogenic and industrial influences. The evaluation of the environmental impact on soil ciliate communities with methods relying on morphology-based identification may be hampered by the large number of samples usually required for a statistically supported, reliable conclusion. Cultivation-independent molecular-biological diagnostic tools are a promising alternative to greatly simplify and accelerate such studies. In this present work a ciliate-specific fingerprint method based on the amplification of a phylogenetic marker gene (i.e. the 18S ribosomal RNA gene) with subsequent analysis by denaturing gradient gel electrophoresis (DGGE) was developed and used to monitor community shifts in a polycyclic aromatic hydrocarbon (PAH) polluted soil. The semi-nested approach generated ciliate-specific amplification products from all soil samples and allowed to distinguish community profiles from a PAH-polluted and a non-polluted control soil. Subsequent sequence analysis of excised bands provided evidence that polluted soil samples are dominated by organisms belonging to the class Colpodea. The general DGGE approach presented in this study might thus in principle serve as a fast and reproducible diagnostic tool, complementing and facilitating future ecological and ecotoxicological monitoring of ciliates in polluted habitats. Copyright 2009 Elsevier B.V. All rights reserved.

  19. A Comparison Between Denaturing Gradient Gel Electrophoresis and Denaturing High Performance Liquid Chromatography in Detecting Mutations in Genes Associated with Hereditary Non-Polyposis Colorectal Cancer (HNPCC and the Identification of 9 New Mutations Previously Unidentified by DGGE

    Directory of Open Access Journals (Sweden)

    Meldrum Cliff J

    2003-12-01

    Full Text Available Abstract Denaturing high performance liquid chromatography is a relatively new method by which heteroduplex structures formed during the PCR amplification of heterozygote samples can be rapidly identified. The use of this technology for mutation detection in hereditary non-polyposis colorectal cancer (HNPCC has the potential to appreciably shorten the time it takes to analyze genes associated with this disorder. Prior to acceptance of this method for screening genes associated with HNPCC, assessment of the reliability of this method should be performed. In this report we have compared mutation and polymorphism detection by denaturing gradient gel electrophoresis (DGGE with denaturing high performance liquid chromatography (DHPLC in a set of 130 families. All mutations/polymorphisms representing base substitutions, deletions, insertions and a 23 base pair inversion were detected by DHPLC whereas DGGE failed to identify four single base substitutions and a single base pair deletion. In addition, we show that DHPLC has been used for the identification of 5 different mutations in exon 7 of hMSH2 that could not be detected by DGGE. From this study we conclude that DHPLC is a more effective and rapid alternative to the detection of mutations in hMSH2 and hMLH1 with the same or better accuracy than DGGE. Furthermore, this technique offers opportunities for automation, which have not been realised for the majority of other methods of gene analysis.

  20. 16S rRNA PCR-Denaturing Gradient Gel Electrophoresis of Oral Lactobacillus casei Group and Their Phenotypic Appearances.

    Science.gov (United States)

    Piwat, S; Teanpaisan, R

    2013-01-01

    This study aimed to develop a 16S rRNA PCR-denaturing gradient gel electrophoresis (DGGE) to identify the species level of Lactobacillus casei group and to investigate their characteristics of acid production and inhibitory effect. PCR-DGGE has been developed based on the 16S rRNA gene, and a set of HDA-1-GC and HDA-2, designed at V2-V3 region, and another set of CARP-1-GC and CARP-2, designed at V1 region, have been used. The bacterial strains included L. casei ATCC 393, L. paracasei CCUG 32212, L. rhamnosus ATCC 7469, L. zeae CCUG 35515, and 46 clinical strains of L. casei/paracasei/rhamnosus. Inhibitory effect against Streptococcus mutans and acid production were examined. Results revealed that each type species strain and identified clinical isolate showed its own unique DGGE pattern using CARP1-GC and CARP2 primers. HDA1-GC and HDA2 primers could distinguish the strains of L. paracasei from L. casei. It was found that inhibitory effect of L. paracasei was stronger than L. casei and L. rhamnosus. The acid production of L. paracasei was lower than L. casei and L. rhamnosus. In conclusion, the technique has been proven to be able to differentiate between closely related species in L. casei group and thus provide reliable information of their phenotypic appearances.

  1. Application of PCR-denaturing-gradient gel electrophoresis (DGGE) method to examine microbial community structure in asparagus fields with growth inhibition due to continuous cropping.

    Science.gov (United States)

    Urashima, Yasufumi; Sonoda, Takahiro; Fujita, Yuko; Uragami, Atsuko

    2012-01-01

    Growth inhibition due to continuous cropping of asparagus is a major problem; the yield of asparagus in replanted fields is low compared to that in new fields, and missing plants occur among young seedlings. Although soil-borne disease and allelochemicals are considered to be involved in this effect, this is still controversial. We aimed to develop a technique for the biological field diagnosis of growth inhibition due to continuous cropping. Therefore, in this study, fungal community structure and Fusarium community structure in continuously cropped fields of asparagus were analyzed by polymerase chain reaction/denaturing-gradient gel electrophoresis (PCR-DGGE). Soil samples were collected from the Aizu region of Fukushima Prefecture, Japan. Soil samples were taken from both continuously cropped fields of asparagus with growth inhibition and healthy neighboring fields of asparagus. The soil samples were collected from the fields of 5 sets in 2008 and 4 sets in 2009. We were able to distinguish between pathogenic and non-pathogenic Fusarium by using Alfie1 and Alfie2GC as the second PCR primers and PCR-DGGE. Fungal community structure was not greatly involved in the growth inhibition of asparagus due to continuous cropping. By contrast, the band ratios of Fusarium oxysporum f. sp. asparagi in growth-inhibited fields were higher than those in neighboring healthy fields. In addition, there was a positive correlation between the band ratios of Fusarium oxysporum f. sp. asparagi and the ratios of missing asparagus plants. We showed the potential of biological field diagnosis of growth inhibition due to continuous cropping of asparagus using PCR-DGGE.

  2. Bacterial Diversity in the Digestive Tracts of Four Indian Air-Breathing Fish Species Investigated by PCR Based Denaturing Gradient Gel Electrophoresis

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    Suxu He

    Full Text Available ABSTRACT An investigation was conducted to identify the allochthonous microbiota (entire intestine and the autochthonous microbiota in proximal intestine (PI and distal intestine (DI of four species of Indian air-breathing fish (climbing perch; Anabas testudineus, murrel; Channa punctatus, walking catfish; Clarias batrachus and stinging catfish; Heteropneustes fossilis by PCR based denaturing gradient gel electrophoresis (DGGE. High similarities of the allochthonous microbiota were observed between climbing perch and murrel, walking catfish and stinging catfish, indicating similar food behavior. The autochthonous microbiota of PI and DI from climbing perch and murrel revealed more similarity, than the result obtained from walking catfish and stinging catfish. The autochthonous microbiota of climbing perch and murrel were similar with regard to the allochthonous microbiota, but no such similarity was observed in case of walking catfish and stinging catfish. The fish genotype and intestinal bacteria are well matched and show co-evolutionary relationship. Three fish species has its unique bacteria; autochthonous Enterobacter cloacae, Edwardsiella tarda and Sphingobium sp. in DI of climbing perch, Pseudomonas sp.; allochthonous and autochthonous in PI of walking catfish and uncultured bacterium (EU697160.1, uncultured bacterium (JF018065.1 and uncultured bacterium (EU697160.1 for stinging catfish. In murrel, no unique bacteria were detected.

  3. Unfolding of hemoglobin variants--insights from urea gradient gel electrophoresis photon correlation spectroscopy and zeta potential measurements

    International Nuclear Information System (INIS)

    Bhattacharya, Jaydeep; GhoshMoulick, Ranjita; Choudhuri, Utpal; Chakrabarty, Prantar; Bhattacharya, Pranab K.; Lahiri, Prabir; Chakraborti, Bikas; Dasgupta, Anjan Kr.

    2004-01-01

    The unfolding pattern of crystal human hemoglobin and variants of hemoglobin obtained from hemolysate were studied using transverse urea gradient gel electrophoresis (TUGGE). A smooth sigmoid like increase of electrophoretic mobility was observed with increasing urea concentrations. A decrease in electrophoretic mobility resulted, if the protein was unfolded with guanidium hydrochloride (GdnHCl). The anomaly was resolved after the Stoke's radii (obtained using the photon correlation spectroscopy) and zeta potential (measured using laser Doppler velocimetry) measurements were made at different denaturant concentrations. Addition of denaturant led to formation of extended structure, irrespective of the nature of the denaturant, as indicated by increase in Stoke's radii in both cases (urea and GdnHCl). The unexpected increase in electrophoretic mobility in case of urea could be explained in terms of a critical redistribution of negative charge at intermediate stages of the unfolding process. In case of GdnHCl, the higher ionic strength masked the charge effect. The mobility, being solely dependent on size, decreased at higher denaturant concentration. Incidentally, folding loci of other hemoglobin variants (e.g. HbE) or that of post-translationally modified hemoglobin (e.g. HbA1c) could be determined by studying the charge distribution and hydrodynamic radius at varying denaturing stress and in each case the gel migration profile could be approximately scaled by the ratio of charge and hydrodynamic diameter of the protein. While unfolding induced charge effect was most pronounced in HbA0 (and crystal ferrous hemoglobin), the unfolding induced aggregation (manifested by the increase in Stoke's radii) was predominantly observed in the variant forms HbE and HbA1c. Representing the proteins by a plot, in which charge and hydrodynamic diameter are on independent axes, may be a useful way of characterizing protein variants having similar migration profiles on native gels

  4. A method for easily customizable gradient gel electrophoresis.

    Science.gov (United States)

    Miller, Andrew J; Roman, Brandon; Norstrom, Eric

    2016-09-15

    Gradient polyacrylamide gel electrophoresis is a powerful tool for the resolution of polypeptides by relative mobility. Here, we present a simplified method for generating polyacrylamide gradient gels for routine analysis without the need for specialized mixing equipment. The method allows for easily customizable gradients which can be optimized for specific polypeptide resolution requirements. Moreover, the method eliminates the possibility of buffer cross contamination in mixing equipment, and the time and resources saved with this method in place of traditional gradient mixing, or the purchase of pre-cast gels, are noteworthy given the frequency with which many labs use gradient gel SDS-PAGE. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Detection of bacteriophage phi 6 minus-strand RNA and novel mRNA isoconformers synthesized in vivo and in vitro, by strand-separating agarose gels

    International Nuclear Information System (INIS)

    Pagratis, N.; Revel, H.R.

    1990-01-01

    Two urea-free agarose gel protocols that resolve the six individual strands of bacteriophage phi 6 dsRNA were developed and used to analyze phage RNA synthesis in vivo and in vitro. Citrate gels separate strands of the large and medium chromosomes while Tris-borate-EDTA (TBE) gels resolve the medium and small dsRNA segments. Minus strands migrate faster than plus strands on citrate gels but are retarded on TBE gels. A study of electrophoretic conditions showed that pH affects strand resolution on citrate gels, and that voltage gradient, agarose concentration, and ethidium bromide significantly alter strand migration on TBE gels. Analysis of native phi 6 RNA synthesized in vivo and in vitro showed that the large and medium message RNAs comigrate with the corresponding plus strands of denatured virion dsRNA. The small messenger RNA is exceptional. Native small mRNA was detected as three isoconformers in vivo and in vitro. The isoconformers were converted by heat denaturation to a single RNA species that comigrates with the virion s+ strand. Minus strands labeled in vivo were detected only after heat denaturation. Minus strand synthesis was detected also in heat-denatured samples from in vitro phi 6 nucleocapsid RNA polymerase reactions at pH values suboptimal for transcription

  6. Unfolding of hemoglobin variants--insights from urea gradient gel electrophoresis photon correlation spectroscopy and zeta potential measurements

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharya, Jaydeep; GhoshMoulick, Ranjita; Choudhuri, Utpal; Chakrabarty, Prantar; Bhattacharya, Pranab K.; Lahiri, Prabir; Chakraborti, Bikas; Dasgupta, Anjan Kr

    2004-09-27

    The unfolding pattern of crystal human hemoglobin and variants of hemoglobin obtained from hemolysate were studied using transverse urea gradient gel electrophoresis (TUGGE). A smooth sigmoid like increase of electrophoretic mobility was observed with increasing urea concentrations. A decrease in electrophoretic mobility resulted, if the protein was unfolded with guanidium hydrochloride (GdnHCl). The anomaly was resolved after the Stoke's radii (obtained using the photon correlation spectroscopy) and zeta potential (measured using laser Doppler velocimetry) measurements were made at different denaturant concentrations. Addition of denaturant led to formation of extended structure, irrespective of the nature of the denaturant, as indicated by increase in Stoke's radii in both cases (urea and GdnHCl). The unexpected increase in electrophoretic mobility in case of urea could be explained in terms of a critical redistribution of negative charge at intermediate stages of the unfolding process. In case of GdnHCl, the higher ionic strength masked the charge effect. The mobility, being solely dependent on size, decreased at higher denaturant concentration. Incidentally, folding loci of other hemoglobin variants (e.g. HbE) or that of post-translationally modified hemoglobin (e.g. HbA1c) could be determined by studying the charge distribution and hydrodynamic radius at varying denaturing stress and in each case the gel migration profile could be approximately scaled by the ratio of charge and hydrodynamic diameter of the protein. While unfolding induced charge effect was most pronounced in HbA0 (and crystal ferrous hemoglobin), the unfolding induced aggregation (manifested by the increase in Stoke's radii) was predominantly observed in the variant forms HbE and HbA1c. Representing the proteins by a plot, in which charge and hydrodynamic diameter are on independent axes, may be a useful way of characterizing protein variants having similar migration profiles on

  7. Dynamics of Vaginal Bacterial Communities in Women Developing Bacterial Vaginosis, Candidiasis, or No Infection, Analyzed by PCR-Denaturing Gradient Gel Electrophoresis and Real-Time PCR▿

    Science.gov (United States)

    Vitali, Beatrice; Pugliese, Ciro; Biagi, Elena; Candela, Marco; Turroni, Silvia; Bellen, Gert; Donders, Gilbert G. G.; Brigidi, Patrizia

    2007-01-01

    The microbial flora of the vagina plays a major role in preventing genital infections, including bacterial vaginosis (BV) and candidiasis (CA). An integrated approach based on PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR was used to study the structure and dynamics of bacterial communities in vaginal fluids of healthy women and patients developing BV and CA. Universal eubacterial primers and Lactobacillus genus-specific primers, both targeted at 16S rRNA genes, were used in DGGE and real-time PCR analysis, respectively. The DGGE profiles revealed that the vaginal flora was dominated by Lactobacillus species under healthy conditions, whereas several potentially pathogenic bacteria were present in the flora of women with BV. Lactobacilli were the predominant bacterial population in the vagina for patients affected by CA, but changes in the composition of Lactobacillus species were observed. Real-time PCR analysis allowed the quantitative estimation of variations in lactobacilli associated with BV and CA diseases. A statistically significant decrease in the relative abundance of lactobacilli was found in vaginal fluids of patients with BV compared to the relative abundance of lactobacilli in the vaginal fluids of healthy women and patients with CA. PMID:17644631

  8. Dynamics of vaginal bacterial communities in women developing bacterial vaginosis, candidiasis, or no infection, analyzed by PCR-denaturing gradient gel electrophoresis and real-time PCR.

    Science.gov (United States)

    Vitali, Beatrice; Pugliese, Ciro; Biagi, Elena; Candela, Marco; Turroni, Silvia; Bellen, Gert; Donders, Gilbert G G; Brigidi, Patrizia

    2007-09-01

    The microbial flora of the vagina plays a major role in preventing genital infections, including bacterial vaginosis (BV) and candidiasis (CA). An integrated approach based on PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR was used to study the structure and dynamics of bacterial communities in vaginal fluids of healthy women and patients developing BV and CA. Universal eubacterial primers and Lactobacillus genus-specific primers, both targeted at 16S rRNA genes, were used in DGGE and real-time PCR analysis, respectively. The DGGE profiles revealed that the vaginal flora was dominated by Lactobacillus species under healthy conditions, whereas several potentially pathogenic bacteria were present in the flora of women with BV. Lactobacilli were the predominant bacterial population in the vagina for patients affected by CA, but changes in the composition of Lactobacillus species were observed. Real-time PCR analysis allowed the quantitative estimation of variations in lactobacilli associated with BV and CA diseases. A statistically significant decrease in the relative abundance of lactobacilli was found in vaginal fluids of patients with BV compared to the relative abundance of lactobacilli in the vaginal fluids of healthy women and patients with CA.

  9. Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology

    Science.gov (United States)

    Koizumi, Yoshikazu; Kelly, John J.; Nakagawa, Tatsunori; Urakawa, Hidetoshi; El-Fantroussi, Said; Al-Muzaini, Saleh; Fukui, Manabu; Urushigawa, Yoshikuni; Stahl, David A.

    2002-01-01

    A mesophilic toluene-degrading consortium (TDC) and an ethylbenzene-degrading consortium (EDC) were established under sulfate-reducing conditions. These consortia were first characterized by denaturing gradient gel electrophoresis (DGGE) fingerprinting of PCR-amplified 16S rRNA gene fragments, followed by sequencing. The sequences of the major bands (T-1 and E-2) belonging to TDC and EDC, respectively, were affiliated with the family Desulfobacteriaceae. Another major band from EDC (E-1) was related to an uncultured non-sulfate-reducing soil bacterium. Oligonucleotide probes specific for the 16S rRNAs of target organisms corresponding to T-1, E-1, and E-2 were designed, and hybridization conditions were optimized for two analytical formats, membrane and DNA microarray hybridization. Both formats were used to characterize the TDC and EDC, and the results of both were consistent with DGGE analysis. In order to assess the utility of the microarray format for analysis of environmental samples, oil-contaminated sediments from the coast of Kuwait were analyzed. The DNA microarray successfully detected bacterial nucleic acids from these samples, but probes targeting specific groups of sulfate-reducing bacteria did not give positive signals. The results of this study demonstrate the limitations and the potential utility of DNA microarrays for microbial community analysis.

  10. Abundance and Diversity of Hydrogenotrophic Microorganisms in the Infant Gut before the Weaning Period Assessed by Denaturing Gradient Gel Electrophoresis and Quantitative PCR

    Directory of Open Access Journals (Sweden)

    Valeria Sagheddu

    2017-06-01

    Full Text Available Delivery mode (natural vs. cesarean and feeding type (breast vs. formula feeding are relevant factors for neonatal gut colonization. Biomolecular methods have shown that the ecological structure of infant microbiota is more complex than previously proposed, suggesting a relevant presence of unculturable bacteria. It has also been postulated that among unculturable bacteria, hydrogenotrophic populations might play a key role in infant health. Sulfate-reducing bacteria (SRB, acetogens, and methanogenic archaea use hydrogenotrophic pathways within the human colon. However, to date, few studies have reported detection of hydrogenotrophic microorganisms in newborns, possibly because of limitations on available group-specific, culture-independent quantification procedures. In the present work, we analyzed 16 fecal samples of healthy babies aged 1–6 months by means of quantitative PCR (qPCR targeting the 16S rRNA or metabolic functional genes and by denaturing gradient gel electrophoresis (DGGE. qPCR data showed quantifiable levels of methanogens, SRB, and acetogens in all samples, indicating that the relative abundances of these microbial groups were not affected by delivery mode (natural vs. caesarian. DGGE revealed a high prevalence of the Blautia genus within the acetogenic bacteria despite strong interindividual variability. Our preliminary results suggest that hydrogenotrophic microorganisms, which have been a neglected group to date, should be included in future ecological and metabolic studies evaluating the infant intestinal microbiota.

  11. Denaturing gradient gel electrophoresis (DGGE as a powerful novel alternative for differentiation of epizootic ISA virus variants.

    Directory of Open Access Journals (Sweden)

    Marisela Carmona

    Full Text Available Infectious Salmon Anemia is a devastating disease critically affecting world-wide salmon production. Chile has been particularly stricken by this disease which in all cases has been directly related with its causative agent, a novel orthomyxovirus which presents specific and distinctive infective features. Among these, two molecular markers have been directly associated with pathogenicity in two of the eight RNA sub genomic coding units of the virus: an insertion hot spot region present in viral segment 5 and a Highly Polymorphic Region (HPR located in viral segment 6. Here we report the successful adaptation of a PCR-dependent denaturing gel electrophoresis technique (DGGE, which enables differentiation of selected reported HPR epizootic variants detected in Chile. At the same time, the technique allows us to distinguish one nucleotide differences in sequences associated with the intriguing, and still not well-understood, insertion events which tend to occur on RNA Segment 5. Thus, the versatility of the technique opens new opportunities for improved understanding of the complex biology of all ISA variants as well as possible applications to other highly variable pathogens.

  12. The use of DNase I, buffer gradient gel, and 35S label for DNA sequencing

    International Nuclear Information System (INIS)

    Hong, G.F.

    1987-01-01

    The use of microcentrifuge tubes and mixing of sequencing reactions and brief centrifugation in racks rather than the original capillary tube method has made sequencing reactions relatively simple. Buffer gradient gels and 15 S label are simple means of increasing the rate of sequence analysis; they add little time to that required for determining the sequences of a given number of clones, need no elaborate equipment, and increase the amount of useful data per gel. The standard approach of running 2- and 4-hr gels generates about 300 bases of sequence. The above improvements allow the same number of bases to be read with more confidence from a single 50-cm gel for each clone sequenced due to the changed spacing between sharpened bands

  13. Protein electrophoretic migration data from custom and commercial gradient gels

    Directory of Open Access Journals (Sweden)

    Andrew J. Miller

    2016-12-01

    Full Text Available This paper presents data related to the article “A method for easily customizable gradient gel electrophoresis” (A.J. Miller, B. Roman, E.M. Norstrom, 2016 [1]. Data is presented on the rate of electrophoretic migration of proteins in both hand-poured and commercially acquired acrylamide gradient gels. For each gel, migration of 9 polypeptides of various masses was measured upon completion of gel electrophoresis. Data are presented on the migration of proteins within separate lanes of the same gel as well as migration rates from multiple gels.

  14. Thermal denaturation of type I collagen vitrified gels

    International Nuclear Information System (INIS)

    Xia, Zhiyong; Calderon-Colon, Xiomara; Trexler, Morgana; Elisseeff, Jennifer; Guo, Qiongyu

    2012-01-01

    Highlights: ► We analyzed the denaturation of vitrigels synthesized under different conditions. ► Overall denaturation kinetics consisted of both reversible and irreversible steps. ► More stable vitrigels were formed under high level of vitrification. - Abstract: The denaturation kinetics of type I collagen vitrigels synthesized under different vitrification time and temperature were analyzed by the classical Kissinger approach and the advanced model free kinetics (AMFK) using the Vyazovkin algorithm. The AMFK successfully elucidated the overall denaturation into reversible and irreversible processes. Depending on vitrification conditions, the activation energy for the irreversible process ranged from 100 to 200 kJ/mol, and the reversible enthalpy ranged from 250 to 300 kJ/mol. All of these values increased with the vitrification time and temperature, indicating that a more stable and complex structure formed with increased vitrification. The classical Kissinger method predicted the presence of a critical temperate of approximately 60 °C for the transition between reversible and irreversible processes. Scanning electron microscopy revealed the presence of fibril structures in vitrigels both before and after full denaturation; however the fibrils had became thicker and rougher after denaturation.

  15. Interchange reaction of disulfides and denaturation of oxytocin by copper(II)/ascorbic acid/O2 system.

    Science.gov (United States)

    Inoue, H; Hirobe, M

    1987-05-29

    The interchange reaction of disulfides was caused by the copper(II)/ascorbic acid/O2 system. The incubation of two symmetric disulfides, L-cystinyl-bis-L-phenylalanine (PP) and L-cystinyl-bis-L-tyrosine (TT), with L-ascorbic acid and CuSO4 in potassium phosphate buffer (pH 7.2, 50 mM) resulted in the formation of an asymmetric disulfide, L-cystinyl-L-phenylalanine-L-tyrosine (PT), and the final ratio of PP:PT:TT was 1:2:1. As the reaction was inhibited by catalase and DMSO only at the initial time, hydroxyl radical generated by the copper(II)/ascorbic acid/O2 system seemed to be responsible for the initiation of the reaction. Oxytocin and insulin were denatured by this system, and catalase and DMSO similarly inhibited these denaturations. As the composition of amino acids was unchanged after the reaction, hydroxyl radical was thought to cause the cleavage and/or interchange reaction of disulfides to denature the peptides.

  16. The application of polymerase chain reaction-denaturing gradient ...

    African Journals Online (AJOL)

    Jane

    2011-05-23

    May 23, 2011 ... dominance in microbial ecology if the corresponding environment samples had been provided. This ... yeast peptone dextrose; PCR, polymerase chain reaction. method, DGGE method ..... Two nuclear mutations that block.

  17. Comparison of automated ribosomal intergenic spacer analysis (ARISA) and denaturing gradient gel electrophoresis (DGGE) techniques for analysing the influence of diet on ruminal bacterial diversity.

    Science.gov (United States)

    Saro, Cristina; Molina-Alcaide, Eduarda; Abecia, Leticia; Ranilla, María José; Carro, María Dolores

    2018-04-01

    The objective of this study was to compare the automated ribosomal intergenic spacer analysis (ARISA) and the denaturing gradient gel electrophoresis (DGGE) techniques for analysing the effects of diet on diversity in bacterial pellets isolated from the liquid (liquid-associated bacteria (LAB)) and solid (solid-associated bacteria (SAB)) phase of the rumen. The four experimental diets contained forage to concentrate ratios of 70:30 or 30:70 and had either alfalfa hay or grass hay as forage. Four rumen-fistulated animals (two sheep and two goats) received the diets in a Latin square design. Bacterial pellets (LAB and SAB) were isolated at 2 h post-feeding for DNA extraction and analysed by ARISA and DGGE. The number of peaks in individual samples ranged from 48 to 99 for LAB and from 41 to 95 for SAB with ARISA, and values of DGGE-bands ranged from 27 to 50 for LAB and from 18 to 45 for SAB. The LAB samples from high concentrate-fed animals tended (p forage-fed animals with ARISA, but no differences were identified with DGGE. The SAB samples from high concentrate-fed animals had lower (p forage diets with ARISA, but only a trend was noticed for these parameters with DGGE (p forage type on LAB diversity was detected by any technique. In this study, ARISA detected some changes in ruminal bacterial communities that were not detected by DGGE, and therefore ARISA was considered more appropriate for assessing bacterial diversity of ruminal bacterial pellets. The results highlight the impact of the fingerprinting technique used to draw conclusions on dietary factors affecting bacterial diversity in ruminal bacterial pellets.

  18. On the mobility of partially denatured DNA in gel electrophoresis: a theoretical investigation

    Science.gov (United States)

    Sean, David

    There are technologies which exploit a rapid reduction of the gel electrophoretic mobility of DNA arising from partial denaturation. The underlying phenomenon behind these experiments---the mechanisms which reduce the mobility---are not very well understood. Such is the purpose of my thesis. The first chapter provides a brief introduction to the field of polymer physics. The subjects covered are carefully chosen to directly relate to the forthcoming research. There is a published semi-empirical formula used to model the rapid decrease of mobility which is largely considered to be consistent with experimental data. The second chapter of this thesis demonstrates that there is a fundamental confusion in the literature regarding the fitting parameter Lr, in the said formula. By going back to the original derivation, a physical interpretation can be given to L r. This interpretation yields theoretical values which are consistent with what has been published. However, we find that an underlying assumption---that the effect of the denaturation does not depend on its position along the DNA fragment---may systematically overestimate experimental observations of Lr. To measure the impact of this assumption, a simulation model of DNA is presented. The article presented in the third chapter reveals that indeed, the position of the denatured region affects the migration of the DNA fragment. A refined version of the formula which takes these factors into account is proposed. The simulations also reveal that, for certain fields, an unexpected conformation completely dominates during migration of the fragment. This surprising result: a squid-like conformation, is explored in chapter four.

  19. An improved silver staining procedure for schizodeme analysis in polyacrylamide gradient gels

    Directory of Open Access Journals (Sweden)

    Antonio M. Gonçalves

    1990-03-01

    Full Text Available A simple protocol is described for the silver staining of polyacrylamide gradient gels used for the separation of restriction fragments of kinetoplast DNA [schizodeme analysis of trypanosomatids (Morel et al., 1980]. The method overcomes the problems of non-uniform staining and strong background color which are frequently encountered when conventional protocols for silver staining of linear gels. The method described has proven to be of general applicability for DNA, RNA and protein separations in gradient gels.

  20. Influence of technological treatments on bacterial communities in ...

    African Journals Online (AJOL)

    Influence of technological treatments on bacterial communities in tilapia ( Oreochromis niloticus ) as determined by 16S rDNA fingerprinting using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)

  1. Spatial variation of bacterial community composition near the Luzon ...

    African Journals Online (AJOL)

    Spatial variation of bacterial community composition near the Luzon strait assessed by polymerase chain reaction-denaturing gradient gel electrophoresis ... chain reaction (PCR)-amplified bacterial 16S ribosomal deoxyribonucleic acid (DNA) gene fragments and interpreted the results; its relationship with physical and ...

  2. Use of pyrosequencing and denaturing gradient gel electrophoresis to examine the effects of probiotics and essential oil blends on digestive microflora in broilers under mixed Eimeria infection.

    Science.gov (United States)

    Hume, Michael E; Barbosa, Nei A; Dowd, Scot E; Sakomura, Nilva K; Nalian, Armen G; Martynova-Van Kley, Alexandra; Oviedo-Rondón, Edgar O

    2011-11-01

    A protective digestive microflora helps prevent and reduce broiler infection and colonization by enteropathogens. In the current experiment, broilers fed diets supplemented with probiotics and essential oil (EO) blends were infected with a standard mixed Eimeria spp. to determine effects of performance enhancers on ileal and cecal microbial communities (MCs). Eight treatment groups included four controls (uninfected-unmedicated [UU], unmedicated-infected, the antibiotic BMD plus the ionophore Coban as positive control, and the ionophore as negative control), and four treatments (probiotics BC-30 and Calsporin; and EO, Crina Poultry Plus, and Crina PoultryAF). Day-old broilers were raised to 14 days in floor pens on used litter and then were moved to Petersime batteries and inoculated at 15 days with mixed Eimeria spp. Ileal and cecal samples were collected at 14 days and 7 days postinfection. Digesta DNA was subjected to pyrosequencing for sequencing of individual cecal bacteria and denaturing gradient gel electrophoresis (DGGE) for determination of changes in ileal and cecal MC according to percentage similarity coefficient (%SC). Pyrosequencing is very sensitive detecting shifts in individual bacterial sequences, whereas DGGE is able to detect gross shifts in entire MC. These combined techniques offer versatility toward identifying feed additive and mild Eimeria infection modulation of broiler MC. Pyrosequencing detected 147 bacterial species sequences. Additionally, pyrosequencing revealed the presence of relatively low levels of the potential human enteropathogens Campylobacter sp. and four Shigella spp. as well as the potential poultry pathogen Clostridiun perfringens. Pre- and postinfection changes in ileal (56%SC) and cecal (78.5%SC) DGGE profiles resulted from the coccidia infection and with increased broiler age. Probiotics and EO changed MC from those seen in UU ilea and ceca. Results potentially reflect the performance enhancement above expectations in

  3. Monomorphism in humans and sequence differences among higher primates for a sequence tagged site (STS) in homeo box cluster 2 as assayed by denaturing gradient electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Ruano, G.; Ruddle, F.H.; Kidd, K.K. (Yale Univ., New Haven, CT (United States)); Gray, M.R. (Tufts Univ., Boston, MA (United States)); Miki, Tetsuro (Osaka Univ. (Japan)); Ferguson-Smith, A.C. (Inst. of Animal Physiology and Genetics Research, Cambridge (United Kingdom))

    1990-03-11

    The human homeo box cluster 2 (HOX2) contains genes coding for DNA binding proteins involved in developmental control and is highly conserved between mouse and man. The authors have applied in concert the Polymerase Chain Reaction (PCR) and Denaturing Gradient Electrophoresis (DGE) to amplify defined primate HOX2 segments and to detect sequence differences among them. They have sequenced a PstI fragment 4 kb upstream from HOX 2.2 and synthesized primers delimiting both halves of 630 bp segment within it PCR on various unrelated humans and SC-PCR on chimpanzee, gorilla, orangutan and gibbon yielded products of the same length for each primer pair.

  4. Evaluation of microbial diversity of different soil layers at a contaminated diesel site

    CSIR Research Space (South Africa)

    Maila, MP

    2005-01-01

    Full Text Available with high TPH removal. Analysis of the microbial diversity in the different soil layers using functional diversity (community-level physiological profile, via Biolog) and genetic diversity using polymerase chain reaction-denaturing gradient gel...

  5. Application of denaturing high-performance liquid chromatography for monitoring sulfate-reducing bacteria in oil fields.

    Science.gov (United States)

    Priha, Outi; Nyyssönen, Mari; Bomberg, Malin; Laitila, Arja; Simell, Jaakko; Kapanen, Anu; Juvonen, Riikka

    2013-09-01

    Sulfate-reducing bacteria (SRB) participate in microbially induced corrosion (MIC) of equipment and H2S-driven reservoir souring in oil field sites. Successful management of industrial processes requires methods that allow robust monitoring of microbial communities. This study investigated the applicability of denaturing high-performance liquid chromatography (DHPLC) targeting the dissimilatory sulfite reductase ß-subunit (dsrB) gene for monitoring SRB communities in oil field samples from the North Sea, the United States, and Brazil. Fifteen of the 28 screened samples gave a positive result in real-time PCR assays, containing 9 × 10(1) to 6 × 10(5) dsrB gene copies ml(-1). DHPLC and denaturing gradient gel electrophoresis (DGGE) community profiles of the PCR-positive samples shared an overall similarity; both methods revealed the same samples to have the lowest and highest diversity. The SRB communities were diverse, and different dsrB compositions were detected at different geographical locations. The identified dsrB gene sequences belonged to several phylogenetic groups, such as Desulfovibrio, Desulfococcus, Desulfomicrobium, Desulfobulbus, Desulfotignum, Desulfonatronovibrio, and Desulfonauticus. DHPLC showed an advantage over DGGE in that the community profiles were very reproducible from run to run, and the resolved gene fragments could be collected using an automated fraction collector and sequenced without a further purification step. DGGE, on the other hand, included casting of gradient gels, and several rounds of rerunning, excising, and reamplification of bands were needed for successful sequencing. In summary, DHPLC proved to be a suitable tool for routine monitoring of the diversity of SRB communities in oil field samples.

  6. Identification of the Bacterial Community Responsible for ...

    African Journals Online (AJOL)

    Identification of bacteria community responsible for decontaminating Eleme petrochemical industrial effluent using 16S PCR denaturing gradient gel electrophoresis (DGGE) was determined. Gene profiles were determined by extracting DNA from bacterial isolates and amplified by polymerase chain reaction (PCR) using ...

  7. Microbiota of Tayohounta , a fermented baobab flavour food of Benin

    African Journals Online (AJOL)

    Tayohounta was also investigated using culture independent techniques, direct DNA extraction, polymerase chain reaction - denaturing gradient gel electrophoresis (PCR-DGGE) and cloning. Isolated microorganisms were tested for their functionality in baobab seed kernels fermentation. Total viable counts were around 9 ...

  8. Reversibility of partial denaturation of DNA

    International Nuclear Information System (INIS)

    Acuna, M.I.; Mingot, F.; Davila, C.A.

    1976-01-01

    The recovery of hypochromicity in a partially denatured DNA sample when salt concentration is suddenly increased at a intermediate stage of the thermal transition is studied. The results of CsCl gradient analysis, PEG/DEX partition analysis, behaviour in a new thermal transition hydrodynamic properties and transforming ability, support the view that the process is an intramolecular double chain denaturation. The degree of denaturation irreversibility is dependent on single chain molecular weight of DNA (discontinuities denisty) and upon the helicity value at which salt concentration jump is performed. Both dependences are formally interpreted according to Elton's model for base distribution in DNA. Kinetically the process behaves as being an hydrodynamically limited rewinding. (author)

  9. Microwave-enhanced folding and denaturation of globular proteins

    DEFF Research Database (Denmark)

    Bohr, Henrik; Bohr, Jakob

    2000-01-01

    It is shown that microwave irradiation can affect the kinetics of the folding process of some globular proteins, especially beta-lactoglobulin. At low temperature the folding from the cold denatured phase of the protein is enhanced, while at a higher temperature the denaturation of the protein from...... its folded state is enhanced. In the latter case, a negative temperature gradient is needed for the denaturation process, suggesting that the effects of the microwaves are nonthermal. This supports the notion that coherent topological excitations can exist in proteins. The application of microwaves...

  10. Application of GelGreen™ in Cesium Chloride Density Gradients for DNA-Stable Isotope Probing Experiments.

    Directory of Open Access Journals (Sweden)

    Jingfeng Gao

    Full Text Available In this study, GelGreen™ was investigated as a replacement for SYBR® Safe to stain DNA in cesium chloride (CsCl density gradients for DNA-stable isotope probing (SIP experiments. Using environmental DNA, the usage of GelGreen™ was optimized for sensitivity compared to SYBR® Safe, its optimal concentration, detection limit for environmental DNA and its application in environmental DNA-SIP assay. Results showed that GelGreen™ was more sensitive than SYBR® Safe, while the optimal dosage (15X concentration needed was approximately one-third of SYBR® Safe, suggesting that its sensitivity was three times more superior than SYBR® Safe. At these optimal parameters, the detection limit of GelGreen™-stained environmental DNA was as low as 0.2 μg, but the usage of 0.5 μg environmental DNA was recommended to produce a more consistent DNA band. In addition, a modified needle extraction procedure was developed to withdraw DNA effectively by fractionating CsCl density gradients into four or five fractions. The successful application of GelGreen™ staining with 13C-labeled DNA from enriched activated sludge suggests that this stain was an excellent alternative of SYBR® Safe in CsCl density gradients for DNA-SIP assays.

  11. Comparison of bacterial communities of tilapia fish from Cameroon ...

    African Journals Online (AJOL)

    Comparison of bacterial communities of tilapia fish from Cameroon and Vietnam using PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) ... The different PCR-DGGE 16S rDNA banding profiles obtained were analysed and results showed that there were specific bands for each geographical ...

  12. Monitoring iron and manganese diagenesis in constructed wetlands with continuous gradient gels

    International Nuclear Information System (INIS)

    Edenborn, H.M.; Brickett, L.A.; Dvorak, D.H.; Edenborn, S.L.

    1993-01-01

    Average removal rates for Fe and Mn in wetlands constructed for the treatment of coal mine drainage have been developed based on field observations, but few details are known about the spatial and temporal variation in metal diagenesis within these wetlands. The heterogeneous distribution of biological activity in constructed wetland sediments makes it difficult to assess the importance of specific diagenetic processes without taking large numbers of samples at great expense. In this study, continuous gradient gels were used to evaluate Pennsylvania. Continuous gradient gels provided rapid and detailed information on the regions of stability of Fe and Mn compounds within the wetland sediments. The resulting data were mapped and used to demonstrate how this technique can be used to assess the overall efficiency of constructed wetlands in the removal of Fe and Mn

  13. A Fast Silver Staining Protocol Enabling Simple and Efficient Detection of SSR Markers using a Non-denaturing Polyacrylamide Gel.

    Science.gov (United States)

    Huang, Ling; Deng, Xiaohui; Li, Ronghua; Xia, Yanshi; Bai, Guihua; Siddique, Kadambot H M; Guo, Peiguo

    2018-04-20

    Simple Sequence Repeat (SSR) is one of the most effective markers used in plant and animal genetic research and molecular breeding programs. Silver staining is a widely used method for the detection of SSR markers in a polyacrylamide gel. However, conventional protocols for silver staining are technically demanding and time-consuming. Like many other biological laboratory techniques, silver staining protocols have been steadily optimized to improve detection efficiency. Here, we report a simplified silver staining method that significantly reduces reagent costs and enhances the detection resolution and picture clarity. The new method requires two major steps (impregnation and development) and three reagents (silver nitrate, sodium hydroxide, and formaldehyde), and only 7 min of processing for a non-denaturing polyacrylamide gel. Compared to previously reported protocols, this new method is easier, quicker and uses fewer chemical reagents for SSR detection. Therefore, this simple, low-cost, and effective silver staining protocol will benefit genetic mapping and marker-assisted breeding by a quick generation of SSR marker data.

  14. Study on the kinetics of gel formation in the radiation crosslinking reaction

    International Nuclear Information System (INIS)

    Wang Mingjun; Liu Yuming

    1988-01-01

    From the kinetic equation of gel formation obtained by the authors, the mechanism of gel formation may be interpreted clearly as follows: (1) When the degree of crosslinking q g , the system is sol and the crosslinking reaction is only carried out between the sol molecules. (q g is the gel point). (2) When q=q g , there exists a beginning point where the gel is coexisted with the sol, and the system is still sol, and the crosslinking reaction is still carried out between the sol molecules. (3) When q>q g , the crosslinking reaction exceeds the gel point and the gel is coexisted with the sol. The kinetic equation shows clearly that the transformation from sol into gel is caused by crosslinking reaction of the uncrosslinked chain units between the sol and gel molecules. As a result the sol molecules are transformed into the gel molecules gradually, and the sol fraction is reduced. When the chain units P-barw(s)S(1-s)dq in sol are crosslinked with gel, the sol fraction in the system is reduced ds (where P-barw(s) is a function of the radiation dose and s is sol frection). The degree of crosslinking per unit dose (q 0 ) is a reduced function of dose (R). The equation for calculating its value for every irradiation dose is obtained. After knowing the correlation between P-bar W(s) vs R and q 0 vs R, the distribution of gel and sol in the process of radiation crosslinking can be discussed as well

  15. New resin gel for uranium determination by diffusive gradient in thin films technique

    International Nuclear Information System (INIS)

    Gregusova, Michaela; Docekal, Bohumil

    2011-01-01

    A new resin gel based on Spheron-Oxin chelating ion-exchanger with anchored 8-hydroxyquinoline functional groups was tested for application in diffusive gradient in thin film technique (DGT) for determination of uranium. Selectivity of uranium uptake from model carbonate loaded solutions of natural water was studied under laboratory conditions and compared with selectivity of the conventional Chelex 100 based resin gel. The affinity of Spheron-Oxin functional groups enables determination of the overall uranium concentration in water containing carbonates up to the concentration level of 10 2 mg L -1 . The effect of uranium binding to the polyacrylamide (APA) and agarose diffusive gels (AGE) was also studied. Uranium is probably bound in both gels by a weak interaction with traces of acrylic acid groups in the structure of APA gel and with pyruvic and sulfonic acid groups in the AGE gel. These sorption effects can be eliminated to the negligible level by prolonged deployment of DGT probes or by disassembling probes after the 1-2 days post-sampling period that is sufficient for release of uranium from diffusive gel and its sorption in resin gel.

  16. New resin gel for uranium determination by diffusive gradient in thin films technique

    Energy Technology Data Exchange (ETDEWEB)

    Gregusova, Michaela, E-mail: gregusova@iach.cz [Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic v.v.i., Veveri 97, 602 00 Brno (Czech Republic); Docekal, Bohumil [Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic v.v.i., Veveri 97, 602 00 Brno (Czech Republic)

    2011-01-17

    A new resin gel based on Spheron-Oxin chelating ion-exchanger with anchored 8-hydroxyquinoline functional groups was tested for application in diffusive gradient in thin film technique (DGT) for determination of uranium. Selectivity of uranium uptake from model carbonate loaded solutions of natural water was studied under laboratory conditions and compared with selectivity of the conventional Chelex 100 based resin gel. The affinity of Spheron-Oxin functional groups enables determination of the overall uranium concentration in water containing carbonates up to the concentration level of 10{sup 2} mg L{sup -1}. The effect of uranium binding to the polyacrylamide (APA) and agarose diffusive gels (AGE) was also studied. Uranium is probably bound in both gels by a weak interaction with traces of acrylic acid groups in the structure of APA gel and with pyruvic and sulfonic acid groups in the AGE gel. These sorption effects can be eliminated to the negligible level by prolonged deployment of DGT probes or by disassembling probes after the 1-2 days post-sampling period that is sufficient for release of uranium from diffusive gel and its sorption in resin gel.

  17. New resin gel for uranium determination by diffusive gradient in thin films technique

    Czech Academy of Sciences Publication Activity Database

    Gregušová, Michaela; Dočekal, Bohumil

    2011-01-01

    Roč. 684, 1-2 (2011), s. 142-146 ISSN 0003-2670 R&D Projects: GA ČR GAP503/10/2002 Institutional research plan: CEZ:AV0Z40310501 Keywords : diffusive gradient in thin film technique * 8-hydroxyquinoline resin gel * uranium determination Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 4.555, year: 2011

  18. Characterization of alkali silica reaction gels using Raman spectroscopy

    International Nuclear Information System (INIS)

    Balachandran, C.; Muñoz, J.F.; Arnold, T.

    2017-01-01

    The ability of Raman spectroscopy to characterize amorphous materials makes this technique ideal to study alkali silica reaction (ASR) gels. The structure of several synthetic ASR gels was thoroughly characterized using Raman Spectroscopy. The results were validated with additional techniques such as Fourier transmission infrared spectroscopy, X-ray powder diffraction and thermogravimetric analysis. The Raman spectra were found to have two broad bands in the 800 to 1200 cm −1 range and the 400 to 700 cm −1 range indicating the amorphous nature of the gel. Important information regarding the silicate polymerization was deduced from both of these spectral regions. An increase in alkali content of the gels caused a depolymerization in the silicate framework which manifested in the Raman spectra as a gradual shift of predominant peaks in both regions. The trends in silicate depolymerization were in agreement with results from a NMR spectroscopy study on similar synthetic ASR gels.

  19. Microfluidic device having an immobilized pH gradient and PAGE gels for protein separation and analysis

    Science.gov (United States)

    Sommer, Gregory J.; Hatch, Anson V.; Singh, Anup K.; Wang, Ying-Chih

    2012-12-11

    Disclosed is a novel microfluidic device enabling on-chip implementation of a two-dimensional separation methodology. Previously disclosed microscale immobilized pH gradients (IPG) are combined with perpendicular polyacrylamide gel electrophoresis (PAGE) microchannels to achieve orthogonal separations of biological samples. Device modifications enable inclusion of sodium dodecyl sulfate (SDS) in the second dimension. The device can be fabricated to use either continuous IPG gels, or the microscale isoelectric fractionation membranes we have also previously disclosed, for the first dimension. The invention represents the first all-gel two-dimensional separation microdevice, with significantly higher resolution power over existing devices.

  20. Coastal microbial mat diversity along a natural salinity gradient.

    Directory of Open Access Journals (Sweden)

    Henk Bolhuis

    Full Text Available The North Sea coast of the Dutch barrier island of Schiermonnikoog is covered by microbial mats that initiate a succession of plant communities that eventually results in the development of a densely vegetated salt marsh. The North Sea beach has a natural elevation running from the low water mark to the dunes resulting in gradients of environmental factors perpendicular to the beach. These gradients are due to the input of seawater at the low water mark and of freshwater from upwelling groundwater at the dunes and rainfall. The result is a natural and dynamic salinity gradient depending on the tide, rainfall and wind. We studied the microbial community composition in thirty three samples taken every ten meters along this natural salinity gradient by using denaturing gradient gel electrophoresis (DGGE of rRNA gene fragments. We looked at representatives from each Domain of life (Bacteria, Archaea and Eukarya and with a particular emphasis on Cyanobacteria. Analysis of the DGGE fingerprints together with pigment composition revealed three distinct microbial mat communities, a marine community dominated by diatoms as primary producers, an intermediate brackish community dominated by Cyanobacteria as primary producers and a freshwater community with Cyanobacteria and freshwater green algae.

  1. Loss of an actin crosslinker uncouples cell spreading from cell stiffening on gels with a gradient of stiffness

    Science.gov (United States)

    Wen, Qi; Byfield, Fitzroy J.; Nordstrom, Kerstin; Arratia, Paulo E.; Miller, R. Tyler; Janmey, Paul A.

    2009-03-01

    We use microfluidics techniques to produce gels with a gradient of stiffness to show the essential function of the actin crosslinker filamin A in cell responses to mechanical stimuli. M2 melanoma cells null for filamin A do not alter their adherent area in response to increased substrate stiffness when they link to the substrate only through collagen receptors, but change adherent area normally when bound through fibronectin receptors. In contrast, filamin A-replete A7 cells change adherent area on both substrates and respond more strongly to collagen 1-coated gels than to fibronectin-coated gels. A7 cells alter their stiffness, as measured by atomic force microscopy, to match the elastic modulus of the substrate immediately adjacent to them on the gradient. M2 cells, in contrast, maintain a constant stiffness on all substrates that is as low as that of A7 cells on the softest gels achievable (1000 Pa). By contrasting the responses of these cell types to different adhesive substrates, cell spreading can be dissociated from stiffening.

  2. Chromatin structure influence of DNA damage measurements by four assays: pulsed- and constant-field gel electrophoresis, DNA precipitation and non-denaturing filter elution

    International Nuclear Information System (INIS)

    Wlodek, D.; Olive, P.L.

    1996-01-01

    The of elution of DNA during non-denaturing filter elution (NFE) often correlates with cell sensitivity to radiation. The elution rate is influenced by two cellular factors: chromatin structure and the number of DNA-strand breaks (DSBs) produced in an intact cell by ionizing radiation. To determine which of the above factors is relevant to cell radiosensitivity, four assays were used to measure induction of DNA damage in three cell lines varying in radiosensitivity (V79, CHO, and L5178Y-R). Each of the assays, neutral filter elution (NFE), DNA precipitation, constant (CFGE) and pulsed field gel electrophoresis (PFGE) have different physical basis for DNA damage measurement and might be differently affected by chromatin structure. Three of the methods used to measure DNA double-strand breaks gave different results: NFE was dependent on cell type and location of DNA relative to the replication fork, gel electrophoresis was independent of cell type but was affected by proximity to the replication fork, and the precipitation assay was independent of both cell type and replication status. Pulsed field gel electrophoresis produced the same results and constant field gel electrophoresis for 3 cell lines examined. Only NFE showed differences in sensitivity which correlated with cell survival following irradiation. The results suggest that three is the same initial amount of DSBs in cells from all three lines and that the sensitivity to radiation is determined by some additional factors, probably chromatin structure. (author). 18 refs, 5 figs

  3. Comparative study of endophytic and endophytic diazotrophic bacterial communities across rice landraces grown in the highlands of northern Thailand

    OpenAIRE

    Rangjaroen, C.; Rerkasem, B.; Teaumroong, N.; Sungthong, R.; Lumyong, S.

    2014-01-01

    Communities of bacterial endophytes within the rice landraces cultivated in the highlands of northern Thailand were studied using fingerprinting data of 16S rRNA and nifH genes profiling by polymerase chain reaction-denaturing gradient gel electrophoresis. The bacterial communities' richness, diversity index, evenness, and stability were varied depending on the plant tissues, stages of growth, and rice cultivars. These indices for the endophytic diazotrophic bacteria within the landrace rice ...

  4. Evaluation of different PCR primers for denaturing gradient gel electrophoresis (DGGE) analysis of fungal community structure in traditional fermentation starters used for Hong Qu glutinous rice wine.

    Science.gov (United States)

    Lv, Xu-Cong; Jiang, Ya-Jun; Liu, Jie; Guo, Wei-Ling; Liu, Zhi-Bin; Zhang, Wen; Rao, Ping-Fan; Ni, Li

    2017-08-16

    Denaturing gradient gel electrophoresis (DGGE) has become a widely used tool to examine microbial community structure. However, when DGGE is applied to evaluate the fungal community of traditional fermentation starters, the choice of hypervariable ribosomal RNA gene regions is still controversial. In the current study, several previously published fungal PCR primer sets were compared and evaluated using PCR-DGGE, with the purpose of screening a suitable primer set to study the fungal community of traditional fermentation starters for Hong Qu glutinous rice wine. Firstly, different primer sets were used to amplify different hypervariable regions from pure fungal cultures. Except NS1/FR1+ and ITS1fGC/ITS4, other primer sets (NL1+/LS2R, NL3A/NL4GC, FF390/FR1+, NS1/GCFung, NS3+/YM951r and ITS1fGC/ITS2r) amplified the target DNA sequences successfully. Secondly, the selected primer sets were further evaluated based on their resolution to distinguish different fungal cultures through DGGE fingerprints. Three primer sets (NL1+/LS2R, NS1/GCFung and ITS1fGC/ITS2r) were finally selected for investigating the fungal community structure of different traditional fermentation starters for Hong Qu glutinous rice wine. The internal transcribed spacer (ITS) region amplified by ITS1fGC/ITS2r, which is more hypervariable than the 18S rRNA gene and 26S rRNA gene, provides an excellent tool to separate amplification products of different fungal species. Results indicated that PCR-DGGE profile using ITS1fGC/ITS2r showed more abundant fungal species than that using NL1+/LS2R and NS1/GCFung. Therefore, ITS1fGC/ITS2r is the most suitable primer set for PCR-DGGE analysis of fungal community structure in traditional fermentation starters for Hong Qu glutinous rice wine. DGGE profiles based on ITS1fGC/ITS2r revealed the presence of twenty-four fungal species in traditional fermentation starter. A significant difference of fungal community can be observed directly from DGGE fingerprints and

  5. Analysis of coupled mass transfer and sol-gel reaction in a two-phase system

    NARCIS (Netherlands)

    Castelijns, H.J.; Huinink, H.P.; Pel, L.; Zitha, P.L.J.

    2006-01-01

    The coupled mass transfer and chemical reactions of a gel-forming compound in a two-phase system were studied in detail. Tetra-methyl-ortho-silicate (TMOS) is often used as a precursor in sol-gel chemistry to produce silica gels in aqueous systems. TMOS can also be mixed with many hydrocarbons

  6. Mapping and identification of interferon gamma-regulated HeLa cell proteins separated by immobilized pH gradient two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Shaw, A.; Larsen, M.; Roepstorff, P.

    1999-01-01

    magnitude of IFN-gamma responsive genes has been reported previously. Our goal is to identify and map IFN-gamma-regulated HeLa cell proteins to the two-dimensional polyacrylamide gel electrophoresis with the immobilized pH gradient (IPG) two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) system...

  7. Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics.

    Science.gov (United States)

    Otero, Toribio F

    2017-01-18

    In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (E a ), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction. This conformational energy becomes an empirical magnitude. E a , k, α and β include and provide quantitative conformational and structural information. The chemical kinetics becomes structural chemical kinetics (SCK) for reactions driving conformational movements of the reactants. The electrochemically stimulated conformational relaxation model describes empirical results and some results from the literature for biochemical reactions. In parallel the development of an emerging technological world of soft, wet, multifunctional and biomimetic tools and anthropomorphic robots driven by reactions of the constitutive material, as in biological organs, can be now envisaged being theoretically supported by the kinetic model.

  8. Effect of free cysteine on the denaturation and aggregation of holo α-lactalbumin

    DEFF Research Database (Denmark)

    Nielsen, Line R.; Lund, Marianne N.; Davies, Michael J.

    2018-01-01

    α-Lactalbumin (α-LA) is a key commercial whey protein for nutritional purposes. The holo protein (calcium saturated) is considered the most heat stable whey protein, capable of refolding from unfolded states under many conditions. This is due to the absence of free thiols (cysteine residues......) that are typically involved in thermal aggregation and thiol–disulphide exchange reactions of other whey proteins. Heating (0–120 min at 90 °C, pH 7.0) holo α-LA generates free thiols through thermal cleavage of disulphide bonds, resulting in aggregates comprising unfolded α-LA species. The addition of free cysteine...... promotes the formation of soluble aggregates, effectively decreasing the holding time required to reach a particular aggregate size in a dose-dependent manner (0.35–1.4 mM cysteine). Excess cysteine (≥14 mM) causes a destabilisation of α-LA, shown by decreased denaturation temperature and gel formation...

  9. Numerical Solutions of Singularly Perturbed Reaction Diffusion Equation with Sobolev Gradients

    Directory of Open Access Journals (Sweden)

    Nauman Raza

    2013-01-01

    Full Text Available Critical points related to the singular perturbed reaction diffusion models are calculated using weighted Sobolev gradient method in finite element setting. Performance of different Sobolev gradients has been discussed for varying diffusion coefficient values. A comparison is shown between the weighted and unweighted Sobolev gradients in two and three dimensions. The superiority of the method is also demonstrated by showing comparison with Newton's method.

  10. Light-induced spatial control of pH-jump reaction at smart gel interface.

    Science.gov (United States)

    Techawanitchai, Prapatsorn; Ebara, Mitsuhiro; Idota, Naokazu; Aoyagi, Takao

    2012-11-01

    We proposed here a 'smart' control of an interface movement of proton diffusion in temperature- and pH-responsive hydrogels using a light-induced spatial pH-jump reaction. A photoinitiated proton-releasing reaction of o-nitrobenzaldehyde (NBA) was integrated into poly(N-isopropylacrylamide-o-2-carboxyisopropylacrylamide) (P(NIPAAm-co-CIPAAm)) hydrogels. NBA-integrated hydrogels demonstrated quick release of proton upon UV irradiation, allowing the pH inside the gel to decrease below the pK(a) of P(NIPAAm-co-CIPAAm) within a minute. The NBA-integrated gel was shown to shrink rapidly upon UV irradiation without polymer "skin layer" formation due to a uniform decrease of pH inside the gel. Spatial control of gel shrinking was also created by irradiating UV light to a limited region of the gel through a photomask. The interface of proton diffusion ("active interface") gradually moved toward non-illuminated area. The apparent position of "active interface", however, did not change remarkably above the LCST, while protons continuously diffused outward direction. This is because the "active interface" also moved inward direction as gel shrank above the LCST. As a result, slow movement of the apparent interface was observed. The NBA-integrated gel was also successfully employed for the controlled release of an entrapped dextran in a light controlled manner. This system is highly promising as smart platforms for triggered and programmed transportation of drugs. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. Molecular diagnostics of periodontitis.

    Science.gov (United States)

    Korona-Głowniak, Izabela; Siwiec, Radosław; Berger, Marcin; Malm, Anna; Szymańska, Jolanta

    2017-01-28

    The microorganisms that form dental plaque are the main cause of periodontitis. Their identification and the understanding of the complex relationships and interactions that involve these microorganisms, environmental factors and the host's health status enable improvement in diagnostics and targeted therapy in patients with periodontitis. To this end, molecular diagnostics techniques (both techniques based on the polymerase chain reaction and those involving nucleic acid analysis via hybridization) come increasingly into use. On the basis of a literature review, the following methods are presented: polymerase chain reaction (PCR), real-time polymerase chain reaction (real-time PCR), 16S rRNA-encoding gene sequencing, checkerboard and reverse-capture checkerboard hybridization, microarrays, denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), as well as terminal restriction fragment length polymorphism (TRFLP) and next generation sequencing (NGS). The advantages and drawbacks of each method in the examination of periopathogens are indicated. The techniques listed above allow fast detection of even small quantities of pathogen present in diagnostic material and prove particularly useful to detect microorganisms that are difficult or impossible to grow in a laboratory.

  12. On the radioimmunological determination of native and heat denaturated protein

    International Nuclear Information System (INIS)

    Menzel, E.J.; Glatz, F.; Technische Univ., Vienna

    1981-01-01

    Precipitation radioimmunoassay, solid phase radioimmunoassay and passive hemagglutination were examined for their efficiency in the determination of native or denaturated soy proteins. Native as well as autoclaved soy protein could be determined quantitatively in the precipitation radioimmunoassay, using antisera directed against the native product. In the solid phase technique only the autoclaved soy protein could be detected with high sensitivity. In the passive hemagglutination reaction, no agglutination could be observed with erythrocytes coated with autoclaved soy protein. Only antisera against the denaturated (autoclaved) soy protein agglutinated these erythrocytes. (orig.) [de

  13. Correlation of acidic and basic carrier ampholyte and immobilized pH gradient two-dimensional gel electrophoresis patterns based on mass spectrometric protein identification

    DEFF Research Database (Denmark)

    Nawrocki, A; Larsen, Martin Røssel; Podtelejnikov, A V

    1998-01-01

    Separation of proteins on either carrier ampholyte-based or immobilized pH gradient-based two-dimensional (2-D) gels gives rise to electrophoretic patterns that are difficult to compare visually. In this paper we have used matrix-assisted laser desorption/ionization mass spectrometry (MALDI......-MS) to determine the identities of 335 protein spots in these two 2-D gel systems, including a substantial number of basic proteins which had never been identified before. Proteins that were identified in both gel systems allowed us to cross-reference the gel patterns. Vector analysis of these cross...

  14. Approach to analysis of single nucleotide polymorphisms by automated constant denaturant capillary electrophoresis

    International Nuclear Information System (INIS)

    Bjoerheim, Jens; Abrahamsen, Torveig Weum; Kristensen, Annette Torgunrud; Gaudernack, Gustav; Ekstroem, Per O.

    2003-01-01

    Melting gel techniques have proven to be amenable and powerful tools in point mutation and single nucleotide polymorphism (SNP) analysis. With the introduction of commercially available capillary electrophoresis instruments, a partly automated platform for denaturant capillary electrophoresis with potential for routine screening of selected target sequences has been established. The aim of this article is to demonstrate the use of automated constant denaturant capillary electrophoresis (ACDCE) in single nucleotide polymorphism analysis of various target sequences. Optimal analysis conditions for different single nucleotide polymorphisms on ACDCE are evaluated with the Poland algorithm. Laboratory procedures include only PCR and electrophoresis. For direct genotyping of individual SNPs, the samples are analyzed with an internal standard and the alleles are identified by co-migration of sample and standard peaks. In conclusion, SNPs suitable for melting gel analysis based on theoretical thermodynamics were separated by ACDCE under appropriate conditions. With this instrumentation (ABI 310 Genetic Analyzer), 48 samples could be analyzed without any intervention. Several institutions have capillary instrumentation in-house, thus making this SNP analysis method accessible to large groups of researchers without any need for instrument modification

  15. Silica Gel-Mediated Organic Reactions under Organic Solvent-Free Conditions

    Directory of Open Access Journals (Sweden)

    Satoaki Onitsuka

    2012-09-01

    Full Text Available Silica gel was found to be an excellent medium for some useful organic transformations under organic solvent-free conditions, such as (1 the Friedel-Crafts-type nitration of arenes using commercial aqueous 69% nitric acid alone at room temperature, (2 one-pot Wittig-type olefination of aldehydes with activated organic halides in the presence of tributyl- or triphenylphosphine and Hunig’s base, and (3 the Morita-Baylis-Hillman reaction of aldehydes with methyl acrylate. After the reactions, the desired products were easily obtained in good to excellent yields through simple manipulation.

  16. LINKAGE ANALYSIS BY 2-DIMENSIONAL DNA TYPING

    NARCIS (Netherlands)

    MEERMAN, GJT; MULLAART, E; VANDERMEULEN, MA; DENDAAS, JHG; MOROLLI, B; UITTERLINDEN, AG; VIJG, J

    1993-01-01

    In two-dimensional (2-D) DNA typing, genomic DNA fragments are separated, first according to size by electrophoresis in a neutral polyacrylamide gel and second according to sequence by denaturing gradient gel electrophoresis, followed by hybridization analysis using micro- and minisatellite core

  17. Linkage analysis by two-dimensional DNA typing

    NARCIS (Netherlands)

    te Meerman, G J; Mullaart, E; Meulen ,van der Martin; den Daas, J H; Morolli, B; Uitterlinden, A G; Vijg, J

    1993-01-01

    In two-dimensional (2-D) DNA typing, genomic DNA fragments are separated, first according to size by electrophoresis in a neutral polyacrylamide gel and second according to sequence by denaturing gradient gel electrophoresis, followed by hybridization analysis using micro- and minisatellite core

  18. Silver and Cyanine Staining of Oligonucleotides in Polyacrylamide Gel.

    Science.gov (United States)

    Tang, Weizhong; Zhou, Huafu; Li, Wei

    2015-01-01

    To explore why some oligonucleotides in denaturing polyacrylamide gel could not be silver-stained, 134 different oligonucleotides were analyzed using denaturing polyacrylamide gel electrophoresis stained with silver and asymmetric cyanine. As a result, we found that the sensitivity of oligos (dA), (dC), (dG) and (dT) to silver staining could be ranged as (dA) > (dG) > (dC) > (dT) from high to low. It was unexpected that oligo (dT) was hard to be silver-stained. Moreover, the silver staining of an oligonucleotide containing base T could be partially or completely inhibited by base T. The inhibition of silver staining by base T was a competitive inhibition which could be affected by the amounts of the argyrophil nucleobase and base T, the cis-distance between the argyrophil nucleobase and base T, and the gel concentration. The changes of the intensity of an oligonucleotide band caused by the changes of DNA base composition were diverse and interesting. The intensity of some oligonucleotide bands would significantly change when the changes of DNA base composition accumulated to a certain extent (usually ≥ 4 nt). The sensitivity of cyanine staining of ≤ 11-nt long oligonucleotides could be enhanced about 250-fold by fixing the gels with methanol fixing solution.

  19. Molecular diagnostics of periodontitis

    Directory of Open Access Journals (Sweden)

    Izabela Korona-Głowniak

    2017-01-01

    Full Text Available The microorganisms that form dental plaque are the main cause of periodontitis. Their identification and the understanding of the complex relationships and interactions that involve these microorganisms, environmental factors and the host’s health status enable improvement in diagnostics and targeted therapy in patients with periodontitis. To this end, molecular diagnostics techniques (both techniques based on the polymerase chain reaction and those involving nucleic acid analysis via hybridization come increasingly into use. On the basis of a literature review, the following methods are presented: polymerase chain reaction (PCR, real-time polymerase chain reaction (real-time PCR, 16S rRNA-encoding gene sequencing, checkerboard and reverse-capture checkerboard hybridization, microarrays, denaturing gradient gel electrophoresis (DGGE, temperature gradient gel electrophoresis (TGGE, as well as terminal restriction fragment length polymorphism (TRFLP and next generation sequencing (NGS. The advantages and drawbacks of each method in the examination of periopathogens are indicated. The techniques listed above allow fast detection of even small quantities of pathogen present in diagnostic material and prove particularly useful to detect microorganisms that are difficult or impossible to grow in a laboratory.

  20. Denatured fuel cycles

    International Nuclear Information System (INIS)

    Till, C.E.

    1979-01-01

    This paper traces the history of the denatured fuel concept and discusses the characteristics of fuel cycles based on the concept. The proliferation resistance of denatured fuel cycles, the reactor types they involve, and the limitations they place on energy generation potential are discussed. The paper concludes with some remarks on the outlook for such cycles

  1. Acetic acid denaturing pulsed field capillary electrophoresis for RNA separation.

    Science.gov (United States)

    Li, Zhenqing; Dou, Xiaoming; Ni, Yi; Sumitomo, Keiko; Yamaguchi, Yoshinori

    2010-10-01

    Based on our previous work of in-capillary denaturing polymer electrophoresis, we present a study of RNA molecular separation up to 6.0 kilo nucleotide by pulsed field CE. This is the first systematic investigation of electrophoresis of a larger molecular mass RNA in linear hydroxyethylcellulose (HEC) under pulsed field conditions. The parameters that may influence the separation performance, e.g. gel polymer concentration, modulation depth and pulse frequency, are analyzed in terms of resolution and mobility. For denaturing and separating RNA in the capillary simultaneously, 2 M acetic acid was added into the HEC polymer to serve as separation buffer. Result shows that (i) in pulsed field conditions, RNA separation can be achieved in a wide range of concentration of HEC polymer, and RNA fragments between 0.3 and 0.6 kilo nucleotide are sensitive to the polymer concentration; (ii) under certain pulsed field conditions, RNA fragments move linearly as the modulation depth increases; (iii) 12.5 Hz is the resonance frequency for RNA reorientation time and applied frequency.

  2. Population Structure and Abundance of Arsenite-Oxidizing Bacteria along an Arsenic Pollution Gradient in Waters of the Upper Isle River Basin, France▿ †

    Science.gov (United States)

    Quéméneur, Marianne; Cébron, Aurélie; Billard, Patrick; Battaglia-Brunet, Fabienne; Garrido, Francis; Leyval, Corinne; Joulian, Catherine

    2010-01-01

    Denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR (qPCR) were successfully developed to monitor functional aoxB genes as markers of aerobic arsenite oxidizers. DGGE profiles showed a shift in the structure of the aoxB-carrying bacterial population, composed of members of the Alpha-, Beta- and Gammaproteobacteria, depending on arsenic (As) and Eh levels in Upper Isle River Basin waters. The highest aoxB gene densities were found in the most As-polluted oxic surface waters but without any significant correlation with environmental factors. Arsenite oxidizers seem to play a key role in As mobility in As-impacted waters. PMID:20453153

  3. Design of Autonomous Gel Actuators

    Directory of Open Access Journals (Sweden)

    Shuji Hashimoto

    2011-01-01

    Full Text Available In this paper, we introduce autonomous gel actuators driven by chemical energy. The polymer gels prepared here have cyclic chemical reaction networks. With a cyclic reaction, the polymer gels generate periodical motion. The periodic motion of the gel is produced by the chemical energy of the oscillatory Belouzov-Zhabotinsky (BZ reaction. We have succeeded in making synthetic polymer gel move autonomously like a living organism. This experimental fact represents the great possibility of the chemical robot.

  4. Electrochemical redox reactions in solvated silica sol-gel glass

    International Nuclear Information System (INIS)

    Opallo, M.

    2002-01-01

    The studies of electrochemical redox reactions in solvated silica sol-gel glass were reviewed. The methodology of the experiments with emphasis on the direct preparation of the solid electrolyte and the application ultra microelectrodes was described. Generally, the level of the electrochemical signal is not much below that observed in liquid electrolyte. The current depends on time elapsed after gelation, namely the longer time, the smaller current. The differences between electrochemical behaviour of the redox couples in monoliths and thin layers were described. (author)

  5. Gel-aided sample preparation (GASP)--a simplified method for gel-assisted proteomic sample generation from protein extracts and intact cells.

    Science.gov (United States)

    Fischer, Roman; Kessler, Benedikt M

    2015-04-01

    We describe a "gel-assisted" proteomic sample preparation method for MS analysis. Solubilized protein extracts or intact cells are copolymerized with acrylamide, facilitating denaturation, reduction, quantitative cysteine alkylation, and matrix formation. Gel-aided sample preparation has been optimized to be highly flexible, scalable, and to allow reproducible sample generation from 50 cells to milligrams of protein extracts. This methodology is fast, sensitive, easy-to-use on a wide range of sample types, and accessible to nonspecialists. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Exploring encapsulation mechanism of DNA and mononucleotides in sol-gel derived silica.

    Science.gov (United States)

    Kapusuz, Derya; Durucan, Caner

    2017-07-01

    The encapsulation mechanism of DNA in sol-gel derived silica has been explored in order to elucidate the effect of DNA conformation on encapsulation and to identify the nature of chemical/physical interaction of DNA with silica during and after sol-gel transition. In this respect, double stranded DNA and dAMP (2'-deoxyadenosine 5'-monophosphate) were encapsulated in silica using an alkoxide-based sol-gel route. Biomolecule-encapsulating gels have been characterized using UV-Vis, 29 Si NMR, FTIR spectroscopy and gas adsorption (BET) to investigate chemical interactions of biomolecules with the porous silica network and to examine the extent of sol-gel reactions upon encapsulation. Ethidium bromide intercalation and leach out tests showed that helix conformation of DNA was preserved after encapsulation. For both biomolecules, high water-to-alkoxide ratio promoted water-producing condensation and prevented alcoholic denaturation. NMR and FTIR analyses confirmed high hydraulic reactivity (water adsorption) for more silanol groups-containing DNA and dAMP encapsulated gels than plain silica gel. No chemical binding/interaction occurred between biomolecules and silica network. DNA and dAMP encapsulated silica gelled faster than plain silica due to basic nature of DNA or dAMP containing buffer solutions. DNA was not released from silica gels to aqueous environment up to 9 days. The chemical association between DNA/dAMP and silica host was through phosphate groups and molecular water attached to silanols, acting as a barrier around biomolecules. The helix morphology was found not to be essential for such interaction. BET analyses showed that interconnected, inkbottle-shaped mesoporous silica network was condensed around DNA and dAMP molecules.

  7. Viscoplastic fracture transition of a biopolymer gel.

    Science.gov (United States)

    Frieberg, Bradley R; Garatsa, Ray-Shimry; Jones, Ronald L; Bachert, John O; Crawshaw, Benjamin; Liu, X Michael; Chan, Edwin P

    2018-06-13

    Physical gels are swollen polymer networks consisting of transient crosslink junctions associated with hydrogen or ionic bonds. Unlike covalently crosslinked gels, these physical crosslinks are reversible thus enabling these materials to display highly tunable and dynamic mechanical properties. In this work, we study the polymer composition effects on the fracture behavior of a gelatin gel, which is a thermoreversible biopolymer gel consisting of denatured collagen chains bridging physical network junctions formed from triple helices. Below the critical volume fraction for chain entanglement, which we confirm via neutron scattering measurements, we find that the fracture behavior is consistent with a viscoplastic type process characterized by hydrodynamic friction of individual polymer chains through the polymer mesh to show that the enhancement in fracture scales inversely with the squared of the mesh size of the gelatin gel network. Above this critical volume fraction, the fracture process can be described by the Lake-Thomas theory that considers fracture as a chain scission process due to chain entanglements.

  8. Single DNA denaturation and bubble dynamics

    DEFF Research Database (Denmark)

    Metzler, Ralf; Ambjörnsson, Tobias; Hanke, Andreas

    2009-01-01

    While the Watson-Crick double-strand is the thermodynamically stable state of DNA in a wide range of temperature and salt conditions, even at physiological conditions local denaturation bubbles may open up spontaneously due to thermal activation. By raising the ambient temperature, titration......, or by external forces in single molecule setups bubbles proliferate until full denaturation of the DNA occurs. Based on the Poland-Scheraga model we investigate both the equilibrium transition of DNA denaturation and the dynamics of the denaturation bubbles with respect to recent single DNA chain experiments...... for situations below, at, and above the denaturation transition. We also propose a new single molecule setup based on DNA constructs with two bubble zones to measure the bubble coalescence and extract the physical parameters relevant to DNA breathing. Finally we consider the interplay between denaturation...

  9. Spatial and vertical distribution of bacteria in the Pearl River estuary ...

    African Journals Online (AJOL)

    Yomi

    2012-01-31

    Jan 31, 2012 ... Key words: Bacterial community structure, the Pearl River estuary, denaturing gradient gel electrophoresis ... change rapidly in response to the change of environ- ..... Chlorinated and polycyclic aromatic hydrocarbons in.

  10. Single DNA denaturation and bubble dynamics

    International Nuclear Information System (INIS)

    Metzler, Ralf; Ambjoernsson, Tobias; Hanke, Andreas; Fogedby, Hans C

    2009-01-01

    While the Watson-Crick double-strand is the thermodynamically stable state of DNA in a wide range of temperature and salt conditions, even at physiological conditions local denaturation bubbles may open up spontaneously due to thermal activation. By raising the ambient temperature, titration, or by external forces in single molecule setups bubbles proliferate until full denaturation of the DNA occurs. Based on the Poland-Scheraga model we investigate both the equilibrium transition of DNA denaturation and the dynamics of the denaturation bubbles with respect to recent single DNA chain experiments for situations below, at, and above the denaturation transition. We also propose a new single molecule setup based on DNA constructs with two bubble zones to measure the bubble coalescence and extract the physical parameters relevant to DNA breathing. Finally we consider the interplay between denaturation bubbles and selectively single-stranded DNA binding proteins.

  11. Bacterial biomass and DNA diversity in an alluvial meadow soil upon long-term fertilization

    NARCIS (Netherlands)

    Naumova, N.B.; Kuikman, P.J.

    2001-01-01

    The denaturing gradient gel-electrophoresis of bacterial DNA fragments and the assessment of bacterial biomass revealed changes in the diversity of the bacterial community in a meadow alluvial soil upon long-term fertilization.

  12. Spectroscopic and electrochemical characterization of cytochrome c encapsulated in a bio sol-gel matrix.

    Science.gov (United States)

    Deriu, Daniela; Pagnotta, Sara Emanuela; Santucci, Roberto; Rosato, Nicola

    2008-08-01

    Sol-gel technique represents a remarkably versatile method for protein encapsulation. To enhance sol-gel biocompatibility, systems envisaging the presence of calcium and phosphates in the sol-gel composition were recently prepared and investigated. Unfortunately, the low pH at which solutions were prepared (pH proteins, because the acidic environment induces protein denaturation. In this paper we apply a new protocol based on the introduction of calcium nitrate to the inorganic phase, with formation of a binary bioactive system. In this case protein encapsulation results versatile and secure, being achieved at a pH close to neutrality (pH 6.0); also, the presence of calcium is expected to enhance system biocompatibility. To determine the properties of the salt-doped sol-gel and the influence exerted on entrapped biosystems, the structural and functional properties of embedded cytochrome c have been investigated. Data obtained indicate that the salt-doped sol-gel induces no significant change in the structure and the redox properties of the embedded protein; also, the matrix increases protein stability. Interestingly, the presence of calcium nitrate appears determinant for refolding of the acid-denatured protein. This is of interest in the perspective of future applications in biosensoristic area.

  13. Apparatus for investigating the reactions of soft-bodied invertebrates to controlled humidity gradients.

    Science.gov (United States)

    Russell, Joshua; Pierce-Shimomura, Jonathan T

    2014-11-30

    While many studies have assayed behavioral responses of animals to chemical, temperature and light gradients, fewer studies have assayed how animals respond to humidity gradients. Our novel humidity chamber has allowed us to study the neuromolecular basis of humidity sensation in the nematode Caenorhabditis elegans (Russell et al., 2014). We describe an easy-to-construct, low-cost humidity chamber to assay the behavior of small animals, including soft-bodied invertebrates, in controlled humidity gradients. We show that our humidity-chamber design is amenable to soft-bodied invertebrates and can produce reliable gradients ranging 0.3-8% RH/cm across a 9-cm long × 7.5-cm wide gel-covered arena. Previous humidity chambers relied on circulating dry and moist air to produce a steep humidity gradient in a small arena (e.g. Sayeed and Benzer, 1996). To remove the confound of moving air that may elicit mechanical responses independent of humidity responses, our chamber controlled the humidity gradient using reservoirs of hygroscopic materials. Additionally, to better observe the behavioral mechanisms for humidity responses, our chamber provided a larger arena. Although similar chambers have been described previously, these approaches were not suitable for soft-bodied invertebrates or for easy imaging of behavior because they required that animals move across wire or fabric mesh. The general applicability of our humidity chamber overcomes limitations of previous designs and opens the door to observe the behavioral responses of soft-bodied invertebrates, including genetically powerful C. elegans and Drosophila larvae. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Quantitative enzyme activity determination with zeptomole sensitivity by microfluidic gradient-gel zymography.

    Science.gov (United States)

    Hughes, Alex J; Herr, Amy E

    2010-05-01

    We describe a sensitive zymography technique that utilizes an automated microfluidic platform to report enzyme molecular weight, amount, and activity (including k(cat) and K(m)) from dilute protein mixtures. Calf intestinal alkaline phosphatase (CIP) is examined in detail as a model enzyme system, and the method is also demonstrated for horseradish peroxidase (HRP). The 40 min assay has a detection limit of 5 zmol ( approximately 3 000 molecules) of CIP. Two-step pore-limit electrophoresis with enzyme assay (PLENZ) is conducted in a single, straight microchannel housing a polyacrylamide (PA) pore-size gradient gel. In the first step, pore limit electrophoresis (PLE) sizes and pseudoimmobilizes resolved proteins. In the second step, electrophoresis transports both charged and neutral substrates into the PLE channel to the entrapped proteins. Arrival of substrate at the resolved enzyme band generates fluorescent product that reveals enzyme molecular weight against a fluorescent protein ladder. Additionally, the PLENZ zymography assay reports the kinetic properties of CIP in a fully quantitative manner. In contrast to covalent enzyme immobilization, physical pseudoimmobilization of CIP in the PA gel does not significantly reduce its maximum substrate turnover rate. However, an 11-fold increase in the Michaelis constant (over the free solution value) is observed, consistent with diffusional limitations on substrate access to the enzyme active site. PLENZ offers a robust platform for rapid and multiplexed functional analysis of heterogeneous protein samples in drug discovery, clinical diagnostics, and biocatalyst engineering.

  15. Colloid molecular weight estimation by gel chromatography/acrylamide gel electrophoresis

    International Nuclear Information System (INIS)

    Liberatore, F.A.; Dearborn, C.; Nigam, S.; Poon, C.; Camin, L.; Liteplo, M.

    1984-01-01

    Size or molecular weight (MW) estimation of radiolabeled collides in aqueous solutions has long been a problem. The authors have prepared several minimicroaggregated albumin colloids (mμAA) by heat denaturation of stannous-containing HSA solutions at pH 7.0, 7.5, and 8.5). The resulting colloids were labeled with Tc-99m and compared with Au-198 colloid and Tc-99m-antimony sulfide colloid (Tc-99m-Sb/sub 2/S3) by gel chromatography and gel electrophoresis. Tc-99mm-mμAA aggregated at pH 7.0 and the Au-198 colloid appeared in the external void volume of a BioRad A5.0 agarose column indicating an apparent MW of > 5 x 10/sup 6/ daltons. The pH7.5 Tc-99m-mμAA, migrated within the filtration range of the column as did a small fraction of Tc-99m-Sb/sub 2/S/sub 3/, suggesting that the MW is between 6 x 10/sup 4/ - 5 x 10/sup 6/ daltons. The Tc-99m-mμAA, aggregated at pH 8.5, had an apparent MW on gel filtration similar to that of untreated albumin, MW 6.6 x 10-/sup 4/ daltons. The mobilities of the colloids, on acrylamide disc gel electrophoresis, were consistent with the results on gel chromatography. The largest colloids, Au-198 colloid and pH 7.0 Tc-99m-mμAA, barely entered the separating gel; intermediate sized colloids, a small fraction of Tc-99m-Sb/sub 2/S/sub 3/ and pH 7.5 Tc-99m-mμAA migrated farther into the separating gel; while pH 8.5 Tc-99m-mμAA had mobility approaching that of untreated albumin. Lymphoscintigraphy studies using these colloids in animals showed the predicted, particle size-related differences in migration and clearance. The authors conclude that gel chromatography and gel electrophoresis are useful methods for estimating the apparent size of the colloidal particles

  16. Development and Characterization of Titanium Dioxide Gel with Encapsulated Bacteriorhodopsin for Hydrogen Production.

    Science.gov (United States)

    Johnson, Kaitlin E; Gakhar, Sukriti; Risbud, Subhash H; Longo, Marjorie L

    2018-06-06

    We study bacteriorhodopsin (BR) in its native purple membrane encapsulated within amorphous titanium dioxide, or titania, gels and in the presence of titania sol-particles to explore this system for hydrogen production. Förster resonance energy transfer between BR and titanium dioxide sol particles was used to conclude that there is nanometer-scale proximity of bacteriorhodopsin to the titanium dioxide. The detection of BR-titania sol aggregates by fluorescence anisotropy and particle sizing indicated the affinity amorphous titania has for BR without the use of additional cross-linkers. UV-Visible spectroscopy of BR-titania gels show that methanol addition did not denature BR at a 25 mM concentration presence as a sacrificial electron donor. Additionally, confinement of BR in the gels significantly limited protein denaturation at higher concentration of added methanol or ethanol. Subsequently, titania gels fabricated through the sol-gel process using a titanium ethoxide precursor, water and the addition of 25 mM methanol were used to encapsulate BR and a platinum reduction catalyst for the production of hydrogen gas under white light irradiation. The inclusion of 5 µM bacteriorhodopsin resulted in a hydrogen production rate of about 3.8 µmole hydrogen mL -1 hr -1 , an increase of 52% compared to gels containing no protein. Electron transfer and proton pumping by BR in close proximity to the titania gel surface are feasible explanations for the enhanced production of hydrogen without the need to crosslink BR to the titania gel. This work sets the stage for further developments of amorphous, rather than crystalline, titania-encapsulated bacteriorhodopsin for solar-driven hydrogen production through water-splitting.

  17. Detection of AGEs as markers for carbohydrate metabolism and protein denaturation.

    Science.gov (United States)

    Nagai, Ryoji; Shirakawa, Jun-Ichi; Fujiwara, Yukio; Ohno, Rei-Ichi; Moroishi, Narumi; Sakata, Noriyuki; Nagai, Mime

    2014-07-01

    Approximately 100 years have passed since the Maillard reaction was first reported in the field of food chemistry as a condensation reaction between reducing sugars and amino acids. This reaction is thought to progress slowly primarily from glucose with proteins in vivo. An early-stage product, called the "Amadori product", is converted into advanced glycation end products. Those accumulate in the body in accordance with age, with such accumulation being enhanced by lifestyle-related diseases that result in the denaturation of proteins. Recent studies have demonstrated that intermediate carbonyls are generated by several pathways, and rapidly generate many glycation products. However, accurate quantification of glycation products in vivo is difficult due to instability and differences in physicochemical properties. In this connection, little is known about the relationship between the structure of glycation products and pathology. Furthermore, the interaction between proteins modified by glycation and receptors for advanced glycation end products is also known to induce the production of several inflammatory cytokines. Therefore, those inhibitors have been developed over the world to prevent lifestyle-related diseases. In this review, we describe the process of protein denaturation induced by glycation and discuss the possibility of using the process as a marker of age-related diseases.

  18. Molecular analysis of the biomass of a fluidized bed reactor treating synthetic vinasse at anaerobic and micro-aerobic conditions

    NARCIS (Netherlands)

    Rodriguez, E.; Lopes, A.; Fdz-Polanco, M.; Stams, A.J.M.; Garcia Encina, P.A.

    2012-01-01

    The microbial communities (Bacteria and Archaea) established in an anaerobic fluidized bed reactor used to treat synthetic vinasse (betaine, glucose, acetate, propionate, and butyrate) were characterized by denaturing gradient gel electrophoresis (DGGE) and phylogenetic analysis. This study was

  19. Comparison between different bio-treatments of a hydrocarbon ...

    African Journals Online (AJOL)

    We investigated the bio-remediation of a hydrocarbon contaminated soil pile that ... Nutrient and microbial amendments did not confer any long-term benefit on the ... Denaturing gradient gel electrophoresis (DGGE) analyses of 16S rDNA and ...

  20. 27 CFR 19.456 - Adding denaturants.

    Science.gov (United States)

    2010-04-01

    ... proprietor shall submit a flow diagram of the intended process or method of adding denaturants. (Sec. 201... OF THE TREASURY LIQUORS DISTILLED SPIRITS PLANTS Denaturing Operations and Manufacture of Articles...

  1. Effect of different salt adaptation strategies on the microbial diversity, activity, and settling of nitrifying sludge in sequencing batch reactors

    NARCIS (Netherlands)

    Bassin, J.P.; Kleerebezem, R.; Muyzer, G.; Rosado, A.S.; Van Loosdrecht, M.C.M.; Dezotti, M.

    2011-01-01

    The effect of salinity on the activity of nitrifying bacteria, floc characteristics, and microbial community structure accessed by fluorescent in situ hybridization and polymerase chain reaction–denaturing gradient gel electrophoresis techniques was investigated. Two sequencing batch reactors (SRB1

  2. Evidence for Vertical Transmission of Bacterial Symbionts from Adult to Embryo in the Caribbean Sponge Svenzea zeai

    KAUST Repository

    Lee, O. O.; Chui, P. Y.; Wong, Y. H.; Pawlik, J. R.; Qian, P.-Y.

    2009-01-01

    to progeny are largely unknown. In this study, both a 16S rRNA gene-based fingerprinting technique (denaturing gradient gel electrophoresis [DGGE]) and clone library analysis were applied to compare the bacterial communities associated with adults and embryos

  3. Synthesis and application of silica gel modified with alkoxyalcohols. Alkoxyalcohol shushoku silica gel no gosei to riyo

    Energy Technology Data Exchange (ETDEWEB)

    Moriguchi, T.; Ishiguro, H.; Matsubara, Y.; Yoshihara, M.; Maeshima, T.; Ito, S. (Kinki University, Osaka (Japan). Faculty of Science and Engineering)

    1991-08-20

    Several kinds of silica gel modified by alkoxyalcohols were synthesized by refluxing and dehyration and the organic reactions were studied when these silica gels were used as the catalyst. It could be confirmed by FT-IR spectra, DTA and elementary analysis that alkoxylalcohols adhere to the surface of silica gels without any decomposition. The acetate was produced by using alkyl halides. It was found that the modified silica gels had clearly the catalytic action for the reaction with n-hexyl bromide and dibromoethane although unmodified silica gels did not show the catalytic action. The reducing reaction of carbonyl compounds was carried out. The reaction proceeded at 25 centigrade for acetophenone, cyclohexanone, 1-indanone and 2-octanone to produce the corresponding reduction products. 11 refs., 5 figs., 4 tabs.

  4. Using fluorescence correlation spectroscopy to study conformational changes in denatured proteins.

    Science.gov (United States)

    Sherman, Eilon; Itkin, Anna; Kuttner, Yosef Yehuda; Rhoades, Elizabeth; Amir, Dan; Haas, Elisha; Haran, Gilad

    2008-06-01

    Fluorescence correlation spectroscopy (FCS) is a sensitive analytical tool that allows dynamics and hydrodynamics of biomolecules to be studied under a broad range of experimental conditions. One application of FCS of current interest is the determination of the size of protein molecules in the various states they sample along their folding reaction coordinate, which can be accessed through the measurement of diffusion coefficients. It has been pointed out that the analysis of FCS curves is prone to artifacts that may lead to erroneous size determination. To set the stage for FCS studies of unfolded proteins, we first show that the diffusion coefficients of small molecules as well as proteins can be determined accurately even in the presence of high concentrations of co-solutes that change the solution refractive index significantly. Indeed, it is found that the Stokes-Einstein relation between the measured diffusion coefficient and solution viscosity holds even in highly concentrated glycerol or guanidinium hydrochloride (GuHCl) solutions. These measurements form the basis for an investigation of the structure of the denatured state of two proteins, the small protein L and the larger, three-domain protein adenylate kinase (AK). FCS is found useful for probing expansion in the denatured state beyond the unfolding transition. It is shown that the denatured state of protein L expands as the denaturant concentration increases, in a process akin to the transition from a globule to a coil in polymers. This process continues at least up to 5 M GuHCl. On the other hand, the denatured state of AK does not seem to expand much beyond 2 M GuHCl, a result that is in qualitative accord with single-molecule fluorescence histograms. Because both the unfolding transition and the coil-globule transition of AK occur at a much lower denaturant concentration than those of protein L, a possible correlation between the two phenomena is suggested.

  5. Effect of reaction solvent on hydroxyapatite synthesis in sol-gel process

    Science.gov (United States)

    Nazeer, Muhammad Anwaar; Yilgor, Emel; Yagci, Mustafa Baris; Unal, Ugur; Yilgor, Iskender

    2017-12-01

    Synthesis of hydroxyapatite (HA) through sol-gel process in different solvent systems is reported. Calcium nitrate tetrahydrate (CNTH) and diammonium hydrogen phosphate (DAHP) were used as calcium and phosphorus precursors, respectively. Three different synthesis reactions were carried out by changing the solvent media, while keeping all other process parameters constant. A measure of 0.5 M aqueous DAHP solution was used in all reactions while CNTH was dissolved in distilled water, tetrahydrofuran (THF) and N,N-dimethylformamide (DMF) at a concentration of 0.5 M. Ammonia solution (28-30%) was used to maintain the pH of the reaction mixtures in the 10-12 range. All reactions were carried out at 40 ± 2°C for 4 h. Upon completion of the reactions, products were filtered, washed and calcined at 500°C for 2 h. It was clearly demonstrated through various techniques that the dielectric constant and polarity of the solvent mixture strongly influence the chemical structure and morphological properties of calcium phosphate synthesized. Water-based reaction medium, with highest dielectric constant, mainly produced β-calcium pyrophosphate (β-CPF) with a minor amount of HA. DMF/water system yielded HA as the major phase with a very minor amount of β-CPF. THF/water solvent system with the lowest dielectric constant resulted in the formation of pure HA.

  6. Two dimensional gel electrophoresis using narrow pH 3-5.6 immobilised pH gradient strips identifies potential novel disease biomarkers in plasma or serum

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Bevin Gangadharan & Nicole Zitzmann ### Abstract Two-dimensional gel electrophoresis (2-DE) is a protein separation technique often used to separate plasma or serum proteins in an attempt to identify novel biomarkers. This protocol describes how to run 2-DE gels using narrow pH 3-5.6 immobilised pH gradient strips to separate 2 mg of serum proteins. pH 3-6 ampholytes are used to enhance the solubility of proteins in this pH range before the serum proteins are separated in the...

  7. "Cooperative collapse" of the denatured state revealed through Clausius-Clapeyron analysis of protein denaturation phase diagrams.

    Science.gov (United States)

    Tischer, Alexander; Machha, Venkata R; Rösgen, Jörg; Auton, Matthew

    2018-02-19

    Protein phase diagrams have a unique potential to identify the presence of additional thermodynamic states even when non-2-state character is not readily apparent from the experimental observables used to follow protein unfolding transitions. Two-state analysis of the von Willebrand factor A3 domain has previously revealed a discrepancy in the calorimetric enthalpy obtained from thermal unfolding transitions as compared with Gibbs-Helmholtz analysis of free energies obtained from the Linear Extrapolation Method (Tischer and Auton, Prot Sci 2013; 22(9):1147-60). We resolve this thermodynamic conundrum using a Clausius-Clapeyron analysis of the urea-temperature phase diagram that defines how ΔH and the urea m-value interconvert through the slope of c m versus T, (∂cm/∂T)=ΔH/(mT). This relationship permits the calculation of ΔH at low temperature from m-values obtained through iso-thermal urea denaturation and high temperature m-values from ΔH obtained through iso-urea thermal denaturation. Application of this equation uncovers sigmoid transitions in both cooperativity parameters as temperature is increased. Such residual thermal cooperativity of ΔH and the m-value confirms the presence of an additional state which is verified to result from a cooperative phase transition between urea-expanded and thermally-compact denatured states. Comparison of the equilibria between expanded and compact denatured ensembles of disulfide-intact and carboxyamidated A3 domains reveals that introducing a single disulfide crosslink does not affect the presence of the additional denatured state. It does, however, make a small thermodynamically favorable free energy (∼-13 ± 1 kJ/mol) contribution to the cooperative denatured state collapse transition as temperature is raised and urea concentration is lowered. The thermodynamics of this "cooperative collapse" of the denatured state retain significant compensations between the enthalpy and entropy contributions to the overall

  8. Preparation and characterization of bismuth ruthenate pyrochlore via solid state reaction and sol-gel methods

    Directory of Open Access Journals (Sweden)

    Mayuree Sansernnivet

    2010-01-01

    Full Text Available Bismuth ruthenate pyrochlores, potential cathode materials for intermediate temperature solid oxide fuel cells(ITSOFCs, were prepared via solid-state and sol-gel method. Effects of the preparation routes and conditions on the phase and microstructures of the materials were investigated in this study using XRD and SEM. The study showed that the preparation method and the adding sequence of the starting meterials have a significant effect on the crystal phase and the particle size obtained. Sol-gel synthesis could yield a material with only pyrochlore structure, i.e. Bi2Ru2O7, while the solid state method yielded powder with a small amount of the secondary RuO2 phase. The sol-gel synthesis resulted in materialswith a finer particle size (~0.3-1.0 μm compared to powder synthesized via the solid state reaction method.

  9. Microbial community changes in biological phosphate-removal systems on altering sludge phosphorus content

    NARCIS (Netherlands)

    Liu, WT; Linning, KD; Nakamura, K; Mino, T; Matsuo, T; Forney, LJ

    Biomarkers (respiratory quinones and cellular fatty acids) and denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes were used to characterize the microbial community structure of lab-scale enhanced biological phosphate-removal (EBPR) systems in response to altering sludge

  10. Microbiota dynamics and diversity at different stages of industrial processing of cocoa beans into cocoa powder

    NARCIS (Netherlands)

    Líma, L.J.R.; Velpen, van der V.; Wolkers-Rooijackers, J.C.M.; Kamphuis, H.J.; Zwietering, M.H.; Nout, M.J.R.

    2012-01-01

    We sampled a cocoa powder production line to investigate the impact of processing on the microbial community size and diversity at different stages. Classical microbiological methods were combined with 16S rRNA gene PCR-denaturing gradient gel electrophoresis, coupled with clone library

  11. Genotyping isolates of the entomopathogenic fungus Beauveria ...

    African Journals Online (AJOL)

    Multi-locus denaturing gradient gel electrophoresis (DGGE) analysis was developed to investigate the genotypes of Beauveria bassiana sensu lato. ... These results demonstrated that multi-locus DGGE is a potentially useful molecular marker for genotyping, identifying and tracking the fates of experimentally released ...

  12. Guanidinium-induced denaturation by breaking of salt bridges

    NARCIS (Netherlands)

    Meuzelaar, H.; Panman, M.R.; Woutersen, S.

    2015-01-01

    Despite its wide use as a denaturant, the mechanism by which guanidinium (Gdm+) induces protein unfolding remains largely unclear. Herein, we show evidence that Gdm+ can induce denaturation by disrupting salt bridges that stabilize the folded conformation. We study the Gdm+-​induced denaturation of

  13. Denatured plutonium: a study of deterrent action. Final report

    International Nuclear Information System (INIS)

    Hutchins, B.A.

    1975-07-01

    The safeguarding of nuclear reactor fuel includes physical security methods as well as technological process options. The purpose of this study was to provide a preliminary evaluation of a technological option; the introduction of denaturing as a deterrent to illicit plutonium diversion. Denaturing is accomplished by coextracting some highly-radioactive fission products with the plutonium during reprocessing of spent fuel. The radioactive denaturant is always in companion with the plutonium through all subsequent fuel cycle steps - and serves as a deterrent to diversion or illicit usage of this fissile source. In concept the denaturing approach is simple and straightforward. This report provides a preliminary analysis of denaturing which can be achieved within the framework of present reprocessing technology. The impact of denaturing is indicated by comparison to a conventional (i.e., non-denatured) light water reacter cycle approach

  14. Guanidinium-Induced Denaturation by Breaking of Salt Bridges.

    Science.gov (United States)

    Meuzelaar, Heleen; Panman, Matthijs R; Woutersen, Sander

    2015-12-07

    Despite its wide use as a denaturant, the mechanism by which guanidinium (Gdm(+) ) induces protein unfolding remains largely unclear. Herein, we show evidence that Gdm(+) can induce denaturation by disrupting salt bridges that stabilize the folded conformation. We study the Gdm(+) -induced denaturation of a series of peptides containing Arg/Glu and Lys/Glu salt bridges that either stabilize or destabilize the folded conformation. The peptides containing stabilizing salt bridges are found to be denatured much more efficiently by Gdm(+) than the peptides containing destabilizing salt bridges. Complementary 2D-infrared measurements suggest a denaturation mechanism in which Gdm(+) binds to side-chain carboxylate groups involved in salt bridges. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Modified lignin: Preparation and use in reversible gel via Diels-Alder reaction.

    Science.gov (United States)

    Zhou, Wanpeng; Zhang, Hui; Chen, Fangeng

    2018-02-01

    In this study, popular soda lignin was modified with either furan or maleimide ring, and the modified lignins were subjected to reversible Diels-Alder reaction. A new process was proposed to prepare the functionalized lignin. A long chain was introduced to the hydroxyl groups of lignin, and then either the furan or maleimide ring was added to the other end of the chain. The test results confirmed that either the furan ring or the maleimide ring was bound to lignin. Furan- and maleimide-functionalized lignins were also combined to generate crosslinking via Diels-Alder [4+2] cycloaddition reaction. Under appropriate conditions, the formation of a gel was identified, which reverted to liquid state after retro Diels-Alder reaction upon heating at 120°C. This study reveals the significant versatility and potential of the developed strategy for the utilization of lignin-based recyclable networks. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Community structure and activity of sulfate-reducing bacteria in an intertidal surface sediment: a multi-method approach

    DEFF Research Database (Denmark)

    Llobet-Brossa, E.; Rabus, R.; Böttcher, M.

    2002-01-01

    by the presence of acid-volatile sulfides (AVS, essentially iron monosulfide). Stable sulfur isotope discrimination between dissolved sulfate and AVS was dominated by sulfate reduction. The diversity of SRB was studied using denaturant gradient gel electrophoresis of 16S rDNA, phospholipid fatty acid analysis...

  17. Fate and effect of ingested Bacillus cereus spores and vegetative cells in the intestinal tract of human-flora-associated rats

    DEFF Research Database (Denmark)

    Wilcks, Andrea; Hansen, Bjarne Munk; Hendriksen, Niels Bohse

    2006-01-01

    The fate and effect of Bacillus cereus F4433/73R in the intestine of human-flora-associated rats was studied using bacteriological culturing techniques and PCR-denaturing gradient gel electrophoresis in combination with cell assays and immunoassays for detection of enterotoxins. In faecal samples...

  18. Gastrointestinal microbiota and local inflammation during oxazolone-induced dermatitis in BALB/cA Mice

    DEFF Research Database (Denmark)

    Lundberg, Randi; Knoth Clausen, Susanne; Pang, Wanyong

    2012-01-01

    -induced skin inflammation model of atopic dermatitis. BALB/cA mice were sensitized with oxazolone over a 28-d period and variation in gastrointestinal microbiota in fecal and cecal samples was assessed by PCR-denaturing gradient gel electrophoresis. Clinical parameters included transepidermal water loss, ear...

  19. Molecularly assessed shifts of Bifidobacterium spp. and less diverse microbial communities are characteristic of 5-year-old allergic children

    NARCIS (Netherlands)

    Stsepetova, J.; Sepp, E.; Julge, K.; Vaughan, E.E.; Mikelsaar, M.; Vos, de W.M.

    2007-01-01

    The composition of intestinal microbiota and the Bifidobacterium group community in 20 allergic and 20 nonallergic 5-year-old children was visualized by PCR-denaturing gradient gel electrophoresis (DGGE). The number of dominant bands in the DGGE profiles was smaller in allergic children than in

  20. Shifts in the Microbial Population in Relation to in situ Caries Progression

    NARCIS (Netherlands)

    Thomas, R. Z.; Zijnge, V.; Cicek, A.; de Soet, J. J.; Harmsen, H. J. M.; Huysmans, M. C. D. N. J. M.

    2012-01-01

    The shift in microbial diversity from young to mature plaque, related to caries activity on sound and restored surfaces, was studied using denaturing gradient gel electrophoresis. During a 20-week in situ study on caries progression 8 subjects wearing restored and unrestored dentin and enamel

  1. Shifts in the microbial population in relation to in situ caries progression

    NARCIS (Netherlands)

    Thomas, R.Z.; Zijnge, V.; Ciçek, A.; de Soet, J.J.; Harmsen, H.J.M.; Huysmans, M.C.D.N.J.M.

    2012-01-01

    The shift in microbial diversity from young to mature plaque, related to caries activity on sound and restored surfaces, was studied using denaturing gradient gel electrophoresis. During a 20-week in situ study on caries progression 8 subjects wearing restored and unrestored dentin and enamel

  2. Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction

    Directory of Open Access Journals (Sweden)

    Consolandi Clarissa

    2002-09-01

    Full Text Available Abstract Background PCR amplification of bacterial 16S rRNA genes provides the most comprehensive and flexible means of sampling bacterial communities. Sequence analysis of these cloned fragments can provide a qualitative and quantitative insight of the microbial population under scrutiny although this approach is not suited to large-scale screenings. Other methods, such as denaturing gradient gel electrophoresis, heteroduplex or terminal restriction fragment analysis are rapid and therefore amenable to field-scale experiments. A very recent addition to these analytical tools is represented by microarray technology. Results Here we present our results using a Universal DNA Microarray approach as an analytical tool for bacterial discrimination. The proposed procedure is based on the properties of the DNA ligation reaction and requires the design of two probes specific for each target sequence. One oligo carries a fluorescent label and the other a unique sequence (cZipCode or complementary ZipCode which identifies a ligation product. Ligated fragments, obtained in presence of a proper template (a PCR amplified fragment of the 16s rRNA gene contain either the fluorescent label or the unique sequence and therefore are addressed to the location on the microarray where the ZipCode sequence has been spotted. Such an array is therefore "Universal" being unrelated to a specific molecular analysis. Here we present the design of probes specific for some groups of bacteria and their application to bacterial diagnostics. Conclusions The combined use of selective probes, ligation reaction and the Universal Array approach yielded an analytical procedure with a good power of discrimination among bacteria.

  3. Spatial and vertical distribution of bacteria in the Pearl River estuary ...

    African Journals Online (AJOL)

    In order to investigate the spatial and vertical change of bacteria community structure in the Pearl River estuary sediment, denaturing gradient gel electrophoresis (DGGE) and multivariate statistical analyses were carried out in this study. Results of multidimensional scaling analyses (MDS) were in good agreement with the ...

  4. Bacterial community structure in the Cerasus sachalinensis Kom ...

    African Journals Online (AJOL)

    Jane

    2011-07-21

    Jul 21, 2011 ... The bacterial community structures of the Cerasus sachalinensis Kom. rhizosphere in wild and cultivated soil were studied and the community changes in different growth stages were analyzed by the PCR-denaturing gradient gel electrophoresis (PCR-DGGE) method. The results showed that the bacterial ...

  5. Analyzing Arthropods for the Presence of Bacteria

    OpenAIRE

    Andrews, Elizabeth S.

    2013-01-01

    Bacteria within arthropods can be identified using culture-independent methods. This unit describes protocols for surface sterilization of arthropods, DNA extraction of whole bodies and tissues, touchdown PCR amplification using 16S rDNA general bacteria primers and profiling the bacterial community using denaturing gradient gel electrophoresis.

  6. Analysis of bacterial and fungal community structure in replant ...

    African Journals Online (AJOL)

    High quality DNA is the basis of analyzing bacterial and fungal community structure in replant strawberry rhizosphere soil with the method of denaturing gradient gel electrophoresis (DGGE). DNA of soil microorganisms was extracted from the rhizosphere soil of strawberries planted in different replanted years (0, two, ...

  7. Bacterial diversity in agricultural soils during litter decomposition

    NARCIS (Netherlands)

    Dilly, O.; Bloem, J.; Vos, A.; Munch, J.C.

    2004-01-01

    Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band.

  8. Effect of Elevated Salt Concentrations on the Aerobic Granular Sludge Process : Linking Microbial Activity with Microbial Community Structure

    NARCIS (Netherlands)

    Bassin, J.P.; Pronk, M.; Muyzer, G.; Kleerebezem, R.; Dezotti, M.; Van Loosdrecht, M.C.M.

    2011-01-01

    The long- and short-term effects of salt on biological nitrogen and phosphorus removal processes were studied in an aerobic granular sludge reactor. The microbial community structure was investigated by PCR-denaturing gradient gel electrophoresis (DGGE) on 16S rRNA and amoA genes. PCR products

  9. Surface grafted chitosan gels. Part II. Gel formation and characterization

    DEFF Research Database (Denmark)

    Liu, Chao; Thormann, Esben; Claesson, Per M.

    2014-01-01

    Responsive biomaterial hydrogels attract significant attention due to their biocompatibility and degradability. In order to make chitosan based gels, we first graft one layer of chitosan to silica, and then build a chitosan/poly(acrylic acid) multilayer using the layer-by-layer approach. After...... cross-linking the chitosan present in the polyelectrolyte multilayer, poly(acrylic acid) is partly removed by exposing the multilayer structure to a concentrated carbonate buffer solution at a high pH, leaving a surface-grafted cross-linked gel. Chemical cross-linking enhances the gel stability against...... detachment and decomposition. The chemical reaction between gluteraldehyde, the cross-linking agent, and chitosan was followed in situ using total internal reflection Raman (TIRR) spectroscopy, which provided a molecular insight into the complex reaction mechanism, as well as the means to quantify the cross...

  10. Polymer gel dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Baldock, C [Institute of Medical Physics, School of Physics, University of Sydney (Australia); De Deene, Y [Radiotherapy and Nuclear Medicine, Ghent University Hospital (Belgium); Doran, S [CRUK Clinical Magnetic Resonance Research Group, Institute of Cancer Research, Surrey (United Kingdom); Ibbott, G [Radiation Physics, UT M D Anderson Cancer Center, Houston, TX (United States); Jirasek, A [Department of Physics and Astronomy, University of Victoria, Victoria, BC (Canada); Lepage, M [Centre d' imagerie moleculaire de Sherbrooke, Departement de medecine nucleaire et de radiobiologie, Universite de Sherbrooke, Sherbrooke, QC (Canada); McAuley, K B [Department of Chemical Engineering, Queen' s University, Kingston, ON (Canada); Oldham, M [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Schreiner, L J [Cancer Centre of South Eastern Ontario, Kingston, ON (Canada)], E-mail: c.baldock@physics.usyd.edu.au, E-mail: yves.dedeene@ugent.be

    2010-03-07

    Polymer gel dosimeters are fabricated from radiation sensitive chemicals which, upon irradiation, polymerize as a function of the absorbed radiation dose. These gel dosimeters, with the capacity to uniquely record the radiation dose distribution in three-dimensions (3D), have specific advantages when compared to one-dimensional dosimeters, such as ion chambers, and two-dimensional dosimeters, such as film. These advantages are particularly significant in dosimetry situations where steep dose gradients exist such as in intensity-modulated radiation therapy (IMRT) and stereotactic radiosurgery. Polymer gel dosimeters also have specific advantages for brachytherapy dosimetry. Potential dosimetry applications include those for low-energy x-rays, high-linear energy transfer (LET) and proton therapy, radionuclide and boron capture neutron therapy dosimetries. These 3D dosimeters are radiologically soft-tissue equivalent with properties that may be modified depending on the application. The 3D radiation dose distribution in polymer gel dosimeters may be imaged using magnetic resonance imaging (MRI), optical-computerized tomography (optical-CT), x-ray CT or ultrasound. The fundamental science underpinning polymer gel dosimetry is reviewed along with the various evaluation techniques. Clinical dosimetry applications of polymer gel dosimetry are also presented. (topical review)

  11. Reduction in beta-myosin heavy chains in stunned myocardium as assessed by nondenaturing gel electrophoresis.

    Science.gov (United States)

    Garcia, S C; Pomblum, V J; Gams, E; Rupp, H; Schipke, J D

    2007-09-01

    Myosin plays a key role in the structure and function of cardiac muscle. Three myosin isoenzymes (V(1), V(2), and V(3)) with different ATPase activities have been identified in mammalian ventricles based on their heavy chain constituents. The relative amount of myosin isoenzymes changes under physiological and pathological conditions. Until now, myosin isoenzymes have frequently been determined using either tube gel (nondenaturing) polyacrylamide gel electrophoresis (PAGE), or gradient or uniform sodium dodecyl sulfate (denaturing) PAGE. Both methods have disadvantages, e.g., a long running time. We developed, therefore, a uniform, nondenaturing PAGE with slab minigel format for analyzing the myosin isoenzymes in normoxic and stunned rabbit hearts. In normoxic hearts of adult rabbits, V(3) predominated over V(1) (46 vs 41%). In turn, in the stunned hearts, V(1) predominated over V(3) (70 vs 30%), and the heterodimeric V(2) was not anymore detectable. This alteration appears to result from a selective loss of myosin heavy chain (MHC)-beta. In parallel, the biochemical markers troponin I and creatine kinase were increased in the stunned hearts. We suggest that alterations of myosin isoenzymes in stunned myocardium can be monitored with native PAGE. The present analysis of myosin isoenzyme appears thus as a new tool for evaluating defects in MHC dimer formation in postischemic hearts.

  12. Obtaining of platinum-titanium alloys by sol-gel and their performance for the detachment reactions and oxygen reduction

    International Nuclear Information System (INIS)

    Regueira R, B. I.

    2011-01-01

    In the present work, platinum-titanium (Pt-Ti) alloys were prepared, characterized and evaluated in acid media as bifunctional electrocatalysts for the oxygen evolution reaction (Oer) and oxygen reduction reactions (Orr) in acid media. The alloys were synthesized by sol-gel method, heating the gel at temperatures of 400 and 600 C. The alloys characterization was realized by X-ray diffraction, scanning electron microscopy and EDS. Both alloys were formed by agglomerates of nanometer particles. The particle sizes were lower for the alloy obtained at 400 C (120 nm to 257 nm) compared to the alloy prepared at 600 C (555 nm to 833 nm). Cyclic and linear voltammetry techniques were used for the electrochemical evaluation of the alloy obtained at both temperatures for the Oer and Orr, in a 0.5 M sulfuric acid solution. The materials have response for both electrochemical reactions, therefore the best performance was for the Pt-Ti alloy, obtained at 400 C and it was stable for the oxygen evolution reaction. The alloy obtained at 400 C presents satisfactory electrocatalytic characteristics to be used as bifunctional material in a unified regenerative fuel cell. (Author)

  13. Metal-silica sol-gel materials

    Science.gov (United States)

    Stiegman, Albert E. (Inventor)

    2002-01-01

    The present invention relates to a single phase metal-silica sol-gel glass formed by the co-condensation of a transition metal with silicon atoms where the metal atoms are uniformly distributed within the sol-gel glass as individual metal centers. Any transition metal may be used in the sol-gel glasses. The present invention also relates to sensor materials where the sensor material is formed using the single phase metal-silica sol-gel glasses. The sensor materials may be in the form of a thin film or may be attached to an optical fiber. The present invention also relates to a method of sensing chemicals using the chemical sensors by monitoring the chromatic change of the metal-silica sol-gel glass when the chemical binds to the sensor. The present invention also relates to oxidation catalysts where a metal-silica sol-gel glass catalyzes the reaction. The present invention also relates to a method of performing oxidation reactions using the metal-silica sol-gel glasses. The present invention also relates to organopolymer metal-silica sol-gel composites where the pores of the metal-silica sol-gel glasses are filled with an organic polymer polymerized by the sol-gel glass.

  14. Fast, three-dimensional, MR Imaging for polymer gel dosimetric applications involving high dose and steep dose gradients

    International Nuclear Information System (INIS)

    Sandilos, Panagiotis; Baras, Panagiotis; Georgiou, Evangelos; Dardoufas, Konstantinos; Karaiskos, Pantelis; Papagiannis, Panagiotis; Paschalis, Theodoros; Tatsis, Elias; Torrens, Michael; Vlahos, Lampros

    2006-01-01

    Polymer gels constitute water equivalent integrating detectors, which, combined with magnetic resonance imaging (MRI), can provide accurate three dimensional (3D) dose distributions in contemporary radiotherapy applications where the small field dimensions and steep dose gradients induce limitations to conventional dosimeters. One of the main obstacles for adapting the method for routine use in the clinical setting is the cost effectiveness of the MRI readout method. Currently, optimized Carr-Purcell-Meiboom-Gill (CPMG) multiple spin echo imaging pulse sequences are commonly used which however result in long imaging times. This work evaluates the efficiency of 3D, dual-echo, k-space segmented turbo spin echo (TSE) scanning sequences for accurate dosimetry with sub-millimetre spatial resolution in strenuous radiation therapy applications. PABIG polymer gel dosimeters were irradiated with an 192 Ir High Dose Rate brachytherapy source, the 4 mm and 8 mm collimator helmets of a gamma knife unit and a custom made x-knife collimator of 1 cm diameter. Profile and dose distribution measurements using TSE are benchmarked against corresponding findings obtained by the commonly used, but time consuming, CPMG sequence as well as treatment planning calculations, Monte Carlo (MC) simulations and film measurements. The implementation of a high Turbo factor was found to provide comparable accuracy, allowing a 64-fold MRI scan acceleration compared to conventional multi-echo sequences. The availability of TSE sequences in typical MRI installations greatly facilitates the introduction of polymer gel dosimetry in the clinical environment as a practicable tool for the determination of full 3D dose distributions in contemporary radiotherapy applications

  15. Fast, three-dimensional, MR Imaging for polymer gel dosimetric applications involving high dose and steep dose gradients

    Energy Technology Data Exchange (ETDEWEB)

    Sandilos, Panagiotis [Department of Radiology, Medical School, University of Athens, Areteion Hospital, 76 Vas. Sofias Ave., 115 28 Athens (Greece); Baras, Panagiotis [Philips Hellas Medical Systems, 44 Kifissias Ave., Maroussi 151 25, Athens (Greece); Georgiou, Evangelos [Medical Physics Department, University of Athens, 75 Mikras Asias, 115 27 Athens (Greece); Dardoufas, Konstantinos [Department of Radiology, Medical School, University of Athens, Areteion Hospital, 76 Vas. Sofias Ave., 115 28 Athens (Greece): Hygeia Hospital, Kiffisias Avenue and 4 Erythrou Stavrou, Marousi, 151 23 Athens (Greece); Karaiskos, Pantelis [Medical Physics Department, University of Athens, 75 Mikras Asias, 115 27 Athens (Greece): Hygeia Hospital, Kiffisias Avenue and 4 Erythrou Stavrou, Marousi, 151 23 Athens (Greece)]. E-mail: p.karaiskos@hygeia.gr; Papagiannis, Panagiotis [Physics Department, Nuclear and Particle Physics Section, University of Athens, Panepistimioupolis, Ilisia, 157 71 Athens (Greece); Paschalis, Theodoros [Department of Radiology, Medical School, University of Athens, Areteion Hospital, 76 Vas. Sofias Ave., 115 28 Athens (Greece); Tatsis, Elias [Department of Radiology, Medical School, University of Athens, Areteion Hospital, 76 Vas. Sofias Ave., 115 28 Athens (Greece); Torrens, Michael [Hygeia Hospital, Kiffisias Avenue and 4 Erythrou Stavrou, Marousi, 151 23 Athens (Greece); Vlahos, Lampros [Department of Radiology, Medical School, University of Athens, Areteion Hospital, 76 Vas. Sofias Ave., 115 28 Athens (Greece)

    2006-12-20

    Polymer gels constitute water equivalent integrating detectors, which, combined with magnetic resonance imaging (MRI), can provide accurate three dimensional (3D) dose distributions in contemporary radiotherapy applications where the small field dimensions and steep dose gradients induce limitations to conventional dosimeters. One of the main obstacles for adapting the method for routine use in the clinical setting is the cost effectiveness of the MRI readout method. Currently, optimized Carr-Purcell-Meiboom-Gill (CPMG) multiple spin echo imaging pulse sequences are commonly used which however result in long imaging times. This work evaluates the efficiency of 3D, dual-echo, k-space segmented turbo spin echo (TSE) scanning sequences for accurate dosimetry with sub-millimetre spatial resolution in strenuous radiation therapy applications. PABIG polymer gel dosimeters were irradiated with an {sup 192}Ir High Dose Rate brachytherapy source, the 4 mm and 8 mm collimator helmets of a gamma knife unit and a custom made x-knife collimator of 1 cm diameter. Profile and dose distribution measurements using TSE are benchmarked against corresponding findings obtained by the commonly used, but time consuming, CPMG sequence as well as treatment planning calculations, Monte Carlo (MC) simulations and film measurements. The implementation of a high Turbo factor was found to provide comparable accuracy, allowing a 64-fold MRI scan acceleration compared to conventional multi-echo sequences. The availability of TSE sequences in typical MRI installations greatly facilitates the introduction of polymer gel dosimetry in the clinical environment as a practicable tool for the determination of full 3D dose distributions in contemporary radiotherapy applications.

  16. Radiation reaction of skin treatment with nucliderm-gel

    International Nuclear Information System (INIS)

    Pandova, V.; Marinova, Ts.; Stefanova, D.; Pantev, T.; Yankova, S.

    1988-01-01

    The process of epithelization and the anticeptic effect of nucliderm-gel applied locally have been studied in 63 oncological patients subjected to radiotherapy. In all cases under study nucliderm-gel promotes skin epithelization and has a high antiseptic effect as compared with the drugs applied hitherto

  17. Unveiling the fungal mycobiota present throughout the cork stopper manufacturing process

    NARCIS (Netherlands)

    Barreto, M.C.; Houbraken, J.; Samson, R.A.; Brito, D.; Gadanho, M.; San Romão, M.V.

    2012-01-01

    A particular fungal population is present in the main stages of the manufacturing process of cork discs. Its diversity was studied using both dependent (isolation) and independent culture methods (denaturing gel gradient electrophoresis and cloning of the ITS1-5.8S-ITS2 region). The mycobiota in the

  18. Molecular monitoring of succession of bacterial communities in human neonates

    NARCIS (Netherlands)

    Favier, C.; Vaughan, E.E.; Vos, de W.M.; Akkermans, A.D.L.

    2002-01-01

    The establishment of bacterial communities in two healthy babies was examined for more than the first 10 months of life by monitoring 16S ribosomal DNA (rDNA) diversity in fecal samples by PCR and denaturing gradient gel electrophoresis (DGGE) and by analyzing the sequences of the major ribotypes.

  19. Thermally responsive silicon nanowire arrays for native/denatured-protein separation

    International Nuclear Information System (INIS)

    Wang Hongwei; Wang Yanwei; Yuan Lin; Wang Lei; Yang Weikang; Wu Zhaoqiang; Li Dan; Chen Hong

    2013-01-01

    We present our findings of the selective adsorption of native and denatured proteins onto thermally responsive, native-protein resistant poly(N-isopropylacrylamide) (PNIPAAm) decorated silicon nanowire arrays (SiNWAs). The PNIPAAm–SiNWAs surface, which shows very low levels of native-protein adsorption, favors the adsorption of denatured proteins. The amount of denatured-protein adsorption is higher at temperatures above the lower critical solution temperature (LCST) of PNIPAAm. Temperature cycling surrounding the LCST, which ensures against thermal denaturation of native proteins, further increases the amount of denatured-protein adsorption. Moreover, the PNIPAAm–SiNWAs surface is able to selectively adsorb denatured protein even from mixtures of different protein species; meanwhile, the amount of native proteins in solution is kept nearly at its original level. It is believed that these results will not only enrich current understanding of protein interactions with PNIPAAm-modified SiNWAs surfaces, but may also stimulate applications of PNIPAAm–SiNWAs surfaces for native/denatured protein separation. (paper)

  20. Schisandra chinensis fruit modulates the gut microbiota composition in association with metabolic markers in obese women: a randomized, double-blind placebo-controlled study.

    Science.gov (United States)

    Song, Mi-young; Wang, Jing-hua; Eom, Taewoong; Kim, Hojun

    2015-08-01

    Schisandra chinensis fruit (SCF) is known to have beneficial effects on metabolic diseases, including obesity, and to affect gut microbiota in in vivo studies. However, in human research, there have been a few studies in terms of its clinical roles in lipid metabolism and modulation of gut microbiota. A double-blind, placebo-controlled study with 28 obese women with SCF or placebo was conducted for 12 weeks. Anthropometry and blood and fecal sampling were performed before and after treatment. Analysis of the gut microbiota in feces was performed using denaturing gradient gel electrophoresis and quantitative polymerase chain reaction. Although the values did not differ significantly between the 2 groups, the SCF group tended to show a greater decrease in waist circumference, fat mass, fasting blood glucose, triglycerides, aspartate aminotransferase, and alanine aminotransferase than the placebo group. Clustering of the denaturing gradient gel electrophoresis fingerprints for total bacteria before and after treatment indicated more separate clustering in SCF group than placebo. In correlation analysis, Bacteroides and Bacteroidetes (both increased by SCF) showed significant negative correlation with fat mass, aspartate aminotransferase, and/or alanine aminotransferase, respectively. Ruminococcus (decreased by SCF) showed negative correlation with high-density lipoprotein cholesterol and fasting blood glucose. In conclusion, administration of SCF for 12 weeks resulted in modulation of the gut microbiota composition in Korean obese women, and significant correlations with some bacterial genera and metabolic parameters were noted. However, in general, SCF was not sufficient to induce significant changes in obesity-related parameters compared with placebo. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. 16S rRNA gene sequence and phylogenetic tree of lactobacillus ...

    African Journals Online (AJOL)

    ... processed by denaturing gradient gel electrophoresis (DGGE). Phylogenetic tree was constructed with the sequences of the V2-V3 region of 16S rRNA gene. Results show two distinct divisions among the Lactobacillus species. The study presents a new understanding of the nature of the Lactobacillus vaginal microbiota ...

  2. A nested PCR approach for improved recovery of archaeal 16S rRNA gene fragments from freshwater samples

    NARCIS (Netherlands)

    Vissers, E.W.; Bodelier, P.L.E.; Muyzer, G.; Laanbroek, R.

    2009-01-01

    In a survey on the presence of archaea in a number of European lakes, it was found that known archaeal primer sets for PCR were not suited for use in freshwater environment, as some lack selectivity, while others were too selective. A nested PCR was developed for denaturing gradient gel

  3. Molecular method to assess the diversity of Burkholderia species in environmental samples

    NARCIS (Netherlands)

    Salles, J.; Souza, de F.A.; Elsas, van J.D.

    2002-01-01

    In spite of the importance of many members of the genus Burkholderia in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. The aim of this work was the development of soil DNA-based PCR-denaturing gradient gel electrophoresis (DGGE), a

  4. 27 CFR 19.464 - Denatured spirits inventories.

    Science.gov (United States)

    2010-04-01

    ... of Articles Inventories § 19.464 Denatured spirits inventories. Each proprietor shall take a physical inventory of all denatured spirits in the processing account at the close of each calendar quarter and at... inventories. 19.464 Section 19.464 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE...

  5. Assessment of local skin reactions with a sequential regimen of cryosurgery followed by ingenol mebutate gel, 0.015%, in patients with actinic keratosis

    Directory of Open Access Journals (Sweden)

    Goldenberg G

    2014-12-01

    Full Text Available Gary Goldenberg,1 Brian Berman2,3 1Department of Dermatology, Mount Sinai School of Medicine, New York, NY, 2Center for Clinical and Cosmetic Research, Aventura, FL, 3Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA Abstract: Lesion-directed and field-directed therapies are used to treat actinic keratosis (AK. Therapeutic approaches that combine both types of therapies may improve the successful elimination of AKs. A randomized, double-blind, vehicle-controlled study evaluated the safety, tolerability, and efficacy of topical field treatment with ingenol mebutate gel, 0.015%, after cryosurgery to AKs on the face and scalp. Patients with 4–8 visible discrete AKs in a 25-cm2 contiguous area received cryosurgery of all AKs at baseline. After a 3-week healing period, patients applied ingenol mebutate gel, 0.015%, or vehicle gel once daily for 3 consecutive days to the treatment area. The incidence, severity, and time course of the development and resolution of local skin reactions were measured from baseline to week 11. Local skin reactions peaked shortly after completion of ingenol mebutate treatment and generally resolved within 2 weeks. The mean (95% confidence interval composite score (maximum range, 0–24 for these reactions was higher in patients with treatment of AKs on the face, 9.3 (8.5–10.1, as compared with the scalp, 5.8 (4.3–7.4. Erythema and flaking/scaling were the major contributors to the composite local skin reaction score. These results show that local skin reactions associated with ingenol mebutate treatment of the face or scalp are well tolerated after recent cryosurgery. Keywords: ingenol mebutate gel, actinic keratosis, field therapy, local skin reaction

  6. A neutral glyoxal gel electrophoresis method for the detection and semi-quantitation of DNA single-strand breaks.

    Science.gov (United States)

    Pachkowski, Brian; Nakamura, Jun

    2013-01-01

    Single-strand breaks are among the most prevalent lesions found in DNA. Traditional electrophoretic methods (e.g., the Comet assay) used for investigating these lesions rely on alkaline conditions to denature DNA prior to electrophoresis. However, the presence of alkali-labile sites in DNA can result in the introduction of additional single-strand breaks upon alkali treatment during DNA sample processing. Herein, we describe a neutral glyoxal gel electrophoresis assay which is based on alkali-free DNA denaturation and is suitable for qualitative and semi-quantitative analyses of single-strand breaks in DNA isolated from different organisms.

  7. Autonomous Oscillation of Nonthermoresponsive Polymers and Gels Induced by the Belousov–Zhabotinsky Reaction

    Directory of Open Access Journals (Sweden)

    Yusuke Hara

    2013-09-01

    Full Text Available This review introduces the self-oscillating behavior of two types of nonthermoresponsive polymer systems with Ru catalyst moieties for the Belousov-Zhabotinsky (BZ reaction: one with a poly-vinylpyrrolidone (PVP main chain, and the other with a poly(2-propenamide (polyacrylamide (PAM main chain. The amplitude of the VP-based self-oscillating polymer chain and the activation energy for self-oscillation are hardly affected by the initial concentrations of the BZ substrates. The influences of the initial concentrations of the BZ substrates and the temperature on the period of the swelling-deswelling self-oscillation are examined in detail. Logarithmic plots of the period against the initial concentration of one BZ substrate, when the concentrations of the other two BZ substrates are fixed, show good linear relationships. The period of the swelling-deswelling self-oscillation decreases with increasing temperature, in accordance with the Arrhenius equation. The maximum frequency (0.5 Hz of the poly(VP-co-Ru(bpy3 gel is 20 times that of the poly(NIPAAm-co-Ru(bpy3 gel. It is also demonstrated that the amplitude of the volume self-oscillation for the gel has a tradeoff with the self-oscillation period. In addition, this review reports the self-oscillating behavior of an AM-based self-oscillating polymer chain as compared to that of the VP-based polymer chain.

  8. Model creation of moving redox reaction boundary in agarose gel electrophoresis by traditional potassium permanganate method.

    Science.gov (United States)

    Xie, Hai-Yang; Liu, Qian; Li, Jia-Hao; Fan, Liu-Yin; Cao, Cheng-Xi

    2013-02-21

    A novel moving redox reaction boundary (MRRB) model was developed for studying electrophoretic behaviors of analytes involving redox reaction on the principle of moving reaction boundary (MRB). Traditional potassium permanganate method was used to create the boundary model in agarose gel electrophoresis because of the rapid reaction rate associated with MnO(4)(-) ions and Fe(2+) ions. MRB velocity equation was proposed to describe the general functional relationship between velocity of moving redox reaction boundary (V(MRRB)) and concentration of reactant, and can be extrapolated to similar MRB techniques. Parameters affecting the redox reaction boundary were investigated in detail. Under the selected conditions, good linear relationship between boundary movement distance and time were obtained. The potential application of MRRB in electromigration redox reaction titration was performed in two different concentration levels. The precision of the V(MRRB) was studied and the relative standard deviations were below 8.1%, illustrating the good repeatability achieved in this experiment. The proposed MRRB model enriches the MRB theory and also provides a feasible realization of manual control of redox reaction process in electrophoretic analysis.

  9. Transport Phenomena in Gel

    Directory of Open Access Journals (Sweden)

    Masayuki Tokita

    2016-05-01

    Full Text Available Gel becomes an important class of soft materials since it can be seen in a wide variety of the chemical and the biological systems. The unique properties of gel arise from the structure, namely, the three-dimensional polymer network that is swollen by a huge amount of solvent. Despite the small volume fraction of the polymer network, which is usually only a few percent or less, gel shows the typical properties that belong to solids such as the elasticity. Gel is, therefore, regarded as a dilute solid because its elasticity is much smaller than that of typical solids. Because of the diluted structure, small molecules can pass along the open space of the polymer network. In addition to the viscous resistance of gel fluid, however, the substance experiences resistance due to the polymer network of gel during the transport process. It is, therefore, of importance to study the diffusion of the small molecules in gel as well as the flow of gel fluid itself through the polymer network of gel. It may be natural to assume that the effects of the resistance due to the polymer network of gel depends strongly on the network structure. Therefore, detailed study on the transport processes in and through gel may open a new insight into the relationship between the structure and the transport properties of gel. The two typical transport processes in and through gel, that is, the diffusion of small molecules due to the thermal fluctuations and the flow of gel fluid that is caused by the mechanical pressure gradient will be reviewed.

  10. Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments.

    Science.gov (United States)

    Chaudhary, Prem Prashant; Brablcová, Lenka; Buriánková, Iva; Rulík, Martin

    2013-09-01

    Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.

  11. EXAFS analysis of a human Cu,Zn SOD isoform focused using non-denaturing gel electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Chevreux, Sylviane; Roudeau, Stephane; Deves, Guillaume; Ortega, Richard [Laboratoire de Chimie Nucleaire Analytique et Bioenvironnementale, CNRS UMR5084, Universite Bordeaux 1, Chemin du Solarium, F-33175 Gradignan cedex (France); Solari, Pier Lorenzo [Synchrotron SOLEIL, L' Orme des Merisiers, BP 48, F-91192 Gif-sur-Yvette cedex, Saint-Aubin (France); Alliot, Isabelle; Testemale, Denis; Hazemann, Jean Louis, E-mail: ortega@cenbg.in2p3.f [FAME, ESRF, 6 rue Jules Horowitz, BP220, F-38043 Grenoble cedex (France)

    2009-11-15

    Isoelectric point isoforms of a metalloprotein, copper-zinc superoxide dismutase (CuZnSOD), separated on electrophoresis gels were analyzed using X-ray Absorption Spectroscopy. Mutations of this protein are involved in familial cases of amyotrophic lateral sclerosis. The toxicity of mutants could be relied to defects in the metallation state. Our purpose is to establish analytical protocols to study metallation state of protein isoforms such as those from CuZnSOD. We previously highlighted differences in the copper oxidation state between CuZnSOD isoforms using XANES. Here, we present the first results for EXAFS analyses performed at Cu and Zn K-edge on the majoritary expressed isoform of human CuZnSOD separated on electrophoresis gels.

  12. EXAFS analysis of a human Cu,Zn SOD isoform focused using non-denaturing gel electrophoresis

    Science.gov (United States)

    Chevreux, Sylviane; Solari, Pier Lorenzo; Roudeau, Stéphane; Deves, Guillaume; Alliot, Isabelle; Testemale, Denis; Hazemann, Jean Louis; Ortega, Richard

    2009-11-01

    Isoelectric point isoforms of a metalloprotein, copper-zinc superoxide dismutase (CuZnSOD), separated on electrophoresis gels were analyzed using X-ray Absorption Spectroscopy. Mutations of this protein are involved in familial cases of amyotrophic lateral sclerosis. The toxicity of mutants could be relied to defects in the metallation state. Our purpose is to establish analytical protocols to study metallation state of protein isoforms such as those from CuZnSOD. We previously highlighted differences in the copper oxidation state between CuZnSOD isoforms using XANES. Here, we present the first results for EXAFS analyses performed at Cu and Zn K-edge on the majoritary expressed isoform of human CuZnSOD separated on electrophoresis gels.

  13. EXAFS analysis of a human Cu,Zn SOD isoform focused using non-denaturing gel electrophoresis

    International Nuclear Information System (INIS)

    Chevreux, Sylviane; Roudeau, Stephane; Deves, Guillaume; Ortega, Richard; Solari, Pier Lorenzo; Alliot, Isabelle; Testemale, Denis; Hazemann, Jean Louis

    2009-01-01

    Isoelectric point isoforms of a metalloprotein, copper-zinc superoxide dismutase (CuZnSOD), separated on electrophoresis gels were analyzed using X-ray Absorption Spectroscopy. Mutations of this protein are involved in familial cases of amyotrophic lateral sclerosis. The toxicity of mutants could be relied to defects in the metallation state. Our purpose is to establish analytical protocols to study metallation state of protein isoforms such as those from CuZnSOD. We previously highlighted differences in the copper oxidation state between CuZnSOD isoforms using XANES. Here, we present the first results for EXAFS analyses performed at Cu and Zn K-edge on the majoritary expressed isoform of human CuZnSOD separated on electrophoresis gels.

  14. Denaturing gradient gel electrophoresis-polymerase chain reaction comparison of chitosan effects on anaerobic cultures of broiler cecal bacteria and Salmonella Typhimurium

    Science.gov (United States)

    Salmonella colonization and product contamination are major poultry industry problems. Alternatives to traditional antibiotics against Salmonella offer the potential to lessen the development of resistance to antibiotics of importance to human health. The chitin derivative chitosan has drawn substa...

  15. Dietary magnesium deficiency affects gut microbiota and anxiety-like behaviour in C57BL/6N mice

    DEFF Research Database (Denmark)

    Pyndt Jørgensen, Bettina; Winther, Gudrun; Kihl, Pernille

    2015-01-01

    and whether there was a link between the two. A total of 20 C57BL/6 mice, fed either a standard diet or a magnesium-deficient diet for 6 weeks, were tested using the light-dark box anxiety test. Gut microbiota composition was analysed by denaturation gradient gel electrophoresis. RESULTS: We demonstrated...

  16. Analyzing Protein Denaturation using Fast Differential Scanning Calorimetry

    NARCIS (Netherlands)

    Splinter, R.; Van Herwaarden, A.W.; Iervolino, E.; Vanden Poel, G.; Istrate, D.; Sarro, P.M.

    2012-01-01

    This paper investigates the possibility to measure protein denaturation with Fast Differential Scanning Calorimetry (FDSC). Cancer can be diagnosed by measuring protein denaturation in blood plasma using Differential Scanning Calorimetry (DSC). FDSC can reduce diagnosis time from hours to minutes,

  17. Experimenting with a Visible Copper-Aluminum Displacement Reaction in Agar Gel and Observing Copper Crystal Growth Patterns to Engage Student Interest and Inquiry

    Science.gov (United States)

    Xu, Xinhua; Wu, Meifen; Wang, Xiaogang; Yang, Yangyiwei; Shi, Xiang; Wang, Guoping

    2016-01-01

    The reaction process of copper-aluminum displacement in agar gel was observed at the microscopic level with a stereomicroscope; pine-like branches of copper crystals growing from aluminum surface into gel at a constant rate were observed. Students were asked to make hypotheses on the pattern formation and design new research approaches to prove…

  18. Use of anionic denaturing detergents to purify insoluble proteins after overexpression

    Directory of Open Access Journals (Sweden)

    Schlager Benjamin

    2012-12-01

    Full Text Available Background Many proteins form insoluble protein aggregates, called “inclusion bodies”, when overexpressed in E. coli. This is the biggest obstacle in biotechnology. Ever since the reversible denaturation of proteins by chaotropic agents such as urea or guanidinium hydrochloride had been shown, these compounds were predominantly used to dissolve inclusion bodies. Other denaturants exist but have received much less attention in protein purification. While the anionic, denaturing detergent sodiumdodecylsulphate (SDS is used extensively in analytical SDS-PAGE, it has rarely been used in preparative purification. Results Here we present a simple and versatile method to purify insoluble, hexahistidine-tagged proteins under denaturing conditions. It is based on dissolution of overexpressing bacterial cells in a buffer containing sodiumdodecylsulfate (SDS and whole-lysate denaturation of proteins. The excess of detergent is removed by cooling and centrifugation prior to affinity purification. Host- and overexpressed proteins do not co-precipitate with SDS and the residual concentration of detergent is compatible with affinity purification on Ni/NTA resin. We show that SDS can be replaced with another ionic detergent, Sarkosyl, during purification. Key advantages over denaturing purification in urea or guanidinium are speed, ease of use, low cost of denaturant and the compatibility of buffers with automated FPLC. Conclusion Ionic, denaturing detergents are useful in breaking the solubility barrier, a major obstacle in biotechnology. The method we present yields detergent-denatured protein. Methods to refold proteins from a detergent denatured state are known and therefore we propose that the procedure presented herein will be of general application in biotechnology.

  19. Thermal stability of chemically denatured green fluorescent protein (GFP) A preliminary study

    Energy Technology Data Exchange (ETDEWEB)

    Nagy, Attila; Malnasi-Csizmadia, Andras; Somogyi, Bela; Lorinczy, Denes

    2004-02-09

    Green fluorescent protein (GFP) is a light emitter in the bioluminescence reaction of the jellyfish Aequorea victoria. The protein consist of 238 amino acids and produces green fluorescent light ({lambda}{sub max}=508 nm), when irradiated with near ultraviolet light. The fluorescence is due to the presence of chromophore consisting of an imidazolone ring, formed by a post-translational modification of the tripeptide -Ser{sup 65}-Tyr{sup 66}-Gly{sup 67}-, which buried into {beta}-barrel. GFP is extremely compact and heat stable molecule. In this work, we present data for the effect of chemical denaturing agent on the thermal stability of GFP. When denaturing agent is applied, global thermal stability and the melting point of the molecule is decreases, that can be monitored with differential scanning calorimetry. The results indicate, that in 1-6 M range of GuHCl the melting temperature is decreasing continuously from 83 to 38 deg. C. Interesting finding, that the calculated calorimetric enthalpy decreases with GuHCl concentration up to 3 M (5.6-0.2 kJ mol{sup -1}), but at 4 M it jumps to 8.4 and at greater concentration it is falling down to 1.1 kJ mol{sup -1}. First phenomena, i.e. the decrease of melting point with increasing GuHCl concentration can be easily explained by the effect of the extended chemical denaturation, when less and less amount of heat required to diminish the remaining hydrogen bonds in {beta}-barrel. The surprising increase of calorimetric enthalpy at 4 M concentration of GuHCl could be the consequence of a dimerization or a formation of stable complex between GFP and denaturing agent as well as a precipitation at an extreme GuHCl concentration. We are planning further experiments to elucidate fluorescent consequence of these processes.

  20. Light water reactors with a denatured thorium fuel cycle

    International Nuclear Information System (INIS)

    1978-05-01

    Discussed in this paper is the performance of denatured thorium fuel cycles in PWR plants of conventional design, such as those currently in operation or under construction. Although some improvement in U 3 O 8 utilization is anticipated in PWRs optimized explicitly for the denatured thorium fuel cycle, this paper is limited to a discussion of the performance of denatured thorium fuels in conventional PWRs and consequently the data presented is representative of the use of thorium fuel in existing PWRs or those presently under construction. In subsequent sections of this paper, the design of the PWR, its performance on the denatured thorium fuel cycle, safety, accident and environmental considerations, and technological status and R and D requirements are discussed

  1. Size distribution of DNA molecules recovered from non-denaturing filter elution

    International Nuclear Information System (INIS)

    Bloecher, D.; Iliakis, G.

    1991-01-01

    DNA fragments removed from the filter during non-denaturing filter elution were collected and loaded on top of neutral sucrose gradients. Their size distribution was determined by low-speed centrifugation in neutral sucrose gradients. The average size of eluted DNA was found to be approximately 110 S; the average size of DNA collected after short elution times was found to be slightly larger than after long elution times. It is concluded that the size of eluted DNA fragments is not correlated with elution rate, and it is proposed that shear forces generated at the filter pores cause degradation of the DNA. Comparison of sedimentation profiles of carefully prepared cellular DNA before and after elution revealed that generated shear forces during elution break down DNA to an extent equivalent to around 20 000 DNA double-strand breaks (dsb) per G 1 cell. The size of DNA fragments decreased with increasing radiation dose; five times more dsb were found than expected after exposure to radiation alone. It is proposed that excess of dsb may derive from the transformation of other radiation-induced lesions to dsb under the action of shear forces generated during elution. (author)

  2. Method of improving heterogeneous oil reservoir polymer flooding effect by positively-charged gel profile control

    Science.gov (United States)

    Zhao, Ling; Xia, Huifen

    2018-01-01

    The project of polymer flooding has achieved great success in Daqing oilfield, and the main oil reservoir recovery can be improved by more than 15%. But, for some strong oil reservoir heterogeneity carrying out polymer flooding, polymer solution will be inefficient and invalid loop problem in the high permeability layer, then cause the larger polymer volume, and a significant reduction in the polymer flooding efficiency. Aiming at this problem, it is studied the method that improves heterogeneous oil reservoir polymer flooding effect by positively-charged gel profile control. The research results show that the polymer physical and chemical reaction of positively-charged gel with the residual polymer in high permeability layer can generate three-dimensional network of polymer, plugging high permeable layer, and increase injection pressure gradient, then improve the effect of polymer flooding development. Under the condition of the same dosage, positively-charged gel profile control can improve the polymer flooding recovery factor by 2.3∼3.8 percentage points. Under the condition of the same polymer flooding recovery factor increase value, after positively-charged gel profile control, it can reduce the polymer volume by 50 %. Applying mechanism of positively-charged gel profile control technology is feasible, cost savings, simple construction, and no environmental pollution, therefore has good application prospect.

  3. Monitoring mass transport in heterogeneously catalyzed reactions by field-gradient NMR for assessing reaction efficiency in a single pellet

    Science.gov (United States)

    Buljubasich, L.; Blümich, B.; Stapf, S.

    2011-09-01

    An important aspect in assessing the performance of a catalytically active reactor is the accessibility of the reactive sites inside the individual pellets, and the mass transfer of reactants and products to and from these sites. Optimal design often requires a suitable combination of micro- and macropores in order to facilitate mass transport inside the pellet. In an exothermic reaction, fluid exchange between the pellet and the surrounding medium is enhanced by convection, and often by the occurrence of gas bubbles. Determining mass flow in the vicinity of a pellet thus represents a parameter for quantifying the reaction efficiency and its dependence on time or external reaction conditions. Field gradient Nuclear Magnetic Resonance (NMR) methods are suggested as a tool for providing parameters sensitive to this mass flow in a contact-free and non-invasive way. For the example of bubble-forming hydrogen peroxide decomposition in an alumina pellet, the dependence of the mean-squared displacement of fluid molecules on spatial direction, observation time and reaction time is presented, and multi-pulse techniques are employed in order to separate molecular displacements from coherent and incoherent motion on the timescale of the experiment. The reaction progress is followed until the complete decomposition of H 2O 2.

  4. Single-molecule denaturation mapping of DNA in nanofluidic channels

    DEFF Research Database (Denmark)

    Reisner, Walter; Larsen, Niels Bent; Silahtaroglu, Asli

    2010-01-01

    Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO (R)-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent "barcode" corresponding to a series of local dips...... and peaks in the intensity trace along the extended molecule. We demonstrate that this structure arises from the physics of local denaturation: statistical mechanical calculations of sequence-dependent melting probability can predict the barcode to be observed experimentally for a given sequence...

  5. Soil microbial community structure across a thermal gradient following a geothermal heating event.

    Science.gov (United States)

    Norris, Tracy B; Wraith, Jon M; Castenholz, Richard W; McDermott, Timothy R

    2002-12-01

    In this study microbial species diversity was assessed across a landscape in Yellowstone National Park, where an abrupt increase in soil temperature had occurred due to recent geothermal activity. Soil temperatures were measured, and samples were taken across a temperature gradient (35 to 65 degrees C at a 15-cm depth) that spanned geothermally disturbed and unimpacted soils; thermally perturbed soils were visually apparent by the occurrence of dead or dying lodgepole pine trees. Changes in soil microbial diversity across the temperature gradient were qualitatively assessed based on 16S rRNA sequence variation as detected by denaturing gradient gel electrophoresis (DGGE) using both ribosomal DNA (rDNA) and rRNA as PCR templates and primers specific for the Bacteria or Archaea domain. The impact of the major heating disturbance was apparent in that DGGE profiles from heated soils appeared less complex than those from the unaffected soils. Phylogenetic analysis of a bacterial 16S rDNA PCR clone library from a recently heated soil showed that a majority of the clones belonged to the Acidobacterium (51%) and Planctomyces (18%) divisions. Agar plate counts of soil suspensions cultured on dilute yeast extract and R2A agar media incubated at 25 or 50 degrees C revealed that thermophile populations were two to three orders of magnitude greater in the recently heated soil. A soil microcosm laboratory experiment simulated the geothermal heating event. As determined by both RNA- and DNA-based PCR coupled with DGGE, changes in community structure (marked change in the DGGE profile) of soils incubated at 50 degrees C occurred within 1 week and appeared to stabilize after 3 weeks. The results of our molecular and culture data suggest that thermophiles or thermotolerant species are randomly distributed in this area within Yellowstone National Park and that localized thermal activity selects for them.

  6. Synthesis and characterization of erbium-doped SiO2-TiO2 thin films prepared by sol-gel and dip-coating techniques onto commercial glass substrates as a route for obtaining active GRadient-INdex materials

    International Nuclear Information System (INIS)

    Gómez-Varela, Ana I.; Castro, Yolanda; Durán, Alicia; De Beule, Pieter A.A.; Flores-Arias, María T.; Bao-Varela, Carmen

    2015-01-01

    In this work, SiO 2 -TiO 2 films doped with erbium were prepared by dip-coating sol-gel process onto commercial glass substrates. The surface morphology of the films was characterized using atomic force microscopy, while thickness, refractive index, extinction coefficient and porosity of the films were determined by ellipsometric measurements in a wavelength region of 400-1000 nm. Optical constants and porosity were found to vary with erbium concentration. The proof of principle presented in this paper is applicable to systems of different nature by tailoring the sol-gel precursors in such a way that active GRadient-INdex media described by a complex, parabolic-like refractive index distribution for beam shaping purposes is obtained. - Highlights: • Sol-gel route for preparation of active GRadient-INdex materials is proposed. • SiO 2 -TiO 2 films doped with erbium were prepared by dipping onto commercial glasses. • Morphological and optical characterization of the samples was performed. • Optical constants and porosity were found to vary with erbium concentration. • Refractive index diminishes with dopant content; the contrary occurs for porosity

  7. Hysteresis in pressure-driven DNA denaturation.

    Directory of Open Access Journals (Sweden)

    Enrique Hernández-Lemus

    Full Text Available In the past, a great deal of attention has been drawn to thermal driven denaturation processes. In recent years, however, the discovery of stress-induced denaturation, observed at the one-molecule level, has revealed new insights into the complex phenomena involved in the thermo-mechanics of DNA function. Understanding the effect of local pressure variations in DNA stability is thus an appealing topic. Such processes as cellular stress, dehydration, and changes in the ionic strength of the medium could explain local pressure changes that will affect the molecular mechanics of DNA and hence its stability. In this work, a theory that accounts for hysteresis in pressure-driven DNA denaturation is proposed. We here combine an irreversible thermodynamic approach with an equation of state based on the Poisson-Boltzmann cell model. The latter one provides a good description of the osmotic pressure over a wide range of DNA concentrations. The resulting theoretical framework predicts, in general, the process of denaturation and, in particular, hysteresis curves for a DNA sequence in terms of system parameters such as salt concentration, density of DNA molecules and temperature in addition to structural and configurational states of DNA. Furthermore, this formalism can be naturally extended to more complex situations, for example, in cases where the host medium is made up of asymmetric salts or in the description of the (helical-like charge distribution along the DNA molecule. Moreover, since this study incorporates the effect of pressure through a thermodynamic analysis, much of what is known from temperature-driven experiments will shed light on the pressure-induced melting issue.

  8. Method of making ionic liquid mediated sol-gel sorbents

    Science.gov (United States)

    Malik, Abdul; Shearrow, Anne M.

    2017-01-31

    Ionic liquid (IL)-mediated sol-gel hybrid organic-inorganic materials present enormous potential for effective use in analytical microextraction. One obstacle to materializing this prospect arises from high viscosity of ILs significantly slowing down sol-gel reactions. A method was developed which provides phosphonium-based, pyridinium-based, and imidazolium-based IL-mediated advanced sol-gel organic-inorganic hybrid materials for capillary microextraction. Scanning electron microscopy results demonstrate that ILs can serve as porogenic agents in sol-gel reactions. IL-mediated sol-gel coatings prepared with silanol-terminated polymers provided up to 28 times higher extractions compared to analogous sol-gel coatings prepared without any IL in the sol solution. This study shows that IL-generated porous morphology alone is not enough to provide effective extraction media: careful choice of the organic polymer and the precursor with close sol-gel reactivity must be made to ensure effective chemical bonding of the organic polymer to the created sol-gel material to be able to provide the desired sorbent characteristics.

  9. Designing Dual-functionalized Gels for Self-reconfiguration and Autonomous Motion

    Science.gov (United States)

    Kuksenok, Olga; Balazs, Anna C.

    2015-04-01

    Human motion is enabled by the concerted expansion and contraction of interconnected muscles that are powered by inherent biochemical reactions. One of the challenges in the field of biomimicry is eliciting this form of motion from purely synthetic materials, which typically do not generate internalized reactions to drive mechanical action. Moreover, for practical applications, this bio-inspired motion must be readily controllable. Herein, we develop a computational model to design a new class of polymer gels where structural reconfigurations and internalized reactions are intimately linked to produce autonomous motion, which can be directed with light. These gels contain both spirobenzopyran (SP) chromophores and the ruthenium catalysts that drive the oscillatory Belousov-Zhabotinsky (BZ) reaction. Importantly, both the SP moieties and the BZ reaction are photosensitive. When these dual-functionalized gels are exposed to non-uniform illumination, the localized contraction of the gel (due to the SP moieties) in the presence of traveling chemical waves (due to the BZ reaction) leads to new forms of spontaneous, self-sustained movement, which cannot be achieved by either of the mono-functionalized networks.

  10. High transparent shape memory gel

    Science.gov (United States)

    Gong, Jin; Arai, Masanori; Kabir, M. H.; Makino, Masato; Furukawa, Hidemitsu

    2014-03-01

    Gels are a new material having three-dimensional network structures of macromolecules. They possess excellent properties as swellability, high permeability and biocompatibility, and have been applied in various fields of daily life, food, medicine, architecture, and chemistry. In this study, we tried to prepare new multi-functional and high-strength gels by using Meso-Decoration (Meso-Deco), one new method of structure design at intermediate mesoscale. High-performance rigid-rod aromatic polymorphic crystals, and the functional groups of thermoreversible Diels-Alder reaction were introduced into soft gels as crosslinkable pendent chains. The functionalization and strengthening of gels can be realized by meso-decorating the gels' structure using high-performance polymorphic crystals and thermoreversible pendent chains. New gels with good mechanical properties, novel optical properties and thermal properties are expected to be developed.

  11. 27 CFR 20.261 - Records of completely denatured alcohol.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Records of completely denatured alcohol. 20.261 Section 20.261 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS DISTRIBUTION AND USE OF DENATURED ALCOHOL AND RUM...

  12. Antigen-antibody reactions of UV-irradiated phage DNA

    International Nuclear Information System (INIS)

    Fink, A.

    1976-01-01

    The observation of others could be confirmed that UV-irradiated DNA is a better immunogen than unirradiated DNA. The author's immune sera contained a high amount of antibodies with a specific action against photoproducts in the DNA. The thymine dimer was identified as relevant photoproduct and thus as antigenic determinant. In comparison, the amount of unspecific antibodies reacting with denaturated DNA was low and varied between sera. Thymin-dimer antibodies showed a high specificity without cross-reaction with other pyrimidine dimers such as anti CC and anti CT; they belong to the class of IgG molecules. UV-irradiated dinucleotide dTpT is sufficient to induce the formation of antibodies reacting with the cis-syn thymine dimers in UV-irradiated DNA. Antibody binding is proportional to the UV doses applied to the DNA. When using completely denaturated DNA, there is a linear increase changing into a plateau at higher doses. The extent of antigen-antibody binding is strongly dependent on the degree of denaturation of the DNA. With increasing denaturation, the antibody binding of the DNA increases. The antigen-antibody reaction can thus be used to estimate the degree of denaturation of the DNA. There were no signs of an influence of the degree of denaturation of the DNA on the quantum yield of thymine dimers. The different amounts of antibodies is therefore due to the masking of thymine dimers in native DNA. When irradiating intact phage particles, there was no sign of an influence of the phages' protein covers on the antibody binding capacity of DNA compared with DNA irradiated in vitro. (orig.) [de

  13. Ternary gradient metal-organic frameworks.

    Science.gov (United States)

    Liu, Chong; Rosi, Nathaniel L

    2017-09-08

    Gradient MOFs contain directional gradients of either structure or functionality. We have successfully prepared two ternary gradient MOFs based on bMOF-100 analogues, namely bMOF-100/102/106 and bMOF-110/100/102, via cascade ligand exchange reactions. The cubic unit cell parameter discrepancy within an individual ternary gradient MOF crystal is as large as ∼1 nm, demonstrating the impressive compatibility and flexibility of the component MOF materials. Because of the presence of a continuum of unit cells, the pore diameters within individual crystals also change in a gradient fashion from ∼2.5 nm to ∼3.0 nm for bMOF-100/102/106, and from ∼2.2 nm to ∼2.7 nm for bMOF-110/100/102, indicating significant porosity gradients. Like previously reported binary gradient MOFs, the composition of the ternary gradient MOFs can be easily controlled by adjusting the reaction conditions. Finally, X-ray diffraction and microspectrophotometry were used to analyse fractured gradient MOF crystals by comparing unit cell parameters and absorbance spectra at different locations, thus revealing the profile of heterogeneity (i.e. gradient distribution of properties) and further confirming the formation of ternary gradient MOFs.

  14. Combining ligation reaction and capillary gel electrophoresis to obtain reliable long DNA probes.

    Science.gov (United States)

    García-Cañas, Virginia; Mondello, Monica; Cifuentes, Alejandro

    2011-05-01

    New DNA amplification methods are continuously developed for sensitive detection and quantification of specific DNA target sequences for, e.g. clinical, environmental or food applications. These new applications often require the use of long DNA oligonucleotides as probes for target sequences hybridization. Depending on the molecular technique, the length of DNA probes ranges from 40 to 450 nucleotides, solid-phase chemical synthesis being the strategy generally used for their production. However, the fidelity of chemical synthesis of DNA decreases for larger DNA probes. Defects in the oligonucleotide sequence result in the loss of hybridization efficiency, affecting the sensitivity and selectivity of the amplification method. In this work, an enzymatic procedure has been developed as an alternative to solid-phase chemical synthesis for the production of long oligonucleotides. The enzymatic procedure for probe production was based on ligation of short DNA sequences. Long DNA probes were obtained from smaller oligonucleotides together with a short sequence that acts as bridge stabilizing the molecular complex for DNA ligation. The ligation reactions were monitored by capillary gel electrophoresis with laser-induced fluorescence detection (CGE-LIF) using a bare fused-silica capillary. The capillary gel electrophoresis-LIF method demonstrated to be very useful and informative for the characterization of the ligation reaction, providing important information about the nature of some impurities, as well as for the fine optimization of the ligation conditions (i.e. ligation cycles, oligonucleotide and enzyme concentration). As a result, the yield and quality of the ligation product were highly improved. The in-lab prepared DNA probes were used in a novel multiplex ligation-dependent genome amplification (MLGA) method for the detection of genetically modified maize in samples. The great possibilities of the whole approach were demonstrated by the specific and sensitive

  15. 27 CFR 20.144 - Packages of completely denatured alcohol.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Packages of completely denatured alcohol. 20.144 Section 20.144 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS DISTRIBUTION AND USE OF DENATURED ALCOHOL AND RUM Sale...

  16. Investigating potential physicochemical errors in polymer gel dosimeters

    International Nuclear Information System (INIS)

    Sedaghat, Mahbod; Lepage, Martin; Bujold, Rachel

    2011-01-01

    Measurement errors in polymer gel dosimetry can originate either during irradiation or scanning. One concern related to the exothermic nature of polymerization reaction was that the heat released in polymer gel dosimeters during irradiation modifies their dose response. In this paper, the effect of heat released from the exothermal polymerization reaction on the dose response of a number of dosimeters was studied. In addition, we investigated whether heat-generated geometric distortion existed in newly proposed gel dosimeters that contain highly thermoresponsive polymers. Our results suggest that despite a significant internal temperature increase in some gel compositions, their dose responses are not affected when oxygen is well expelled mechanically from the gel mixture. We also report on significant pre-irradiation instability in some recently developed polymer gel dosimeters but that geometric distortions were not observed. Data obtained by a set of small calibration vials are compared to those obtained from larger phantoms, and potential physicochemical causes of deviations between them are identified.

  17. Investigating potential physicochemical errors in polymer gel dosimeters

    Energy Technology Data Exchange (ETDEWEB)

    Sedaghat, Mahbod; Lepage, Martin [Centre d' imagerie moleculaire de Sherbrooke, Departement de medecine nucleaire et radiobiologie, Universite de Sherbrooke, Sherbrooke, QC (Canada); Bujold, Rachel, E-mail: martin.lepage@usherbrooke.ca [Service de radio-oncologie, Centre hospitalier universitaire de Sherbrooke, Sherbrooke, QC (Canada)

    2011-09-21

    Measurement errors in polymer gel dosimetry can originate either during irradiation or scanning. One concern related to the exothermic nature of polymerization reaction was that the heat released in polymer gel dosimeters during irradiation modifies their dose response. In this paper, the effect of heat released from the exothermal polymerization reaction on the dose response of a number of dosimeters was studied. In addition, we investigated whether heat-generated geometric distortion existed in newly proposed gel dosimeters that contain highly thermoresponsive polymers. Our results suggest that despite a significant internal temperature increase in some gel compositions, their dose responses are not affected when oxygen is well expelled mechanically from the gel mixture. We also report on significant pre-irradiation instability in some recently developed polymer gel dosimeters but that geometric distortions were not observed. Data obtained by a set of small calibration vials are compared to those obtained from larger phantoms, and potential physicochemical causes of deviations between them are identified.

  18. Preparation of a gel of zirconium molybdate for use in the generators of 99 Mo - 99m Tc prepared with 99 Mo produced by the 98 Mo(n,γ)99 Mo reaction

    International Nuclear Information System (INIS)

    Osso Junior, Joao A.; Lima, Ana Lucia V.P.; Silva, Nestor C. da; Nieto, Renata C.; Velosa, Adriana C. de

    1998-01-01

    IPEN develops a project concerning the preparation of a gel of Zirconium Molybdate for use in the generators of 99 Mo- 99m Tc . 99m Tc is the most used radioisotope in nuclear medicine diagnosis procedures and nowadays the generators are being prepared with imported 99 Mo, produced by 235 U fission. The production of 99 Mo by the 98 Mo(n, γ) 99 Mo reaction is now possible because of the power upgrade of IPEN's IEA-R1 reactor, from 2 to 5 MW. This work describes the preparation method of Zirconium Molybdate gel that will be used in the 99 Mo- 99m Tc generators. The gel is prepared by the chemical reaction between Mo, in Mo O 3 form, and Zr, in Zr O Cl 2 .8H 2 O form. After the reaction, the gel is filtered, dried and cracked with saline solution. The product is then loaded into glass columns for use as 99m Tc generator. The results showed the good quality of the gel prepared at laboratory level and of the generators evaluated. (author)

  19. Electrophoretic analysis of proteins from Mycoplasma hominis strains detected by SDS-PAGE, two-dimensional gel electrophoresis and immunoblotting

    DEFF Research Database (Denmark)

    Andersen, H; Birkelund, Svend; Christiansen, Gunna

    1987-01-01

    The proteins of 14 strains of Mycoplasma hominis were compared by SDS-PAGE in gradient gels, by two-dimensional (2D) gel electrophoresis of extracts of 35S-labelled cells and by immunoblot analysis of cell proteins. The strains examined included the M. hominis type strain PG21 and 13 others...... isolated variously from genital tract, mouth, blood, upper urinary tract and a wound. These 14 strains shared 76-99% of proteins in SDS-gradient gel analysis and 41-72% in the 2D gels. As expected, the immunoblot analysis likewise revealed the existence of an extensive common protein pattern in M. hominis...

  20. Microfluidics of soft granular gels

    Science.gov (United States)

    Nixon, Ryan; Bhattacharjee, Tapomoy; Sawyer, W. Gregory; Angelini, Thomas E.

    Microfluidic methods for encapsulating cells and particles typically involve drop making with two immiscible fluids. The main materials constraint in this approach is surface tension, creating inherent instability between the two fluids. We can eliminate this instability by using miscible inner and outer phases. This is achieved by using granular micro gels which are chemically miscible but physically do not mix. These microgels are yield stress materials, so they flow as solid plugs far from shear gradients, and fluidize where gradients are generated - near an injection nozzle for example. We have found that tuning the yield stress of the material by varying polymer concentration, device performance can be controlled. The solid like behavior of the gel allows us to produces infinitely stable jets that maintain their integrity and configuration over long distances and times. These properties can be combined and manipulated to produce discrete particulate bunches of an inner phase, flowing inside of an outer phase, well enough even to print a Morse code message suspended within flow chambers about a millimeter in diameter moving at millimeters a second.

  1. A PCR-denaturing gradient gel electrophoresis (DGGE) approach to assess Fusarium diversity in asparagus

    NARCIS (Netherlands)

    Yergeau, E.; Filion, M.; Vujanovic, V.; St-Arnaud, M.

    2005-01-01

    In North America, asparagus (Asparagus officinalis) production suffers from a crown and root rot disease mainly caused by Fusarium oxysporum f. sp. asparagi and F. proliferatum. Many other Fusarium species are also found in asparagus fields, whereas accurate detection and identification of these

  2. Microbial Succession in Co-Composting of Chipped-Ground Oil Palm Frond and Palm Oil Mill Effluent

    International Nuclear Information System (INIS)

    Mohd Najib Ahmad; Siti Ramlah Ahmad Ali; Mohd Ali Hassan

    2016-01-01

    Succession and phylogenetic profile of microbial communities during co-composting of chipped-ground oil palm frond (CG-OPF) and palm oil mill effluent (POME) were studied by apply-ing polymerase chain reaction-denaturant gel gradient electrophoresis (PCR-DGGE) analysis. The results indicated that the dominant microbial community detected was γ-Pro bacteria such as Pseudomonas sp. at almost throughout the composting process. Whilst Bacillales such as Bacillus psychrodurans were found toward the end of the composting process. Bacteroidetes such as Pedobacter solani were detected at the final stage of composting. This study contributed to a better understanding of microbial shifting and functioning throughout CG-OPF composting. Therefore, PCR-DGGE is recommended to be used as a tool to identify potential microbes that can contribute to a better performance of composting process. (author)

  3. Isolate PM1 populations are dominant and novel methyl tert-butyl ether-degrading bacterial in compost biofilter enrichments.

    Science.gov (United States)

    Bruns, M A; Hanson, J R; Mefford, J; Scow, K M

    2001-03-01

    The gasoline additive MTBE, methyl tert-butyl ether, is a widespread and persistent groundwater contaminant. MTBE undergoes rapid mineralization as the sole carbon and energy source of bacterial strain PM1, isolated from an enrichment culture of compost biofilter material. In this report, we describe the results of microbial community DNA profiling to assess the relative dominance of isolate PM1 and other bacterial strains cultured from the compost enrichment. Three polymerase chain reaction (PCR)-based profiling approaches were evaluated: denaturing gradient gel electrophoresis (DGGE) analysis of 230 bp 16S rDNA fragments; thermal gradient gel electrophoresis (TGGE) analysis of 575 bp 16S rDNA fragments; and non-denaturing polyacrylamide gel electrophoresis of 300-1,500 bp fragments containing 16S/23S ribosomal intergenic transcribed spacer (ITS) regions. Whereas all three DNA profiling approaches indicated that PM1-like bands predominated in mixtures from MTBE-grown enrichments, ITS profiling provided the most abundant and specific sequence data to confirm strain PM1's presence in the enrichment. Moreover, ITS profiling did not produce non-specific PCR products that were observed with T/DGGE. A further advantage of ITS community profiling over other methods requiring restriction digestion (e.g. terminal restriction fragment length polymorphisms) was that it did not require an additional digestion step or the use of automated sequencing equipment. ITS bands, excised from similar locations in profiles of the enrichment and PM1 pure culture, were 99.9% identical across 750 16S rDNA positions and 100% identical across 691 spacer positions. BLAST comparisons of nearly full-length 16S rDNA sequences showed 96% similarity between isolate PM1 and representatives of at least four different genera in the Leptothrix subgroup of the beta-Proteobacteria (Aquabacterium, Leptothrix, Rubrivivax and Ideonella). Maximum likelihood and parsimony analyses of 1,249 nucleotide

  4. The generation of denatured reactor plutonium by different options of the fuel cycle

    Energy Technology Data Exchange (ETDEWEB)

    Broeders, C.H.M.; Kessler, G. [Inst. for Neutron Physics and Reactor Technology, Research Center Karlsruhe (Germany)

    2006-11-15

    Denatured (proliferation resistant) reactor plutonium can be generated in a number of different fuel cycle options. First denatured reactor plutonium can be obtained if, instead of low enriched U-235 PWR fuel, re-enriched U-235/U-236 from reprocessed uranium is used (fuel type A). Also the envisaged existing 2,500 t of reactor plutonium (being generated world wide up to the year 2010), mostly stored in intermediate fuel storage facilities at present, could be converted during a transition phase into denatured reactor plutonium by the options fuel type B and D. Denatured reactor plutonium could have the same safeguards standard as present low enriched (<20% U-235) LWR fuel. It could be incinerated by recycling once or twice in PWRs and subsequently by multi-recycling in FRs (CAPRA type or IFRs). Once denatured, such reactor plutonium could remain denatured during multiple recycling. In a PWR, e.g., denatured reactor plutonium could be destroyed at a rate of about 250 kg/GWey. While denatured reactor plutonium could be recycled and incinerated under relieved IAEA safeguards, neptunium would still have to be monitored by the IAEA in future for all cases in which considerable amounts of neptunium are produced. (orig.)

  5. Gels and gel-derived glasses in the system Na2O-B2O3-SiO2

    Science.gov (United States)

    Mukherjee, S. P.

    1983-01-01

    The containerless melting of high-purity multicomponent homogeneous gels and gel monoliths offers a unique approach to making ultrapure multicomponent optical glasses in the reduced gravity environment of space. Procedures for preparing and characterizing gels and gel-derived glasses in the system Na2O-B2O3-SiO2 are described. Preparation is based on the polymerization reactions of alkoxysilane with trimethyl borate or boric acid and a suitable sodium compound. The chemistry of the gelling process is discussed in terms of process parameters and the gel compositions. The physicochemical nature of gels prepared by three different procedures was found to be significantly different. Infrared absorption spectra indicate finite differences in the molecular structures of the different gels. The melting of the gel powders and the transformation of porous gel monoliths to transparent 'glass' without melting are described.

  6. Comparison of DNA double-strand break rejoining as measured by pulsed field gel electrophoresis, neutral sucrose gradient centrifugation and non-unwinding filter elution in irradiated plateau-phase CHO cells

    International Nuclear Information System (INIS)

    Iliakis, G.; Metzger, L.; Pantelias, G.

    1991-01-01

    The initial (up to 30 min) rate of DNA double-strand break (dsb) rejoining was measured in irradiated plateau-phase CHO cells, in a set of parallel experiments using the same cell suspension, by means of non-unwinding filter elution, neutral sucrose gradient centrifugation, and two pulsed-field gel electrophoresis assays: asymmetric field inversion gel electrophoresis (AFIGE) and clamped homogeneous electric field (CHEF) gel electrophoresis. The rate of DNA dsb rejoining was compared to the rate of rejoining of chromatin breaks measured, also in the same cell population, using the technique of premature chromosome condensation (PCC). Two radiation exposures, 25 Gy and/or 50 Gy, were used and applied to the individual parts of the experiments according to the sensitivity of the assay under investigation. The results suggest all major techniques currently used for assaying rejoining of DNA dsb give similar results, and indicate that more information is required before a direct correlation between rejoining of DNA dsb and rejoining of chromatin breaks can be established. (author)

  7. Diversity and Stability of Lactic Acid Bacteria in Rye Sourdoughs of Four Bakeries with Different Propagation Parameters

    OpenAIRE

    Viiard, Ene; Bessmeltseva, Marianna; Simm, Jaak; Talve, Tiina; Aasp?llu, Anu; Paalme, Toomas; Sarand, Inga

    2016-01-01

    We identified the lactic acid bacteria within rye sourdoughs and starters from four bakeries with different propagation parameters and tracked their dynamics for between 5-28 months after renewal. Evaluation of bacterial communities was performed using plating, denaturing gradient gel electrophoresis, and pyrosequencing of 16S rRNA gene amplicons. Lactobacillus amylovorus and Lactobacillus frumenti or Lactobacillus helveticus, Lactobacillus pontis and Lactobacillus panis prevailed in sourdoug...

  8. Isolation of Methylophaga spp. from Marine Dimethylsulfide-Degrading Enrichment Cultures and Identification of Polypeptides Induced during Growth on Dimethylsulfide▿

    OpenAIRE

    Schäfer, Hendrik

    2007-01-01

    Dimethylsulfide (DMS)-degrading enrichment cultures were established from samples of coastal seawater, nonaxenic Emiliania huxleyi cultures, and mixed marine methyl halide-degrading enrichment cultures. Bacterial populations from a broad phylogenetic range were identified in the mixed DMS-degrading enrichment cultures by denaturing gradient gel electrophoresis (DGGE). Sequences of dominant DGGE bands were similar to those of members of the genera Methylophaga and Alcanivorax. Several closely ...

  9. Lessons Learned on Bioaugmentation of DNAPL Source Zone Areas

    Science.gov (United States)

    2007-10-01

    but rather have stringers, ganglia or blobs that can create an “effective pool length”. As the leading edge of these discontinuous DNAPL free-phases...terminal restriction fragment length polymorphism (T-RFLP), denaturing gradient gel electrophoresis (DGGE), and fluorescent in situ hybridization ( FISH ...question of interest (e.g. PCR, FISH , DGGE); (ii) sampling location(s); (iii) an appropriate sampling procedure; and (iv) an appropriate sample handling

  10. Microbial community analysis of perchlorate-reducing cultures growing on zero-valent iron

    International Nuclear Information System (INIS)

    Son, Ahjeong; Schmidt, Carl J.; Shin, Hyejin; Cha, Daniel K.

    2011-01-01

    Anaerobic microbial mixed cultures demonstrated its ability to completely remove perchlorate in the presence of zero-valent iron. In order to understand the major microbial reaction in the iron-supported culture, community analysis comprising of microbial fatty acids and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) techniques was performed for perchlorate reducing cultures. Analysis of fatty acid methyl esters (FAMEs) and subsequent principal component analysis (PCA) showed clear distinctions not only between iron-supported perchlorate reducing culture and seed bacteria, but also among perchlorate-reducing cultures receiving different electron donors. The DGGE pattern targeting the chlorite dismutase (cld) gene showed that iron-supported perchlorate reducing culture is similar to hydrogen-fed cultures as compared to acetate-fed culture. The phylogenetic tree suggested that the dominant microbial reaction may be a combination of the autotrophic and heterotrophic reduction of perchlorate. Both molecular and chemotaxonomic experimental results support further understanding in the function of zero-valent iron as an adequate electron source for enhancing the microbial perchlorate reduction in natural and engineered systems.

  11. Microbial community analysis of perchlorate-reducing cultures growing on zero-valent iron

    Energy Technology Data Exchange (ETDEWEB)

    Son, Ahjeong, E-mail: ason@auburn.edu [Department of Civil Engineering, Auburn University, Auburn, AL 36849 (United States); Schmidt, Carl J. [Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716 (United States); Shin, Hyejin [Department of Mathematics and Statistics, Auburn University, Auburn, AL 36849 (United States); Cha, Daniel K. [Department of Civil and Environmental Engineering, University of Delaware, Newark, DE 19716 (United States)

    2011-01-30

    Anaerobic microbial mixed cultures demonstrated its ability to completely remove perchlorate in the presence of zero-valent iron. In order to understand the major microbial reaction in the iron-supported culture, community analysis comprising of microbial fatty acids and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) techniques was performed for perchlorate reducing cultures. Analysis of fatty acid methyl esters (FAMEs) and subsequent principal component analysis (PCA) showed clear distinctions not only between iron-supported perchlorate reducing culture and seed bacteria, but also among perchlorate-reducing cultures receiving different electron donors. The DGGE pattern targeting the chlorite dismutase (cld) gene showed that iron-supported perchlorate reducing culture is similar to hydrogen-fed cultures as compared to acetate-fed culture. The phylogenetic tree suggested that the dominant microbial reaction may be a combination of the autotrophic and heterotrophic reduction of perchlorate. Both molecular and chemotaxonomic experimental results support further understanding in the function of zero-valent iron as an adequate electron source for enhancing the microbial perchlorate reduction in natural and engineered systems.

  12. Computer simulation of immobilized pH gradients at acidic and alkaline extremes - A quest for extended pH intervals

    Science.gov (United States)

    Mosher, Richard A.; Bier, Milan; Righetti, Pier Giorgio

    1986-01-01

    Computer simulations of the concentration profiles of simple biprotic ampholytes with Delta pKs 1, 2, and 3, on immobilized pH gradients (IPG) at extreme pH values (pH 3-4 and pH 10-11) show markedly skewed steady-state profiles with increasing kurtosis at higher Delta pK values. Across neutrality, all the peaks are symmetric irrespective of their Delta pK values, but they show very high contribution to the conductivity of the background gel and significant alteration of the local buffering capacity. The problems of skewness, due to the exponential conductivity profiles at low and high pHs, and of gel burning due to a strong electroosmotic flow generated by the net charges in the gel matrix, also at low and high pHs, are solved by incorporating in the IPG gel a strong viscosity gradient. This is generated by a gradient of linear polyacrylamide which is trapped in the gel by the polymerization process.

  13. Molecular characterization of microbial population dynamics during sildenafil citrate degradation.

    Science.gov (United States)

    De Felice, Bruna; Argenziano, Carolina; Guida, Marco; Trifuoggi, Marco; Russo, Francesca; Condorelli, Valerio; Inglese, Mafalda

    2009-02-01

    Little is known about pharmaceutical and personal care products pollutants (PPCPs), but there is a growing interest in how they might impact the environment and microbial communities. The widespread use of Viagra (sildenafil citrate) has attracted great attention because of the high usage rate, the unpredictable disposal and the unknown potential effects on wildlife and the environment. Until now information regarding the impact of Viagra on microbial community in water environment has not been reported. In this research, for the first time, the genetic profile of the microbial community, developing in a Viagra polluted water environment, was evaluated by means of the 16S and 18S rRNA genes, for bacteria and fungi, respectively, amplified by polymerase chain reaction (PCR) and separated using the denaturing gradient gel electrophoresis (DGGE) technique. The DGGE results revealed a complex microbial community structure with most of the population persisting throughout the experimental period. DNA sequences from bands observed in the different denaturing gradient gel electrophoresis profiles exhibited the highest degree of identity to uncultured bacteria and fungi found previously mainly in polluted environmental and treating bioreactors. Biotransformation ability of sildenafil citrate by the microbial pool was studied and the capability of these microorganisms to detoxify a polluted water ecosystem was assessed. The bacterial and fungal population was able to degrade sildenafil citrate entirely. Additionally, assays conducted on Daphnia magna, algal growth inhibition assay and cell viability determination on HepG2 human cells showed that biotransformation products obtained from the bacterial growth was not toxic. The higher removal efficiency for sildenafil citrate and the lack of toxicity by the biotransformation products obtained showed that the microbial community identified here represented a composite population that might have biotechnological relevance to

  14. Micro-CT imaging of denatured chitin by silver to explore honey bee and insect pathologies.

    Directory of Open Access Journals (Sweden)

    Peter R Butzloff

    Full Text Available BACKGROUND: Chitin and cuticle coatings are important to the environmental and immune defense of honey bees and insect pollinators. Pesticides or environmental effects may target the biochemistry of insect chitin and cuticle coating. Denaturing of chitin involves a combination of deacetylation, intercalation, oxidation, Schweiger-peeling, and the formation of amine hydrochloride salt. The term "denatured chitin" calls attention to structural and property changes to the internal membranes and external carapace of organisms so that some properties affecting biological activities are diminished. METHODOLOGY/PRINCIPAL FINDINGS: A case study was performed on honey bees using silver staining and microscopic computer-tomographic x-ray radiography (micro-CT. Silver nitrate formed counter-ion complexes with labile ammonium cations and reacted with amine hydrochloride. Silver was concentrated in the peritrophic membrane, on the abdomen, in the glossa, at intersegmental joints (tarsi, at wing attachments, and in tracheal air sacs. Imaged mono-esters and fatty acids from cuticle coating on external surfaces were apparently reduced by an alcohol pretreatment. CONCLUSIONS/SIGNIFICANCE: The technique provides 3-dimensional and sectional images of individual honey bees consistent with the chemistries of silver reaction and complex formation with denatured chitin. Environmental exposures and influences such as gaseous nitric oxide intercalant, trace oxidants such as ozone gas, oligosachharide salt conversion, exposure to acid rain, and chemical or biochemical denaturing by pesticides may be studied using this technique. Peritrophic membranes, which protect against food abrasion, microorganisms, and permit efficient digestion, were imaged. Apparent surface damage to the corneal lenses of compound eyes by dilute acid exposure consistent with chitin amine hydrochloride formation was imaged. The technique can contribute to existing insect pathology research, and may

  15. Micro-CT Imaging of Denatured Chitin by Silver to Explore Honey Bee and Insect Pathologies

    Science.gov (United States)

    Butzloff, Peter R.

    2011-01-01

    Background Chitin and cuticle coatings are important to the environmental and immune defense of honey bees and insect pollinators. Pesticides or environmental effects may target the biochemistry of insect chitin and cuticle coating. Denaturing of chitin involves a combination of deacetylation, intercalation, oxidation, Schweiger-peeling, and the formation of amine hydrochloride salt. The term “denatured chitin” calls attention to structural and property changes to the internal membranes and external carapace of organisms so that some properties affecting biological activities are diminished. Methodology/Principal Findings A case study was performed on honey bees using silver staining and microscopic computer-tomographic x-ray radiography (micro-CT). Silver nitrate formed counter-ion complexes with labile ammonium cations and reacted with amine hydrochloride. Silver was concentrated in the peritrophic membrane, on the abdomen, in the glossa, at intersegmental joints (tarsi), at wing attachments, and in tracheal air sacs. Imaged mono-esters and fatty acids from cuticle coating on external surfaces were apparently reduced by an alcohol pretreatment. Conclusions/Significance The technique provides 3-dimensional and sectional images of individual honey bees consistent with the chemistries of silver reaction and complex formation with denatured chitin. Environmental exposures and influences such as gaseous nitric oxide intercalant, trace oxidants such as ozone gas, oligosachharide salt conversion, exposure to acid rain, and chemical or biochemical denaturing by pesticides may be studied using this technique. Peritrophic membranes, which protect against food abrasion, microorganisms, and permit efficient digestion, were imaged. Apparent surface damage to the corneal lenses of compound eyes by dilute acid exposure consistent with chitin amine hydrochloride formation was imaged. The technique can contribute to existing insect pathology research, and may provide an

  16. Modeling chemical gradients in sediments under losing and gaining flow conditions: The GRADIENT code

    Science.gov (United States)

    Boano, Fulvio; De Falco, Natalie; Arnon, Shai

    2018-02-01

    Interfaces between sediments and water bodies often represent biochemical hotspots for nutrient reactions and are characterized by steep concentration gradients of different reactive solutes. Vertical profiles of these concentrations are routinely collected to obtain information on nutrient dynamics, and simple codes have been developed to analyze these profiles and determine the magnitude and distribution of reaction rates within sediments. However, existing publicly available codes do not consider the potential contribution of water flow in the sediments to nutrient transport, and their applications to field sites with significant water-borne nutrient fluxes may lead to large errors in the estimated reaction rates. To fill this gap, the present work presents GRADIENT, a novel algorithm to evaluate distributions of reaction rates from observed concentration profiles. GRADIENT is a Matlab code that extends a previously published framework to include the role of nutrient advection, and provides robust estimates of reaction rates in sediments with significant water flow. This work discusses the theoretical basis of the method and shows its performance by comparing the results to a series of synthetic data and to laboratory experiments. The results clearly show that in systems with losing or gaining fluxes, the inclusion of such fluxes is critical for estimating local and overall reaction rates in sediments.

  17. Effects of sterilization, packaging, and storage on vitamin C degradation, protein denaturation, and glycation in fortified milks.

    Science.gov (United States)

    Gliguem, H; Birlouez-Aragon, I

    2005-03-01

    Monitoring the nutritional quality of dietetic milk throughout its shelf life is particularly important due to the high susceptibility of some vitamins to oxidation, and the continuous development of the Maillard reaction during storage. The objective of this paper was to evaluate the vitamin C content and protein modification by denaturation and glycation on fortified milk samples (growth milks) destined for 1- to 3-yr-old children. The influences of the sterilization process, formulation, packaging, and storage duration at ambient temperature in the dark were studied. Vitamin C degradation was particularly influenced by type of packaging. The use of a 3-layered opaque bottle was associated with complete oxidation of vitamin C after 1 mo of storage, whereas in the 6-layered opaque bottle, which has an oxygen barrier, the vitamin C content slowly decreased to reach 25% of the initial concentration after 4 mo of storage. However, no significant effect of vitamin C degradation during storage could be observed in terms of Maillard reaction, despite the fact that a probable impact occurred during sterilization. Furosine content and the FAST (fluorescence of advanced Maillard products and soluble tryptophan) index-indicators of the early and advanced Maillard reaction, respectively-were significantly higher in the in-bottle sterilized milk samples compared with UHT samples, and in fortified milk samples compared with cow milk. However, after 1 mo, the impact of storage was predominant, increasing the furosine level and the FAST index at similar levels for the differently processed samples. The early Maillard reaction developed continuously throughout the storage period.In conclusion, only packaging comprising an oxygen and light barrier is compatible with vitamin C fortification of milk. Furthermore, short storage time or low storage temperature is needed to retard vitamin C degradation, protein denaturation, and development of the Maillard reaction.

  18. Study on the mechanism of toxicity development by analysis of interactions among RI-labelled biopolymers

    International Nuclear Information System (INIS)

    Koizumi, Shinji

    1997-01-01

    In order to find the directly targetting molecule(s) of toxic substances which are produced in various working environments and to elucidate the natural functions of such molecules in the body. The interactions between an assumed target molecule, ZRF and a sequence in metallothionein II A gene, MRE were investigated using electrophoresis. When double stranded DNA of which binding region was labelled with 32 P was mixed with ZRF, any DNA-protein complex was not detectable on denatured polyacrylamide gel electrophoresis, but Zn-dependent complex formation was observed when labelled in the presence of BrdUTP and the specific band disappeared after the treatment with nuclease. And UV radiation was essential for the complex formation under the conditions of denatured gel, however the complex formed by un-denatured gel electrophoresis was markedly reduced by UV radiation, indicating that the cross-linking reaction should be done at a low dose of UV. Since the nuclease preparation used was contaminated with protease, it was needed to choose an appropriate amount of the preparation. Although there remain some problems, it was found that the present procedure by SDS-polyacrylamide gel electrophoresis was available for detection of the cross-linking between DNA and protein. (M.N.)

  19. Energy-Efficient Bioalcohol Recovery by Gel Stripping

    Science.gov (United States)

    Godbole, Rutvik; Ma, Lan; Hedden, Ronald

    2014-03-01

    Design of energy-efficient processes for recovering butanol and ethanol from dilute fermentations is a key challenge facing the biofuels industry due to the high energy consumption of traditional multi-stage distillation processes. Gel stripping is an alternative purification process by which a dilute alcohol is stripped from the fermentation product by passing it through a packed bed containing particles of a selectively absorbent polymeric gel material. The gel must be selective for the alcohol, while swelling to a reasonable degree in dilute alcohol-water mixtures. To accelerate materials optimization, a combinatorial approach is taken to screen a matrix of copolymer gels having orthogonal gradients in crosslinker concentration and hydrophilicity. Using a combination of swelling in pure solvents, the selectivity and distribution coefficients of alcohols in the gels can be predicted based upon multi-component extensions of Flory-Rehner theory. Predictions can be validated by measuring swelling in water/alcohol mixtures and conducting h HPLC analysis of the external liquid. 95% + removal of butanol from dilute aqueous solutions has been demonstrated, and a mathematical model of the unsteady-state gel stripping process has been developed. NSF CMMI Award 1335082.

  20. Heavy water reactors on the denatured thorium cycles

    International Nuclear Information System (INIS)

    1978-05-01

    This paper presents preliminary technical and economic data to INFCE on the denatured U-233/Thorium fuel cycle for use in early comparisons of alternate nuclear systems. The once-through uranium fuel cycle is discussed in a companion paper. In presenting this preliminary information at this time, it is recognized that there are several other denatured thorium fuel cycles of potential interest, such as the U-235/thorium cycle which could be implemented at an earlier date. Information on these alternate cycles is currently being developed, and will be provided to INFCE when available

  1. Synthesis and characterization of erbium-doped SiO{sub 2}-TiO{sub 2} thin films prepared by sol-gel and dip-coating techniques onto commercial glass substrates as a route for obtaining active GRadient-INdex materials

    Energy Technology Data Exchange (ETDEWEB)

    Gómez-Varela, Ana I. [Microoptics and GRIN Optics Group, Department of Applied Physics, Faculty of Optics and Optometry and Faculty of Physics, Universidade de Santiago de Compostela, Campus Vida s/n, Santiago de Compostela E-15782 (Spain); Castro, Yolanda, E-mail: castro@icv.csic.es [Instituto de Cerámica y Vidrio (CSIC), Kelsen 5, Campus de Cantoblanco, Madrid 28049 (Spain); Durán, Alicia [Instituto de Cerámica y Vidrio (CSIC), Kelsen 5, Campus de Cantoblanco, Madrid 28049 (Spain); De Beule, Pieter A.A. [Applied Nano-Optics Laboratory, International Iberian Nanotechnology Laboratory, Braga 4715-330 (Portugal); Flores-Arias, María T. [Microoptics and GRIN Optics Group, Department of Applied Physics, Faculty of Optics and Optometry and Faculty of Physics, Universidade de Santiago de Compostela, Campus Vida s/n, Santiago de Compostela E-15782 (Spain); Bao-Varela, Carmen, E-mail: carmen.bao@usc.es [Microoptics and GRIN Optics Group, Department of Applied Physics, Faculty of Optics and Optometry and Faculty of Physics, Universidade de Santiago de Compostela, Campus Vida s/n, Santiago de Compostela E-15782 (Spain)

    2015-05-29

    In this work, SiO{sub 2}-TiO{sub 2} films doped with erbium were prepared by dip-coating sol-gel process onto commercial glass substrates. The surface morphology of the films was characterized using atomic force microscopy, while thickness, refractive index, extinction coefficient and porosity of the films were determined by ellipsometric measurements in a wavelength region of 400-1000 nm. Optical constants and porosity were found to vary with erbium concentration. The proof of principle presented in this paper is applicable to systems of different nature by tailoring the sol-gel precursors in such a way that active GRadient-INdex media described by a complex, parabolic-like refractive index distribution for beam shaping purposes is obtained. - Highlights: • Sol-gel route for preparation of active GRadient-INdex materials is proposed. • SiO{sub 2}-TiO{sub 2} films doped with erbium were prepared by dipping onto commercial glasses. • Morphological and optical characterization of the samples was performed. • Optical constants and porosity were found to vary with erbium concentration. • Refractive index diminishes with dopant content; the contrary occurs for porosity.

  2. Irreversible denaturation of maltodextrin glucosidase studied by differential scanning calorimetry, circular dichroism, and turbidity measurements.

    Science.gov (United States)

    Goyal, Megha; Chaudhuri, Tapan K; Kuwajima, Kunihiro

    2014-01-01

    Thermal denaturation of Escherichia coli maltodextrin glucosidase was studied by differential scanning calorimetry, circular dichroism (230 nm), and UV-absorption measurements (340 nm), which were respectively used to monitor heat absorption, conformational unfolding, and the production of solution turbidity. The denaturation was irreversible, and the thermal transition recorded at scan rates of 0.5-1.5 K/min was significantly scan-rate dependent, indicating that the thermal denaturation was kinetically controlled. The absence of a protein-concentration effect on the thermal transition indicated that the denaturation was rate-limited by a mono-molecular process. From the analysis of the calorimetric thermograms, a one-step irreversible model well represented the thermal denaturation of the protein. The calorimetrically observed thermal transitions showed excellent coincidence with the turbidity transitions monitored by UV-absorption as well as with the unfolding transitions monitored by circular dichroism. The thermal denaturation of the protein was thus rate-limited by conformational unfolding, which was followed by a rapid irreversible formation of aggregates that produced the solution turbidity. It is thus important to note that the absence of the protein-concentration effect on the irreversible thermal denaturation does not necessarily means the absence of protein aggregation itself. The turbidity measurements together with differential scanning calorimetry in the irreversible thermal denaturation of the protein provided a very effective approach for understanding the mechanisms of the irreversible denaturation. The Arrhenius-equation parameters obtained from analysis of the thermal denaturation were compared with those of other proteins that have been reported to show the one-step irreversible thermal denaturation. Maltodextrin glucosidase had sufficiently high kinetic stability with a half-life of 68 days at a physiological temperature (37°C).

  3. Design of Self-Oscillating Gels and Application to Biomimetic Actuators

    Directory of Open Access Journals (Sweden)

    Ryo Yoshida

    2010-03-01

    Full Text Available As a novel biomimetic polymer, we have developed polymer gels with an autonomous self-oscillating function. This was achieved by utilizing oscillating chemical reactions, called the Belousov-Zhabotinsky (BZ reaction, which is recognized as a chemical model for understanding several autonomous phenomena in biological systems. Under the coexistence of the reactants, the polymer gel undergoes spontaneous swelling-deswelling changes without any on-off switching by external stimuli. In this review, our recent studies on the self-oscillating polymer gels and application to biomimetic actuators are summarized.

  4. Interim assessment of the denatured 233U fuel cycle: feasibility and nonproliferation characteristics

    International Nuclear Information System (INIS)

    Abbott, L.S.; Bartine, D.E.; Burns, T.J.

    1979-12-01

    A fuel cycle that employs 233 U denatured with 238 U and mixed with thorium fertile material is examined with respect to its proliferation-resistance characteristics and its technical and economic feasibility. The rationale for considering the denatured 233 U fuel cycle is presented, and the impact of the denatured fuel on the performance of Light-Water Reactors, Spectral-Shift-Controlled Reactors, Gas-Cooled Reactors, Heavy-Water Reactors, and Fast Breeder Reactors is discussed. The scope of the R, D and D programs to commercialize these reactors and their associated fuel cycles is also summarized and the resource requirements and economics of denatured 233 U cycles are compared to those of the conventional Pu/U cycle. In addition, several nuclear power systems that employ denatured 233 U fuel and are based on the energy center concept are evaluated

  5. Succession of Selected Strains of Acetobacter pasteurianus and Other Acetic Acid Bacteria in Traditional Balsamic Vinegar

    OpenAIRE

    Gullo, M.; De Vero, L.; Giudici, P.

    2009-01-01

    The application of a selected Acetobacter pasteurianus strain for traditional balsamic vinegar production was assessed. Genomic DNA was extracted from biofilms after enrichment cultures on GYC medium (10% glucose, 1.0% yeast extract, 2.0% calcium carbonate) and used for PCR/denaturing gradient gel electrophoresis, 16S rRNA gene sequencing, and enterobacterial repetitive intergenic consensus/PCR sequencing. Results suggested that double-culture fermentation is suitable for traditional balsamic...

  6. Molecular Detection and Ecological Significance of the Cyanobacterial Genera Geitlerinema and Leptolyngbya in Black Band Disease of Corals▿ †

    OpenAIRE

    Myers, Jamie L.; Sekar, Raju; Richardson, Laurie L.

    2007-01-01

    Black band disease (BBD) is a pathogenic, sulfide-rich microbial mat dominated by filamentous cyanobacteria that infect corals worldwide. We isolated cyanobacteria from BBD into culture, confirmed their presence in the BBD community by using denaturing gradient gel electrophoresis (DGGE), and demonstrated their ecological significance in terms of physiological sulfide tolerance and photosynthesis-versus-irradiance values. Twenty-nine BBD samples were collected from nine host coral species, fo...

  7. Influence of Artisan Bakery- or Laboratory-Propagated Sourdoughs on the Diversity of Lactic Acid Bacterium and Yeast Microbiotas

    OpenAIRE

    Minervini, Fabio; Lattanzi, Anna; De Angelis, Maria; Di Cagno, Raffaella; Gobbetti, Marco

    2012-01-01

    Seven mature type I sourdoughs were comparatively back-slopped (80 days) at artisan bakery and laboratory levels under constant technology parameters. The cell density of presumptive lactic acid bacteria and related biochemical features were not affected by the environment of propagation. On the contrary, the number of yeasts markedly decreased from artisan bakery to laboratory propagation. During late laboratory propagation, denaturing gradient gel electrophoresis (DGGE) showed that the DNA ...

  8. Effects of zinc pyrithione and copper pyrithione on microbial community function and structure in sediments

    DEFF Research Database (Denmark)

    Petersen, DG; Dahllof, I.; Nielsen, LP

    2004-01-01

    incorporation) were used, whereas molecular fingerprinting methods (polymerase chain reaction/ denaturing gradient gel electrophoresis) were used to describe the bacterial community structure. The lowest-observed-effect concentration (LOEC) for ZPT was 0.001 nmol/g dry sediment for the phosphate flux and total...... DNA content, whereas the LOEC for CPT was 0.1 nmol/g dry sediment for the nitrate flux and total DNA content. Nitrate fluxes increased significantly following additions of both ZPT and CPT, whereas ammonium fluxes decreased significantly after ZPT addition, suggesting changes in the nitrification...... and denitrification processes. The total DNA content decreased significantly following addition of both ZPT and CPT, but at the highest addition of ZPT (10 nmol ZPT/g dry sediment), an increase in total DNA content was found. Increased protein synthesis and bacterial diversity were also observed at this concentration...

  9. Microbial degradation. Mass transfer in the system pollutant - water - sediment; Mikrobieller Abbau. Massentransfer im System Schadstoff - Wasser - Sediment

    Energy Technology Data Exchange (ETDEWEB)

    Tiehm, Andreas [Technologiezentrum Wasser (TZW), Karlsruhe (Germany). Abt. Umweltbiotechnologie und Altlasten; Kranzioch, Irene; Stoll, Claudia

    2011-09-15

    The microbial degradation of pollutants in the aquatic environment essentially is influenced by the prevailing redox conditions and mass exchange processes (bioavailability). Within a new project, the Technologiezentrum Wasser TZW (Karlsruhe, Federal Republic of Germany) deals with the microbial conversion under dynamic conditions such as those expected in the area of the Three Gorges Dam at the Yangtze River. In particular, molecular-biological methods (PCR, polymerase chain reaction and DGGE Denatured gradient gel electrophoresis) are used for a targeted monitoring and further developed. The focus of the investigation initially focuses on the degradation of halogenated substances which are used as main substances for understanding the mass exchange between sediment and water as well as the microbial conversion processes. An enhanced understanding of the process and the compilation of the dynamic sales performance can be defined as a target.

  10. Use of Psychrotolerant Lactic Acid Bacteria (Lactobacillus spp. and Leuconostoc spp.) Isolated from Chinese Traditional Paocai for the Quality Improvement of Paocai Products.

    Science.gov (United States)

    Liu, Aiping; Li, Xiaoyan; Pu, Biao; Ao, Xiaolin; Zhou, Kang; He, Li; Chen, Shujuan; Liu, Shuliang

    2017-03-29

    To improve the quality of Chinese traditional Paocai, two psychrotolerant lactic acid bacteria (LAB) strains were isolated from Paocai, and the quality of Chinese Paocai product using these two strains as starter cultures was compared to a control sample fermented with aged brine at 10 °C. The results suggested that the physicochemical and sensory features of Paocai fermented with psychrotolerant LAB were more suitable for industrial applications. The nitrite content of Paocai fermented with psychrotolerant LAB was 1 mg/kg, which was significantly lower than that of the control Paocai (P products. Additionally, Paocai fermented with psychrotolerant LAB harbored relatively simple microbial flora as revealed by polymerase chain reaction-denaturing gradient gel electrophoresis. This study provides a basis for improving the quality of Chinese traditional Paocai and the large-scale production of low-temperature Chinese traditional Paocai products.

  11. Influence of ionic constituents and electrical conductivity on the propagation of charged nanoscale objects in passivated gel electrophoresis.

    Science.gov (United States)

    Bikos, Dimitri A; Mason, Thomas G

    2018-01-01

    When determining the electric field E acting on charged objects in gel electrophoresis, the electrical conductivity of the buffer solution is often overlooked; E is typically calculated by dividing the applied voltage by a separation distance between electrodes. However, as a consequence of electrolytic reactions, which occur at the electrodes, gradients in the ionic content of the buffer solution and its conductivity can potentially develop over time, thereby impacting E and affecting propagation velocities of charged objects, v, directly. Here, we explore how the types and concentrations of ionic constituents of the buffer solution, which largely control its conductivity, when used in passivated gel electrophoresis (P-gelEP), can influence E, thereby altering v of charged nanospheres propagating through large-pore gels. We measure the conductivity of the buffer solution in the center of the gel region near propagating bands of nanospheres, and we show that predictions of E based on conductivity closely correlate with v. We also explore P-gelEP involving two different types of passivation agents: nonionic polyethylene glycol (PEG) and anionic sodium dodecyl sulfate (SDS). Our observations indicate that using a conductivity model to determine E from the local current density and the conductivity where spheres are propagating can lead to a better estimate than the standard approach of a voltage divided by a separation. Moreover, this conductivity model also provides a starting point for interpreting the complex behavior created by amphiphilic ionic passivation agents, such as SDS, on propagating nanospheres used in some P-gelEP experiments. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Obtaining of platinum-titanium alloys by sol-gel and their performance for the detachment reactions and oxygen reduction; Obtencion de aleaciones de platino-titanio por sol-gel y su desempeno para las reacciones de desprendimiento y reduccion de oxigeno

    Energy Technology Data Exchange (ETDEWEB)

    Regueira R, B. I.

    2011-07-01

    In the present work, platinum-titanium (Pt-Ti) alloys were prepared, characterized and evaluated in acid media as bifunctional electrocatalysts for the oxygen evolution reaction (Oer) and oxygen reduction reactions (Orr) in acid media. The alloys were synthesized by sol-gel method, heating the gel at temperatures of 400 and 600 C. The alloys characterization was realized by X-ray diffraction, scanning electron microscopy and EDS. Both alloys were formed by agglomerates of nanometer particles. The particle sizes were lower for the alloy obtained at 400 C (120 nm to 257 nm) compared to the alloy prepared at 600 C (555 nm to 833 nm). Cyclic and linear voltammetry techniques were used for the electrochemical evaluation of the alloy obtained at both temperatures for the Oer and Orr, in a 0.5 M sulfuric acid solution. The materials have response for both electrochemical reactions, therefore the best performance was for the Pt-Ti alloy, obtained at 400 C and it was stable for the oxygen evolution reaction. The alloy obtained at 400 C presents satisfactory electrocatalytic characteristics to be used as bifunctional material in a unified regenerative fuel cell. (Author)

  13. The effect of reaction temperature on the room temperature ferromagnetic property of sol-gel derived tin oxide nanocrystal

    Science.gov (United States)

    Sakthiraj, K.; Hema, M.; Balachandra Kumar, K.

    2018-06-01

    In the present study, nanocrystalline tin oxide materials were prepared using sol-gel method with different reaction temperatures (25 °C, 50 °C, 75 °C & 90 °C) and the relation between the room temperature ferromagnetic property of the sample with processing temperature has been analysed. The X-ray diffraction pattern and infrared absorption spectra of the as-prepared samples confirm the purity of the samples. Transmission electron microscopy images visualize the particle size variation with respect to reaction temperature. The photoluminescence spectra of the samples demonstrate that luminescence process in materials is originated due to the electron transition mediated by defect centres. The room temperature ferromagnetic property is observed in all the samples with different amount, which was confirmed using vibrating sample magnetometer measurements. The saturation magnetization value of the as-prepared samples is increased with increasing the reaction temperature. From the photoluminescence & magnetic measurements we accomplished that, more amount of surface defects like oxygen vacancy and tin interstitial are created due to the increase in reaction temperature and it controls the ferromagnetic property of the samples.

  14. Response of Soft Continuous Structures and Topological Defects to a Temperature Gradient.

    Science.gov (United States)

    Kurita, Rei; Mitsui, Shun; Tanaka, Hajime

    2017-09-08

    Thermophoresis, which is mass transport induced by a temperature gradient, has recently attracted considerable attention as a new way to transport materials. So far the study has been focused on the transport of discrete structures such as colloidal particles, proteins, and polymers in solutions. However, the response of soft continuous structures such as membranes and gels to a temperature gradient has been largely unexplored. Here we study the behavior of a lamellar phase made of stacked surfactant bilayer membranes under a temperature gradient. We find the migration of membranes towards a low-temperature region, causing the increase in the degree of membrane undulation fluctuations towards that direction. This is contrary to our intuition that the fluctuations are weaker at a lower temperature. We show that this can be explained by temperature-gradient-induced migration of membranes under the topological constraint coming from the connectivity of each membrane. We also reveal that the pattern of an edge dislocation array formed in a wedge-shaped cell can be controlled by a temperature gradient. These findings suggest that application of a temperature gradient provides a novel way to control the organization of soft continuous structures such as membranes, gels, and foams, in a manner essentially different from the other types of fields, and to manipulate topological defects.

  15. 27 CFR 20.148 - Manufacture of articles with completely denatured alcohol.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Manufacture of articles with completely denatured alcohol. 20.148 Section 20.148 Alcohol, Tobacco Products and Firearms ALCOHOL... ALCOHOL AND RUM Sale and Use of Completely Denatured Alcohol § 20.148 Manufacture of articles with...

  16. Modification of Clays by Sol-Gel Reaction and Their Use in the Ethylene In Situ Polymerization for Obtaining Nanocomposites

    Directory of Open Access Journals (Sweden)

    E. Moncada

    2012-01-01

    Full Text Available The nanocomposites formation by in situ polymerization used a metallocene catalyst (butyl-2-cyclopentadienyl zirconium 2-chlorines and a hectorite synthetic clay type which is discussed. This research was carried out in two phases. The first phase consisted of mixing the components of the metallocenic polymerization reaction (metallocene-methylaluminoxane-ethylene with clay in a reactor. In the second phase, the metallocenic catalytic system was supported by clay particles and then a polymerization reaction was made. In this second phase, the clay particles were modified using a sol-gel reaction with different pH values: pH = 3, pH = 8, and pH = 12. The results were compared in terms of the catalytic activity in the different systems (phase 1 and phase 2 and the nanoparticle morphology of nanocomposites generated in this study.

  17. Transurethral radiofrequency collagen denaturation for the treatment of women with urinary incontinence.

    Science.gov (United States)

    Kang, Diana; Han, Julia; Neuberger, Molly M; Moy, M Louis; Wallace, Sheila A; Alonso-Coello, Pablo; Dahm, Philipp

    2015-03-18

    Transurethral radiofrequency collagen denaturation is a relatively novel, minimally invasive device-based intervention used to treat individuals with urinary incontinence (UI). No systematic review of the evidence supporting its use has been published to date. To evaluate the efficacy of transurethral radiofrequency collagen denaturation, compared with other interventions, in the treatment of women with UI.Review authors sought to compare the following.• Transurethral radiofrequency collagen denaturation versus no treatment/sham treatment.• Transurethral radiofrequency collagen denaturation versus conservative physical treatment.• Transurethral radiofrequency collagen denaturation versus mechanical devices (pessaries for UI).• Transurethral radiofrequency collagen denaturation versus drug treatment.• Transurethral radiofrequency collagen denaturation versus injectable treatment for UI.• Transurethral radiofrequency collagen denaturation versus other surgery for UI. We conducted a systematic search of the Cochrane Incontinence Group Specialised Register (searched 19 December 2014), EMBASE and EMBASE Classic (January 1947 to 2014 Week 50), Google Scholar and three trials registries in December 2014, along with reference checking. We sought to identify unpublished studies by handsearching abstracts of major gynaecology and urology meetings, and by contacting experts in the field and the device manufacturer. Randomised and quasi-randomised trials of transurethral radiofrequency collagen denaturation versus no treatment/sham treatment, conservative physical treatment, mechanical devices, drug treatment, injectable treatment for UI or other surgery for UI in women were eligible. We screened search results and selected eligible studies for inclusion. We assessed risk of bias and analysed dichotomous variables as risk ratios (RRs) with 95% confidence intervals (CIs) and continuous variables as mean differences (MDs) with 95% CIs. We rated the quality of

  18. Denaturing gradient gel electrophoresis as a fingerprinting method for the analysis of soil microbial communities

    Czech Academy of Sciences Publication Activity Database

    Valášková, Vendula; Baldrian, Petr

    2009-01-01

    Roč. 55, č. 10 (2009), s. 413-423 ISSN 1214-1178 R&D Projects: GA ČR GA526/08/0751; GA MŠk LC06066 Institutional research plan: CEZ:AV0Z50200510 Keywords : DGGE * bacteria * fungi Subject RIV: EE - Microbiology, Virology Impact factor: 0.697, year: 2009

  19. Preparation of denatured protein bone sterilized with gamma radiation

    International Nuclear Information System (INIS)

    Luna Z, D.

    2005-01-01

    The bone is one of the tissues more transplanted in the entire world by that the bone necessity for transplant every day becomes bigger. In the Bank of tissues Radio sterilized of the ININ the amnion and the pig skin are routinely processed. The tissue with which will be continued is with bone. Due to that in our country it doesn't have enough bone of human origin for the necessities required in the bone transplant, an option is the bone of bovine. Of this bone one can obtain denatured protein bone, with the same characteristics of the denatured protein human bone, the one which has been proven that it has good acceptance and incorporation in the human body when is transplanted. The method for the obtaining of the denatured protein bone of bovine, with the confirmation of the final product by means of X-ray diffraction is described. The radiosterilization of this bone with gamma rays and the determination of the lead content. (Author)

  20. Functionality screen of streptavidin mutants by non-denaturing SDS-PAGE using biotin-4-fluorescein.

    Science.gov (United States)

    Humbert, Nicolas; Ward, Thomas R

    2008-01-01

    Site-directed mutagenesis or directed evolution of proteins often leads to the production of inactive mutants. For streptavidin and related proteins, mutations may lead to the loss of their biotin-binding properties. With high-throughput screening methodologies in mind, it is imperative to detect, prior to the high-density protein production, the bacteria that produce non-functional streptavidin isoforms. Based on the incorporation of biotin-4-fluorescein in streptavidin mutants present in Escherichia coli bacterial extracts, we detail a functional screen that allows the identification of biotin-binding streptavidin variants. Bacteria are cultivated in a small volume, followed by a rapid treatment of the cells; biotin-4-fluorescein is added to the bacterial extract and loaded on an Sodium Dodecyl Sulfate Poly-Acrylamide Gel Electrophoresis (SDS-PAGE) under non-denaturing conditions. Revealing is performed using a UV transilluminator. This screen is thus easy to implement, cheap and requires only readily available equipment.

  1. Mutation of charged residues to neutral ones accelerates urea denaturation of HP-35.

    Science.gov (United States)

    Wei, Haiyan; Yang, Lijiang; Gao, Yi Qin

    2010-09-16

    Following the studies of urea denaturation of β-hairpins using molecular dynamics, in this paper, molecular dynamics simulations of two peptides, a 35 residue three helix bundle villin headpiece protein HP-35 and its doubly norleucine-substituent mutant (Lys24Nle/Lys29Nle) HP-35 NleNle, were undertaken in urea solutions to understand the molecular mechanism of urea denaturation of α-helices. The mutant HP-35 NleNle was found to denature more easily than the wild type. During the expansion of the small hydrophobic core, water penetration occurs first, followed by that of urea molecules. It was also found that the initial hydration of the peptide backbone is achieved through water hydrogen bonding with the backbone CO groups during the denaturation of both polypeptides. The mutation of the two charged lysine residues to apolar norleucine enhances the accumulation of urea near the hydrophobic core and facilitates the denaturation process. Urea also interacts directly with the peptide backbone as well as side chains, thereby stabilizing nonnative conformations. The mechanism revealed here is consistent with the previous study on secondary structure of β-hairpin polypeptide, GB1, PEPTIDE 1, and TRPZIP4, suggesting that there is a general mechanism in the denaturation of protein backbone hydrogen bonds by urea.

  2. Interim assessment of the denatured 233U fuel cycle: feasibility and nonproliferation characteristics

    International Nuclear Information System (INIS)

    Abbott, L.S.; Bartine, D.E.; Burns, T.J.

    1978-12-01

    A fuel cycle that employs 233 U denatured with 238 U and mixed with thorium fertile material is examined with respect to its proliferation-resistance characteristics and its technical and economic feasibility. The rationale for considering the denatured 233 U fuel cycle is presented, and the impact of the denatured fuel on the performance of Light-Water Reactors, Spectral-Shift-Controlled Reactors, Gas-Cooled Reactors, Heavy-Water Reactors, and Fast Breeder Reactors is discussed. The scope of the R, D and D programs to commercialize these reactors and their associated fuel cycles is also summarized and the resource requirements and economics of denatured 233 U cycles are compared to those of the conventional Pu/U cycle. In addition, several nuclear power systems that employ denatured 233 U fuel and are based on the energy center concept are evaluated. Under this concept, dispersed power reactors fueled with denatured or low-enriched uranium fuel are supported by secure energy centers in which sensitive activities of the nuclear cycle are performed. These activities include 233 U production by Pu-fueled transmuters (thermal or fast reactors) and reprocessing. A summary chapter presents the most significant conclusions from the study and recommends areas for future work

  3. Dapsone gel 5% in combination with adapalene gel 0.1%, benzoyl peroxide gel 4% or moisturizer for the treatment of acne vulgaris: a 12-week, randomized, double-blind study.

    Science.gov (United States)

    Fleischer, Alan B; Shalita, Alan; Eichenfield, Lawrence F; Abramovits, William; Lucky, Anne; Garrett, Steven

    2010-01-01

    To evaluate the safety and efficacy of dapsone gel 5% in the treatment of acne when used in combination with adapalene gel 0.1%, benzoyl peroxide gel 4% or moisturizer. This was a twelve-week, randomized, double-blind study. Patients aged 12 years and older (n=301) applied dapsone gel twice daily and were randomly assigned (1:1:1) to one of three additional treatments, applied once daily. By week 12, dapsone gel combined with any of the three additional treatments reduced the mean number of inflammatory lesions. However, the authors did not detect a significant difference in the reduction of inflammatory lesions when dapsone was used in combination with adapalene gel or with benzoyl peroxide gel compared to the dapsone plus moisturizer combination group (P=0.052 for both versus moisturizer combination). Patients treated with dapsone gel combined with adapalene showed a significantly better response in reduction in non-inflammatory and total acne lesion count than those who received the moisturizer combination. Local adverse reactions in all three treatment groups were minimal and generally mild in severity. Dapsone gel in combination with adapalene gel or benzoyl peroxide gel is safe and well tolerated for the treatment of acne vulgaris.

  4. Allopurinol gel mitigates radiation-induced mucositis and dermatitis

    International Nuclear Information System (INIS)

    Kitagawa, Junichi; Nasu, Masanori; Okumura, Hayato; Matsumoto, Shigeji; Shibata, Akihiko; Makino, Kimiko; Terada, Hiroshi

    2008-01-01

    It has not been verified whether allopurinol application is beneficial in decreasing the severity of radiation-induced oral mucositis and dermatitis. Rats were divided into 4 groups and received 15 Gy irradiation on the left whisker pad. Group 1 received only irradiation. Group 2 was maintained by applying allopurinol/carrageenan-mixed gel (allopurinol gel) continuously from 2 days before to 20 days after irradiation. Group 3 had allopurinol gel applied for 20 days after radiation. Group 4 was maintained by applying carrageenan gel continuously from 2 days before to 20 days after irradiation. The intra oral mucosal and acute skin reactions were assessed daily using mucositis and skin score systems. The escape thresholds for mechanical stimulation to the left whisker pad were measured daily. In addition, the irradiated tissues at the endpoint of this study were compared with naive tissue. Escape threshold in group 2 was significantly higher than that in group 1, and mucositis and skin scores were much improved compared with those of group 1. Concerning escape threshold, mucositis and skin scores in group 3 began to improve 10 days after irradiation. Group 4 showed severe symptoms of mucositis and dermatitis to the same extent as that observed in group 1. In the histopathological study, the tissues of group 1 showed severe inflammatory reactions, compared with those of group 2. These results suggest that allopurinol gel application can mitigate inflammation reactions associated with radiation-induced oral mucositis and dermatitis. (author)

  5. Gels and gel-derived glasses in the Na2O-B2O3-SiO2 system. [containerless melting in space

    Science.gov (United States)

    Mukherjee, S. P.

    1982-01-01

    The containerless melting of high-purity multicomponent homogeneous gels and gel-monoliths offers a unique approach to making ultrapure multicomponent optical glasses in the reduced gravity environment of space. Procedures for preparing and characterizing gels and gel-derived glasses in the Na2O-B2O3-SiO2 system are described. Preparation is based on the polymerization reactions of alkoxysilane with trimethyl borate or boric acid and a suitable sodium compound. The chemistry of the gelling process is discussed in terms of process parameters and the gel compositions. The physicochemical nature of gels prepared by three different procedures were found to be significantly different. IR absorption spectra indicate finite differences in the molecular structures of the different gels. The melting of the gel powders and the transformation of porous gel-monoliths to transparent 'glass' without melting are described.

  6. Complex Surface Concentration Gradients by Stenciled "Electro Click Chemistry"

    DEFF Research Database (Denmark)

    Hansen, Thomas Steen; Lind, Johan Ulrik; Daugaard, Anders Egede

    2010-01-01

    Complex one- or two-dimensional concentration gradients of alkynated molecules are produced on azidized conducting polymer substrates by stenciled "electro click chemistry". The latter describes the local electrochemical generation of catalytically active Cu(I) required to complete a "click...... reaction" between alkynes and azides at room temperature. A stencil on the counter electrode defines the shape and multiplicity of the gradient(s) on the conducting polymer substrate, while the specific reaction conditions control gradient steepness and the maximum concentration deposited. Biologically...

  7. Feasibility of CBCT dosimetry for IMRT using a normoxic polymethacrylic-acid gel dosimeter

    Science.gov (United States)

    Bong, Ji Hye; Kwon, Soo-Il; Kim, Kum Bae; Kim, Mi Suk; Jung, Hai Jo; Ji, Young Hoon; Ko, In Ok; Park, Ji Ae; Kim, Kyeong Min

    2013-09-01

    The purpose of this study is to evaluate the availability of cone-beam computed tomography(CBCT) for gel dosimetry. The absorbed dose was analyzed by using intensity-modulated radiation therapy(IMRT) to irradiate several tumor shapes with a calculated dose and several tumor acquiring images with CBCT in order to verify the possibility of reading a dose on the polymer gel dosimeter by means of the CBCT image. The results were compared with those obtained using magnetic resonance imaging(MRI) and CT. The linear correlation coefficients at doses less than 10 Gy for the polymer gel dosimeter were 0.967, 0.933 and 0.985 for MRI, CT and CBCT, respectively. The dose profile was symmetric on the basis of the vertical axis in a circular shape, and the uniformity was 2.50% for the MRI and 8.73% for both the CT and the CBCT. In addition, the gradient in the MR image of the gel dosimeter irradiated in an H shape was 109.88 while the gradients of the CT and the CBCT were 71.95 and 14.62, respectively. Based on better image quality, the present study showed that CBCT dosimetry for IMRT could be restrictively performed using a normoxic polymethacrylic-acid gel dosimeter.

  8. Urea-temperature phase diagrams capture the thermodynamics of denatured state expansion that accompany protein unfolding

    Science.gov (United States)

    Tischer, Alexander; Auton, Matthew

    2013-01-01

    We have analyzed the thermodynamic properties of the von Willebrand factor (VWF) A3 domain using urea-induced unfolding at variable temperature and thermal unfolding at variable urea concentrations to generate a phase diagram that quantitatively describes the equilibrium between native and denatured states. From this analysis, we were able to determine consistent thermodynamic parameters with various spectroscopic and calorimetric methods that define the urea–temperature parameter plane from cold denaturation to heat denaturation. Urea and thermal denaturation are experimentally reversible and independent of the thermal scan rate indicating that all transitions are at equilibrium and the van't Hoff and calorimetric enthalpies obtained from analysis of individual thermal transitions are equivalent demonstrating two-state character. Global analysis of the urea–temperature phase diagram results in a significantly higher enthalpy of unfolding than obtained from analysis of individual thermal transitions and significant cross correlations describing the urea dependence of and that define a complex temperature dependence of the m-value. Circular dichroism (CD) spectroscopy illustrates a large increase in secondary structure content of the urea-denatured state as temperature increases and a loss of secondary structure in the thermally denatured state upon addition of urea. These structural changes in the denatured ensemble make up ∼40% of the total ellipticity change indicating a highly compact thermally denatured state. The difference between the thermodynamic parameters obtained from phase diagram analysis and those obtained from analysis of individual thermal transitions illustrates that phase diagrams capture both contributions to unfolding and denatured state expansion and by comparison are able to decipher these contributions. PMID:23813497

  9. Effect of the exothermal polymerization reaction on polymer gel dosimetric measurements

    International Nuclear Information System (INIS)

    Sedaghat, Mahbod; Bujold, Rachel; Lepage, Martin

    2010-01-01

    Discrepancies in polymer gel dosimetric measurements have been observed between containers of different sizes receiving the same radiation dose. We hypothesized that these deviations are caused by a change in the rate of polymerization due to internal heat increase in the gel containers resulting from the exothermic polymerization of monomers. Here, we test this hypothesis in a polyacrylamide gel dosimeter by recording the temperature in glass phantoms of different sizes during and after irradiation. The dose response of the samples was determined with magnetic resonance imaging. The difference of R 2 values along the depth of the containers was below ±1%. We discuss that this small difference can be attributed to variations in the rate of gelatin cooling during manufacture rather than to the measured heat increase during irradiation.

  10. PCR-DGGE Analysis of Bacterial Population Attached to the Bovine Rumen Wall

    OpenAIRE

    Lukáš, F. (Filip); Šimůnek, J. (Jiří); Mrázek, J. (Jakub); Kopečný, J. (Jan)

    2010-01-01

    We isolated and amplified by PCR 16S rDNA from bacteria attached to the bovine rumen wall and analyzed it by denaturing gradient gel electrophoresis (DGGE) with subsequent sequence analysis. The attached bacterial community differed from the bacteria of rumen content; however, no differences were observed among the five epithelial sampling sites taken from each animal. The DGGE profile of the bacterial population attached to the rumen wall represented a high inter-animal variation.

  11. Impact of salinomycin on the intestinal microflora of broiler chickens

    DEFF Research Database (Denmark)

    Johansen, Charlotte; Friis-Holm, Lotte Bjerrum; Pedersen, Karl

    2007-01-01

    jejuni infection and on the composition of the caecal microflora in broiler chickens. Methods: An experimental infection study was carried out in isolators and the intestinal microflora was analyzed using quantitative cultivation, denaturant gradient gel electrophoresis (DGGE), cloning and sequencing...... treated chickens compared to un-treated controls. Conclusion: Termination of the use of ionophore coccidiostats will not affect food safety related to campylobacter, but will increase the risk of necrotic enteritis in the broilers....

  12. Alteration of the Canine Small-Intestinal Lactic Acid Bacterium Microbiota by Feeding of Potential Probiotics

    OpenAIRE

    Manninen, Titta J. K.; Rinkinen, Minna L.; Beasley, Shea S.; Saris, Per E. J.

    2006-01-01

    Five potentially probiotic canine fecal lactic acid bacterium (LAB) strains, Lactobacillus fermentum LAB8, Lactobacillus salivarius LAB9, Weissella confusa LAB10, Lactobacillus rhamnosus LAB11, and Lactobacillus mucosae LAB12, were fed to five permanently fistulated beagles for 7 days. The survival of the strains and their potential effects on the indigenous intestinal LAB microbiota were monitored for 17 days. Denaturing gradient gel electrophoresis (DGGE) demonstrated that the five fed LAB ...

  13. Mesoscopic modeling of DNA denaturation rates: Sequence dependence and experimental comparison

    Energy Technology Data Exchange (ETDEWEB)

    Dahlen, Oda, E-mail: oda.dahlen@ntnu.no; Erp, Titus S. van, E-mail: titus.van.erp@ntnu.no [Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Realfagbygget D3-117 7491 Trondheim (Norway)

    2015-06-21

    Using rare event simulation techniques, we calculated DNA denaturation rate constants for a range of sequences and temperatures for the Peyrard-Bishop-Dauxois (PBD) model with two different parameter sets. We studied a larger variety of sequences compared to previous studies that only consider DNA homopolymers and DNA sequences containing an equal amount of weak AT- and strong GC-base pairs. Our results show that, contrary to previous findings, an even distribution of the strong GC-base pairs does not always result in the fastest possible denaturation. In addition, we applied an adaptation of the PBD model to study hairpin denaturation for which experimental data are available. This is the first quantitative study in which dynamical results from the mesoscopic PBD model have been compared with experiments. Our results show that present parameterized models, although giving good results regarding thermodynamic properties, overestimate denaturation rates by orders of magnitude. We believe that our dynamical approach is, therefore, an important tool for verifying DNA models and for developing next generation models that have higher predictive power than present ones.

  14. Role of cyclobutane dimers in UV-denaturation of DNA

    International Nuclear Information System (INIS)

    Zavil'gel'skij, G.B.; Zuev, A.V.

    1978-01-01

    UV irradiation of double-stranded DNA produces local denatured regions. The evidence presented indicates that these single-stranded regions arise from photoproducts other than pyrimidine dimers. The irradiation of T2 DNA at 8x10 4 erg/mm 2 (254 nm) produces 6-8% thymine dimers, amd Tsub(mel) drops by 12-14 deg C, accompanied by a significant broadening of the transition profile. The kinetics of denatured region formation and lowering Tsub(mel) corresponds to that of formation of crosslinkages and differs markedly from the kinetics of formation of cyclobutane pyrimidine dimers. Treatment of UV-irradiated DNA with light in the presence of yeast photoreactivating enzyme monomerizes almost all thymine dimers but does not change the Tsub(mel). Local denatured regions are detected in UV-irradiated DNA and are absent from AcPhM-sensibilized DNA, which contains 20-25% thymine dimers, as determined by the accridine orange fluorescence technique. S1 nuclease from Aspergillis oryzae produces single-strand breaks in UV-irradiated DNA of phage PM2 but is not active on AcPhM-treated PM2 DNA, which contains about 50 thymine dimers. It is supposed that the formation of a cyclobutane dimer only weakens the hydrogen bonds in the AT base pair rather than breaks them. Local denatured regions are thought to arise from the accumulation in UV-irradiated DNA (254 nm) of the sufficient number of photoproducts with impaired ability to base pairing

  15. Thermal denaturation of protein studied by terahertz time-domain spectroscopy

    Science.gov (United States)

    Fu, Xiuhua; Li, Xiangjun; Liu, Jianjun; Du, Yong; Hong, Zhi

    2012-12-01

    In this study, the absorption spectra of native or thermal protein were measured in 0.2-1.4THz using terahertz time-domain spectroscopy (THz-TDS) system at room temperature, their absorption spectra and the refractive spectra were obtained. Experimental results indicate that protein both has strong absorption but their characteristics were not distinct in the THz region, and the absorption decreased during thermal denatured state. In order to prove protein had been denatured, we used Differential scanning calorimeter (DSC) measured their denatured temperature, from their DSC heating traces, collagen Td=101℃, Bovine serum albumin Td=97℃. While we also combined the Fourier transform infrared spectrometer (FTIR) to investigate their secondary and tertiary structure before and after denatuation, but the results did not have the distinct changes. We turned the absorption spectra and the refractive spectra to the dielectric spectra, and used the one-stage Debye model simulated the terahertz dielectric spectra of protein before and after denaturation. This research proved that the terahertz spectrum technology is feasible in testing protein that were affected by temperature or other factors which can provide theoretical foundation in the further study about the THz spectrum of protein and peptide temperature stability.

  16. The expression and proangiogenic effect of nucleolin during the recovery of heat-denatured HUVECs.

    Science.gov (United States)

    Liang, Pengfei; Jiang, Bimei; Lv, Chunliu; Huang, Xu; Sun, Li; Zhang, Pihong; Huang, Xiaoyuan

    2013-10-01

    The present study aims to examine the expression patterns and roles of nucleolin during the recovery of heat-denatured human umbilical vein endothelial cells (HUVECs). Deep partial thickness burn model in Sprague-Dawley rats and the heat denatured cell model (52°C, 35s) were used. The expression of nucleolin was measured using Western blot analysis and real-time PCR. Angiogenesis was assessed using in vitro parameters including endothelial cell proliferation, transwell migration assay, and scratched wound healing. Gene transfection and RNA interference approaches were employed to investigate the roles of nucleolin. Nucleolin mRNA and protein expression showed a time-dependent increase during the recovery of heat-denatured dermis and HUVECs. Heat-denaturation time-dependently promoted cell growth, adhesion, migration, scratched wound healing and formation of tube-like structures in HUVECs. These effects of heat denaturation on endothelial wound healing and formation of tube-like structures were prevented by knockdown of nucleolin, whereas over-expression of nucleolin increased cell growth, migration, and formation of tube-like structures in cultured HUVEC endothelial cells. In addition, we found that the expression of vascular endothelial growth factor (VEGF) increased during the recovery of heat-denatured dermis and HUVECs, and nucleolin up-regulated VEGF in HUVECs. The present study reveals that the expression of nucleolin is up-regulated, and plays a pro-angiogenic role during the recovery of heat-denatured dermis and its mechanism is probably dependent on production of VEGF. We find a novel and important pro-angiogenic role of nucleolin during the recovery of heat-denatured dermis. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. Improvement in the accuracy of polymer gel dosimeters using scintillating fibers

    International Nuclear Information System (INIS)

    Tremblay, Nicolas M; Hubert-Tremblay, Vincent; Bujold, Rachel; Beaulieu, Luc; Lepage, Martin

    2010-01-01

    We propose a novel method for the absolute calibration of polyacrylamide gel (PAG) dosimeters with one or more reference scintillating fiber dosimeters inserted inside the gel. Four calibrated scintillating fibers were inserted into a cylindrical glass container filled with a PAG dosimeter irradiated with a wedge filtered 6 MV photon beam. Calibration curves using small glass vials containing the same gel as the cylindrical containers were used to obtain a first calibration curve. This calibration curve was then adjusted with the dose measured with one of the scintillating fibers in a low gradient part of the field using different approaches. Among these, it was found that a translation of the gel calibration curve yielded the highest accuracy with PAG dosimeters.

  18. Cation-Induced Stabilization and Denaturation of DNA Origami Nanostructures in Urea and Guanidinium Chloride.

    Science.gov (United States)

    Ramakrishnan, Saminathan; Krainer, Georg; Grundmeier, Guido; Schlierf, Michael; Keller, Adrian

    2017-11-01

    The stability of DNA origami nanostructures under various environmental conditions constitutes an important issue in numerous applications, including drug delivery, molecular sensing, and single-molecule biophysics. Here, the effect of Na + and Mg 2+ concentrations on DNA origami stability is investigated in the presence of urea and guanidinium chloride (GdmCl), two strong denaturants commonly employed in protein folding studies. While increasing concentrations of both cations stabilize the DNA origami nanostructures against urea denaturation, they are found to promote DNA origami denaturation by GdmCl. These inverse behaviors are rationalized by a salting-out of Gdm + to the hydrophobic DNA base stack. The effect of cation-induced DNA origami denaturation by GdmCl deserves consideration in the design of single-molecule studies and may potentially be exploited in future applications such as selective denaturation for purification purposes. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Alcohol-induced structural transitions in the acid-denatured Bacillus licheniformis α-amylase

    Directory of Open Access Journals (Sweden)

    Adyani Azizah Abd Halim

    2017-01-01

    Full Text Available Alcohol-induced structural changes in the acid-denatured Bacillus licheniformis α-amylase (BLA at pH 2.0 were studied by far-ultra violet circular dichroism, intrinsic, three-dimensional and 8-anilino-1-naphthalene sulfonic acid (ANS fluorescence, acrylamide quenching and thermal denaturation. All the alcohols used in this study produced partial refolding in the acid-denatured BLA as evident from the increased mean residue ellipticity at 222 nm, increased intrinsic fluorescence and decreased ANS fluorescence. The order of effectiveness of these alcohols to induce a partially folded state of BLA was found to be: 2,2,2-trifluoroethanol/tert-butanol > 1-propanol/2-propanol > 2-chloroethanol > ethanol > methanol. Three-dimensional fluorescence and acrylamide quenching results obtained in the presence of 5.5 M tert-butanol also suggested formation of a partially folded state in the acid-denatured BLA. However, 5.5 M tert-butanol-induced state of BLA showed a non-cooperative thermal transition. All these results suggested formation of a partially folded state of the acid-denatured BLA in the presence of these alcohols. Furthermore, their effectiveness was found to be guided by their chain length, position of methyl groups and presence of the substituents.

  20. Testing the limits of gradient sensing.

    Directory of Open Access Journals (Sweden)

    Vinal Lakhani

    2017-02-01

    Full Text Available The ability to detect a chemical gradient is fundamental to many cellular processes. In multicellular organisms gradient sensing plays an important role in many physiological processes such as wound healing and development. Unicellular organisms use gradient sensing to move (chemotaxis or grow (chemotropism towards a favorable environment. Some cells are capable of detecting extremely shallow gradients, even in the presence of significant molecular-level noise. For example, yeast have been reported to detect pheromone gradients as shallow as 0.1 nM/μm. Noise reduction mechanisms, such as time-averaging and the internalization of pheromone molecules, have been proposed to explain how yeast cells filter fluctuations and detect shallow gradients. Here, we use a Particle-Based Reaction-Diffusion model of ligand-receptor dynamics to test the effectiveness of these mechanisms and to determine the limits of gradient sensing. In particular, we develop novel simulation methods for establishing chemical gradients that not only allow us to study gradient sensing under steady-state conditions, but also take into account transient effects as the gradient forms. Based on reported measurements of reaction rates, our results indicate neither time-averaging nor receptor endocytosis significantly improves the cell's accuracy in detecting gradients over time scales associated with the initiation of polarized growth. Additionally, our results demonstrate the physical barrier of the cell membrane sharpens chemical gradients across the cell. While our studies are motivated by the mating response of yeast, we believe our results and simulation methods will find applications in many different contexts.

  1. Molecular identification of Mango, Mangifera indica L.var. totupura

    Science.gov (United States)

    Jagarlamudi, Sankar; G, Rosaiah; Kurapati, Ravi Kumar; Pinnamaneni, Rajasekhar

    2011-01-01

    Mango (>Mangifera indica) belonging to Anacardiaceae family is a fruit that grows in tropical regions. It is considered as the King of fruits. The present work was taken up to identify a tool in identifying the mango species at the molecular level. The chloroplast trnL-F region was amplified from extracted total genomic DNA using the polymerase chain reaction (PCR) and sequenced. Sequence of the dominant DGGE band revealed that Mangifera indica in tested leaves was Mangifera indica (100% similarity to the ITS sequences of Mangifera indica). This sequence was deposited in NCBI with the accession no. GQ927757. Abbreviations AFLP - Amplified fragment length polymorphism , cpDNA - Chloroplast DNA, DDGE - Denaturing gradient gel electrophoresis, DNA - Deoxyribo nucleic acid, EDTA - Ethylenediamine tetraacetic acid, HCl - Hydrochloric acid, ISSR - Inter simple sequence repeats, ITS - Internal transcribed spacer, MATAB - Methyl Ammonium Bromide, Na2SO3 - Sodium sulphite, NaCl - Sodium chloride, NCBI - National Centre for Biotechnology Information, PCR - Polymerase chain reaction, PEG - Polyethylene glycol, RAPD - Randomly amplified polymorphic DNA, trnL-F - Transfer RNA genes start codon- termination codon. PMID:21423885

  2. Visualization of early events in acetic acid denaturation of HIV-1 protease: a molecular dynamics study.

    Directory of Open Access Journals (Sweden)

    Aditi Narendra Borkar

    Full Text Available Protein denaturation plays a crucial role in cellular processes. In this study, denaturation of HIV-1 Protease (PR was investigated by all-atom MD simulations in explicit solvent. The PR dimer and monomer were simulated separately in 9 M acetic acid (9 M AcOH solution and water to study the denaturation process of PR in acetic acid environment. Direct visualization of the denaturation dynamics that is readily available from such simulations has been presented. Our simulations in 9 M AcOH reveal that the PR denaturation begins by separation of dimer into intact monomers and it is only after this separation that the monomer units start denaturing. The denaturation of the monomers is flagged off by the loss of crucial interactions between the α-helix at C-terminal and surrounding β-strands. This causes the structure to transit from the equilibrium dynamics to random non-equilibrating dynamics. Residence time calculations indicate that denaturation occurs via direct interaction of the acetic acid molecules with certain regions of the protein in 9 M AcOH. All these observations have helped to decipher a picture of the early events in acetic acid denaturation of PR and have illustrated that the α-helix and the β-sheet at the C-terminus of a native and functional PR dimer should maintain both the stability and the function of the enzyme and thus present newer targets for blocking PR function.

  3. Analysis of spatial diffusion of ferric ions in PVA-GTA gel dosimeters through magnetic resonance imaging

    Energy Technology Data Exchange (ETDEWEB)

    Marrale, Maurizio [Dipartimento di Fisica e Chimica, Universitá di Palermo, Viale delle Scienze, Edificio 18, 90128 Palermo (Italy); Istituto Nazionale di Fisica Nucleare (INFN) – Gruppo V Sezione di Catania, Via Santa Sofia, 64, 95123 Catania (Italy); ATeN Center, Università di Palermo, Viale delle Scienze, Edificio 18, 90128 Palermo (Italy); Collura, Giorgio [Dipartimento di Fisica e Chimica, Universitá di Palermo, Viale delle Scienze, Edificio 18, 90128 Palermo (Italy); Istituto Nazionale di Fisica Nucleare (INFN) – Gruppo V Sezione di Catania, Via Santa Sofia, 64, 95123 Catania (Italy); Gallo, Salvatore, E-mail: salvatore.gallo05@unipa.it [Dipartimento di Fisica e Chimica, Universitá di Palermo, Viale delle Scienze, Edificio 18, 90128 Palermo (Italy); Istituto Nazionale di Fisica Nucleare (INFN) – Gruppo V Sezione di Catania, Via Santa Sofia, 64, 95123 Catania (Italy); Dipartimento di Fisica, Universitá di Milano, Via Giovanni Celoria 16, 20133 Milano (Italy); Nici, Stefania [Dipartimento di Fisica e Chimica, Universitá di Palermo, Viale delle Scienze, Edificio 18, 90128 Palermo (Italy); Tranchina, Luigi [ATeN Center, Università di Palermo, Viale delle Scienze, Edificio 18, 90128 Palermo (Italy); Abbate, Boris Federico [U.O.C. Fisica Sanitaria, A.R.N.A.S., Ospedale Civico Palermo, Piazza Nicola Leotta 4, 90127 Palermo (Italy); Marineo, Sandra; Caracappa, Santo [Istituto Zooprofilattico Sperimentale della Sicilia (IZS), Via Gino Marinuzzi, 3, 90129 Palermo (Italy); and others

    2017-04-01

    Highlights: • Analysis of ferric ions diffusion throughout the gel matrix in PVA-GTA samples. • Measurements with preclinical 7T MRI scanner with spatial resolution of 200 μm. • Diffusion process is much slower for PVA-GTA gels than for agarose ones. - Abstract: This work focused on the analysis of the temporal diffusion of ferric ions through PVA-GTA gel dosimeters. PVA-GTA gel samples, partly exposed with 6 MV X-rays in order to create an initial steep gradient, were mapped using magnetic resonance imaging on a 7T MRI scanner for small animals. Multiple images of the gels were acquired over several hours after irradiation and were analyzed to quantitatively extract the signal profile. The spatial resolution achieved is 200 μm and this makes this technique particularly suitable for the analysis of steep gradients of ferric ion concentration. The results obtained with PVA-GTA gels were compared with those achieved with agarose gels, which is a standard dosimetric gel formulation. The analysis showed that the diffusion process is much slower (more than five times) for PVA-GTA gels than for agarose ones. Furthermore, it is noteworthy that the diffusion coefficient value obtained through MRI analysis is significantly consistent with that obtained in separate study Marini et al. (Submitted for publication) using a totally independent method such as spectrophotometry. This is a valuable result highlighting that the good dosimetric features of this gel matrix not only can be reproduced but also can be measured through independent experimental techniques based on different physical principles.

  4. Neutronics calculations for denatured molten salt reactors: Assessing resource requirements and proliferation-risk attributes

    International Nuclear Information System (INIS)

    Ahmad, Ali; McClamrock, Edward B.; Glaser, Alexander

    2015-01-01

    Highlights: • We study the proliferation-risk and resource attributes of denatured MSRs. • MSRs offer significantly better resource efficiency compared to light-water reactors. • Denatured single-fluid MSRs reactors offer promising non-proliferation attributes. - Abstract: Molten salt reactors (MSRs) are often advocated as a radical but worthwhile alternative to traditional reactor concepts based on solid fuels. This article builds upon the existing research into MSRs to model and simulate the operation of thorium-fueled single-fluid and two-fluid reactors. The analysis is based on neutronics calculations and focuses on denatured MSR systems. Resource utilization and basic proliferation-risk attributes are compared to those of standard light-water reactors. Depending on specific design choices, even fully denatured reactors could reduce uranium and enrichment requirements by a factor of 3–4. Overall, denatured single-fluid designs appear as the most promising candidate technology minimizing both design complexity and overall proliferation risks despite being somewhat less attractive from the perspective of resource utilization

  5. Neutron detector based on lithiated sol-gel glass

    CERN Document Server

    Wallace, S; Miller, L F; Dai, S

    2002-01-01

    A neutron detector technology is demonstrated based on sup 6 Li/ sup 1 sup 0 B doped sol-gel glass. The detector is a sol-gel glass film coated silicon surface barrier detector (SBD). The ionized charged particles from (n, alpha) reactions in the sol-gel film enter the SBD and are counted. Data showing that gamma-ray pulse amplitudes interfere with identifying charged particles that exit the film layer with energies below the gamma-ray energy is presented. Experiments were performed showing the effect of sup 1 sup 3 sup 7 Cs and sup 6 sup 0 Co gamma rays on the SBD detector. The reaction product energies of the triton and alpha particles from sup 6 Li are significantly greater than the energies of the Compton electrons from high-energy gamma rays, allowing the measurement of neutrons in a high gamma background. The sol-gel radiation detection technology may be applicable to the characterization of transuranic waste, spent nuclear fuel and to the monitoring of stored plutonium.

  6. Analysis of microbial diversity in Shenqu with different fermentation times by PCR-DGGE

    Directory of Open Access Journals (Sweden)

    Tengfei Liu

    Full Text Available Abstract Shenqu is a fermented product that is widely used in traditional Chinese medicine (TCM to treat indigestion; however, the microbial strains in the fermentation process are still unknown. The aim of this study was to investigate microbial diversity in Shenqu using different fermentation time periods. DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis profiles indicated that a strain of Pediococcus acidilactici (band 9 is the predominant bacteria during fermentation and that the predominant fungi were uncultured Rhizopus, Aspergillus oryzae, and Rhizopus oryzae. In addition, pathogenic bacteria, such as Enterobacter cloacae, Klebsiella oxytoca, Erwinia billingiae, and Pantoea vagan were detected in Shenqu. DGGE analysis showed that bacterial and fungal diversity declined over the course of fermentation. This determination of the predominant bacterial and fungal strains responsible for fermentation may contribute to further Shenqu research, such as optimization of the fermentation process.

  7. The effectiveness of the biodegradation of raw and processed polystyrene by mealworms

    Science.gov (United States)

    Leluk, Karol; Hanus-Lorenz, Beata; Rybak, Justyna; Bożek, Magdalena

    2017-11-01

    In our studies biodegradation of four variants of polystyrene was performed. We tested: raw material (PS), processed polystyrene (PSr), building insulation material (EPS) and food packaging boxes (PSp). Materials were characterized by means melt flow ratio (MFR), shore hardness and gloss. The biochemical assessment of macromolecules (proteins, lipids and sugars) in the mealworms organisms fed with tested forms of polystyrene allowed us to set how efficient and beneficial the biodegradation of types of polystyrene is. We also evaluated the variability of bacterial community in larval guts by the use of denaturing gradient gel electrophoresis (DGGE) on the bacterial DNA of 16S rRNA genes amplified in polymerase chain reaction (PCR). The results suggest that EPS and PSp polystyrene are the most digestible for T. molitor larvae. The metabolic degradation of polystyrene is probably strictly connected with the changes in biodiversity of gut bacteria.

  8. Analysis of the bacterial community changes in soil for septic tank effluent treatment in response to bio-clogging.

    Science.gov (United States)

    Nie, J Y; Zhu, N W; Zhao, K; Wu, L; Hu, Y H

    2011-01-01

    Soil columns were set up to survey the bacterial community in the soil for septic tank effluent treatment. When bio-clogging occurred in the soil columns, the effluent from the columns was in poorer quality. To evaluate changes of the soil bacterial community in response to bio-clogging, the bacterial community was characterized by DNA gene sequences from soil samples after polymerase chain reaction coupled with denaturing gradient gel electrophoresis process. Correspondence analysis showed that Proteobacteria related bacteria were the main bacteria within the soil when treating septic tank effluent. However, Betaproteobacteria related bacteria were the dominant microorganisms in the normal soil, whereas Alphaproteobacteria related bacteria were more abundant in the clogged soil. This study provided insight into changes of the soil bacterial community in response to bio-clogging. The results can supply some useful information for the design and management of soil infiltration systems.

  9. The effectiveness of the biodegradation of raw and processed polystyrene by mealworms

    Directory of Open Access Journals (Sweden)

    Leluk Karol

    2017-01-01

    Full Text Available In our studies biodegradation of four variants of polystyrene was performed. We tested: raw material (PS, processed polystyrene (PSr, building insulation material (EPS and food packaging boxes (PSp. Materials were characterized by means melt flow ratio (MFR, shore hardness and gloss. The biochemical assessment of macromolecules (proteins, lipids and sugars in the mealworms organisms fed with tested forms of polystyrene allowed us to set how efficient and beneficial the biodegradation of types of polystyrene is. We also evaluated the variability of bacterial community in larval guts by the use of denaturing gradient gel electrophoresis (DGGE on the bacterial DNA of 16S rRNA genes amplified in polymerase chain reaction (PCR. The results suggest that EPS and PSp polystyrene are the most digestible for T. molitor larvae. The metabolic degradation of polystyrene is probably strictly connected with the changes in biodiversity of gut bacteria.

  10. Microchip capillary gel electrophoresis using programmed field strength gradients for the ultra-fast analysis of genetically modified organisms in soybeans.

    Science.gov (United States)

    Kim, Yun-Jeong; Chae, Joon-Seok; Chang, Jun Keun; Kang, Seong Ho

    2005-08-12

    We have developed a novel method for the ultra-fast analysis of genetically modified organisms (GMOs) in soybeans by microchip capillary gel electrophoresis (MCGE) using programmed field strength gradients (PFSG) in a conventional glass double-T microchip. Under the programmed electric field strength and 0.3% poly(ethylene oxide) sieving matrix, the GMO in soybeans was analyzed within only 11 s of the microchip. The MCGE-PFSG method was a program that changes the electric field strength during GMO analysis, and was also applied to the ultra-fast analysis of PCR products. Compared to MCGE using a conventional and constantly applied electric field, the MCGE-PFSG analysis generated faster results without the loss of resolving power and reproducibility for specific DNA fragments (100- and 250-bp DNA) of GM-soybeans. The MCGE-PFSG technique may prove to be a new tool in the GMO analysis due to its speed, simplicity, and high efficiency.

  11. Actuator device utilizing a conductive polymer gel

    Science.gov (United States)

    Chinn, Douglas A.; Irvin, David J.

    2004-02-03

    A valve actuator based on a conductive polymer gel is disclosed. A nonconductive housing is provided having two separate chambers separated by a porous frit. The conductive polymer is held in one chamber and an electrolyte solution, used as a source of charged ions, is held in the second chamber. The ends of the housing a sealed with a flexible elastomer. The polymer gel is further provide with electrodes with which to apply an electrical potential across the gel in order to initiate an oxidation reaction which in turn drives anions across the porous frit and into the polymer gel, swelling the volume of the gel and simultaneously contracting the volume of the electrolyte solution. Because the two end chambers are sealed the flexible elastomer expands or contracts with the chamber volume change. By manipulating the potential across the gel the motion of the elastomer can be controlled to act as a "gate" to open or close a fluid channel and thereby control flow through that channel.

  12. Interim assessment of the denatured /sup 233/U fuel cycle: feasibility and nonproliferation characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Abbott, L.S.; Bartine, D.E.; Burns, T.J. (eds.)

    1978-12-01

    A fuel cycle that employs /sup 233/U denatured with /sup 238/U and mixed with thorium fertile material is examined with respect to its proliferation-resistance characteristics and its technical and economic feasibility. The rationale for considering the denatured /sup 233/U fuel cycle is presented, and the impact of the denatured fuel on the performance of Light-Water Reactors, Spectral-Shift-Controlled Reactors, Gas-Cooled Reactors, Heavy-Water Reactors, and Fast Breeder Reactors is discussed. The scope of the R, D and D programs to commercialize these reactors and their associated fuel cycles is also summarized and the resource requirements and economics of denatured /sup 233/U cycles are compared to those of the conventional Pu/U cycle. In addition, several nuclear power systems that employ denatured /sup 233/U fuel and are based on the energy center concept are evaluated. Under this concept, dispersed power reactors fueled with denatured or low-enriched uranium fuel are supported by secure energy centers in which sensitive activities of the nuclear cycle are performed. These activities include /sup 233/U production by Pu-fueled transmuters (thermal or fast reactors) and reprocessing. A summary chapter presents the most significant conclusions from the study and recommends areas for future work.

  13. Synthesis of palladium-doped silica nanofibers by sol-gel reaction and electrospinning process

    Energy Technology Data Exchange (ETDEWEB)

    San, Thiam Hui; Daud, Wan Ramli Wan; Kadhum, Abdul Amir Hassan; Mohamad, Abu Bakar; Kamarudin, Siti Kartom; Shyuan, Loh Kee; Majlan, Edy Herianto [Fuel Cell Institute, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor (Malaysia); Fuel Cell Institute, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia and Department of Chemical and Process Engineering, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor (Malaysia); Fuel Cell Institute, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor (Malaysia)

    2012-06-29

    Nanofiber is drawing great attention nowadays with their high surface area per volume and flexibility in surface functionalities that make them favorable as a proton exchange membrane in fuel cell application. In this study, incorporation of palladium nanoparticles in silica nanofibers was prepared by combination of a tetraorthosilane (TEOS) sol-gel reaction with electrospinning process. This method can prevent the nanoparticles from aggregation by direct mixing of palladium nanoparticles in silica sol. The as-produced electrospun fibers were thermally treated to remove poly(vinyl pyrrolidone) (PVP) and condensation of silanol in silica framework. PVP is chosen as fiber shaping agent because of its insulting and capping properties for various metal nanoparticles. Scanning electron microscopy (SEM), energy dispersive spectrometer (EDS) and Fourier transform infrared spectroscopy (FTIR) were used to characterize the silica fibers and Pd nanoparticles on the fibers. Spun fibers with average diameter ranged from 100nm to 400nm were obtained at optimum operating condition and distribution of Pd nanoparticles on silica fibers was investigated.

  14. Sol-gel antireflective coating on plastics

    Science.gov (United States)

    Ashley, Carol S.; Reed, Scott T.

    1990-01-01

    An antireflection film made from a reliquified sol-gel hydrolyzation, condensation polymeric reaction product of a silicon, alkoxides and/or metal alkoxides, or mixtures thereof. The film is particularly useful for coating plastics.

  15. Growth, characterization and dielectric property studies of gel grown ...

    Indian Academy of Sciences (India)

    Administrator

    chemical reaction method. Plate-like single ... Barium succinate; gel growth; single crystals; dielectric constant; dielectric loss. 1. .... The chemical reaction involved in the birth of a new .... due to the displacement of electrons and ions, respec-.

  16. Fluctuating partially native-like topologies in the acid denatured ensemble of autolysis resistant HIV-1 protease.

    Science.gov (United States)

    Rout, Manoj Kumar; Hosur, Ramakrishna V

    2009-02-01

    Folding, in-vivo, starts from a denatured state and thus the nature of the denatured state would play an important role in directing the folding of a protein. We report here NMR characterization of the acid-denatured state of a mutant of HIV-1 protease, designed to prevent autolysis (Q7K, L33I, L63I) and to prevent cysteine oxidation (C67A and C95A). Secondary chemical shifts, TALOS analysis of chemical shifts and (15)N relaxation data (R(1), R(2), NOE) coupled with AABUF and hydrophobicity calculations, suggest formation of hydrophobic clusters and possibility of some partially native-like topologies in the acid denatured state of the protease. The structural and dynamics characteristics of the acid denatured PR seem to be considerably different from those of the guanidine or urea denatured states of some variants of PR. These would have implications for the folding and auto-processing of the enzyme in-vivo.

  17. Down-regulation of triose phosphate isomerase in Vineristine-resistant gastric cancer SGC7901 cell line identified by immobilized pH gradient two-dimensional gel electrophoresis and mierosequencing

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Objective:To exkplore new multidrug-resistance-related proteins in gastric SC7901 cells and clarify their mechanisms.Methods:Two-dimensional(2-D) polyacrylamide gel electrophoresis with immobilized pH gradients(IPG) was applied to compare the differential expression of multidrug-resistance-related proteins in gastric cancer SGC7901 cells and Vineristine-resistant SGC7901 cells (SGC7901/VCR) induced by vincristine sulfate.The 2-D gels were silver-stained.Then,preparative 2-D PAGE was performed.The differential proteins of PVDF membranes were cxcised and identified by N-terminal microsequencing.The mRNA expressions of differential proteins were detected in SGC 7901 cells and SGC7901/VCR cells by RT-PCR.Results:Approximatedly 680 protein sports were resolved on each 2-D gel by silver staining.Most protein spots showed no difference in composition,shape or density.25 proteins differed in abundance (6 higher in SGC7901/VCR cells;19 higher in 7901 cells);5 proteins were unique to one kind of cell or the othe(3 in SGC7901/VRC cells,2 in 7901 cells).One drug-resistance-related protein,which was down-regulated in SGC7901/VCR cells,was identified as trisephosphate isomerase(TPI),a glycolytic pathway enzyme.Conclusions:the results suggest that these differential proteins including TPI may be related to the Vincristine-resistant mechanism in human gastric cancer SGC7901/VCR cell line.

  18. 9 CFR 325.13 - Denaturing procedures.

    Science.gov (United States)

    2010-01-01

    ... the appropriate agent shall be used to give the material a distinctive color, odor, or taste so that... thoroughly mixing therein denaturing oil, No. 2 fuel oil, brucine dissolved in a mixture of alcohol and pine... distinctive a color, odor, or taste that it cannot be confused with an article of human food. [35 FR 15605...

  19. Comparative mutagenesis in human cells in vitro and in vivo: First progress report for the period 15 July 1986-30 June 1987

    International Nuclear Information System (INIS)

    Thilly, W.G.

    1987-06-01

    We used the technique of denaturing gradient electrophoresis to produce a pure mutant sequence so that we were able to directly sequence the mutant without bacterial cloning. As part of our continuing studies of the hprt locus in human cells, we have isolated a series of chemically induced mutant DNA sequences in HPRT exon 3 which had been selected by 6-thioguanine resistance. Using denaturing gradient gels to study the amount and kinds of mutations induced in vitro by certain DNA polymerases, we modified polymerase chain reaction (PCR) DNA amplification to our studies of mutation in the human hprt gene. We studied the nature of T 4 DNA polymerase errors and discovered a means to overcome the principle source of noise in amplifying sequences from the human genome. We initiated studies of multi-copy sequences in the human genome so that mutational spectra may be obtained from small numbers of human cells. We worked out novel statistical modes of analysis for planning and evaluating long term low dose human cell mutation studies, and mutational spectra from cell-based or DNA sequence-based studies. We have characterized the positions of large deletion mutations, confirming 6TG resistance in human cells and have found an intron of hprt which has an apparently high density of deletion endpoints within it. We used exon specific probes to discover which exons are present in each of the four pseudogenes of hprt which are scattered over three human autosomes. 41 refs., 8 figs., 10 tabs

  20. Rubber-like poly(vinyl alcohol) gel

    Energy Technology Data Exchange (ETDEWEB)

    Nambu, Masao (Nippon Oil Co. Ltd., Yokohama (Japan). Central Technical Research Lab.)

    1990-09-01

    Anomalous poly (vinyl alcohol) gel has been found in our laboratory since 1980. The gel is prepared by repeated freezing (or freeze-dehydration) of aqueous poly (vinyl alcohol). Experiments establish the fact that anomalous gel is never produced in the course of freezing, but during sustained thawing the gelation does occur. Moreover, it was found that the softening point of the gel increases at 37degC. It is assumed that crystal nuclei are generated on freezing, then on thawing, some of them grow to very fine crystals which act as polymer network-knots (cross-linking). Additional freezing provide other seeds, which grow similarly, and these are accumulated until rubber-like gel is produced. The gel was always water-resistant at 37degC, and the potassium permanganate consumption of the extracted water layer remained far below the official restricted value for medical materials. The gel can be sterilized with gamma-rays or chlorhexidine. Moreover, it satisfies the official standards of acute toxicity, pyrogen, intracutaneous reaction, hemolyzation, and intracorporeal implantation, respectively. Applications to adhesion-preventing membrane (for joint or pericardium), tamponade (for jaw defects), electrode (for electroretinogram or artificial inner ear), artificial denture base and phantoms for magnetic resonance imaging were examined. (author) 54 refs.

  1. The effect of residual water on antacid properties of sucralfate gel dried by microwaves.

    Science.gov (United States)

    Gainotti, Alessandro; Losi, Elena; Colombo, Paolo; Santi, Patrizia; Sonvico, Fabio; Baroni, Daniela; Massimo, Gina; Colombo, Gaia; Del Gaudio, Pasquale

    2006-03-01

    The aim of this work was to study the acid neutralization characteristics of microwave-dried sucralfate gel in relation to the water content and physical structure of the substance. Several dried sucralfate gels were compared with humid sucralfate gel and sucralfate nongel powder in terms of neutralization rate and buffering capacity. Humid sucralfate gel and microwave-dried gel exhibited antacid effectiveness. In particular, the neutralization rate of dried gel powders was inversely related to the water content: as the water content of dried powders decreased, the acid reaction rate linearly increased. The relationship was due to the different morphology of dried sucralfate gels. In fact, the porosity of the dried samples increased with the water reduction. However, the acid neutralization equivalent revealed that the dried sucralfate gel became more resistant to acid attack in the case of water content below 42%. Then, the microwave drying procedure had the opposite effect on the reactivity of the aluminum hydroxide component of dried sucralfate gel powders, since the rate of the reaction increased whereas the buffering capacity decreased as the amount of water was reduced.

  2. DGT/DET Gel partition features of humic acid/metal species

    NARCIS (Netherlands)

    Veeken, van der P.L.R.; Leeuwen, van H.P.

    2010-01-01

    Gel layer based sensors are increasingly employed for dynamic trace metal speciation analysis in aquatic and soil media, in which humic and fulvic acid species are generally known to be relevant. In DGT (diffusive gradient in thin film), polyacrylamide hydrogels are commonly used for the diffusive

  3. The alkali-aggregate reaction - concrete microstructure evolution

    International Nuclear Information System (INIS)

    Regourd, M.; Hornain, H.; Poitevin, P.

    1981-01-01

    The alkali-aggregate reaction has been studied by scanning electron microscopy and energy dispersive X-ray analysis, electron probe microanalysis, and X-ray diffraction in concretes containing glass aggregates or hornfels and greywacke aggregates. The surface reaction of the natural aggregates in alkaline solutions has been analysed by X-ray photo-electron spectrometry. The study of concretes with glass aggregates stored at 20 degrees Celcius and 100 percent relative humidity has revealed, irrespective of alkali content and type of cement, the formation of a gel containing SiO 2 , Na 2 O, CaO, MgO and Al 2 O 3 . Under heat and pressure (210 degrees Celcius at MPa for 48 hours), the gel crystallizes and yields silicates not very different from tobermorite found in autoclaved normal concretes but cotaining Na and K in solid solutions. The alkali reaction in two natural aggregate concretes, is also shown by the formation of gels and silicate crystals. The progressive structuring of the gels in silicate crystals is promoted by an increase in temperature. Ettringite and Ca(OH) 2 reinforce the alkali-aggregate reaction which may be looked upon as a hydration reaction, partially of the pozzolanic type

  4. Meso-decorated self-healing gels: network structure and properties

    Science.gov (United States)

    Gong, Jin; Sawamura, Kensuke; Igarashi, Susumu; Furukawa, Hidemitsu

    2013-04-01

    Gels are a new material having three-dimensional network structures of macromolecules. They possess excellent properties as swellability, high permeability and biocompatibility, and have been applied in various fields of daily life, food, medicine, architecture, and chemistry. In this study, we tried to prepare new multi-functional and high-strength gels by using Meso-Decoration (Meso-Deco), one new method of structure design at intermediate mesoscale. High-performance rigid-rod aromatic polymorphic crystals, and the functional groups of thermoreversible Diels-Alder reaction were introduced into soft gels as crosslinkable pendent chains. The functionalization and strengthening of gels can be realized by meso-decorating the gels' structure using high-performance polymorphic crystals and thermoreversible pendent chains. New gels with good mechanical properties, novel optical properties and thermal properties are expected to be developed.

  5. Radiotherapy gel dosimetry

    International Nuclear Information System (INIS)

    Baldock, C.

    2002-01-01

    shapes and sizes while sparing normal tissue. The situation is further complicated if the normal tissues are critical organs or are particularly sensitive to radiation. Radiotherapy techniques employed to obtain a closer conformation of the dose distribution to the tumour volume are referred to as conformal radiotherapy techniques. The clinical implementation of conformal therapy has been delayed by limitations in the verification of conformal dose distributions calculated by treatment planning systems prior to the irradiation of the patient and the verification of complex treatments during its delivery to the patient. There are several aspects of conformal therapy that complicate dose verification. To achieve the dose distributions conforming to complex 3D volumes, high dose gradients arise in the treatment volume. Further, overdose or underdose regions can exist when separate radiation fields are used to deliver additional radiation. These aspects require that practical dose measurement (dosimetry) techniques be able to integrate dose over time and easily measure dose distributions in 3D with high spatial resolution. Traditional dosimeters, such as ion chambers, thermoluminescent dosimeters and radiographic film do not fulfil these requirements. Novel gel dosimetry techniques are being developed in which dose distributions can potentially be determined in vitro in 3D using anthropomorphic phantoms to simulate a clinically irradiated situation. As long ago as the 1950's, radiation-induced colour change in dyes was used to investigate radiation doses in gels. It was subsequently shown that radiation induced changes in nuclear magnetic resonance (NMR) relaxation properties of gels infused with conventional Fricke dosimetry solutions could be measured using magnetic resonance imaging (MRI). In Fricke gels, Fe 2+ ions in ferrous sulphate solutions are usually dispersed throughout a gelatin, agarose or PVA matrix. Radiation-induced changes in the dosimeters are considered to

  6. Impact of organic and inorganic nanomaterials in the soil microbial community structure

    Energy Technology Data Exchange (ETDEWEB)

    Nogueira, Veronica; Lopes, Isabel [Department of Biology, University of Aveiro, Campus Universitario de Santiago, P-3810-193 Aveiro (Portugal); CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus de Santiago 3810-193 Aveiro (Portugal); Rocha-Santos, Teresa [ISEIT/Viseu, Instituto Piaget, Estrada do Alto do Gaio, Galifonge, 3515-776 Lordosa, Viseu (Portugal); Santos, Ana L. [Department of Biology, University of Aveiro, Campus Universitario de Santiago, P-3810-193 Aveiro (Portugal); CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus de Santiago 3810-193 Aveiro (Portugal); Rasteiro, Graca M.; Antunes, Filipe [CIEPQPF, Department of Chemical Engineering, Faculty of Science and Technology, Polo II, University of Coimbra, 3030-290 Coimbra (Portugal); Goncalves, Fernando; Soares, Amadeu M.V.M.; Cunha, Angela; Almeida, Adelaide [Department of Biology, University of Aveiro, Campus Universitario de Santiago, P-3810-193 Aveiro (Portugal); CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus de Santiago 3810-193 Aveiro (Portugal); Gomes, Newton N.C.M., E-mail: gomesncm@ua.pt [Department of Biology, University of Aveiro, Campus Universitario de Santiago, P-3810-193 Aveiro (Portugal); CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus de Santiago 3810-193 Aveiro (Portugal); Pereira, Ruth [Department of Biology, Faculty of Science, University of Porto, Rua do Campo Alegre 4169-007 Porto (Portugal); CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus de Santiago 3810-193 Aveiro (Portugal)

    2012-05-01

    In this study the effect of organic and inorganic nanomaterials (NMs) on the structural diversity of the soil microbial community was investigated by Denaturing Gradient Gel Electrophoresis, after amplification with universal primers for the bacterial region V6-V8 of 16S rDNA. The polymers of carboxylmethyl-cellulose (CMC), of hydrophobically modified CMC (HM-CMC), and hydrophobically modified polyethylglycol (HM-PEG); the vesicles of sodium dodecyl sulphate/didodecyl dimethylammonium bromide (SDS/DDAB) and of monoolein/sodium oleate (Mo/NaO); titanium oxide (TiO{sub 2}), titanium silicon oxide (TiSiO{sub 4}), CdSe/ZnS quantum dots, gold nanorods, and Fe/Co magnetic fluid were the NMs tested. Soil samples were incubated, for a period of 30 days, after being spiked with NM suspensions previously characterized by Dynamic Light Scattering (DLS) or by an ultrahigh-resolution scanning electron microscope (SEM). The analysis of similarities (ANOSIM) of DGGE profiles showed that gold nanorods, TiO{sub 2}, CMC, HM-CMC, HM-PEG, and SDS/DDAB have significantly affected the structural diversity of the soil bacterial community. - Highlights: Black-Right-Pointing-Pointer Organic and inorganic nanomaterials on soil microbial community. Black-Right-Pointing-Pointer Structural diversity was investigated by Denaturing Gradient Gel Electrophoresis. Black-Right-Pointing-Pointer All the organic nanomaterials, TiO{sub 2} and gold nanorods significantly affected the structural diversity.

  7. Impact of organic and inorganic nanomaterials in the soil microbial community structure

    International Nuclear Information System (INIS)

    Nogueira, Verónica; Lopes, Isabel; Rocha-Santos, Teresa; Santos, Ana L.; Rasteiro, Graça M.; Antunes, Filipe; Gonçalves, Fernando; Soares, Amadeu M.V.M.; Cunha, Angela; Almeida, Adelaide; Gomes, Newton N.C.M.; Pereira, Ruth

    2012-01-01

    In this study the effect of organic and inorganic nanomaterials (NMs) on the structural diversity of the soil microbial community was investigated by Denaturing Gradient Gel Electrophoresis, after amplification with universal primers for the bacterial region V6–V8 of 16S rDNA. The polymers of carboxylmethyl-cellulose (CMC), of hydrophobically modified CMC (HM-CMC), and hydrophobically modified polyethylglycol (HM-PEG); the vesicles of sodium dodecyl sulphate/didodecyl dimethylammonium bromide (SDS/DDAB) and of monoolein/sodium oleate (Mo/NaO); titanium oxide (TiO 2 ), titanium silicon oxide (TiSiO 4 ), CdSe/ZnS quantum dots, gold nanorods, and Fe/Co magnetic fluid were the NMs tested. Soil samples were incubated, for a period of 30 days, after being spiked with NM suspensions previously characterized by Dynamic Light Scattering (DLS) or by an ultrahigh-resolution scanning electron microscope (SEM). The analysis of similarities (ANOSIM) of DGGE profiles showed that gold nanorods, TiO 2 , CMC, HM-CMC, HM-PEG, and SDS/DDAB have significantly affected the structural diversity of the soil bacterial community. - Highlights: ► Organic and inorganic nanomaterials on soil microbial community. ► Structural diversity was investigated by Denaturing Gradient Gel Electrophoresis. ► All the organic nanomaterials, TiO 2 and gold nanorods significantly affected the structural diversity.

  8. Development and dosimetric evaluation of radiochromic PCDA vesicle gel dosimeters

    International Nuclear Information System (INIS)

    Sun, P.; Fu, Y.C.; Hu, J.; Hao, N.; Huang, W.; Jiang, B.

    2016-01-01

    The gel dosimeter has the unique capacity in recording radiation dose distribution in three dimensions (3D), which has the specific advantages in dosimetry measurements where steep dose gradients exist, such as in intensity-modulated radiation therapy (IMRT), brachytherapy and so on. Some 3D dosimeters, such as Fricke gel dosimeters, polymer gel dosimeters, the PRESAGE plastic dosimeters and micelle gel dosimeters have appeared recently. However, there are several disadvantages of these 3D dosimeters limit their application in radiotherapy dose verification. In this study, a novel radiochromic gel dosimeter for 3D dose verification of radiotherapy was developed by dispersing nanovesicles self-assembled by 10,12-pentacosadiynoic acid (PCDA) into the tissue equivalence gel matrix. The characteristics of radiochromic PCDA vesicle gel dosimeters were evaluated. The results indicate that these radiochromic gel dosimeters have good linear dose response to X-ray irradiation in the dose range of 2–100 Gy. In addition, the radiochromic gel dosimeters breakthrough the limitations of the existing gel dosimeters such as diffusion effect, post-radiation effect, and poor forming ability. The response of the gel dosimeter does not show any dose rate dependence, energy dependence and temperature effect, and there was no obvious difference in the gel response between single and cumulative dose of fractional irradiation. Hence, the radiochromic PCDA vesicle gel dosimeters developed in this study could be generally applied to 3D dose verification in radiotherapy. - Highlights: • A novel radiochromic gel dosimeter was developed by dispersing PCDA nanovesicles into the tissue equivalence gel matrix. • This nanovesicle overcomes the dose image blurring caused by the diffusion of monomer molecules. • This nanovesicle limits the polymer chain growth, so as to reduce the post-radiation effect. • The gel matrixes possess excellent tissue equivalence and elastic strength, which

  9. Ternary Phase-Separation Investigation of Sol-Gel Derived Silica from Ethyl Silicate 40

    Science.gov (United States)

    Wang, Shengnan; Wang, David K.; Smart, Simon; Diniz da Costa, João C.

    2015-01-01

    A ternary phase-separation investigation of the ethyl silicate 40 (ES40) sol-gel process was conducted using ethanol and water as the solvent and hydrolysing agent, respectively. This oligomeric silica precursor underwent various degrees of phase separation behaviour in solution during the sol-gel reactions as a function of temperature and H2O/Si ratios. The solution composition within the immiscible region of the ES40 phase-separated system shows that the hydrolysis and condensation reactions decreased with decreasing reaction temperature. A mesoporous structure was obtained at low temperature due to weak drying forces from slow solvent evaporation on one hand and formation of unreacted ES40 cages in the other, which reduced network shrinkage and produced larger pores. This was attributed to the concentration of the reactive sites around the phase-separated interface, which enhanced the condensation and crosslinking. Contrary to dense silica structures obtained from sol-gel reactions in the miscible region, higher microporosity was produced via a phase-separated sol-gel system by using high H2O/Si ratios. This tailoring process facilitated further condensation reactions and crosslinking of silica chains, which coupled with stiffening of the network, made it more resistant to compression and densification. PMID:26411484

  10. Alteration of proteins and pigments influence the function of photosystem I under iron deficiency from Chlamydomonas reinhardtii.

    Directory of Open Access Journals (Sweden)

    Venkateswarlu Yadavalli

    Full Text Available BACKGROUND: Iron is an essential micronutrient for all organisms because it is a component of enzyme cofactors that catalyze redox reactions in fundamental metabolic processes. Even though iron is abundant on earth, it is often present in the insoluble ferric [Fe (III] state, leaving many surface environments Fe-limited. The haploid green alga Chlamydomonas reinhardtii is used as a model organism for studying eukaryotic photosynthesis. This study explores structural and functional changes in PSI-LHCI supercomplexes under Fe deficiency as the eukaryotic photosynthetic apparatus adapts to Fe deficiency. RESULTS: 77K emission spectra and sucrose density gradient data show that PSI and LHCI subunits are affected under iron deficiency conditions. The visible circular dichroism (CD spectra associated with strongly-coupled chlorophyll dimers increases in intensity. The change in CD signals of pigments originates from the modification of interactions between pigment molecules. Evidence from sucrose gradients and non-denaturing (green gels indicates that PSI-LHCI levels were reduced after cells were grown for 72 h in Fe-deficient medium. Ultrafast fluorescence spectroscopy suggests that red-shifted pigments in the PSI-LHCI antenna were lost during Fe stress. Further, denaturing gel electrophoresis and immunoblot analysis reveals that levels of the PSI subunits PsaC and PsaD decreased, while PsaE was completely absent after Fe stress. The light harvesting complexes were also susceptible to iron deficiency, with Lhca1 and Lhca9 showing the most dramatic decreases. These changes in the number and composition of PSI-LHCI supercomplexes may be caused by reactive oxygen species, which increase under Fe deficiency conditions. CONCLUSIONS: Fe deficiency induces rapid reduction of the levels of photosynthetic pigments due to a decrease in chlorophyll synthesis. Chlorophyll is important not only as a light-harvesting pigment, but also has a structural role

  11. A theory for fracture of polymeric gels

    Science.gov (United States)

    Mao, Yunwei; Anand, Lallit

    2018-06-01

    A polymeric gel is a cross-linked polymer network swollen with a solvent. If the concentration of the solvent or the deformation is increased to substantial levels, especially in the presence of flaws, then the gel may rupture. Although various theoretical aspects of coupling of fluid permeation with large deformation of polymeric gels are reasonably well-understood and modeled in the literature, the understanding and modeling of the effects of fluid diffusion on the damage and fracture of polymeric gels is still in its infancy. In this paper we formulate a thermodynamically-consistent theory for fracture of polymeric gels - a theory which accounts for the coupled effects of fluid diffusion, large deformations, damage, and also the gradient effects of damage. The particular constitutive equations for fracture of a gel proposed in our paper, contain two essential new ingredients: (i) Our constitutive equation for the change in free energy of a polymer network accounts for not only changes in the entropy, but also changes in the internal energy due the stretching of the Kuhn segments of the polymer chains in the network. (ii) The damage and failure of the polymer network is taken to occur by chain-scission, a process which is driven by the changes in the internal energy of the stretched polymer chains in the network, and not directly by changes in the configurational entropy of the polymer chains. The theory developed in this paper is numerically implemented in an open-source finite element code MOOSE, by writing our own application. Using this simulation capability we report on our study of the fracture of a polymeric gel, and some interesting phenomena which show the importance of the diffusion of the fluid on fracture response of the gel are highlighted.

  12. Phagocytosis by macrophages mediated by receptors for denatured proteins - dependence on tyrosine protein kinases

    Directory of Open Access Journals (Sweden)

    M.R. Hespanhol

    2002-03-01

    Full Text Available Previous studies have demonstrated that some components of the leukocyte cell membrane, CR3 (Mac-1, CD11b/CD18 and p150/95, are able to bind to denatured proteins. Thus, it is of interest to know which effector functions of these cells can be triggered by these receptors when they interact with particles or surfaces covered with denatured proteins. In the present study we analyzed their possible role as mediators of phagocytosis of red cells covered with denatured bovine serum albumin (BSA by mouse peritoneal macrophages. We observed that a macrophages are able to recognize (bind to these red cells, b this interaction can be inhibited by denatured BSA in the fluid phase, c there is no phagocytosis of these particles by normal macrophages, d phagocytosis mediated by denatured BSA can be, however, effectively triggered in inflammatory macrophages induced by glycogen or in macrophages activated in vivo with LPS, and e this phagocytic capacity is strongly dependent on the activity of tyrosine protein kinases in its signal transduction pathway, as demonstrated by using three kinds of enzyme inhibitors (genistein, quercetin and herbimycin A.

  13. [Inactivating Effect of Heat-Denatured Lysozyme on Murine Norovirus in Bread Fillings].

    Science.gov (United States)

    Takahashi, Michiko; Yasuda, Yuka; Takahashi, Hajime; Takeuchi, Akira; Kuda, Takashi; Kimura, Bon

    2018-01-01

    In this study, we investigated the viability of murine norovirus strain 1 (MNV-1), a surrogate for human norovirus, in bread fillings used for making stuffed buns and pastries. The inactivating effect of heat-denatured lysozyme, which was recently reported to have an antiviral effect, on MNV-1 contaminating the bread fillings was also examined. MNV-1 was inoculated into two types of fillings (chocolate cream, marmalade jam) at 4.5 log PFU/g, and the bread fillings were stored at 4℃ for 5 days. MNV-1 remained viable in the bread fillings during storage. However, addition of 1% heat-denatured lysozyme to the fillings resulted in a decrease of MNV-1 infectivity immediately after inoculation, in both fillings. On the fifth day of storage, MNV-1 infectivity was decreased by 1.2 log PFU/g in chocolate cream and by 0.9 log PFU/g in marmalade jam. Although the mechanism underlying the anti-norovirus effect of heat-denatured lysozyme has not been clarified, our results suggest that heat-denatured lysozyme can be used as an inactivating agent against norovirus in bread fillings.

  14. Evaluation of the denaturing gradient gel electrophoresis-apparatus as a parameter influencing soil microbial community fingerprinting

    Czech Academy of Sciences Publication Activity Database

    Ascher, J.; Ceccherini, M.T.; Chroňáková, Alica; Jirout, Jiří; Borgogni, F.; Elhottová, Dana; Šimek, Miloslav; Pietramellara, G.

    2010-01-01

    Roč. 26, č. 9 (2010), s. 1721-1726 ISSN 0959-3993 R&D Projects: GA MŠk LC06066; GA AV ČR IAA600660605 Institutional research plan: CEZ:AV0Z60660521 Keywords : cattle impact * DGGE * DGGE interfering factors Subject RIV: EH - Ecology, Behaviour Impact factor: 1.214, year: 2010

  15. Association of Stremptomyces community composition determined by PCR-denaturing gradient gel electrophoresis with indoor mold status.

    Science.gov (United States)

    Abstract Both Streptomyces species and mold species have previously been isolated from moisture-damaged building materials; however, an association between these two groups of microorganisms in indoor environments is not clear. In this study, we used a cultureindependent met...

  16. Spatiotemporal variability in archaeal communities of tropical coastal waters

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, S.K.

    properties on SST biases and the South Asian summer monsoon in a coupled GCM. Clim Dyn 39:811–826 Urakawa H, Martens-Habbena W, Stahl DA (2010) High abundance of ammonia-oxidizing archaea in coastal waters, determined using a modified DNA extraction method...- ments suggests that archaea play a major role in the global nitrification process (Francis et al. 2005; Prosser and Nicol 2008; Wuchter et al. 2006). Denaturing gradient gel electrophoresis (DGGE) is among the reliable techniques for microbial...

  17. Screening for mutations in human alpha-globin genes by nonradioactive single-strand conformation polymorphism

    Directory of Open Access Journals (Sweden)

    Jorge S.B.

    2003-01-01

    Full Text Available Point mutations and small insertions or deletions in the human alpha-globin genes may produce alpha-chain structural variants and alpha-thalassemia. Mutations can be detected either by direct DNA sequencing or by screening methods, which select the mutated exon for sequencing. Although small (about 1 kb, 3 exons and 2 introns, the alpha-globin genes are duplicate (alpha2 and alpha1 and highy G-C rich, which makes them difficult to denature, reducing sequencing efficiency and causing frequent artifacts. We modified some conditions for PCR and electrophoresis in order to detect mutations in these genes employing nonradioactive single-strand conformation polymorphism (SSCP. Primers previously described by other authors for radioactive SSCP and phast-SSCP plus denaturing gradient gel electrophoresis were here combined and the resultant fragments (6 new besides 6 original per alpha-gene submitted to silver staining SSCP. Nine structural and one thalassemic mutations were tested, under different conditions including two electrophoretic apparatus (PhastSystem(TM and GenePhor(TM, Amersham Biosciences, different polyacrylamide gel concentrations, run temperatures and denaturing agents, and entire and restriction enzyme cut fragments. One hundred percent of sensitivity was achieved with four of the new fragments formed, using the PhastSystem(TM and 20% gels at 15ºC, without the need of restriction enzymes. This nonradioactive PCR-SSCP approach showed to be simple, rapid and sensitive, reducing the costs involved in frequent sequencing repetitions and increasing the reliability of the results. It can be especially useful for laboratories which do not have an automated sequencer.

  18. 27 CFR 19.41 - Claims on spirits, denatured spirits, articles, or wines lost or destroyed in bond.

    Science.gov (United States)

    2010-04-01

    ..., denatured spirits, articles, or wines lost or destroyed in bond. 19.41 Section 19.41 Alcohol, Tobacco... DISTILLED SPIRITS PLANTS Taxes Claims § 19.41 Claims on spirits, denatured spirits, articles, or wines lost..., relating to the destruction or loss of spirits, denatured spirits, articles, or wines in bond, shall be...

  19. Drying and denaturation characteristics of whey protein isolate in the presence of lactose and trehalose.

    Science.gov (United States)

    Haque, M Amdadul; Chen, Jie; Aldred, Peter; Adhikari, Benu

    2015-06-15

    The denaturation kinetics of whey protein isolate (WPI), in the presence and absence of lactose and trehalose, was quantified in a convective air-drying environment. Single droplets of WPI, WPI-lactose and WPI-trehalose were dried in conditioned air (2.5% RH, 0.5m/s air velocity) at two temperatures (65°C and 80°C) for 500s. The initial solid concentration of these solutions was 10% (w/v) in all the samples. Approximately 68% of WPI was denatured when it was dried in the absence of sugars. Addition of 20% trehalose prevented the irreversible denaturation of WPI at both temperatures. Thirty percent lactose was required to prevent denaturation of WPI at 65°C and the same amount of lactose protected only 70% of WPI from denaturation at 80°C. The secondary structures of WPI were found to be altered by the drying-induced stresses, even in the presence of 20% trehalose and 30% lactose. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. The efficacy of denaturing actinide elements as a means of decreasing materials attractiveness

    Energy Technology Data Exchange (ETDEWEB)

    Hase, K.R.; Bathke, C.G. [Los Alamos National Laboratory: P.O. Box 1663, Los Alamos, NM 87545 (United States); Ebbinghaus, B.B.; Sleaford, B.W.; Robel, M. [Lawrence Livermore National Laboratory: P.O. Box 808, Livermore, CA 94551 (United States); Collins, B.A.; Prichard, A.W. [Pacific Northwest National Laboratory: P.O. Box 999, Richland, WA 99352 (United States)

    2013-07-01

    This study considers the concept of denaturing as applied to the actinide elements present in spent fuel as a means to reduce materials attractiveness. Highly attractive materials generally have low values of bare critical mass, heat content, and dose. To denature an attractive element, its spent-fuel isotopic composition (isotopic vector) is intentionally modified by introducing sufficient quantities of a significantly less attractive isotope to dilute the concentration of a highly attractive isotope so that the overall attractiveness of the element is reduced. The authors used FOM (Figure of Merit) formula as the material attractiveness metric for their parametric determination of the attractiveness of the Pu and U. Materials attractiveness needs to be considered in three distinct phases in the process to construct a nuclear explosive device (NED): the acquisition phase, processing phase, and utilization phase. The results show that denaturing uranium with {sup 238}U is actually an effective means of reducing the attractiveness. For uranium with a large minority of {sup 235}U, a mixture of 80% {sup 238}U to 20% {sup 235}U is required to reduce the attractiveness to low. For uranium with a large concentration of {sup 233}U, a mixture of 88% {sup 238}U to 12% {sup 233}U is required to reduce the attractiveness to low. The results also show that denaturing plutonium with {sup 238}Pu is less effective than denaturing uranium with {sup 238}U. Using {sup 238}Pu as the denaturing agent would require 80% or more by mass in order to reduce the attractiveness to low. No amount of {sup 240}Pu is enough to reduce the plutonium attractiveness below medium. The combination of {sup 238}Pu and {sup 240}Pu would require approximately 70% {sup 238}Pu and 25% {sup 240}Pu by mass to reduce the plutonium attractiveness to low.

  1. The efficacy of denaturing actinide elements as a means of decreasing materials attractiveness

    International Nuclear Information System (INIS)

    Hase, K.R.; Bathke, C.G.; Ebbinghaus, B.B.; Sleaford, B.W.; Robel, M.; Collins, B.A.; Prichard, A.W.

    2013-01-01

    This study considers the concept of denaturing as applied to the actinide elements present in spent fuel as a means to reduce materials attractiveness. Highly attractive materials generally have low values of bare critical mass, heat content, and dose. To denature an attractive element, its spent-fuel isotopic composition (isotopic vector) is intentionally modified by introducing sufficient quantities of a significantly less attractive isotope to dilute the concentration of a highly attractive isotope so that the overall attractiveness of the element is reduced. The authors used FOM (Figure of Merit) formula as the material attractiveness metric for their parametric determination of the attractiveness of the Pu and U. Materials attractiveness needs to be considered in three distinct phases in the process to construct a nuclear explosive device (NED): the acquisition phase, processing phase, and utilization phase. The results show that denaturing uranium with 238 U is actually an effective means of reducing the attractiveness. For uranium with a large minority of 235 U, a mixture of 80% 238 U to 20% 235 U is required to reduce the attractiveness to low. For uranium with a large concentration of 233 U, a mixture of 88% 238 U to 12% 233 U is required to reduce the attractiveness to low. The results also show that denaturing plutonium with 238 Pu is less effective than denaturing uranium with 238 U. Using 238 Pu as the denaturing agent would require 80% or more by mass in order to reduce the attractiveness to low. No amount of 240 Pu is enough to reduce the plutonium attractiveness below medium. The combination of 238 Pu and 240 Pu would require approximately 70% 238 Pu and 25% 240 Pu by mass to reduce the plutonium attractiveness to low

  2. 27 CFR 19.32 - Assessment of tax on spirits, denatured spirits, or wines in bond which are lost, destroyed or...

    Science.gov (United States)

    2010-04-01

    ... spirits, denatured spirits, or wines in bond which are lost, destroyed or removed without authorization... spirits, denatured spirits, or wines in bond which are lost, destroyed or removed without authorization. When spirits, denatured spirits, or wines in bond are lost or destroyed (except spirits, denatured...

  3. Caffeine-catalyzed gels.

    Science.gov (United States)

    DiCiccio, Angela M; Lee, Young-Ah Lucy; Glettig, Dean L; Walton, Elizabeth S E; de la Serna, Eva L; Montgomery, Veronica A; Grant, Tyler M; Langer, Robert; Traverso, Giovanni

    2018-07-01

    Covalently cross-linked gels are utilized in a broad range of biomedical applications though their synthesis often compromises easy implementation. Cross-linking reactions commonly utilize catalysts or conditions that can damage biologics and sensitive compounds, producing materials that require extensive post processing to achieve acceptable biocompatibility. As an alternative, we report a batch synthesis platform to produce covalently cross-linked materials appropriate for direct biomedical application enabled by green chemistry and commonly available food grade ingredients. Using caffeine, a mild base, to catalyze anhydrous carboxylate ring-opening of diglycidyl-ether functionalized monomers with citric acid as a tri-functional crosslinking agent we introduce a novel poly(ester-ether) gel synthesis platform. We demonstrate that biocompatible Caffeine Catalyzed Gels (CCGs) exhibit dynamic physical, chemical, and mechanical properties, which can be tailored in shape, surface texture, solvent response, cargo release, shear and tensile strength, among other potential attributes. The demonstrated versatility, low cost and facile synthesis of these CCGs renders them appropriate for a broad range of customized engineering applications including drug delivery constructs, tissue engineering scaffolds, and medical devices. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. Nonsurgical Transurethral Radiofrequency Collagen Denaturation: Results at Three Years after Treatment

    Directory of Open Access Journals (Sweden)

    Denise M. Elser

    2011-01-01

    Full Text Available Objective. To assess treatment efficacy and quality of life in women with stress urinary incontinence 3 years after treatment with nonsurgical transurethral radiofrequency collagen denaturation. Methods. This prospective study included 139 women with stress urinary incontinence due to bladder outlet hypermobility. Radiofrequency collagen denaturation was performed using local anesthesia in an office setting. Assessments included incontinence quality of life (I-QOL and urogenital distress inventory (UDI-6 instruments. Results. In total, 139 women were enrolled and 136 women were treated (mean age, 47 years. At 36 months, intent-to-treat analysis (n=139 revealed significant improvements in quality of life. Mean I-QOL score improved 17 points from baseline (P=.0004, while mean UDI-6 score improved (decreased 19 points (P=.0005. Conclusions. Transurethral collagen denaturation is a low-risk, office-based procedure that results in durable quality-of-life improvements in a significant proportion of women for as long as 3 years.

  5. Enhanced biodegradation of antibiotic combinations via the sequential treatment of the sludge resulting from pharmaceutical wastewater treatment using white-rot fungi Trametes versicolor and Bjerkandera adusta.

    Science.gov (United States)

    Aydin, Sevcan

    2016-07-01

    While anaerobic treatment is capable of treating pharmaceutical wastewater and removing antibiotics in liquid phases, solid phases may still contain significant amounts of antibiotics following this treatment. The main goal of this study was to evaluate the use of white-rot fungi to remove erythromycin, sulfamethoxazole, and tetracycline combinations from biosolids. The degradation potential of Trametes versicolor and Bjerkandera adusta was evaluated via the sequential treatment of anaerobic sludge. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses were used to identify competition between the autochthonous microbial communities and white-rot fungi. Solid-phase treatment using white-rot fungi substantially reduced antibiotic concentrations and toxicity in sludge. According to PCR-DGGE results, there is an association between species of fungus and antibiotic type as a result of the different transformation pathways of fungal strains. Fungal post-treatment of sludge represents a promising method of removing antibiotic combinations, therefore holding a significant promise as an environmentally friendly means of degrading the antibiotics present in sludge.

  6. Evaluation of biochars from different stock materials as carriers of bacterial strain for remediation of heavy metal-contaminated soil.

    Science.gov (United States)

    Wang, Ting; Sun, Hongwen; Ren, Xinhao; Li, Bing; Mao, Hongjun

    2017-09-21

    Two kinds of biochars, one derived from corn straw and one from pig manure, were studied as carriers of a mutant genotype from Bacillus subtilis (B38) for heavy metal contaminated soil remediation. After amendment with biochar, the heavy metal bioavailability decreased. Moreover, the heavy metal immobilization ability of the biochar was enhanced by combining it with B38. The simultaneous application of B38 and pig manure-derived biochar exhibited a superior effect on the promotion of plant growth and the immobilization of heavy metals in soil. The plant biomass increased by 37.9% and heavy metal concentrations in the edible part of lettuce decreased by 69.9-96.1%. The polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) profiles revealed that pig manure-derived biochar could enhance the proliferation of both exotic B38 and native microbes. These results suggest that B38 carried by pig manure-derived biochar may be a promising candidate for the remediation of soils contaminated by multiple heavy metals.

  7. Enhancement of sludge reduction and methane production by removing extracellular polymeric substances from waste activated sludge.

    Science.gov (United States)

    Nguyen, Minh Tuan; Mohd Yasin, Nazlina Haiza; Miyazaki, Toshiki; Maeda, Toshinari

    2014-12-01

    The management of waste activated sludge (WAS) recycling is a concern that affects the development of the future low-carbon society, particularly sludge reduction and biomass utilization. In this study, we investigated the effect of removing extracellular polymeric substances (EPS), which play important roles in the adhesion and flocculation of WAS, on increased sludge disintegration, thereby enhancing sludge reduction and methane production by anaerobic digestion. EPS removal from WAS by ethylenediaminetetraacetic acid (EDTA) significantly enhanced sludge reduction, i.e., 49 ± 5% compared with 27 ± 1% of the control at the end the digestion process. Methane production was also improved in WAS without EPS by 8881 ± 109 CH4 μmol g(-1) dry-weight of sludge. Microbial activity was determined by denaturing gradient gel electrophoresis and real-time polymerase chain reaction, which showed that the hydrolysis and acetogenesis stages were enhanced by pretreatment with 2% EDTA, with a larger methanogenic community and better methane production. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. The impact of shrimp farming effluent on bacterial communities in mangrove waters, Ceará, Brazil.

    Science.gov (United States)

    Sousa, O V; Macrae, A; Menezes, F G R; Gomes, N C M; Vieira, R H S F; Mendonça-Hagler, L C S

    2006-12-01

    The effects of shrimp farm effluents on bacterial communities in mangroves have been infrequently reported. Classic and molecular biology methods were used to survey bacterial communities from four mangroves systems. Water temperature, salinity, pH, total heterotrophic bacteria and maximum probable numbers of Vibrio spp. were investigated. Genetic profiles of bacterial communities were also characterized by polymerase chain reaction (PCR) amplification of eubacterial and Vibrio 16S rDNA using denaturing gradient gel electrophoresis (DGGE). Highest heterotrophic counts were registered in the mangrove not directly polluted by shrimp farming. The Enterobacteriaceae and Chryseomonas luteola dominated the heterotrophic isolates. Vibrio spp. pathogenic to humans and shrimps were identified. Eubacterial genetic profiles suggest a shared community structure independent of mangrove system. Vibrio genetic profiles were mangrove specific. Neither microbial counts nor genetic profiling revealed a significant decrease in species richness associated with shrimp farm effluent. The complex nature of mangrove ecosystems and their microbial communities is discussed.

  9. Study of the diversity of microbial communities in a sequencing batch reactor oxic-settling-anaerobic process and its modified process.

    Science.gov (United States)

    Sun, Lianpeng; Chen, Jianfan; Wei, Xiange; Guo, Wuzhen; Lin, Meishan; Yu, Xiaoyu

    2016-05-01

    To further reveal the mechanism of sludge reduction in the oxic-settling-anaerobic (OSA) process, the polymerase chain reaction - denaturing gradient gel electrophoresis protocol was used to study the possible difference in the microbial communities between a sequencing batch reactor (SBR)-OSA process and its modified process, by analyzing the change in the diversity of the microbial communities in each reactor of both systems. The results indicated that the structure of the microbial communities in aerobic reactors of the 2 processes was very different, but the predominant microbial populations in anaerobic reactors were similar. The predominant microbial population in the aerobic reactor of the SBR-OSA belonged to Burkholderia cepacia, class Betaproteobacteria, while those of the modified process belonged to the classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. These 3 types of microbes had a cryptic growth characteristic, which was the main cause of a greater sludge reduction efficiency achieved by the modified process.

  10. ANALYSIS OF BACTERIAL COMMUNITIES IN SEAGRASS BED SEDIMENTS BY DOUBLE-GRADIENT DENATURING GRADIENT GEL ELECTROPHORESIS OF PCR-AMPLIFIED 16SRRNA GENES

    Science.gov (United States)

    Bacterial communities associated with seagrass bed sediments are not well studied. The work presented here investigated several factors, including the presence or absence of vegetation, depth into sediment, and season, and their impact on bacterial community diversity. Double gra...

  11. Sol–gel synthesized mesoporous anatase titanium dioxide ...

    Indian Academy of Sciences (India)

    for dye sensitized solar cell (DSSC) applications. R GOVINDARAJ1,∗, M ... DSSC than rutile phase. In this work, we have synthesized hierarchically structured ... Hydrolysis and polycondensation reaction mechanism of sol–gel process. 2.

  12. The expression of miR-125b regulates angiogenesis during the recovery of heat-denatured HUVECs.

    Science.gov (United States)

    Zhou, Situo; Zhang, Pihong; Liang, Pengfei; Huang, Xiaoyuan

    2015-06-01

    In previous studies we found that miR-125b was down-regulated in denatured dermis of deep partial thickness burn patients. Moreover, miR-125b inhibited tumor-angiogenesis associated with the decrease of ERBB2 and VEGF expression in ovarian cancer cells and breast cancer cells, etc. In this study, we investigated the expression patterns and roles of miR-125b during the recovery of denatured dermis and heat-denatured human umbilical vein endothelial cells (HUVECs). Deep partial thickness burns in Sprague-Dawley rats and the heat-denatured cells (52°C, 35 s) were used for analysis. Western blot analysis and real-time PCR were applied to evaluate the expression of miR-125b and ERBB2 and VEGF. The ability of angiogenesis in heat-denatured HUVECs was analyzed by scratch wound healing and tube formation assay after pri-miR-125b or anti-miR-125b transfection. miR-125b expression was time-dependent during the recovery of heat-denatured dermis and HUVECs. Moreover, miR-125b regulated ERBB2 mRNA and Protein Expression and regulated angiogenesis association with regulating the expression of VEGF in heat-denatured HUVECs. Taken together our results show that the expression of miR-125b is time-dependent and miR-125b plays a regulatory role of angiogenesis during wound healing after burns. Copyright © 2014 Elsevier Ltd and ISBI. All rights reserved.

  13. Complement-fixing antibodies against denatured HLA and MICA antigens are associated with antibody mediated rejection.

    Science.gov (United States)

    Cai, Junchao; Terasaki, Paul I; Zhu, Dong; Lachmann, Nils; Schönemann, Constanze; Everly, Matthew J; Qing, Xin

    2016-02-01

    We have found antibodies against denatured HLA class I antigens in the serum of allograft recipients which were not significantly associated with graft failure. It is unknown whether transplant recipients also have denatured HLA class II and MICA antibodies. The effects of denatured HLA class I, class II, and MICA antibodies on long-term graft outcome were further investigated based on their ability to fix complement c1q. In this 4-year retrospective cohort study, post-transplant sera from 975 kidney transplant recipients were tested for antibodies against denatured HLA/MICA antigens and these antibodies were further classified based on their ability to fix c1q. Thirty percent of patients had antibodies against denatured HLA class I, II, or MICA antigens. Among them, 8.5% and 21.5% of all patients had c1q-fixing and non c1q-fixing antibodies respectively. There was no significant difference on graft survival between patients with or without antibodies against denatured HLA/MICA. However, when these antibodies were further classified according to their ability to fix c1q, patients with c1q-fixing antibodies had a significantly lower graft survival rate than patients without antibodies or patients with non c1q-fixing antibodies (p=0.008). In 169 patients who lost renal grafts, 44% of them had c1q-fixing antibodies against denatured HLA/MICA antigens, which was significantly higher than that in patients with functioning renal transplants (25%, pantibodies were more significantly associated with graft failure caused by AMR (72.73%) or mixed AMR/CMR (61.9%) as compared to failure due to CMR (35.3%) or other causes (39.2%) (p=0.026). Transplant recipients had antibodies against denatured HLA class I, II, and MICA antigens. However, only c1q-fixing antibodies were associated with graft failure which was related to antibody mediated rejection. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Ultrasound-assisted sol-gel synthesis of ZrO2.

    Science.gov (United States)

    Guel, Marlene Lariza Andrade; Jiménez, Lourdes Díaz; Hernández, Dora Alicia Cortés

    2017-03-01

    Synthesis of tetragonal ZrO 2 by both conventional sol-gel and ultrasound-assisted sol-gel methods and using a non-ionic surfactant Tween-20, was performed. A porous microstructure composed of nanometric particles was observed. Tetragonal ZrO 2 was obtained using a low heat treatment temperature of powders, 500°C by both methods. A higher crystallinity and a shorter reaction time were observed when ultrasound was used in the sol-gel method due to the cavitation phenomenon. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Protein denaturation and functional properties of Lenient Steam Injection heat treated whey protein concentrate

    DEFF Research Database (Denmark)

    Dickow, Jonatan Ahrens; Kaufmann, Niels; Wiking, Lars

    2012-01-01

    Whey protein concentrate (WPC) was heat treated by use of the novel heat treatment method of Lenient Steam Injection (LSI) to elucidate new functional properties in relation to heat-induced gelation of heat treated WPC. Denaturation was measured by both DSC and FPLC, and the results of the two...... methods were highly correlated. Temperatures of up to 90 °C were applicable using LSI, whereas only 68 °C could be reached by plate heat exchange before coagulation/fouling. Denaturation of whey proteins increased with increasing heat treatment temperature up to a degree of 30–35% denaturation at 90 °C...

  16. How Chain Length and Charge Affect Surfactant Denaturation of Acyl Coenzyme A Binding Protein (ACBP)

    DEFF Research Database (Denmark)

    Andersen, Kell Kleiner; Otzen, Daniel

    2009-01-01

    maltoside (DDM). The aim has been to determine how surfactant chain length and micellar charge affect the denaturation mechanism. ACBP denatures in two steps irrespective of surfactant chain length, but with increasing chain length, the potency of the denaturant rises more rapidly than the critical micelle......Using intrinsic tryptophan fluorescence, equilibria and kinetics of unfolding of acyl coenzyme A binding protein (ACBP) have been investigated in sodium alkyl sulfate surfactants of different chain length (8-16 carbon atoms) and with different proportions of the nonionic surfactant dodecyl...... constants increases linearly with denaturant concentration below the cmc but declines at higher concentrations. Both shortening chain length and decreasing micellar charge reduce the overall kinetics of unfolding and makes the dependence of unfolding rate constants on surfactant concentration more complex...

  17. Pseudomonas aeruginosa cytochrome c551 denaturation by five systematic urea derivatives that differ in the alkyl chain length.

    Science.gov (United States)

    Kobayashi, Shinya; Fujii, Sotaro; Koga, Aya; Wakai, Satoshi; Matubayasi, Nobuyuki; Sambongi, Yoshihiro

    2017-07-01

    Reversible denaturation of Pseudomonas aeruginosa cytochrome c 551 (PAc 551 ) could be followed using five systematic urea derivatives that differ in the alkyl chain length, i.e. urea, N-methylurea (MU), N-ethylurea (EU), N-propylurea (PU), and N-butylurea (BU). The BU concentration was the lowest required for the PAc 551 denaturation, those of PU, EU, MU, and urea being gradually higher. Furthermore, the accessible surface area difference upon PAc 551 denaturation caused by BU was found to be the highest, those by PU, EU, MU, and urea being gradually lower. These findings indicate that urea derivatives with longer alkyl chains are stronger denaturants. In this study, as many as five systematic urea derivatives could be applied for the reversible denaturation of a single protein, PAc 551 , for the first time, and the effects of the alkyl chain length on protein denaturation were systematically verified by means of thermodynamic parameters.

  18. Fabrication and Crystal Structure of Sol-Gel Deposited BST Thin Films with Compositional Gradient

    Directory of Open Access Journals (Sweden)

    Czekaj D.

    2017-06-01

    Full Text Available In the present research technology of compositionally graded barium strontium titanate Ba1-xSrxTiO3 thin films deposited on stainless steel substrates by sol-gel spin coating followed with thermal annealing at T = 650°C is reported. Results of thermal behavior of the sol-gel derived powders with compositions used for fabrication of graded structure (i.e. with Sr mole fraction x = 0.5, 0.4 and 0.3 are described. X-ray diffraction studies of the phase composition and crystal structure of such complex thin film configuration are given. It was found that gel powders exhibited a large total weight loss of about Δm ≈ 44-47%. Three stages of weight loss took place at temperature ranges: below T ≈ 300°C, at ΔT ≈ 300-500°C and between T = 600°C and T = 800°C. Phase analysis has shown that the dominating phase is Ba0.67Sr0.33TiO3 compound while the second phase is Ba0.7Sr0.3TiO3 or Ba0.5Sr0.5TiO3 for “up-graded” and “down-graded” structure, respectively.

  19. On the Use of Potential Denaturing Agents for Ethanol in Direct Ethanol Fuel Cells

    Directory of Open Access Journals (Sweden)

    Domnik Bayer

    2011-01-01

    Full Text Available Acidic or alkaline direct ethanol fuel cells (DEFCs can be a sustainable alternative for power generation if they are fuelled with bio-ethanol. However, in order to keep the fuel cheap, ethanol has to be exempted from tax on spirits by denaturing. In this investigation the potential denaturing agents fusel oil, tert-butyl ethyl ether, and Bitrex were tested with regard to their compatibility with fuel cells. Experiments were carried out both in sulphuric acid and potassium hydroxide solution. Beside, basic electrochemical tests, differential electrochemical mass spectrometry (DEMS and fuel cell tests were conducted. It was found that fusel oil is not suitable as denaturing agent for DEFC. However, tert-butyl ethyl ether does not seem to hinder the ethanol conversion as much. Finally, a mixture of tert-butyl ethyl ether and Bitrex can be proposed as promising candidate as denaturing agent for use in acidic and alkaline DEFC.

  20. Denaturation of membrane proteins and hyperthermic cell killing

    NARCIS (Netherlands)

    Burgman, Paulus Wilhelmus Johannes Jozef

    1993-01-01

    Summarizing: heat induced denaturation of membrane proteins is probably related to hyperthermic cell killing. Induced resistance of heat sensitive proteins seems to be involved in the development of thermotolerance. Although many questions remain still to be answered, it appears that HSP72, when

  1. Rapid DNA sequencing by horizontal ultrathin gel electrophoresis.

    OpenAIRE

    Brumley, R L; Smith, L M

    1991-01-01

    A horizontal polyacrylamide gel electrophoresis apparatus has been developed that decreases the time required to separate the DNA fragments produced in enzymatic sequencing reactions. The configuration of this apparatus and the use of circulating coolant directly under the glass plates result in heat exchange that is approximately nine times more efficient than passive thermal transfer methods commonly used. Bubble-free gels as thin as 25 microns can be routinely cast on this device. The appl...

  2. Identification of Cysteine Proteases and Screening of Cysteine Protease Inhibitors in Biological Samples by a Two-Dimensional Gel System of Zymography and Reverse Zymography

    OpenAIRE

    Saitoh, Eiichi; Yamamoto, Shinya; Okamoto, Eishiro; Hayakawa, Yoshimi; Hoshino, Takashi; Sato, Ritsuko; Isemura, Satoko; Ohtsubo, Sadami; Taniguchi, Masayuki

    2007-01-01

    We have developed a two-dimensional (2D-) gel system of zymography and reverse zymography for the detection and characterization of proteases and protease inhibitors. Isoelectric focusing (IEF) agarose gels with pH gradients were employed for separation in the fi rst-dimension and sodium dodecyl sulfate (SDS)-polyacrylamide gel copolymerized with gelatin used for the second dimension. Proteases and protease inhibitors separated by IEF gel were applied on the second gel without trichloroacetic...

  3. Product-selective blot: a technique for measuring enzyme activities in large numbers of samples and in native electrophoresis gels

    International Nuclear Information System (INIS)

    Thompson, G.A.; Davies, H.M.; McDonald, N.

    1985-01-01

    A method termed product-selective blotting has been developed for screening large numbers of samples for enzyme activity. The technique is particularly well suited to detection of enzymes in native electrophoresis gels. The principle of the method was demonstrated by blotting samples from glutaminase or glutamate synthase reactions into an agarose gel embedded with ion-exchange resin under conditions favoring binding of product (glutamate) over substrates and other substances in the reaction mixture. After washes to remove these unbound substances, the product was measured using either fluorometric staining or radiometric techniques. Glutaminase activity in native electrophoresis gels was visualized by a related procedure in which substrates and products from reactions run in the electrophoresis gel were blotted directly into a resin-containing image gel. Considering the selective-binding materials available for use in the image gel, along with the possible detection systems, this method has potentially broad application

  4. Effects of thermally induced denaturation on technological-functional properties of whey protein isolate-based films.

    Science.gov (United States)

    Schmid, M; Krimmel, B; Grupa, U; Noller, K

    2014-09-01

    This study examined how and to what extent the degree of denaturation affected the technological-functional properties of whey protein isolate (WPI)-based coatings. It was observed that denaturation affected the material properties of WPI-coated films significantly. Surface energy decreased by approximately 20% compared with native coatings. Because the surface energy of a coating should be lower than that of the substrate, this might result in enhanced wettability characteristics between WPI-based solution and substrate surface. Water vapor barrier properties increased by about 35% and oxygen barrier properties increased by approximately 33%. However, significant differences were mainly observed between coatings made of fully native WPI and ones with a degree of denaturation of 25%. Higher degrees of denaturation did not lead to further improvement of material properties. This observation offers cost-saving potential: a major share of denatured whey proteins may be replaced by fully native ones that are not exposed to energy-intensive heat treatment. Furthermore, native WPI solutions can be produced with higher dry matter content without gelatinizing. Hence, less moisture has to be removed through drying, resulting in reduced energy consumption. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  5. Diversity, Dynamics, and Activity of Bacterial Communities during Production of an Artisanal Sicilian Cheese as Evaluated by 16S rRNA Analysis†

    OpenAIRE

    Randazzo, Cinzia L.; Torriani, Sandra; Akkermans, Antoon D. L.; de Vos, Willem M.; Vaughan, Elaine E.

    2002-01-01

    The diversity and dynamics of the microbial communities during the manufacturing of Ragusano cheese, an artisanal cheese produced in Sicily (Italy), were investigated by a combination of classical and culture-independent approaches. The latter included PCR, reverse transcriptase-PCR (RT-PCR), and denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes (rDNA). Bacterial and Lactobacillus group-specific primers were used to amplify the V6 to V8 and V1 to V3 regions of the 16S rRNA gene...

  6. Different Fecal Microbiotas and Volatile Organic Compounds in Treated and Untreated Children with Celiac Disease▿ †

    OpenAIRE

    Di Cagno, Raffaella; Rizzello, Carlo G.; Gagliardi, Francesca; Ricciuti, Patrizia; Ndagijimana, Maurice; Francavilla, Ruggiero; Guerzoni, M. Elisabetta; Crecchio, Carmine; Gobbetti, Marco; De Angelis, Maria

    2009-01-01

    This study aimed at investigating the fecal microbiotas of children with celiac disease (CD) before (U-CD) and after (T-CD) they were fed a gluten-free diet and of healthy children (HC). Brothers or sisters of T-CD were enrolled as HC. Each group consisted of seven children. PCR-denaturing gradient gel electrophoresis (DGGE) analysis with V3 universal primers revealed a unique profile for each fecal sample. PCR-DGGE analysis with group- or genus-specific 16S rRNA gene primers showed that the ...

  7. Investigation of optimal scanning protocol for X-ray computed tomography polymer gel dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Sellakumar, P. [Bangalore Institute of Oncology, 44-45/2, II Cross, RRMR Extension, Bangalore 560 027 (India)], E-mail: psellakumar@rediffmail.com; James Jebaseelan Samuel, E. [School of Science and Humanities, VIT University, Vellore 632 014 (India); Supe, Sanjay S. [Department of Radiation Physics, Kidwai Memorial Institute of Oncology, Hosur Road, Bangalore 560 027 (India)

    2007-11-15

    X-ray computed tomography is one of the potential tool used to evaluate the polymer gel dosimeters in three dimensions. The purpose of this study is to investigate the factors which affect the image noise for X-ray CT polymer gel dosimetry. A cylindrical water filled phantom was imaged with single slice Siemens Somatom Emotion CT scanner. The imaging parameters like tube voltage, tube current, slice scan time, slice thickness and reconstruction algorithm were varied independently to study the dependence of noise on each other. Reductions of noise with number of images to be averaged and spatial uniformity of the image were also investigated. Normoxic polymer gel PAGAT was manufactured and irradiated using Siemens Primus linear accelerator. The radiation induced change in CT number was evaluated using X-ray CT scanner. From this study it is clear that image noise is reduced with increase in tube voltage, tube current, slice scan time, slice thickness and also reduced with increasing the number of images averaged. However to reduce the tube load and total scan time, it was concluded that tube voltage of 130 kV, tube current of 200 mA, scan time of 1.5 s, slice thickness of 3 mm for high dose gradient and 5 mm for low dose gradient were optimal scanning protocols for this scanner. Optimum number of images to be averaged was concluded to be 25 for X-ray CT polymer gel dosimetry. Choice of reconstruction algorithm was also critical. From the study it is also clear that CT number increase with imaging tube voltage and shows the energy dependency of polymer gel dosimeter. Hence for evaluation of polymer gel dosimeters with X-ray CT scanner needs the optimization of scanning protocols to reduce the image noise.

  8. Development of an injectable chitosan/marine collagen composite gel

    International Nuclear Information System (INIS)

    Wang Wei; Itoh, Soichiro; Aizawa, Tomoyasu; Demura, Makoto; Okawa, Atsushi; Sakai, Katsuyoshi; Ohkuma, Tsuneo

    2010-01-01

    A chitosan/marine-originated collagen composite has been developed. This composite gel was characterized and its biocompatibility, as well as an inflammatory reaction, was observed. The chitosan gel including N-3-carboxypropanoil-6-O-(carboxymethyl) chitosan of 3 mol%, 6-O-(carboxymethyl) chitosan of 62 mol% and 6-O-(carboxymethyl) chitin of 35 mol% was prepared and compounded with the salmon atelocollagen (SA) gel at different mixture ratios. The composite gels were injected subcutaneously in to the back of rats. The specimens were harvested for a histological survey as well as a tumor necrosis factor-alpha (TNF-α) assay by ELISA. The inflammatory cell infiltration and release of TNF-α were successively controlled low with the ratio of SA to chitosan at 10:90 or 20:80. The SA gel first, within 2 weeks, and then chitosan in the composite gel were slowly absorbed after implantation, followed by soft tissue formation. It is expected that this composite gel will be available as a carrier for tissue filler and drug delivery systems.

  9. Spectral shift controlled reactors, denatured U-233/thorium cycle

    International Nuclear Information System (INIS)

    1978-05-01

    This paper presents technical and economic data on the SSCR which may be of use in the International Fuel Cycle Evaluation Program to intercompare alternative nuclear systems. Included in this paper are data on the denatured U-233/thorium cycle. This cycle shows a proliferation advantage over more classical thorium fuel cycle (e.g., highly-enriched U-235/thorium or plutonium/thorium) due to the elimination of chemically-separable, concentrated fissile material from unirradiated nuclear fuel. The U-233 is denatured by mixing with depleted uranium to a concentration no greater than 12 w/o. An exogenous source of U-233 is assumed in this paper, since U-233 does not occur in nature and only a limited supply has been produced to date for research and development work

  10. Modified denatured lysozyme effectively solubilizes fullerene c60 nanoparticles in water

    Science.gov (United States)

    Siepi, Marialuisa; Politi, Jane; Dardano, Principia; Amoresano, Angela; De Stefano, Luca; Monti, Daria Maria; Notomista, Eugenio

    2017-08-01

    Fullerenes, allotropic forms of carbon, have very interesting pharmacological effects and engineering applications. However, a very low solubility both in organic solvents and water hinders their use. Fullerene C60, the most studied among fullerenes, can be dissolved in water only in the form of nanoparticles of variable dimensions and limited stability. Here the effect on the production of C60 nanoparticles by a native and denatured hen egg white lysozyme, a highly basic protein, has been systematically studied. In order to obtain a denatured, yet soluble, lysozyme derivative, the four disulfides of the native protein were reduced and exposed cysteines were alkylated by 3-bromopropylamine, thus introducing eight additional positive charges. The C60 solubilizing properties of the modified denatured lysozyme proved to be superior to those of the native protein, allowing the preparation of biocompatible highly homogeneous and stable C60 nanoparticles using lower amounts of protein, as demonstrated by dynamic light scattering, transmission electron microscopy and atomic force microscopy studies. This lysozyme derivative could represent an effective tool for the solubilization of other carbon allotropes.

  11. Versatile action of picomolar gradients of progesterone on different sperm subpopulations.

    Directory of Open Access Journals (Sweden)

    Diego Rafael Uñates

    Full Text Available High step concentrations of progesterone may stimulate various sperm physiological processes, such as priming and the acrosome reaction. However, approaching the egg, spermatozoa face increasing concentrations of the hormone, as it is secreted by the cumulus cells and then passively diffuses along the cumulus matrix and beyond. In this context, several questions arise: are spermatozoa sensitive to the steroid gradients as they undergo priming and the acrosome reaction? If so, what are the functional gradual concentrations of progesterone? Do spermatozoa in different physiological states respond differentially to steroid gradients? To answer these questions, spermatozoa were confronted with progesterone gradients generated by different hormone concentrations (1 pM to 100 µM. Brief exposure to a 10 pM progesterone gradient stimulated priming for the acrosome reaction in one sperm subpopulation, and simultaneously induced the acrosome reaction in a different sperm subpopulation. This effect was not observed in non-capacitated cells or when progesterone was homogeneously distributed. The results suggest a versatile role of the gradual distribution of very low doses of progesterone, which selectively stimulate the priming and the acrosome reaction in different sperm subpopulations.

  12. Characterisation of Maillard reaction products derived from LEKFD--a pentapeptide found in β-lactoglobulin sequence, glycated with glucose--by tandem mass spectrometry, molecular orbital calculations and gel filtration chromatography coupled with continuous photodiode array.

    Science.gov (United States)

    Yamaguchi, Keiko; Homma, Takeshi; Nomi, Yuri; Otsuka, Yuzuru

    2014-02-15

    Maillard reaction peptides (MRPs) contribute to taste, aroma, colour, texture and biological activity. However, peptide degradation or the cross-linking of MRPs in the Maillard reaction has not been investigated clearly. A peptide of LEKFD, a part of β-lactoglobulin, was heated at 110 °C for 24h with glucose and the reaction products were analysed by HPLC with ODS, ESI-MS, ESI-MS/MS and HPLC with gel-filtration column and DAD detector. In the HPLC fractions, an imminium ion of LEK*FD, a pyrylium ion or a hydroxymethyl furylium ion of LEK*FD, and KFD and EK were detected by ESI-MS. Therefore, those products may be produced by the Maillard reaction. The molecular orbital of glycated LEKFD at the lysine epsilon-amino residue with Schiff base form was calculated by MOPAC. HPLC with gel-filtration column showed cross-linking and degradation of peptides. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. 3D Architectured polyazomethine gel synthesis: its self-assembled ...

    Indian Academy of Sciences (India)

    2018-03-28

    Mar 28, 2018 ... Schiff's base reactions are well-known organic reactions that are the main source of ... it difficult to ver- satile applications and the determination of their structural ... Since non-covalent gel phase materials are formed through weak and .... nitrogen as major elements in the composition, which proves that the ...

  14. Gel/Space Ratio Evolution in Ternary Composite System Consisting of Portland Cement, Silica Fume, and Fly Ash.

    Science.gov (United States)

    Wu, Mengxue; Li, Chen; Yao, Wu

    2017-01-11

    In cement-based pastes, the relationship between the complex phase assemblage and mechanical properties is usually described by the "gel/space ratio" descriptor. The gel/space ratio is defined as the volume ratio of the gel to the available space in the composite system, and it has been widely studied in the cement unary system. This work determines the gel/space ratio in the cement-silica fume-fly ash ternary system (C-SF-FA system) by measuring the reaction degrees of the cement, SF, and FA. The effects that the supplementary cementitious material (SCM) replacements exert on the evolution of the gel/space ratio are discussed both theoretically and practically. The relationship between the gel/space ratio and compressive strength is then explored, and the relationship disparities for different mix proportions are analyzed in detail. The results demonstrate that the SCM replacements promote the gel/space ratio evolution only when the SCM reaction degree is higher than a certain value, which is calculated and defined as the critical reaction degree (CRD). The effects of the SCM replacements can be predicted based on the CRD, and the theological predictions agree with the test results quite well. At low gel/space ratios, disparities in the relationship between the gel/space ratio and the compressive strength are caused by porosity, which has also been studied in cement unary systems. The ratio of cement-produced gel to SCM-produced gel ( G C to G S C M ratio) is introduced for use in analyzing high gel/space ratios, in which it plays a major role in creating relationship disparities.

  15. Gel/Space Ratio Evolution in Ternary Composite System Consisting of Portland Cement, Silica Fume, and Fly Ash

    Directory of Open Access Journals (Sweden)

    Mengxue Wu

    2017-01-01

    Full Text Available In cement-based pastes, the relationship between the complex phase assemblage and mechanical properties is usually described by the “gel/space ratio” descriptor. The gel/space ratio is defined as the volume ratio of the gel to the available space in the composite system, and it has been widely studied in the cement unary system. This work determines the gel/space ratio in the cement-silica fume-fly ash ternary system (C-SF-FA system by measuring the reaction degrees of the cement, SF, and FA. The effects that the supplementary cementitious material (SCM replacements exert on the evolution of the gel/space ratio are discussed both theoretically and practically. The relationship between the gel/space ratio and compressive strength is then explored, and the relationship disparities for different mix proportions are analyzed in detail. The results demonstrate that the SCM replacements promote the gel/space ratio evolution only when the SCM reaction degree is higher than a certain value, which is calculated and defined as the critical reaction degree (CRD. The effects of the SCM replacements can be predicted based on the CRD, and the theological predictions agree with the test results quite well. At low gel/space ratios, disparities in the relationship between the gel/space ratio and the compressive strength are caused by porosity, which has also been studied in cement unary systems. The ratio of cement-produced gel to SCM-produced gel ( G C to G S C M ratio is introduced for use in analyzing high gel/space ratios, in which it plays a major role in creating relationship disparities.

  16. Quantitative assessments of the distinct contributions of polypeptide backbone amides versus sidechain groups to chain expansion via chemical denaturation

    Science.gov (United States)

    Holehouse, Alex S.; Garai, Kanchan; Lyle, Nicholas; Vitalis, Andreas; Pappu, Rohit V.

    2015-01-01

    In aqueous solutions with high concentrations of chemical denaturants such as urea and guanidinium chloride (GdmCl) proteins expand to populate heterogeneous conformational ensembles. These denaturing environments are thought to be good solvents for generic protein sequences because properties of conformational distributions align with those of canonical random coils. Previous studies showed that water is a poor solvent for polypeptide backbones and therefore backbones form collapsed globular structures in aqueous solvents. Here, we ask if polypeptide backbones can intrinsically undergo the requisite chain expansion in aqueous solutions with high concentrations of urea and GdmCl. We answer this question using a combination of molecular dynamics simulations and fluorescence correlation spectroscopy. We find that the degree of backbone expansion is minimal in aqueous solutions with high concentrations denaturants. Instead, polypeptide backbones sample conformations that are denaturant-specific mixtures of coils and globules, with a persistent preference for globules. Therefore, typical denaturing environments cannot be classified as good solvents for polypeptide backbones. How then do generic protein sequences expand in denaturing environments? To answer this question, we investigated the effects of sidechains using simulations of two archetypal sequences with amino acid compositions that are mixtures of charged, hydrophobic, and polar groups. We find that sidechains lower the effective concentration of backbone amides in water leading to an intrinsic expansion of polypeptide backbones in the absence of denaturants. Additional dilution of the effective concentration of backbone amides is achieved through preferential interactions with denaturants. These effects lead to conformational statistics in denaturing environments that are congruent with those of canonical random coils. Our results highlight the role of sidechain-mediated interactions as determinants of the

  17. Isothermal chemical denaturation of large proteins: Path-dependence and irreversibility.

    Science.gov (United States)

    Wafer, Lucas; Kloczewiak, Marek; Polleck, Sharon M; Luo, Yin

    2017-12-15

    State functions (e.g., ΔG) are path independent and quantitatively describe the equilibrium states of a thermodynamic system. Isothermal chemical denaturation (ICD) is often used to extrapolate state function parameters for protein unfolding in native buffer conditions. The approach is prudent when the unfolding/refolding processes are path independent and reversible, but may lead to erroneous results if the processes are not reversible. The reversibility was demonstrated in several early studies for smaller proteins, but was assumed in some reports for large proteins with complex structures. In this work, the unfolding/refolding of several proteins were systematically studied using an automated ICD instrument. It is shown that: (i) the apparent unfolding mechanism and conformational stability of large proteins can be denaturant-dependent, (ii) equilibration times for large proteins are non-trivial and may introduce significant error into calculations of ΔG, (iii) fluorescence emission spectroscopy may not correspond to other methods, such as circular dichroism, when used to measure protein unfolding, and (iv) irreversible unfolding and hysteresis can occur in the absence of aggregation. These results suggest that thorough confirmation of the state functions by, for example, performing refolding experiments or using additional denaturants, is needed when quantitatively studying the thermodynamics of protein unfolding using ICD. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Heat-denaturation and aggregation of quinoa (Chenopodium quinoa) globulins as affected by the pH value.

    Science.gov (United States)

    Mäkinen, Outi E; Zannini, Emanuele; Koehler, Peter; Arendt, Elke K

    2016-04-01

    The influence of heating (100 °C; 0-15 min) on the relative molecular mass, protein unfolding and secondary structure of quinoa globulins was studied at pH 6.5 (low solubility), 8.5 and 10.5 (high solubility). The patterns of denaturation and aggregation varied with pH. Heating triggered the disruption of the disulfide bonds connecting the acidic and basic chains of the chenopodin subunits at pH 8.5 and 10.5, but not at pH 6.5. Large aggregates unable to enter a 4% SDS-PAGE gel were formed at pH 6.5 and 8.5, which became soluble under reducing conditions. Heating at pH 10.5 lead to a rapid dissociation of the native chenopodin and to the disruption of the subunits, but no SDS-insoluble aggregates were formed. No major changes in secondary structure occurred during a 15 min heating, but an increase in hydrophobicity indicated unfolding of the tertiary structure in all samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Cellulose gels produced in room temperature ionic liquids by ionizing radiation

    International Nuclear Information System (INIS)

    Kimura, Atsushi; Nagasawa, Naotsugu; Taguchi, Mitsumasa

    2014-01-01

    Cellulose-based gels were produced in room temperature ionic liquids (RTILs) by ionizing radiation. Cellulose was dissolved at the initial concentration of 20 wt% in 1-ethyl-3-methylimidazolium (EMI)-acetate or N,N-diethyl-N-methyl-N-(2-methoxyethyl)ammonium (DEMA)-formate with a water content of 18 wt%, and irradiated with γ-rays under aerated condition to produce new cellulose gels. The gel fractions of the cellulose gels obtained in EMI-acetate and DEMA-formate at a dose of 10 kGy were 13% and 19%, respectively. The formation of gel fractions was found to depend on the initial concentration of cellulose, water content, and irradiation temperature. The obtained gel readily absorbed water, methanol, ethanol, dichloromethane, N,N-dimethylacetamide, and RTILs. - Highlights: • Cellulose gels were produced in room temperature ionic liquids (RTILs). • Water plays a crucial role in the cross-linking reaction. • Cellulose gels swollen with RTILs show good electronic conductivity (3.0 mS cm −1 )

  20. Fluorography--limitations on its use for the quantitative detection of 3H- and 14-C-labeled proteins in polyacrylamide gels

    International Nuclear Information System (INIS)

    Harding, C.R.; Scott, I.R.

    1983-01-01

    The suitability of fluorography for the detection of 3 H- and 14 C-labeled proteins on polyacrylamide gradient gels has been investigated. If was found that the absorbance of the fluorographic film image produced by a given level of radioactivity decreased as the acrylamide concentration in the gel increased. The use of Coomassie brilliant blue protein dyes to stain the gel prior to fluorography reduced the absorbance of the fluorographic image. It is concluded that quantitative fluorography can only be applied to unstained gels of a uniform acrylamide concentration

  1. Sol-gel precursors and products thereof

    Science.gov (United States)

    Warren, Scott C.; DiSalvo, Jr., Francis J.; Weisner, Ulrich B.

    2017-02-14

    The present invention provides a generalizable single-source sol-gel precursor capable of introducing a wide range of functionalities to metal oxides such as silica. The sol-gel precursor facilitates a one-molecule, one-step approach to the synthesis of metal-silica hybrids with combinations of biological, catalytic, magnetic, and optical functionalities. The single-source precursor also provides a flexible route for simultaneously incorporating functional species of many different types. The ligands employed for functionalizing the metal oxides are derived from a library of amino acids, hydroxy acids, or peptides and a silicon alkoxide, allowing many biological functionalities to be built into silica hybrids. The ligands can coordinate with a wide range of metals via a carboxylic acid, thereby allowing direct incorporation of inorganic functionalities from across the periodic table. Using the single-source precursor a wide range of functionalized nanostructures such as monolith structures, mesostructures, multiple metal gradient mesostructures and Stober-type nanoparticles can be synthesized. ##STR00001##

  2. Dynamic partitioning of nanoparticulate metal species between gel layers and aqueous media

    NARCIS (Netherlands)

    Veeken, van der P.L.R.

    2010-01-01

    This thesis deals with several aspects of the use of Diffusive Gradient in Thin film (DGT) and Diffusive Equilibriation in Thin film (DET) in dynamic metal speciation analysis. It has a clear focus on the properties of the diffusive gel layer, and their possible impact on metal speciation

  3. U.S. leans toward denatured thorium cycle

    International Nuclear Information System (INIS)

    Smock, R.

    1977-01-01

    Denatured thorium appears to be the most promising among the nonproliferating alternatives to the plutonium cycle, which the Carter Administration is trying to cancel. Criteria for a better system include uranium utilization comparable to current light water reactors and minimal separation of fissile material into the waste stream. Comparisons with other systems conclude that thorium is preferable because it can lead to an acceptable fast breeder. The thorium cycle can be placed in energy centers for sensitive facilities and can also be introduced into ongoing light water systems. Reprocessing can be handled in the centers, where thorium can be mixed with plutonium for use in reactors within the center, while light water reactors operate on the outside. Any fuel leaving the center would be unsuitable for weapons. Later adaptation to in-center fast breeders will extend energy supplies, although a thorium breeder will be less efficient than a plutonium fast breeder. Denatured thorium is a technical answer to a complex political problem, but those in the nuclear industry see the U.S. goal of a nonproliferating fuel as futile in the light of world politics and breeder efforts in other countries

  4. Investigation on lithium migration for treating alkali-silica reaction affected concrete

    NARCIS (Netherlands)

    Silva De Souza, L.M.; Polder, R.B.; Copuroglu, O.

    2014-01-01

    Alkali-silica reaction (ASR) is one of the major deterioration mechanisms that affect numerous concrete structures worldwide. During the reaction, hydroxyl and alkali (sodium and potassium ) ions react with certain siliceous compounds in the aggregate, forming a hygroscopic gel. The gel absorbs

  5. Vanadium dioxide formed by the sol-gel process

    International Nuclear Information System (INIS)

    Potember, R.S.; Speck, K.R.; Hu, H.S.

    1990-01-01

    This patent describes a process for the deposition of a crystalline vanadium dioxide thin film. It comprises: providing a solution comprising a vanadium tetraalkoxide and solvent; allowing hydrolysis and condensation reactions to progressively form a homogeneous sol from the solution, applying a coating of the sol to the substrate; allowing a gel to form from the sol on the substrate by evaporating the solvent; dehydrating the gel by heat treatment under an inert atmosphere to form the crystalline vanadium dioxide film

  6. Partially folded intermediates during trypsinogen denaturation

    Directory of Open Access Journals (Sweden)

    Martins N.F.

    1999-01-01

    Full Text Available The equilibrium unfolding of bovine trypsinogen was studied by circular dichroism, differential spectra and size exclusion HPLC. The change in free energy of denaturation was = 6.99 ± 1.40 kcal/mol for guanidine hydrochloride and = 6.37 ± 0.57 kcal/mol for urea. Satisfactory fits of equilibrium unfolding transitions required a three-state model involving an intermediate in addition to the native and unfolded forms. Size exclusion HPLC allowed the detection of an intermediate population of trypsinogen whose Stokes radii varied from 24.1 ± 0.4 Å to 26.0 ± 0.3 Å for 1.5 M and 2.5 M guanidine hydrochloride, respectively. During urea denaturation, the range of Stokes radii varied from 23.9 ± 0.3 Å to 25.7 ± 0.6 Å for 4.0 M and 6.0 M urea, respectively. Maximal intrinsic fluorescence was observed at about 3.8 M urea with 8-aniline-1-naphthalene sulfonate (ANS binding. These experimental data indicate that the unfolding of bovine trypsinogen is not a simple transition and suggest that the equilibrium intermediate population comprises one intermediate that may be characterized as a molten globule. To obtain further insight by studying intermediates representing different stages of unfolding, we hope to gain a better understanding of the complex interrelations between protein conformation and energetics.

  7. Interaction of ATP with acid-denatured cytochrome c via coupled folding-binding mechanism

    International Nuclear Information System (INIS)

    Ahluwalia, Unnati; Deep, Shashank

    2012-01-01

    Highlights: ► Interaction between ATP and cyt c takes place via coupled binding–folding mechanism. ► Binding of ATP to cyt c is endothermic. ► GTP and CTP induce similar level of helicity in acid-denatured cyt c as with ATP. ► Compactness induced by ATP is far greater than ADP or AMP. - Abstract: The non-native conformations of the cytochrome c (cyt c) are believed to play key roles in a number of physiological processes. Nucleotides are supposed to act as allosteric effectors in these processes by regulating structural transitions among different conformations of cyt c. To understand the interaction between acid denatured cytochrome c and nucleotides, spectroscopic and calorimetric techniques were utilized to observe the structural features of the induced conformation and the energetics of interaction of acid denatured cyt c with different nucleotides. Structure induction in the acid denatured cyt c was observed on the addition of the ∼1 mM nucleotide tri-phosphates (ATP/GTP/CTP) at 25 °C, however, not in the presence of 1 mM nucleotide mono and diphosphates. ATP-bound cyt c at pH 2.0 is likely to have a conformation that has intact α-helical domain. However, Met80-Fe(III) axial bond is still ruptured. Observed thermodynamics reflect interaction between nucleotide and cyt c via coupled binding–folding mechanism. DSC data suggest the preferential binding of the ATP to the folded conformation with respect to the acid denatured cyt c. ITC data indicate that the exothermic folding of cyt c was accompanied by endothermic binding of ATP to cyt c.

  8. Cold denaturation of the HIV-1 protease monomer

    DEFF Research Database (Denmark)

    Rösner, Heike Ilona; Caldarini, Martina; Prestel, Andreas

    2017-01-01

    The HIV-1-protease is a complex protein which in its active form adopts a homodimer dominated by -sheet structures. We have discovered a cold-denatured state of the monomeric subunit of HIV-1-protease which is populated above 0ºC and therefore directly accessible to various spectroscopic approac...

  9. Agarose gel electrophoresis for the separation of DNA fragments.

    Science.gov (United States)

    Lee, Pei Yun; Costumbrado, John; Hsu, Chih-Yuan; Kim, Yong Hoon

    2012-04-20

    Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb(1). Agarose is isolated from the seaweed genera Gelidium and Gracilaria, and consists of repeated agarobiose (L- and D-galactose) subunits(2). During gelation, agarose polymers associate non-covalently and form a network of bundles whose pore sizes determine a gel's molecular sieving properties. The use of agarose gel electrophoresis revolutionized the separation of DNA. Prior to the adoption of agarose gels, DNA was primarily separated using sucrose density gradient centrifugation, which only provided an approximation of size. To separate DNA using agarose gel electrophoresis, the DNA is loaded into pre-cast wells in the gel and a current applied. The phosphate backbone of the DNA (and RNA) molecule is negatively charged, therefore when placed in an electric field, DNA fragments will migrate to the positively charged anode. Because DNA has a uniform mass/charge ratio, DNA molecules are separated by size within an agarose gel in a pattern such that the distance traveled is inversely proportional to the log of its molecular weight(3). The leading model for DNA movement through an agarose gel is "biased reptation", whereby the leading edge moves forward and pulls the rest of the molecule along(4). The rate of migration of a DNA molecule through a gel is determined by the following: 1) size of DNA molecule; 2) agarose concentration; 3) DNA conformation(5); 4) voltage applied, 5) presence of ethidium bromide, 6) type of agarose and 7) electrophoresis buffer. After separation, the DNA molecules can be visualized under uv light after staining with an appropriate dye. By following this protocol, students should be able to: Understand the mechanism by which DNA fragments are separated within a gel matrix Understand how conformation of the DNA molecule will determine its mobility through a gel matrix Identify an agarose solution of appropriate

  10. Distribution, transition and thermodynamic stability of protein conformations in the denaturant-induced unfolding of proteins.

    Science.gov (United States)

    Bian, Liujiao; Ji, Xu

    2014-01-01

    Extensive and intensive studies on the unfolding of proteins require appropriate theoretical model and parameter to clearly illustrate the feature and characteristic of the unfolding system. Over the past several decades, four approaches have been proposed to describe the interaction between proteins and denaturants, but some ambiguity and deviations usually occur in the explanation of the experimental data. In this work, a theoretical model was presented to show the dependency of the residual activity ratio of the proteins on the molar denaturant concentration. Through the characteristic unfolding parameters ki and Δmi in this model, the distribution, transition and thermodynamic stability of protein conformations during the unfolding process can be quantitatively described. This model was tested with the two-state unfolding of bovine heart cytochrome c and the three-state unfolding of hen egg white lysozyme induced by both guanidine hydrochloride and urea, the four-state unfolding of bovine carbonic anhydrase b induced by guanidine hydrochloride and the unfolding of some other proteins induced by denaturants. The results illustrated that this model could be used accurately to reveal the distribution and transition of protein conformations in the presence of different concentrations of denaturants and to evaluate the unfolding tendency and thermodynamic stability of different conformations. In most denaturant-induced unfolding of proteins, the unfolding became increasingly hard in next transition step and the proteins became more unstable as they attained next successive stable conformation. This work presents a useful method for people to study the unfolding of proteins and may be used to describe the unfolding and refolding of other biopolymers induced by denaturants, inducers, etc.

  11. Reduction of nitrogen oxides by gamma-irradiated hemoproteins. Pt. 2. Reduction of nitrite by immobilized gamma-irradiated hemoprotein

    International Nuclear Information System (INIS)

    Oku, Tadatake; Sato, Hitoshi; Ichikawa, Yoshinobu; Kaneko, Junko; Goto, Mituhiro; Nishio, Toshiyuki; Ito, Teiichiro; Kume, Tamikazu.

    1994-01-01

    Sodium and potassium nitrites are used for coloration and pasteurization of meat products as food additives. Recently, removal of nitrite in water has been one of the research area in environmental science because of the necessity of reducing water pollution. The horse cardiac cytochrome c in 0.1mM aqueous solution was denatured by gamma-irradiation at a dose of 10kGy in the presence of air, and was immobilized by lattice entrapment method in the polyacrylamide gel. The immobilized irradiated cytochrome c was reacted with nitrite in the presence of reducing agent (sodium hydrosulfite) and electron carrier (methyl viologen) at 30degC. The remaining nitrite was determined by diazo-reaction. Immobilized irradiated cytochrome c could be used as a substituent of nitrite reductase, and especially high nitrite reducing activity under nitrogen atmosphere in acidic range, and entrapment in 15% gel made possible to reuse denatured cytochrome c several times. (J.P.N.)

  12. TP53 mutations in clinically normal mucosa adjacent to oral carcinomas

    DEFF Research Database (Denmark)

    Thode, Christenze; Bilde, Anders; von Buchwald, Christian

    2010-01-01

    BACKGROUND: The tumour-suppressor protein p53 often accumulates in histologically normal epithelium adjacent to oral squamous cell carcinomas (OSCC). We investigated whether this was associated with mutations in TP53, the gene for p53, and might implicate impending malignancy. METHODS: Specimens...... products were separated by denatured gradient gel electrophoresis. Fragments with a deviant DGEE pattern were sequenced. RESULTS: TP53 mutations were found in six of 18 tumours. Fourteen specimens contained histologically normal mucosa adjacent to the tumour; 13 of these showed small clusters of p53...

  13. Blood grouping based on PCR methods and agarose gel electrophoresis.

    Science.gov (United States)

    Sell, Ana Maria; Visentainer, Jeane Eliete Laguila

    2015-01-01

    The study of erythrocyte antigens continues to be an intense field of research, particularly after the development of molecular testing methods. More than 300 specificities have been described by the International Society for Blood Transfusion as belonging to 33 blood group systems. The polymerase chain reaction (PCR) is a central tool for red blood cells (RBC) genotyping. PCR and agarose gel electrophoresis are low cost, easy, and versatile in vitro methods for amplifying defined target DNA (RBC polymorphic region). Multiplex-PCR, AS-PCR (Specific Allele Polymerase Chain Reaction), and RFLP-PCR (Restriction Fragment Length Polymorphism-Polymerase Chain Reaction) techniques are usually to identify RBC polymorphisms. Furthermore, it is an easy methodology to implement. This chapter describes the PCR methodology and agarose gel electrophoresis to identify the polymorphisms of the Kell, Duffy, Kidd, and MNS blood group systems.

  14. The Influence of Conditioning Agent on Phosphate Diffusion Coefficient through Polyacrylamide and Agarose Gel

    Directory of Open Access Journals (Sweden)

    Layta Dinira

    2013-03-01

    Full Text Available Excess phosphate in natural water can cause algae grow rapidly, to the extent causing many fish deaths that led to the extinction of certain species. Therefore, an analysis or periodic observations of phosphate levels in the water is needed. The commonly used method is diffusive gradient in thin films (DGT technique. The DGT technique is based on the ability of analyte to diffuse through a gel, which have a value named diffusion coefficient. This research was conducted in order to study the effect of different storage solution to the phosphate diffusion coefficient through polyacrylamide and agarose gels. Initial research performed with making the polyacrylamide and agarose gels. To observe the effect of different storage solutions, the gels partly stored in distilled water gel while the others are stored in a NaCl solution of 0.01 M. Phosphate diffusion coefficient was determined using Fick's Law after analyze the phosphate concentration using UV-Visible spectrophotometer. The results showed that phosphate diffusion coefficient was highest when polyacrylamide and agarose gels stored in NaCl solution of 0.01 M.

  15. Comparison of the effectiveness of polymer gel dosimeters (Magic ...

    African Journals Online (AJOL)

    demonstrate that the gel dosimeters are best suited for nuclear medicine. Keywords: Magic ... International Pharmaceutical Abstract, Chemical Abstracts, Embase, Index Copernicus, EBSCO, African. Index Medicus .... Reaction rate. 2.15E-6.

  16. Sulphur-oxidizing and sulphate-reducing communities in Brazilian mangrove sediments.

    Science.gov (United States)

    Varon-Lopez, Maryeimy; Dias, Armando Cavalcante Franco; Fasanella, Cristiane Cipolla; Durrer, Ademir; Melo, Itamar Soares; Kuramae, Eiko Eurya; Andreote, Fernando Dini

    2014-03-01

    Mangrove soils are anaerobic environments rich in sulphate and organic matter. Although the sulphur cycle is one of the major actors in this ecosystem, little is known regarding the sulphur bacteria communities in mangrove soils. We investigated the abundance, composition and diversity of sulphur-oxidizing (SOB) and sulphate-reducing (SRB) bacteria in sediments from three Brazilian mangrove communities: two contaminated, one with oil (OilMgv) and one with urban waste and sludge (AntMgv), and one pristine (PrsMgv). The community structures were assessed using quantitative real-time polymerase chain reaction (qPCR), polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and clone libraries, using genes for the enzymes adenosine-5'-phosphosulphate reductase (aprA) and sulphite reductase (Dsr) (dsrB). The abundance for qPCR showed the ratio dsrB/aprA to be variable among mangroves and higher according to the gradient observed for oil contamination in the OilMgv. The PCR-DGGE patterns analysed by Nonmetric Multidimensional Scaling revealed differences among the structures of the three mangrove communities. The clone libraries showed that Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria were the most abundant groups associated with sulphur cycling in mangrove sediments. We conclude that the microbial SOB and SRB communities in mangrove soils are different in each mangrove forest and that such microbial communities could possibly be used as a proxy for contamination in mangrove forests. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

  17. A cost-effective device for the rapid transfer of gel-separated proteins onto membranes.

    Science.gov (United States)

    Tam, Hann W; Huang, Yu-Chen; Tam, Ming F

    2009-03-01

    We describe here the fabrication of a cost-effective semi-dry blotting apparatus for the transfer of proteins onto membranes. Graphite sheets were used as electrodes. Protein mixtures were separated on NuPAGE 4% to 12% polyacrylamide gradient gels. With a Tris-bicine buffer, we demonstrated that close to 80% of the proteins with apparent molecular mass of 80kDa or less were removed from the gels after 8min of blotting. The process is much faster than the techniques reported previously in the literature.

  18. Membrane bridging and hemifusion by denaturated Munc18.

    Directory of Open Access Journals (Sweden)

    Yi Xu

    Full Text Available Neuronal Munc18-1 and members of the Sec1/Munc18 (SM protein family play a critical function(s in intracellular membrane fusion together with SNARE proteins, but the mechanism of action of SM proteins remains highly enigmatic. During experiments designed to address this question employing a 7-nitrobenz-2-oxa-1,3-diazole (NBD fluorescence de-quenching assay that is widely used to study lipid mixing between reconstituted proteoliposomes, we observed that Munc18-1 from squid (sMunc18-1 was able to increase the apparent NBD fluorescence emission intensity even in the absence of SNARE proteins. Fluorescence emission scans and dynamic light scattering experiments show that this phenomenon arises at least in part from increased light scattering due to sMunc18-1-induced liposome clustering. Nuclear magnetic resonance and circular dichroism data suggest that, although native sMunc18-1 does not bind significantly to lipids, sMunc18-1 denaturation at 37 °C leads to insertion into membranes. The liposome clustering activity of sMunc18-1 can thus be attributed to its ability to bridge two membranes upon (perhaps partial denaturation; correspondingly, this activity is hindered by addition of glycerol. Cryo-electron microscopy shows that liposome clusters induced by sMunc18-1 include extended interfaces where the bilayers of two liposomes come into very close proximity, and clear hemifusion diaphragms. Although the physiological relevance of our results is uncertain, they emphasize the necessity of complementing fluorescence de-quenching assays with alternative experiments in studies of membrane fusion, as well as the importance of considering the potential effects of protein denaturation. In addition, our data suggest a novel mechanism of membrane hemifusion induced by amphipathic macromolecules that does not involve formation of a stalk intermediate.

  19. Molecular structure effects on the post irradiation diffusion in polymer gel dosimeters

    Energy Technology Data Exchange (ETDEWEB)

    Mattea, F.; Romero, M.; Strumia, M. [Instituto Multidisciplinario de Biologia Vegetal / CONICET, Universidad Nacional de Cordoba, Departamento de Quimica Organica, Ciudad Universitaria, 5000 Cordoba (Argentina); Vedelago, J. [Laboratorio de Investigaciones e Instrumentacion en Fisica Aplicada a la Medicina e Imagenes por Rayos X, Laboratorio 448 FaMAF - UNC, Ciudad Universitaria, 5000 Cordoba (Argentina); Quiroga, A. [Centro de Investigacion y Estudios de Matematica / CONICET, Oficina 318 FaMAF - UNC, Ciudad Universitaria, 5000 Cordoba (Argentina); Valente, M., E-mail: fmattea@gmail.com [Instituto de Fisica E. Gaviola / CONICET, LIIFAMIRx, Oficina 102 FaMAF - UNC, 5000 Cordoba (Argentina)

    2014-08-15

    Polymer gel dosimeters have specific advantages for recording 3D radiation dose distribution representing a key factor for most of the therapeutic and diagnostic radiation techniques. Radiation-induced polymerization and crosslinking reactions that take place in the dosimeter have been studied for different monomers like acrylamide and N,N-methylene-bis acrylamide (Bis) and most recently for less toxic monomers like N-isopropylacrylamide and Bis. In this work a novel system based on itaconic acid and Bis is proposed, the radical polymerization or gel formation of these monomers has been already studied for the formation of an hydrogel for non dosimetric applications and their reactivity are comparable with the already mentioned systems. Although the 3D structure is maintained after the dosimeter has been irradiated, it is not possible to eliminate the diffusion of the reacted and monomer species in regions of dose gradients within the gel after irradiation. As a consequence the dose information of the dosimeters loose quality over time. The mobility within the gelatin structure of the already mentioned species is related to their chemical structure, and nature. In this work the effect of changes in the chemical structure of the monomers over the dosimetric sensitivity and over the post-irradiation diffusion of species is studied. One of the acrylic acid groups of the itaconic acid molecule is modified to obtain molecules with similar reactivity but different molecular sizes. Dosimetric systems with these modified species, Bis, an antioxidant to avoid oxygen polymerization inhibition, water and gelatin are irradiated in an X-ray tomography at different doses, and the resulting dosimeters are characterized by Raman spectroscopy and optical absorbance to study their feasibility and capabilities as dosimetric systems, and by optical-CT to analyze the diffusion degree after being irradiated. (Author)

  20. Molecular structure effects on the post irradiation diffusion in polymer gel dosimeters

    International Nuclear Information System (INIS)

    Mattea, F.; Romero, M.; Strumia, M.; Vedelago, J.; Quiroga, A.; Valente, M.

    2014-08-01

    Polymer gel dosimeters have specific advantages for recording 3D radiation dose distribution representing a key factor for most of the therapeutic and diagnostic radiation techniques. Radiation-induced polymerization and crosslinking reactions that take place in the dosimeter have been studied for different monomers like acrylamide and N,N-methylene-bis acrylamide (Bis) and most recently for less toxic monomers like N-isopropylacrylamide and Bis. In this work a novel system based on itaconic acid and Bis is proposed, the radical polymerization or gel formation of these monomers has been already studied for the formation of an hydrogel for non dosimetric applications and their reactivity are comparable with the already mentioned systems. Although the 3D structure is maintained after the dosimeter has been irradiated, it is not possible to eliminate the diffusion of the reacted and monomer species in regions of dose gradients within the gel after irradiation. As a consequence the dose information of the dosimeters loose quality over time. The mobility within the gelatin structure of the already mentioned species is related to their chemical structure, and nature. In this work the effect of changes in the chemical structure of the monomers over the dosimetric sensitivity and over the post-irradiation diffusion of species is studied. One of the acrylic acid groups of the itaconic acid molecule is modified to obtain molecules with similar reactivity but different molecular sizes. Dosimetric systems with these modified species, Bis, an antioxidant to avoid oxygen polymerization inhibition, water and gelatin are irradiated in an X-ray tomography at different doses, and the resulting dosimeters are characterized by Raman spectroscopy and optical absorbance to study their feasibility and capabilities as dosimetric systems, and by optical-CT to analyze the diffusion degree after being irradiated. (Author)

  1. Dynamics of Ionic Liquid-Assisted Refolding of Denatured Cytochrome c: A Study of Preferential Interactions toward Renaturation.

    Science.gov (United States)

    Singh, Upendra Kumar; Patel, Rajan

    2018-05-25

    In vitro refolding of denatured protein and the influence of the alkyl chain on the refolding of a protein were tested using long chain imidazolium chloride salts, 1-methyl-3-octylimidazolium chloride [C 8 mim][Cl], and 1-decyl-3-methylimidazolium chloride [C 10 mim][Cl]. The horse heart cytochrome c (h-cyt c) was denatured by urea and guanidinium hydrochloride (GdnHCl), as well as by base-induced denaturation at pH 13, to provide a broad overview of the overall refolding behavior. The variation in the alkyl chain of the ionic liquids (ILs) showed a profound effect on the refolding of denatured h-cyt c. The ligand-induced refolding was correlated to understand the mechanism of the conformational stability of proteins in aqueous solutions of ILs. The results showed that the long chain ILs having the [C 8 mim] + and [C 10 mim] + cations promote the refolding of alkali-denatured h-cyt c. The IL having the [C 10 mim] + cation efficiently refolded the alkali-denatured h-cyt c with the formation of the MG state, whereas the IL having the [C 8 mim] + cation, which is known to be compatible for protein stability, shows slight refolding and forms a different transition state. The lifetime results show successful refolding of alkaline-denatured h-cyt c by both of the ILs, however, more refolding was observed in the case of [C 10 mim][Cl], and this was correlated with the fast and medium lifetimes (τ 1 and τ 2 ) obtained, which show an increase accompanied by an increase in secondary structure. The hydrophobic interactions plays an important role in the refolding of chemically and alkali-denatured h-cyt c by long chain imidazolium ILs. The formation of the MG state by [C 10 mim][Cl] was also confirmed, as some regular structure exists far below the CMC of IL. The overall results suggested that the [C 10 mim] + cation bound to the unfolded h-cyt c triggers its refolding by electrostatic and hydrophobic interactions that stabilize the MG state.

  2. Communication: Control of chemical reactions using electric field gradients

    Energy Technology Data Exchange (ETDEWEB)

    Deshmukh, Shivaraj D.; Tsori, Yoav, E-mail: tsori@bgu.ac.il [Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105 (Israel)

    2016-05-21

    We examine theoretically a new idea for spatial and temporal control of chemical reactions. When chemical reactions take place in a mixture of solvents, an external electric field can alter the local mixture composition, thereby accelerating or decelerating the rate of reaction. The spatial distribution of electric field strength can be non-trivial and depends on the arrangement of the electrodes producing it. In the absence of electric field, the mixture is homogeneous and the reaction takes place uniformly in the reactor volume. When an electric field is applied, the solvents separate and the reactants are concentrated in the same phase or separate to different phases, depending on their relative miscibility in the solvents, and this can have a large effect on the kinetics of the reaction. This method could provide an alternative way to control runaway reactions and to increase the reaction rate without using catalysts.

  3. Communication: Control of chemical reactions using electric field gradients.

    Science.gov (United States)

    Deshmukh, Shivaraj D; Tsori, Yoav

    2016-05-21

    We examine theoretically a new idea for spatial and temporal control of chemical reactions. When chemical reactions take place in a mixture of solvents, an external electric field can alter the local mixture composition, thereby accelerating or decelerating the rate of reaction. The spatial distribution of electric field strength can be non-trivial and depends on the arrangement of the electrodes producing it. In the absence of electric field, the mixture is homogeneous and the reaction takes place uniformly in the reactor volume. When an electric field is applied, the solvents separate and the reactants are concentrated in the same phase or separate to different phases, depending on their relative miscibility in the solvents, and this can have a large effect on the kinetics of the reaction. This method could provide an alternative way to control runaway reactions and to increase the reaction rate without using catalysts.

  4. Comparison of polyacrylamide and agarose gel thin-layer isoelectric focusing for the characterization of beta-lactamases.

    Science.gov (United States)

    Vecoli, C; Prevost, F E; Ververis, J J; Medeiros, A A; O'Leary, G P

    1983-08-01

    Plasmid-mediated beta-lactamases from strains of Escherichia coli and Pseudomonas aeruginosa were separated by isoelectric focusing on a 0.8-mm thin-layer agarose gel with a pH gradient of 3.5 to 9.5. Their banding patterns and isoelectric points were compared with those obtained with a 2.0-mm polyacrylamide gel as the support medium. The agarose method produced banding patterns and isoelectric points which corresponded to the polyacrylamide gel data for most samples. Differences were observed for HMS-1 and PSE-1 beta-lactamases. The HMS-1 sample produced two highly resolvable enzyme bands in agarose gels rather than the single faint enzyme band observed on polyacrylamide gels. The PSE-1 sample showed an isoelectric point shift of 0.2 pH unit between polyacrylamide and agarose gel (pI 5.7 and 5.5, respectively). The short focusing time, lack of toxic hazard, and ease of formulation make agarose a practical medium for the characterization of beta-lactamases.

  5. Heat denaturation of soy glycinin : Influence of pH and ionic strength on molecular structure

    NARCIS (Netherlands)

    Lakemond, C.M.M.; Jongh, de H.H.J.; Hessing, M.; Gruppen, H.; Voragen, A.G.J.

    2000-01-01

    The 7S/11S glycinin equilibrium as found in Lakemond et al. (J. Agric. Food Chem. 2000, 48, xxxx-xxxx) at ambient temperatures influences heat denaturation. It is found that the 7S form of glycinin denatures at a lower temperature than the 11S form, as demonstrated by a combination of calorimetric

  6. Fractional order analysis of Sephadex gel structures: NMR measurements reflecting anomalous diffusion

    Science.gov (United States)

    Magin, Richard L.; Akpa, Belinda S.; Neuberger, Thomas; Webb, Andrew G.

    2011-12-01

    We report the appearance of anomalous water diffusion in hydrophilic Sephadex gels observed using pulse field gradient (PFG) nuclear magnetic resonance (NMR). The NMR diffusion data was collected using a Varian 14.1 Tesla imaging system with a home-built RF saddle coil. A fractional order analysis of the data was used to characterize heterogeneity in the gels for the dynamics of water diffusion in this restricted environment. Several recent studies of anomalous diffusion have used the stretched exponential function to model the decay of the NMR signal, i.e., exp[-( bD) α], where D is the apparent diffusion constant, b is determined the experimental conditions (gradient pulse separation, durations and strength), and α is a measure of structural complexity. In this work, we consider a different case where the spatial Laplacian in the Bloch-Torrey equation is generalized to a fractional order model of diffusivity via a complexity parameter, β, a space constant, μ, and a diffusion coefficient, D. This treatment reverts to the classical result for the integer order case. The fractional order decay model was fit to the diffusion-weighted signal attenuation for a range of b-values (0 < b < 4000 s mm -2). Throughout this range of b values, the parameters β, μ and D, were found to correlate with the porosity and tortuosity of the gel structure.

  7. Kinetic evidence for a two-stage mechanism of protein denaturation by guanidinium chloride.

    Science.gov (United States)

    Jha, Santosh Kumar; Marqusee, Susan

    2014-04-01

    Dry molten globular (DMG) intermediates, an expanded form of the native protein with a dry core, have been observed during denaturant-induced unfolding of many proteins. These observations are counterintuitive because traditional models of chemical denaturation rely on changes in solvent-accessible surface area, and there is no notable change in solvent-accessible surface area during the formation of the DMG. Here we show, using multisite fluorescence resonance energy transfer, far-UV CD, and kinetic thiol-labeling experiments, that the guanidinium chloride (GdmCl)-induced unfolding of RNase H also begins with the formation of the DMG. Population of the DMG occurs within the 5-ms dead time of our measurements. We observe that the size and/or population of the DMG is linearly dependent on [GdmCl], although not as strongly as the second and major step of unfolding, which is accompanied by core solvation and global unfolding. This rapid GdmCl-dependent population of the DMG indicates that GdmCl can interact with the protein before disrupting the hydrophobic core. These results imply that the effect of chemical denaturants cannot be interpreted solely as a disruption of the hydrophobic effect and strongly support recent computational studies, which hypothesize that chemical denaturants first interact directly with the protein surface before completely unfolding the protein in the second step (direct interaction mechanism).

  8. Fractal dimensions of silica gels generated using reactive molecular dynamics simulations

    International Nuclear Information System (INIS)

    Bhattacharya, Sudin; Kieffer, John

    2005-01-01

    We have used molecular dynamics simulations based on a three-body potential with charge transfer to generate nanoporous silica aerogels. Care was taken to reproduce the sol-gel condensation reaction that forms the gel backbone as realistically as possible and to thereby produce credible gel structures. The self-similarity of aerogel structures was investigated by evaluating their fractal dimension from geometric correlations. For comparison, we have also generated porous silica glasses by rupturing dense silica and computed their fractal dimension. The fractal dimension of the porous silica structures was found to be process dependent. Finally, we have determined that the effect of supercritical drying on the fractal nature of condensed silica gels is not appreciable

  9. The effect of Na+ and K+ on the thermal denaturation of Na+ and + K+-dependent ATPase.

    Science.gov (United States)

    Fischer, T H

    1983-01-01

    To increase our understanding of the physical nature of the Na+ and K+ forms of the Na+ + K+-dependent ATPase, thermal-denaturation studies were conducted in different types of ionic media. Thermal-denaturation measurements were performed by measuring the regeneration of ATPase activity after slow pulse exposure to elevated temperatures. Two types of experiments were performed. First, the dependence of the thermal-denaturation rate on Na+ and K+ concentrations was examined. It was found that both cations stabilized the pump protein. Also, K+ was a more effective stabilizer of the native state than was Na+. Secondly, a set of thermodynamic parameters was obtained by measuring the temperature-dependence of the thermal-denaturation rate under three ionic conditions: 60 mM-K+, 150 mM-Na+ and no Na+ or K+. It was found that ion-mediated stabilization of the pump protein was accompanied by substantial increases in activation enthalpy and entropy, the net effect being a less-pronounced increase in activation free energy. PMID:6309139

  10. Denaturing of plutonium by transmutation of minor-actinides for enhancement of proliferation resistance

    International Nuclear Information System (INIS)

    Sagara, Hiroshi; Saito, Masaki; Peryoga, Yoga; Ezoubtchenko, Alexey; Takivayev, Alan

    2005-01-01

    Feasibility study for the plutonium denaturing by utilizing minor-actinide transmutation in light water reactors has been performed. And the intrinsic feature of proliferation resistance of plutonium has been discussed based on IAEA's publication and Kessler's proposal. The analytical results show that not only 238 Pu but also other plutonium isotopes with even-mass-number have very important role for denaturing of plutonium due to their relatively large critical mass and noticeably high spontaneous fission neutron generation. With the change of the minor-actinide doping ratio in U-Pu mix oxide fuel and moderator to fuel ratio, it is found that the reactor-grade plutonium from conventional light water reactors can be denatured to satisfy the proliferation resistance criterion based on the Kessler's proposal but not to be sufficient for the criterion based on IAEA's publication. It has been also confirmed that all the safety coefficients take negative value throughout the irradiation. (author)

  11. Improved protocol for isolation of Campylobacter spp. from retail broiler meat and use of pulsed field gel electrophoresis for the typing of isolates.

    Science.gov (United States)

    Oyarzabal, Omar A; Williams, Aretha; Zhou, Ping; Samadpour, Mansour

    2013-10-01

    To improve the detection of Campylobacter spp. in retail broiler meat, a reference method (R subsamples) based on the enrichment of 25 g of meat in Bolton broth at 42°C under microaerobiosis was compared with an alternative method (A subsamples) consisting in the rinsing of meat samples for 30s in buffered peptone water with antimicrobials with incubation at 42°C under aerobiosis. One piece of meat (breasts, tenderloins and thighs) was rinse in experiment 1 (A1) and two pieces in experiment 2 (A2). Campylobacter spp. were isolated on agar plates and identified by PCR. Retail samples in Alabama had less prevalence (P ≤ 0.05) than samples in the state of Washington. The percentage of positive was higher (P ≤ 0.05) in A than in R subsamples and rinsing two pieces of meat yielded the highest percentage of positive subsamples. R subsamples showed variations in the prevalence by product. However, A subsamples had similar prevalence of positives among products compare to the result from reference method. More Campylobacter coli isolates were collected in A2 subsamples. Pulse field gel electrophoresis (PFGE) was used as subtyping method to study the genome similarity among the isolates from all methods. A larger diversity of isolates were detected by PFGE in A2 subsamples. Denaturing gradient gel electrophoresis analysis suggested that the initial bacterial populations of the meat samples impact the final bacterial profile after enrichment. Rinsing broiler meats was less time consuming, required less sample preparation and was more sensitive than the reference method for the isolation of naturally occurring Campylobacter spp. This new method could help with epidemiological and intervention studies to control Campylobacter spp. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Capability of NIPAM polymer gel in recording dose from the interaction of 10B and thermal neutron in BNCT

    International Nuclear Information System (INIS)

    Khajeali, Azim; Reza Farajollahi, Ali; Kasesaz, Yaser; Khodadadi, Roghayeh; Khalili, Assef; Naseri, Alireza

    2015-01-01

    The capability of N-isopropylacrylamide (NIPAM) polymer gel to record the dose resulting from boron neutron capture reaction in BNCT was determined. In this regard, three compositions of the gel with different concentrations of 10 B were prepared and exposed to gamma radiation and thermal neutrons. Unlike irradiation with gamma rays, the boron-loaded gels irradiated by neutron exhibited sensitivity enhancement compared with the gels without 10 B. It was also found that the neutron sensitivity of the gel increased by the increase of concentration of 10 B. It can be concluded that NIPAM gel might be suitable for the measurement of the absorbed dose enhancement due to 10 B and thermal neutron reaction in BNCT. - Highlights: • Three compositions of NIPAM gel with different concentration of 10 B have been exposed by gamma and thermal neutron. • The vials containing NIPAM gel have been irradiated by an automatic system capable of providing for dose uniformity. • Suitability of NIPAM polymer gel in measuring radiation doses in BNCT has been investigated.

  13. The Power of Non-Hydrolytic Sol-Gel Chemistry: A Review

    Directory of Open Access Journals (Sweden)

    Ales Styskalik

    2017-05-01

    Full Text Available This review is devoted to non-hydrolytic sol-gel chemistry. During the last 25 years, non-hydrolytic sol-gel (NHSG techniques were found to be attractive and versatile methods for the preparation of oxide materials. Compared to conventional hydrolytic approaches, the NHSG route allows reaction control at the atomic scale resulting in homogeneous and well defined products. Due to these features and the ability to design specific materials, the products of NHSG reactions have been used in many fields of application. The aim of this review is to present an overview of NHSG research in recent years with an emphasis on the syntheses of mixed oxides, silicates and phosphates. The first part of the review highlights well known condensation reactions with some deeper insights into their mechanism and also presents novel condensation reactions established in NHSG chemistry in recent years. In the second section we discuss porosity control and novel compositions of selected materials. In the last part, the applications of NHSG derived materials as heterogeneous catalysts and supports, luminescent materials and electrode materials in Li-ion batteries are described.

  14. Thermal denaturation of sunflower globulins in low moisture conditions

    International Nuclear Information System (INIS)

    Rouilly, A.; Orliac, O.; Silvestre, F.; Rigal, L.

    2003-01-01

    DSC analysis in pressure resisting pans of sunflower oil cake makes appear the endothermic peak of sunflower globulins denaturation. Its temperature decreases from 189.5 to 119.9 deg. C while the corresponding enthalpy increases from 2.6 to 3.3 J/g of sample, or from 6.7 to 12.2 J/g of dry protein, when the samples moisture content varies from 0 to 30.0% of the total weight. The plot of the denaturation temperature versus the moisture content is not linear but has a rounded global shape and seems to follow the hydration behavior of the proteins, modeled with the sorption isotherm. As it can be seen on scanning electron microscopy (SEM) micrographs, protein corpuscles 'melt' after such a thermal treatment and large aggregates form by coagulation. Moisture dependence of the 'fusion' temperature of native proteic organization, in low moisture conditions, offers so a new characterization method for the use of vegetable proteins in agro-materials

  15. Thermal denaturation of sunflower globulins in low moisture conditions

    Energy Technology Data Exchange (ETDEWEB)

    Rouilly, A.; Orliac, O.; Silvestre, F.; Rigal, L

    2003-03-05

    DSC analysis in pressure resisting pans of sunflower oil cake makes appear the endothermic peak of sunflower globulins denaturation. Its temperature decreases from 189.5 to 119.9 deg. C while the corresponding enthalpy increases from 2.6 to 3.3 J/g of sample, or from 6.7 to 12.2 J/g of dry protein, when the samples moisture content varies from 0 to 30.0% of the total weight. The plot of the denaturation temperature versus the moisture content is not linear but has a rounded global shape and seems to follow the hydration behavior of the proteins, modeled with the sorption isotherm. As it can be seen on scanning electron microscopy (SEM) micrographs, protein corpuscles 'melt' after such a thermal treatment and large aggregates form by coagulation. Moisture dependence of the 'fusion' temperature of native proteic organization, in low moisture conditions, offers so a new characterization method for the use of vegetable proteins in agro-materials.

  16. Evaluation of gasoline-denatured ethanol as a carbon source for denitrification.

    Science.gov (United States)

    Kazasi, Anna; Boardman, Gregory D; Bott, Charles B

    2013-06-01

    In this study concerning denitrification, the performance of three carbon sources, methanol (MeOH), ethanol (EtOH) and gasoline-denatured ethanol (dEtOH), was compared and evaluated on the basis of treatment efficiency, inhibition potential and cost. The gasoline denaturant considered here contained mostly aliphatic compounds and little of the components that typically boost the octane rating, such as benzene, toluene, ethylbenzene and xylenes. Results were obtained using three lab-scale SBRs operated at SRT of 12.0 +/- 0.9 days. After biomass was acclimated, denitrification rates with dEtOH were similar to those of EtOH (201 +/- 50 and 197 +/- 28 NO3-N/g MLVSS x d, respectively), and higher than those of MeOH (165 +/- 49 mg NO3-N/g MLVSS x d). The denaturant did not affect biomass production, nitrification or denitrification. Effluent soluble COD concentrations were always less than the analytical detection limit. Although the cost of dEtOH ($2.00/kg nitrate removed) was somewhat higher than that of methanol ($1.63/kg nitrate removed), the use of dEtOH is very promising and utilities will have to decide if it is worth paying a little extra to take advantage of its benefits.

  17. Sodium dodecyl sulfate-capillary gel electrophoresis of polyethylene glycolylated interferon alpha.

    Science.gov (United States)

    Na, Dong H; Park, Eun J; Youn, Yu S; Moon, Byung W; Jo, Yeong W; Lee, Sung H; Kim, Won-Bae; Sohn, Yeowon; Lee, Kang C

    2004-02-01

    Sodium dodecyl sulfate-capillary gel electrophoresis (SDS-CGE) using a hydrophilic replaceable polymer network matrix was applied to characterize the polyethylene glycol(PEG)ylated interferon alpha (PEG-IFN). The SDS-CGE method resulted in a clearer resolution in both the PEG-IFN species and the native IFN species. The distribution profile of PEGylation determined by SDS-CGE was consistent with that obtained by SDS-polyacrylamide gel electrophoresis (PAGE) with Coomassie blue or barium iodide staining. The result was also compared using matrix-assisted laser desorption/ionization-time of flight-mass spectrometry. SDS-CGE was also useful for monitoring the PEGylation reaction to optimize the reaction conditions, such as reaction molar ratio. This study shows the potential of SDS-CGE as a new method for characterizing the PEGylated proteins with advantages of speed, minimal sample consumption and high resolution.

  18. Enhancement of the electrochemical performance in LiFePO4 cathode materials synthesized by using the sol-gel method

    Directory of Open Access Journals (Sweden)

    Kyong-Soo Hong

    2010-11-01

    Full Text Available LiFePO4 powders were synthesized by using the sol-gel and the solid-state reaction methods. The chemical states of Fe ions were studied by using XPS, and their electrochemical properties according to the oxidation states of Fe ions were compared. The average oxidation state of Fe ions in LiFePO4 powders synthesized by using the solid-state reaction method was found to be Fe3+, on the other hand, that of Fe ions synthesized by using the sol-gel method was found to be Fe2+. The obtained discharge capacities were 50 mAh/g and 120 mAh/g at a rate 0.1 C in LiFePO4 synthesized by using the solid-state reaction and sol-gel methods, respectively. Relatively a good cycling stability was observed in sol-gel prepared powder.

  19. Different Applications of Rheological Techniques in Studies of Physical Gels

    DEFF Research Database (Denmark)

    Hvidt, Søren

    of associating protein filaments with the characteristic function of individual filaments. The proteins enable the cell to regulate the mechanical properties of the cell by sol-gel transition and a variety of crosslinking reactions. In the food industry texture of products are regulated by addition of gel......, respectively, are particularly useful for investigating slow motions in gels and long-time properties. An example of how these different techniques have been used to investigate the rheological properties of sputum [4] will be discussed. The results demonstrate that sputum is a viscoelastic material...... are dominated by repulsive interactions between micelles, and oscillatory measurements allow a determination of the repulsive potential between micelles. Oscillatory bulk modulus measurements have been used to determine the dynamics of unimer-micelle motions. The strain properties of physical gels are of major...

  20. Ionic conductivity of polymer gels deriving from alkali metal ionic liquids and negatively charged polyelectrolytes

    International Nuclear Information System (INIS)

    Ogihara, Wataru; Sun Jiazeng; Forsyth, Maria; MacFarlane, Douglas R.; Yoshizawa, Masahiro; Ohno, Hiroyuki

    2004-01-01

    We have prepared polymer gel electrolytes with alkali metal ionic liquids (AMILs) that inherently contain alkali metal ions. The AMIL consisted of sulfate anion, imidazolium cation, and alkali metal cation. AMILs were mixed directly with poly(3-sulfopropyl acrylate) lithium salt or poly(2-acrylamido-2-methylpropanesulfonic acid) lithium salt to form polymer gels. The ionic conductivity of these gels decreased with increasing polymer fraction, as in general ionic liquid/polymer mixed systems. At low polymer concentrations, these gels displayed excellent ionic conductivity of 10 -4 to 10 -3 S cm -1 at room temperature. Gelation was found to cause little change in the 7 Li diffusion coefficient of the ionic liquid, as measured by pulse-field-gradient NMR. These data strongly suggest that the lithium cation migrates in successive pathways provided by the ionic liquids

  1. On the Formation and Properties of Interstrand DNA-DNA Cross-links Forged by Reaction of an Abasic Site With the Opposing Guanine Residue of 5′-CAp Sequences in Duplex DNA

    Science.gov (United States)

    Johnson, Kevin M.; Price, Nathan E.; Wang, Jin; Fekry, Mostafa I.; Dutta, Sanjay; Seiner, Derrick R.; Wang, Yinsheng; Gates, Kent S.

    2014-01-01

    We recently reported that the aldehyde residue of an abasic (Ap) site in duplex DNA can generate an interstrand cross-link via reaction with a guanine residue on the opposing strand. This finding is intriguing because the highly deleterious nature of interstrand cross-links suggests that even small amounts of Ap-derived cross-links could make a significant contribution to the biological consequences stemming from the generation of Ap sites in cellular DNA. Incubation of 21-bp duplexes containing a central 5′-CAp sequence under conditions of reductive amination (NaCNBH3, pH 5.2) generated much higher yields of cross-linked DNA than reported previously. At pH 7, in the absence of reducing agents, these Ap-containing duplexes also produced cross-linked duplexes that were readily detected on denaturing polyacrylamide gels. Cross-link formation was not highly sensitive to reaction conditions and, once formed, the cross-link was stable to a variety of work-up conditions. Results of multiple experiments including MALDI-TOF mass spectrometry, gel mobility, methoxyamine capping of the Ap aldehyde, inosine-for-guanine replacement, hydroxyl radical footprinting, and LCMS/MS were consistent with a cross-linking mechanism involving reversible reaction of the Ap aldehyde residue with the N2-amino group of the opposing guanine residue in 5′-CAp sequences to generate hemiaminal, imine, or cyclic hemiaminal cross-links (7-10) that were irreversibly converted under conditions of reductive amination (NaCNBH3/pH 5.2) to a stable amine linkage. Further support for the importance of the exocyclic N2-amino group in this reaction was provided by an experiment showing that installation of a 2-aminopurine-thymine base pair at the cross-linking site produced high yields (15-30%) of a cross-linked duplex at neutral pH, in the absence of NaCNBH3. PMID:23215239

  2. Comparison of Excretory-Secretory and Somatic Antigens of Ornithobilharzia turkestanicum in Agar Gel Diffusion Test

    Directory of Open Access Journals (Sweden)

    H Miranzadeh

    2008-12-01

    Full Text Available Background: Ornithobilharziosis as one of the parasitic infections may give rise to serious economic problems in animal husbandry. The Aim of the study was to prepare and compare the somatic and excretory-secretory (ES antigens of O. tur­kestanicum in gel diffusion test. Methods: Excretory-secretory (ES and somatic antigens of Ornithobilharzia turkestanicum were prepared from collected worms from mesentric blood vessels of infected sheep. The laboratory bred rabbits were immunized with antigens and then antisera were prepared. The reaction of antigens and antisera was observed in gel diffusion test. Results: ES antigens of this species showed positive reaction with antisera raised against ES and also somatic antigens. Somatic antigens also showed positive reaction with antisera raised against somatic and also ES antigens. Conclusion: The antigenicity of O. turkestanicum ES and somatic antigens is the same in gel diffusion test.

  3. Manufacture of Regularly Shaped Sol-Gel Pellets

    Science.gov (United States)

    Leventis, Nicholas; Johnston, James C.; Kinder, James D.

    2006-01-01

    An extrusion batch process for manufacturing regularly shaped sol-gel pellets has been devised as an improved alternative to a spray process that yields irregularly shaped pellets. The aspect ratio of regularly shaped pellets can be controlled more easily, while regularly shaped pellets pack more efficiently. In the extrusion process, a wet gel is pushed out of a mold and chopped repetitively into short, cylindrical pieces as it emerges from the mold. The pieces are collected and can be either (1) dried at ambient pressure to xerogel, (2) solvent exchanged and dried under ambient pressure to ambigels, or (3) supercritically dried to aerogel. Advantageously, the extruded pellets can be dropped directly in a cross-linking bath, where they develop a conformal polymer coating around the skeletal framework of the wet gel via reaction with the cross linker. These pellets can be dried to mechanically robust X-Aerogel.

  4. Unravelling the hydrophobicity of urea in water using thermodiffusion: implications for protein denaturation.

    Science.gov (United States)

    Niether, Doreen; Di Lecce, Silvia; Bresme, Fernando; Wiegand, Simone

    2018-01-03

    Urea is widely used as a protein denaturant in aqueous solutions. Experimental and computer simulation studies have shown that it dissolves in water almost ideally at high concentrations, introducing little disruption in the water hydrogen bonded structure. However, at concentrations of the order of 5 M or higher, urea induces denaturation in a wide range of proteins. The origin of this behaviour is not completely understood, but it is believed to stem from a balance between urea-protein and urea-water interactions, with urea becoming possibly hydrophobic at a specific concentration range. The small changes observed in the water structure make it difficult to connect the denaturation effects to the solvation properties. Here we show that the exquisite sensitivity of thermodiffusion to solute-water interactions allows the identification of the onset of hydrophobicity of urea-water mixtures. The hydrophobic behaviour is reflected in a sign reversal of the temperature dependent slope of the Soret coefficient, which is observed, both in experiments and non-equilibrium computer simulations at ∼5 M concentration of urea in water. This concentration regime corresponds to the one where abrupt changes in the denaturation of proteins are commonly observed. We show that the onset of hydrophobicity is intrinsically connected to the urea-water interactions. Our results allow us to identify correlations between the Soret coefficient and the partition coefficient, log P, hence establishing the thermodiffusion technique as a powerful approach to study hydrophobicity.

  5. Removal mechanism of tritium by variously pretreated silica gel

    International Nuclear Information System (INIS)

    Nakashima, M.; Tachikawa, E.; Saeki, M.; Aratono, Y.

    1981-01-01

    Removal mechanisms of HTO from variously pretreated and non-pretreated silica gel columns were investigated with pulse-loading with tritiated water vapor. With non-pretreated silica gel, the HTO physisorbed on the upper part of the column comes into contact with surface hydroxyl groups while passing downward the column, so that in each equilibration a part of the tritium is incorporated into hydroxyl groups by H/T isotopic exchange reactions. With the silica gel pretreated at a temperature below 400 0 C, most of tritium in the applied HTO is easily incorporated into surface hydroxyl groups in the upper part of the column either by H/T isotopic exchange reactions or by rehydration of the dehydrated surface (siloxyl linkage). In the pretreatment above 400 0 C, essentially all the tritium is trapped by siloxyl groups of various stabilities. The ease of rehydration of siloxyl groups by applied HTO depends on their stabilities, which, in turn, depend on the pretreatment temperature. As a general trend, treatment at higher temperature promotes annealing of the constrained siloxyl groups and thus the rate of rehydration becomes slower. (author)

  6. A correlated Walks' theory for DNA denaturation

    International Nuclear Information System (INIS)

    Mejdani, R.

    1994-08-01

    We have shown that by using a correlated Walks' theory for the lattice gas model on a one-dimensional lattice, we can study, beside the saturation curves obtained before for the enzyme kinetics, also the DNA denaturation process. In the limit of no interactions between sites the equation for melting curves of DNA reduces to the random model equation. Thus our leads naturally to this classical equation in the limiting case. (author). 22 refs, 3 figs

  7. Development of two dimensional electrophoresis method using single chain DNA

    International Nuclear Information System (INIS)

    Ikeda, Junichi; Hidaka, So

    1998-01-01

    By combining a separation method due to molecular weight and a method to distinguish difference of mono-bases, it was aimed to develop a two dimensional single chain DNA labeled with Radioisotope (RI). From electrophoretic pattern difference of parent and variant strands, it was investigated to isolate the root module implantation control gene. At first, a Single Strand Conformation Polymorphism (SSCP) method using concentration gradient gel was investigated. As a result, it was formed that intervals between double chain and single chain DNAs expanded, but intervals of both single chain DNAs did not expand. On next, combination of non-modified acrylic amide electrophoresis method and Denaturing Gradient-Gel Electrophoresis (DGGE) method was examined. As a result, hybrid DNA developed by two dimensional electrophoresis arranged on two lines. But, among them a band of DNA modified by high concentration of urea could not be found. Therefore, in this fiscal year's experiments, no preferable result could be obtained. By the used method, it was thought to be impossible to detect the differences. (G.K.)

  8. Characterization and Biocompatibility of Chitosan Gels with Silver and Gold Nanoparticles

    Directory of Open Access Journals (Sweden)

    C. Sámano-Valencia

    2014-01-01

    Full Text Available The presence of bacterial resistance to antibiotics is a very important issue and the search of new alternatives is necessary. In this work, a combination of chitosan gel with silver or gold nanoparticles was prepared and characterized using thermal, rheology, bactericide, and biocompatibility analyses. ESEM images were also taken to visualize the incorporation of the nanoparticles into the gel matrix. Thermal analysis showed a better thermal stability in the chitosan-gold nanoparticles gels compared to the chitosan-silver nanoparticles gels. Rheology analyses showed that the viscosity of the gels decreased when velocity increased and there were differences in viscosity when silver and gold nanoparticles concentrations change. ESEM images showed the presence of agglomerates of silver and gold nanoparticles into the gel matrix with a good distribution; in some cases the formation of microstructures was found. Bactericide results show that these materials present an antibacterial activity against S. aureus, S. mutans, and E. coli. The biocompatibility test showed neither negative reaction nor wound healing delay after the application of the gels in an in vivo test. The gels with silver and gold nanoparticles could be used to treat wound infections in oral or skin applications.

  9. Ionogel Electrolytes through Sol-Gel Processing

    Science.gov (United States)

    Horowitz, Ariel I.

    Electrical energy needs have intensified due to the ubiquity of personal electronics, the decarbonization of energy services through electrification, and the use of intermittent renewable energy sources. Despite developments in mechanical and thermal methods, electrochemical technologies are the most convenient and effective means of storing electrical energy. These technologies include both electrochemical cells, commonly called batteries, and electrochemical double-layer capacitors, or "supercapacitors", which store energy electrostatically. Both device types require an ion-conducting electrolyte. Current devices use solutions of complex salts in organic solvents, leading to both toxicity and flammability concerns. These drawbacks can be avoided by replacing conventional electrolytes with room-temperature molten salts, known as ionic liquids (ILs). ILs are non-volatile, non-flammable, and offer high conductivity and good electrochemical stability. Device mass can be reduced by combining ILs with a solid scaffold material to form an "ionogel," further improving performance metrics. In this work, sol-gel chemistry is explored as a means of forming ionogel electrolytes. Sol-gel chemistry is a solution-based, industrially-relevant, well-studied technique by which solids such as silica can be formed in situ. Previous works used a simple acid-catalyzed sol-gel reaction to create brittle, glassy ionogels. Here, both the range of products that can be accomplished through sol-gel processing and the understanding of interactions between ILs and the sol-gel reaction network are greatly expanded. This work introduces novel ionogel materials, including soft and compliant silica-supported ionogels and PDMS-supported ionogels. The impacts of the reactive formulation, IL identity, and casting time are detailed. It is demonstrated that variations in formulation can lead to rapid gelation and open pore structures in the silica scaffold or slow gelation and more dense silica

  10. On the Use of Potential Denaturing Agents for Ethanol in Direct Ethanol Fuel Cells

    OpenAIRE

    Domnik Bayer; Florina Jung; Birgit Kintzel; Martin Joos; Carsten Cremers; Dierk Martin; Jörg Bernard; Jens Tübke

    2011-01-01

    Acidic or alkaline direct ethanol fuel cells (DEFCs) can be a sustainable alternative for power generation if they are fuelled with bio-ethanol. However, in order to keep the fuel cheap, ethanol has to be exempted from tax on spirits by denaturing. In this investigation the potential denaturing agents fusel oil, tert-butyl ethyl ether, and Bitrex were tested with regard to their compatibility with fuel cells. Experiments were carried out both in sulphuric acid and potassium hydroxide solution...

  11. Synthesis and characterization of gel-grown cobalt tartrate crystals

    Indian Academy of Sciences (India)

    ... in electronics, optics and industries. A series of pure and mixed crystals ... bility method. A few researchers reported the growth of crystals of strontium tartrate ... grow it by chemical reaction method using the gel technique. The crystallization ...

  12. Silver-Stained Fibrin Zymography: Separation of Proteases and Activity Detection Using a Single Substrate-Containing Gel.

    Science.gov (United States)

    Park, Chang-Su; Kang, Dae-Ook; Choi, Nack-Shick

    2017-01-01

    Silver-stained fibrin zymography for separation of protease bands and activity detection using a single substrate gel was designed. The method takes advantage of the nano-scale sensitivity of both zymography and silver staining. After sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) in a gel containing fibrin (protease substrate), the gel was incubated in enzyme reaction buffer and the zymogram gel was silver-stained. Bands with protease activity were stained with silver in clear areas where the protein substrate had been degraded. The molecular sizes of proteases were accurately determined.

  13. Hydroponics gel as a new electrolyte gelling agent for alkaline zinc-air cells

    Science.gov (United States)

    Othman, R.; Basirun, W. J.; Yahaya, A. H.; Arof, A. K.

    The viability of hydroponics gel as a new alkaline electrolyte gelling agent is investigated. Zinc-air cells are fabricated employing 12 wt.% KOH electrolyte immobilised with hydroponics gel. The cells are discharged at constant currents of 5, 50 and 100 mA. XRD and SEM analysis of the anode plates after discharge show that the failure mode is due to the formation of zinc oxide insulating layers and not due to any side reactions between the gel and the plate or the electrolyte.

  14. A modified {sup 99} Mo- {sup 99} Tc generator on Zirconium molybdo- phosphate-{sup 99} Mo gel. Vol. 3

    Energy Technology Data Exchange (ETDEWEB)

    El-Kolaly, M T; Talaat, H [Labelled Compounds Department, Cairo (Egypt); Botros, N [Radioistspe and Generator Department, Radioisotope Production and Sealed Source Division, Hot Laboratories Center, Atomic Energy Authority, Cairo (Egypt)

    1996-03-01

    A modified {sup 99} Mo - {sup 99} Tc gel generator is described. The new generator is based on the use of zirconium molybdophosphate - {sup 99} Mo gel in which {sup 99} Mo chemically combined in the gel structure, where {sup 99m}Tc can be easily eluted with distilled water or saline. The gel was prepared via chemical reaction between zirconyl chloride and molybdophosphate - {sup 99} Mo solution. The PH of the reaction mixture was adjusted with NaOH. Different gels have been prepared by varying the molar ratio of Mo:Zr:p. The PH and time of digeston on complete gel formation was also investigated in order to optimize the condition of gel preparation. Molybdophosphate {sup 32} P solution was used to determine the phosphorous content in the gel and in the {sup 99m}Tc eluate. The temperature and time of drying of the gel and their effect on {sup 99m}Tc elution efficiency were also studied. From the data obtained, the optimum conditions for routine production of {sup 99} Mo - {sup 99m}Tc generator are presented and discussed. 2 figs., 6 tabs.

  15. Bioremediation assessment of diesel-biodiesel-contaminated soil using an alternative bioaugmentation strategy.

    Science.gov (United States)

    Colla, Tatiana Simonetto; Andreazza, Robson; Bücker, Francielle; de Souza, Marcela Moreira; Tramontini, Letícia; Prado, Gerônimo Rodrigues; Frazzon, Ana Paula Guedes; Camargo, Flávio Anastácio de Oliveira; Bento, Fátima Menezes

    2014-02-01

    This study investigated the effectiveness of successive bioaugmentation, conventional bioaugmentation, and biostimulation of biodegradation of B10 in soil. In addition, the structure of the soil microbial community was assessed by polymerase chain reaction-denaturing gradient gel electrophoresis. The consortium was inoculated on the initial and the 11th day of incubation for successive bioaugmentation and only on the initial day for bioaugmentation and conventional bioaugmentation. The experiment was conducted for 32 days. The microbial consortium was identified based on sequencing of 16S rRNA gene and consisted as Pseudomonas aeruginosa, Achromobacter xylosoxidans, and Ochrobactrum intermedium. Nutrient introduction (biostimulation) promoted a positive effect on microbial populations. The results indicate that the edaphic community structure and dynamics were different according to the treatments employed. CO2 evolution demonstrated no significant difference in soil microbial activity between biostimulation and bioaugmentation treatments. The total petroleum hydrocarbon (TPH) analysis indicated a biodegradation level of 35.7 and 32.2 % for the biostimulation and successive bioaugmentation treatments, respectively. Successive bioaugmentation displayed positive effects on biodegradation, with a substantial reduction in TPH levels.

  16. The occurrence of spoilage yeasts in cream-filled bakery products.

    Science.gov (United States)

    Osimani, Andrea; Milanović, Vesna; Taccari, Manuela; Cardinali, Federica; Pasquini, Marina; Aquilanti, Lucia; Clementi, Francesca

    2017-04-01

    Filling creams can provide an adequate substrate for spoilage yeasts because some yeasts can tolerate the high osmotic stress in these products. To discover the source of spoilage of a cream-filled baked product, end products, raw materials, indoor air and work surfaces were subjected to microbiological and molecular analyses. The efficacy of disinfectants against spoilage yeasts was also assessed. The analyses on end products revealed the presence of the closest relatives to Zygosaccharomyces bailii with counts ranging from 1.40 to 4.72 log cfu g -1 . No spoilage yeasts were found in the indoor air and work surfaces. Polymerase chain reaction-denaturing gradient gel electrophoresis analysis, carried out directly on filling creams collected from unopened cans, showed the presence of bands ascribed to the closest relatives to Z. bailii sensu lato, although with counts products, reliable and sensitive methods must be used. Moreover, hygiene and the application of good manufacturing practices represent the most efficient way for the prevention and minimization of cross-contamination. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  17. The synergy of permeable pavements and geothermal heat pumps for stormwater treatment and reuse.

    Science.gov (United States)

    Tota-Maharaj, K; Scholz, M; Ahmed, T; French, C; Pagaling, E

    2010-12-14

    The use of permeable pavement systems with integrated geothermal heat pumps for the treatment and recycling of urban runoff is novel and timely. This study assesses the efficiency of the combined technology for controlled indoor and uncontrolled outdoor experimental rigs. Water quality parameters such as biochemical oxygen demand, nutrients, total viable heterotrophic bacteria and total coliforms were tested before and after treatment in both rigs. The water borne bacterial community genomic deoxyribonucleic acid (DNA) was analyzed by polymerase chain reaction (PCR) amplification followed by denaturing gradient gel electrophoresis (DGGE) and was further confirmed by DNA sequencing techniques. Despite the relatively high temperatures in the indirectly heated sub-base of the pavement, potentially pathogenic organisms such as Salmonella spp., Escherichia coli, faecal Streptococci and Legionella were not detected. Moreover, mean removal rates of 99% for biochemical oxygen demand, 97% for ammonia-nitrogen and 95% for orthophosphate-phosphates were recorded. This research also supports decision-makers in assessing public health risks based on qualitative molecular microbiological data associated with the recycling of treated urban runoff.

  18. Effect of changing temperature on anaerobic hydrogen production and microbial community composition in an open-mixed culture bioreactor

    Energy Technology Data Exchange (ETDEWEB)

    Karadag, Dogan; Puhakka, Jaakko A. [Department of Chemistry and Bioengineering, Tampere University of Technology, Tampere (Finland)

    2010-10-15

    The temperature effect (37-65 C) on H{sub 2} production from glucose in an open-mixed culture bioreactor using an enrichment culture from a hot spring was studied. The dynamics of microbial communities was investigated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). At 45 and 60 C the H{sub 2} production was the highest i.e. 1.71 and 0.85 mol H{sub 2}/mol glucose, respectively. No H{sub 2} was produced at temperatures 50 and 55 C. At 37-45 C, H{sub 2} production was produced by butyrate type fermentation while fermentation mechanism changed to ethanol type at 60 C. Clostridium species were dominant at 37-45 C while at 50-55 C and 60 C the culture was dominated by Bacillus coagulans and Thermoanaerobacterium, respectively. In the presence of B. Coagulans the metabolism was directed to lactate production. The results show that the mixed culture had two optima for H{sub 2} production and that the microbial communities and metabolic patterns promptly changed according to changing temperatures. (author)

  19. Comparative study of endophytic and endophytic diazotrophic bacterial communities across rice landraces grown in the highlands of northern Thailand.

    Science.gov (United States)

    Rangjaroen, Chakrapong; Rerkasem, Benjavan; Teaumroong, Neung; Sungthong, Rungroch; Lumyong, Saisamorn

    2014-01-01

    Communities of bacterial endophytes within the rice landraces cultivated in the highlands of northern Thailand were studied using fingerprinting data of 16S rRNA and nifH genes profiling by polymerase chain reaction-denaturing gradient gel electrophoresis. The bacterial communities' richness, diversity index, evenness, and stability were varied depending on the plant tissues, stages of growth, and rice cultivars. These indices for the endophytic diazotrophic bacteria within the landrace rice Bue Wah Bo were significantly the lowest. The endophytic bacteria revealed greater diversity by cluster analysis with seven clusters compared to the endophytic diazotrophic bacteria (three clusters). Principal component analysis suggested that the endophytic bacteria showed that the community structures across the rice landraces had a higher stability than those of the endophytic diazotrophic bacteria. Uncultured bacteria were found dominantly in both bacterial communities, while higher generic varieties were observed in the endophytic diazotrophic bacterial community. These differences in bacterial communities might be influenced either by genetic variation in the rice landraces or the rice cultivation system, where the nitrogen input affects the endophytic diazotrophic bacterial community.

  20. Arbuscular mycorrhizal fungal communities in the rhizosphere of a continuous cropping soybean system at the seedling stage.

    Science.gov (United States)

    Cui, Jiaqi; Bai, Li; Liu, Xiaorui; Jie, Weiguang; Cai, Baiyan

    Arbuscular mycorrhizae (AM) fungi play a crucial role in the growth of soybean; however, the planting system employed is thought to have an effect on AM fungal communities in the rhizosphere. This study was performed to explore the influence of continuous soybean cropping on the diversity of Arbuscular mycorrhizal (AM) fungi, and to identify the dominant AM fungus during the seedling stage. Three soybean cultivars were planted under two and three years continuous cropping, respectively. The diversity of AM fungi in the rhizosphere soil at the seedling stage was subsequently analyzed using polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE). The results showed that an increase in cropping years improved the colonization rate of AM in all three soybean cultivars. Moreover, the dominant species were found to be Funneliformis mosseae and Glomus species. The results of cluster analysis further confirmed that the number of years of continuous cropping significantly affected the composition of rhizospheric AM fungal communities in different soybean cultivars. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  1. Effects of mannan oligosaccharide and virginiamycin on the cecal microbial community and intestinal morphology of chickens raised under suboptimal conditions.

    Science.gov (United States)

    Pourabedin, Mohsen; Xu, Zhengxin; Baurhoo, Bushansingh; Chevaux, Eric; Zhao, Xin

    2014-05-01

    There is an increasing movement against use of antibiotic growth promoters in animal feed. Prebiotic supplementation is a potential alternative to enhance the host's natural defense through modulation of gut microbiota. In the present study, the effect of mannan oligosaccharide (MOS) and virginiamycin (VIRG) on cecal microbial ecology and intestinal morphology of broiler chickens raised under suboptimal conditions was evaluated. MOS and VIRG induced different bacterial community structures, as revealed by denaturing gradient gel electrophoresis of 16S rDNA. The antibiotic treatment reduced cecal microbial diversity while the community equitability increased. A higher bacterial diversity was observed in the cecum of MOS-supplemented birds. Quantitative polymerase chain reaction results indicated that MOS changed the cecal microbiota in favor of the Firmicutes population but not the Bacteroidetes population. No difference was observed in total bacterial counts among treatments. MOS promoted the growth of Lactobacillus spp. and Bifidobacterium spp. in the cecum and increased villus height and goblet cell numbers in the ileum and jejunum. These results provide a deeper insight into the microbial ecological changes after supplementation of MOS prebiotic in poultry diets.

  2. The assessment of the coke wastewater treatment efficacy in rotating biological contractor.

    Science.gov (United States)

    Cema, G; Żabczyński, S; Ziembińska-Buczyńska, A

    2016-01-01

    Coke wastewater is known to be relatively difficult for biological treatment. Nonetheless, biofilm-based systems seem to be promising tool for such treatment. That is why a rotating biological contactor (RBC) system focused on the Anammox process was used in this study. The experiment was divided into two parts with synthetic and then real wastewater. It was proven that it is possible to treat coke wastewater with RBC but such a procedure requires a very long start-up period for the nitritation (190 days), as well as for the Anammox process, where stable nitrogen removal over 70% was achieved after 400 days of experiment. Interestingly, it was possible at a relatively low (20.2 ± 2.2 °C) temperature. The polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) based monitoring of the bacterial community showed that its biodiversity decreased when the real wastewater was treated and it was composed mainly of GC-rich genotypes, probably because of the modeling influence of this wastewater and the genotypes specialization.

  3. In vitro fermentation behaviors of fucosylated chondroitin sulfate from Pearsonothuria graeffei by human gut microflora.

    Science.gov (United States)

    Wei, Chao-Yang; Liao, Ning-Bo; Zhang, Yu; Ye, Xing-Qian; Li, Shan; Hu, Ya-Qin; Liu, Dong-Hong; Linhardt, Robert J; Wang, Xin; Chen, Shi-Guo

    2017-09-01

    A fucosylated chondroitin sulfate (FCS-pg) with highly repeated structure from Pearsonothuria graeffei was subjected to a in vitro fermentation model to investigate its fermentability and effects on human gut microflora. High performance liquid chromatography (HPLC) measurement found FCS-pg can be fermented to short chain fatty acids (SCFAs) by gut microflora from partial human fecal samples. 16S rRNA gene-based polymerase chain reaction-based denaturing gradient gel electrophoresis (PCR-DGGE) profiling and real-time quantitative PCR analysis showed that FCS-pg mainly increased the proportions of Clostridium cluster XI, Bacteriodes prevotella group, Bifidobacterium genus, Clostridium cluster I and Clostridium cluster XIVab, whereas the numbers of the Enterobacteriaceae and Lactobacillus decreased. These results indicated that FCS-pg was mainly fermented by Bacteroides, Bifidobacterium and Clostridium. It increased the content of probiotics bacteria in achieving health-enhancing effect, was slightly different than most sulfated polysaccharides from marine animals. The current study provides useful new information on the mechanism of absorption and functional activity on FCS-pg within the gastrointestinal tract of the human body. Copyright © 2017. Published by Elsevier B.V.

  4. Performance and microbial community structures of hydrolysis acidification process treating azo and anthraquinone dyes in different stages.

    Science.gov (United States)

    Liu, Na; Xie, Xuehui; Yang, Bo; Zhang, Qingyun; Yu, Chengzhi; Zheng, Xiulin; Xu, Leyi; Li, Ran; Liu, Jianshe

    2017-01-01

    In this study, performance of hydrolysis acidification process treating simulated dyeing wastewater containing azo and anthraquinone dyes in different stages was investigated. The decolorization ratio, COD Cr removal ratio, BOD 5 /COD Cr value, and volatile fatty acids (VFAs) production were almost better in stage 1 than that in stage 2. Fourier transform infrared spectroscopy (FTIR) and gas chromatography-mass spectrometry (GC-MS) confirmed the biodegradation of Reactive Black 5 (RB5) and Remazol Brilliant Blue R (RBBR) in hydrolysis acidification process. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses revealed that significant difference of microbial community structures existed in stage 1 and 2. The dominant species in stage 1 was related to Bacteroidetes group, while the dominant species in stage 2 was related to Bacteroidetes and Firmicutes groups. From the results, it could be speculated that different dyes' structures might have significant influence on the existence and function of different bacterial species, which might supply information for bacteria screening and acclimation in the treatment of actual dyeing wastewater.

  5. Denaturation of proteins by surfactants studied by the Taylor dispersion analysis.

    Directory of Open Access Journals (Sweden)

    Aldona Jelińska

    Full Text Available We showed that the Taylor Dispersion Analysis (TDA is a fast and easy to use method for the study of denaturation proteins. We applied TDA to study denaturation of β-lactoglobulin, transferrin, and human insulin by anionic surfactant sodium dodecyl sulfate (SDS. A series of measurements at constant protein concentration (for transferrin was 1.9 x 10-5 M, for β- lactoglobulin was 7.6 x 10-5 M, and for insulin was 1.2 x 10-4 M and varying SDS concentrations were carried out in the phosphate-buffered saline (PBS. The structural changes were analyzed based on the diffusion coefficients of the complexes formed at various surfactant concentrations. The concentration of surfactant was varied in the range from 1.2 x 10-4 M to 8.7 x 10-2 M. We determined the minimum concentration of the surfactant necessary to change the native conformation of the proteins. The minimal concentration of SDS for β-lactoglobulin and transferrin was 4.3 x 10-4 M and for insulin 2.3 x 10-4 M. To evaluate the TDA as a novel method for studying denaturation of proteins we also applied other methods i.e. electronic circular dichroism (ECD and dynamic light scattering (DLS to study the same phenomenon. The results obtained using these methods were in agreement with the results from TDA.

  6. Successive changes in community structure of an ethylbenzene-degrading sulfate-reducing consortium.

    Science.gov (United States)

    Nakagawa, Tatsunori; Sato, Shinya; Yamamoto, Yoko; Fukui, Manabu

    2002-06-01

    The microbial community structure and successive changes in a mesophilic ethylbenzene-degrading sulfate-reducing consortium were for the first time clarified by the denaturing gradient gel electrophoresis (DGGE) analysis of the PCR amplified 16S rRNA gene fragments. At least ten bands on the DGGE gel were detected in the stationary phase. Phylogenetic analysis of the DGGE bands revealed that the consortium consisted of different eubacterial phyla including the delta subgroup of Proteobacteria, the order Sphingobacteriales, the order Spirochaetales, and the unknown bacterium. The most abundant band C was closely related to strain mXyS1, an m-xylene-degrading sulfate-reducing bacterium (SRB), and occurred as a sole band on DGGE gels in the logarithmic growth phase that 40% ethylbenzene was consumed accompanied by sulfide production. During further prolonged incubation, the dominancy of band C did not change. These results suggest that SRB corresponds to the most abundant band C and contributes mainly to the degradation of ethylbenzene coupled with sulfate reduction.

  7. The production and repair of double strand breaks in cells from normal humans and patients with ataxia telangiectasia

    International Nuclear Information System (INIS)

    Lehman, A.R.; Stevens, S.

    1977-01-01

    The production and repair of double strand breaks induced by γ-rays in the DNA of human fibroblasts have been measured by sedimentation in sucrose gradients under non-denaturing conditions. Unirradiated DNA formed a rapidly sedimenting gel. Low doses of radiation released freely sedimenting DNA molecules from this gel. Higher doses reduced the rate of sedimentation of the free DNA due to the introduction of double strand breaks. The breakage efficiency was 1 break/1.3x10 10 daltons of DNA/krad. Postirradiation incubation after a high dose of radiation resulted in an increase in molecular weight of the free DNA molecules, and after a low dose the rapidly-sedimenting gel was reformed. These data suggest that double strand breaks are repaired in human fibroblasts. No significant differences were found between fibroblasts from two normal donors and four patients with the radiosensitive disorder, ataxia telangiectasia, in either the production or repair of double strand breaks

  8. Effect of heating strategies on whey protein denaturation--Revisited by liquid chromatography quadrupole time-of-flight mass spectrometry.

    Science.gov (United States)

    Akkerman, M; Rauh, V M; Christensen, M; Johansen, L B; Hammershøj, M; Larsen, L B

    2016-01-01

    Previous standards in the area of effect of heat treatment processes on milk protein denaturation were based primarily on laboratory-scale analysis and determination of denaturation degrees by, for example, electrophoresis. In this study, whey protein denaturation was revisited by pilot-scale heating strategies and liquid chromatography quadrupole time-of-flight mass spectrometer (LC/MC Q-TOF) analysis. Skim milk was heat treated by the use of 3 heating strategies, namely plate heat exchanger (PHE), tubular heat exchanger (THE), and direct steam injection (DSI), under various heating temperatures (T) and holding times. The effect of heating strategy on the degree of denaturation of β-lactoglobulin and α-lactalbumin was determined using LC/MC Q-TOF of pH 4.5-soluble whey proteins. Furthermore, effect of heating strategy on the rennet-induced coagulation properties was studied by oscillatory rheometry. In addition, rennet-induced coagulation of heat-treated micellar casein concentrate subjected to PHE was studied. For skim milk, the whey protein denaturation increased significantly as T and holding time increased, regardless of heating method. High denaturation degrees were obtained for T >100°C using PHE and THE, whereas DSI resulted in significantly lower denaturation degrees, compared with PHE and THE. Rennet coagulation properties were impaired by increased T and holding time regardless of heating method, although DSI resulted in less impairment compared with PHE and THE. No significant difference was found between THE and PHE for effect on rennet coagulation time, whereas the curd firming rate was significantly larger for THE compared with PHE. Micellar casein concentrate possessed improved rennet coagulation properties compared with skim milk receiving equal heat treatment. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  9. Mineralogical Control on Microbial Diversity in a Weathered Granite?

    Science.gov (United States)

    Gleeson, D.; Clipson, N.; McDermott, F.

    2003-12-01

    Mineral transformation reactions and the behaviour of metals in rock and soils are affected not only by physicochemical parameters but also by biological factors, particularly by microbial activity. Microbes inhabit a wide range of niches in surface and subsurface environments, with mineral-microbe interactions being generally poorly understood. The focus of this study is to elucidate the role of microbial activity in the weathering of common silicate minerals in granitic rocks. A site in the Wicklow Mountains (Ireland) has been identified that consists of an outcrop surface of Caledonian (ca. 400 million years old) pegmatitic granite from which large intact crystals of variably weathered muscovite, plagioclase, K-feldspar and quartz were sampled, together with whole-rock granite. Culture-based microbial approaches have been widely used to profile microbial communities, particularly from copiotrophic environments, but it is now well established that for oligotrophic environments such as those that would be expected on weathering faces, perhaps less than 1% of microbial diversity can be profiled by cultural means. A number of culture-independent molecular based approaches have been developed to profile microbial diversity and community structure. These rely on successfully isolating environmental DNA from a given environment, followed by the use of the polymerase chain reaction (PCR) to amplify the typically small quantities of extracted DNA. Amplified DNA can then be analysed using cloning based approaches as well as community fingerprinting systems such as denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP) and ribosomal intergenic spacer analysis (RISA). Community DNA was extracted and the intergenic spacer region (ITS) between small (16S) and large (23S) bacterial subunit rRNA genes was amplified. RISA fragments were then electrophoresed on a non-denaturing polyacrylamide gel. Banding patterns suggest that

  10. Ion-ion interactions in the denatured state contribute to the stabilization of CutA1 proteins.

    Science.gov (United States)

    Yutani, Katsuhide; Matsuura, Yoshinori; Naitow, Hisashi; Joti, Yasumasa

    2018-05-16

    In order to elucidate features of the denatured state ensembles that exist in equilibrium with the native state under physiological conditions, we performed 1.4-μs molecular dynamics (MD) simulations at 400 K and 450 K using the monomer subunits of three CutA1 mutants from Escherichia coli: an SH-free mutant (Ec0SH) with denaturation temperature (T d ) = 85.6 °C, a hydrophobic mutant (Ec0VV) with T d  = 113.3 °C, and an ionic mutant (Ec0VV_6) with T d  = 136.8 °C. The occupancy of salt bridges by the six substituted charged residues in Ec0VV_6 was 140.1% at 300 K and 89.5% at 450 K, indicating that even in the denatured state, salt bridge occupancy was high, approximately 60% of that at 300 K. From these results, we can infer that proteins from hyperthermophiles with a high ratio of charged residues are stabilized by a decrease in conformational entropy due to ion-ion interactions in the denatured state. The mechanism must be comparable to the stabilization conferred by disulfide bonds within a protein. This suggests that introduction of charged residues, to promote formation of salt bridges in the denatured state, would be a simple way to rationally design stability-enhanced mutants.

  11. Computational design of active, self-reinforcing gels.

    Science.gov (United States)

    Yashin, Victor V; Kuksenok, Olga; Balazs, Anna C

    2010-05-20

    Many living organisms have evolved a protective mechanism that allows them to reversibly alter their stiffness in response to mechanical contact. Using theoretical modeling, we design a mechanoresponsive polymer gel that exhibits a similar self-reinforcing behavior. We focus on cross-linked gels that contain Ru(terpy)(2) units, where both terpyridine ligands are grafted to the chains. The Ru(terpy)(2) complex forms additional, chemoresponsive cross-links that break and re-form in response to a repeated oxidation and reduction of the Ru. In our model, the periodic redox variations of the anchored metal ion are generated by the Belousov-Zhabotinsky (BZ) reaction. Our computer simulations reveal that compression of the BZ gel leads to a stiffening of the sample due to an increase in the cross-link density. These findings provide guidelines for designing biomimetic, active coatings that send out a signal when the system is impacted and use this signaling process to initiate the self-protecting behavior.

  12. Denaturation/Renaturation of Organophosphorus Acid Anhydrolase (OPAA) Using Guanidinium Hydrochloride and Urea

    National Research Council Canada - National Science Library

    Ong, K. K; Sun, Z; Cheng, T. C; Wei, Y; Yuan, J. M; Yin, R

    2004-01-01

    .... Using organophosphorus acid anhydrolase (OPAA) as the model protein, a guanidinium hydrochloride and urea denaturation/renaturation study was conducted and measured both optically and enzymatically...

  13. Denaturation/Renaturation of Organophosphorus Acid Anhydrolase (OPAA) Using Guanidinium Hydrochloride and Urea

    National Research Council Canada - National Science Library

    Ong, K. K; Sun, Z; Cheng, T. C; Wei, Y; Yuan, J. M; Yin, R

    2004-01-01

    ...; thereby indicating conformational changes. Similar results were obtained with circular dichroism as the peak representing the alpha-helix conformation decreased as denaturant concentration was increased...

  14. 3D MR gel dosimetry with lung equivalent gel

    International Nuclear Information System (INIS)

    Scherer, J.; Solleder, M.; Schiessl, I.; Bogner, L.; Herbst, M.

    1998-01-01

    The MR gel dosimetry is used to verify complex 3D treatment plans. Till now this method served only for dose evaluation in homogeneous phantoms. On the way to build a heterogeneous anthropomorphic gel phantom, a lung equivalent gel with the density 0.4 g/cm 3 was developed. First experiments show a 1.55 times higher dose reponse in the low density gel (LD gel). The comparison of a dose distribution in a gel/LD gel/gel slab phantom with Monte Carlo calculations shows good agreement within 5%. More over the accuray of the measuring device magnetic resonance imager was studied in respect to the now exclusive digital image processing with the software MRD (MR dosimetry). Because of the dimensions of the Fricke gel phantom an artefact correction, based on the data from the unirradiated phantom proved to be essential. (orig.) [de

  15. Behavior of Heat-Denatured Whey: Buttermilk Protein Aggregates during the Yogurt-Making Process and Their Influence on Set-Type Yogurt Properties

    Directory of Open Access Journals (Sweden)

    Maxime Saffon

    2013-09-01

    Full Text Available The objective of this study was to assess the impact of using heat-denatured whey:buttermilk protein aggregate in acid-set type yogurt production. Whey and buttermilk (25:75 protein concentrate was adjusted to pH 4.6, heated at 90 °C for 5 min, homogenized and freeze-dried. Set-type yogurts were prepared from skim milk standardized to 15% (w/v total solids and 4.2% (w/v protein using different levels of powdered skim milk or freeze-dried protein aggregate. The use of the protein aggregate significantly modified yogurt texture, but did not affect the water-holding capacity of the gel. Confocal laser-scanning microscope images showed the presence of large particles in milk enriched with protein aggregate, which directly affected the homogeneity of the clusters within the protein matrix. Thiol groups were freed during heating of the protein aggregate suspended in water, suggesting that the aggregates could interact with milk proteins during heating.

  16. Electrolyte transport in neutral polymer gels embedded with charged inclusions

    Science.gov (United States)

    Hill, Reghan

    2005-11-01

    Ion permeable membranes are the basis of a variety of molecular separation technologies, including ion exchange, gel electrophoresis and dialysis. This work presents a theoretical model of electrolyte transport in membranes comprised of a continuous polymer gel embedded with charged spherical inclusions, e.g., biological cells and synthetic colloids. The microstructure mimics immobilized cell cultures, where electric fields have been used to promote nutrient transport. Because several important characteristics can, in principle, be carefully controlled, the theory provides a quantitative framework to help tailor the bulk properties for enhanced molecular transport, microfluidic pumping, and physicochemical sensing applications. This talk focuses on the electroosmotic flow driven by weak electric fields and electrolyte concentration gradients. Also of importance is the influence of charge on the effective ion diffusion coefficients, bulk electrical conductivity, and membrane diffusion potential.

  17. Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription-PCR in temperature gradient gel electrophoresis fingerprints.

    Science.gov (United States)

    Felske, A; Akkermans, A D; De Vos, W M

    1998-11-01

    A novel approach was developed to quantify rRNA sequences in complex bacterial communities. The main bacterial 16S rRNAs in Drentse A grassland soils (The Netherlands) were amplified by reverse transcription (RT)-PCR with bacterium-specific primers and were separated by temperature gradient gel electrophoresis (TGGE). The primer pair used (primers U968-GC and L1401) was found to amplify with the same efficiency 16S rRNAs from bacterial cultures containing different taxa and cloned 16S ribosomal DNA amplicons from uncultured soil bacteria. The sequence-specific efficiency of amplification was determined by monitoring the amplification kinetics by kinetic PCR. The primer-specific amplification efficiency was assessed by competitive PCR and RT-PCR, and identical input amounts of different 16S rRNAs resulted in identical amplicon yields. The sequence-specific detection system used for competitive amplifications was TGGE, which also has been found to be suitable for simultaneous quantification of more than one sequence. We demonstrate that this approach can be applied to TGGE fingerprints of soil bacteria to estimate the ratios of the bacterial 16S rRNAs.

  18. Endometriosis and Type I Interferon & Characterization of a Mammalian Flippase

    DEFF Research Database (Denmark)

    Vestergaard, Anna Lindeløv

    2010-01-01

    endometriosis lesion. Human papillomavirus (HPV) is the causative agent of cervix cancer, and DNA viruses might play a role in endometriosis. DNA purified from tissue samples were subjected to highly sensitive PCR tests detecting HPV types, the herpes family viruses HSV-1 and -2, CMV, and EBV......, and ERa, when analyzed by bisulfate PCR and melting curve analysis. Also, no mutations of BRAF, HRAS, NRAS, CTNNB1, CDK4, FGFR3, PIK3CA, P53, and PTEN were detected by PCR denaturing gradient gel electrophoresis analysis. A well-known cancer-associated mutation in KRAS was detected in a single...

  19. Manipulation of the gut microbiota in C57BL/6 mice changes glucose tolerancewithout affecting weight development and gut mucosal immunity

    DEFF Research Database (Denmark)

    Bech-Nielsen, Gunilla Veslemöy; Hansen, Camilla Hartmann Friis; Hufeldt, Majbritt Ravn

    2012-01-01

    Inflammatory diseases such as type 2 diabetes (T2D) in humans and mice are under the influence of the composition of the gut microbiota (GM). It was previously demonstrated that treating Lepob mice with antibiotics improved glucose tolerance. However, wild type C57BL/6J mice may also exhibit plasma...... glucose tolerance without significantly affecting the weight or the number of gut mucosal regulatory T cells, tolerogenic dendritic cells or T helper cells type 1. 16S rRNA gene based denaturing gradient gel electrophoresis profiles clearly clustered according to treatment and showed that antibiotic...

  20. A viable electrode material for use in microbial fuel cells for tropical regions

    DEFF Research Database (Denmark)

    Offei, Felix; Thygesen, Anders; Mensah, Moses

    2016-01-01

    of this material is also targeted at introducing an inexpensive and durable electrode material, which can be produced in rural communities to improve the viability of MFCs. The maximum voltage and power density obtained (under 1000 Ω load) using an H-shaped MFC with AC as both anode and cathode electrode material...... was 0.66 V and 1.74 W/m3, respectively. The power generated by AC was as high as 86% of the value obtained with the extensively used carbon paper. Scanning electron microscopy and Denaturing Gradient Gel Electrophoresis (DGGE) analysis of AC anode biofilms confirmed that electrogenic bacteria were...

  1. Silica Sol-Gel Entrapment of the Enzyme Chloro peroxidase

    International Nuclear Information System (INIS)

    Le, T.; Chan, S.; Ebaid, B.; Sommerhalter, M.

    2015-01-01

    The enzyme chloro peroxidase (CPO) was immobilized in silica sol-gel beads prepared from tetramethoxysilane. The average pore diameter of the silica host structure (∼3 nm) was smaller than the globular CPO diameter (∼6 nm) and the enzyme remained entrapped after sol-gel maturation. The catalytic performance of the entrapped enzyme was assessed via the pyrogallol peroxidation reaction. Sol-gel beads loaded with 4 μg CPO per mL sol solution reached 9-12% relative activity compared to free CPO in solution. Enzyme kinetic analysis revealed a decrease in K_cat but no changes in K_M or K_I . Product release or enzyme damage might thus limit catalytic performance. Yet circular dichroism and visible absorption spectra of transparent CPO sol-gel sheets did not indicate enzyme damage. Activity decline due to methanol exposure was shown to be reversible in solution. To improve catalytic performance the sol-gel protocol was modified. The incorporation of 5, 20, or 40% methyltrimethoxysilane resulted in more brittle sol-gel beads but the catalytic performance increased to 14% relative to free CPO in solution. The use of more acidic casting buffers (ph 4.5 or 5.5 instead of 6.5) resulted in a more porous silica host reaching up to 18% relative activity

  2. Sol-gel synthesis of magnesium oxide-silicon dioxide glass compositions

    Science.gov (United States)

    Bansal, Narottam P.

    1988-01-01

    MgO-SiO2 glasses containing up to 15 mol pct MgO, which could not have been prepared by the conventional glass melting method due to the presence of stable liquid-liquid immiscibility, were synthesized by the sol-gel technique. Clear and transparent gels were obtained from the hydrolysis and polycondensation of silicon tetraethoxide (TEOS) and magnesium nitrate hexahydrate when the water/TEOS mole ratio was four or more. The gelling time decreased with increase in magnesium content, water/TEOS ratio, and reaction temperature. Magnesium nitrate hexahydrate crystallized out of the gels containing 15 and 20 mol pct MgO on slow drying. This problem was partially alleviated by drying the gels quickly at higher temperatures. Monolithic gel samples were prepared using glycerol as the drying control additive. The gels were subjected to various thermal treatments and characterized by several methods. No organic groups could be detected in the glasses after heat treatments to approx. 800 C, but trace amounts of hydroxyl groups were still present. No crystalline phase was found from X-ray diffraction in the gel samples to approx. 890 C. At higher temperatures, alpha quartz precipitated out as the crystalline phase in gels containing up to 10 mol pct MgO. The overall activation energy for gel formation in 10MgO-90SiO2 (mol pct) system for water/TEOS mole ratio of 7.5 was calculated to be 58.7 kJ/mol.

  3. Sustained subconjunctival protein delivery using a thermosetting gel delivery system.

    Science.gov (United States)

    Rieke, Erin R; Amaral, Juan; Becerra, S Patricia; Lutz, Robert J

    2010-02-01

    An effective treatment modality for posterior eye diseases would provide prolonged delivery of therapeutic agents, including macromolecules, to eye tissues using a safe and minimally invasive method. The goal of this study was to assess the ability of a thermosetting gel to deliver a fluorescently labeled protein, Alexa 647 ovalbumin, to the choroid and retina of rats following a single subconjunctival injection of the gel. Additional experiments were performed to compare in vitro to in vivo ovalbumin release rates from the gel. The ovalbumin content of the eye tissues was monitored by spectrophotometric assays of tissue extracts of Alexa 647 ovalbumin from dissected sclera, choroid, and retina at time points ranging from 2 h to 14 days. At the same time points, fluorescence microscopy images of tissue samples were also obtained. Measurement of intact ovalbumin was verified by LDS-PAGE analysis of the tissue extract solutions. In vitro release of Alexa 488 ovalbumin into 37 degrees C PBS solutions from ovalbumin-loaded gel pellets was also monitored over time by spectrophotometric assay. In vivo ovalbumin release rates were determined by measurement of residual ovalbumin extracted from gel pellets removed from rat eyes at various time intervals. Our results indicate that ovalbumin concentrations can be maintained at measurable levels in the sclera, choroid, and retina of rats for up to 14 days using the thermosetting gel delivery system. The concentration of ovalbumin exhibited a gradient that decreased from sclera to choroid and to retina. The in vitro release rate profiles were similar to the in vivo release profiles. Our findings suggest that the thermosetting gel system may be a feasible method for safe and convenient sustained delivery of proteins to choroidal and retinal tissue in the posterior segments of the eye.

  4. Identification of active methanotrophs in a landfill cover soil through detection of expression of 16S rRNA and functional genes.

    Science.gov (United States)

    Chen, Yin; Dumont, Marc G; Cébron, Aurélie; Murrell, J Colin

    2007-11-01

    Active methanotrophs in a landfill soil were revealed by detecting the 16S rRNA of methanotrophs and the mRNA transcripts of key genes involved in methane oxidation. New 16S rRNA primers targeting type I and type II methanotrophs were designed and optimized for analysis by denaturing gradient gel electrophoresis. Direct extraction of RNA from soil enabled the analysis of the expression of the functional genes: mmoX, pmoA and mxaF, which encode subunits of soluble methane monooxygenase, particulate methane monooxygenase and methanol dehydrogenase respectively. The 16S rRNA polymerase chain reaction (PCR) primers for type I methanotrophs detected Methylomonas, Methylosarcina and Methylobacter sequences from both soil DNA and cDNA which was generated from RNA extracted directly from the landfill cover soil. The 16S rRNA primers for type II methanotrophs detected primarily Methylocella and some Methylocystis 16S rRNA genes. Phylogenetic analysis of mRNA recovered from the soil indicated that Methylobacter, Methylosarcina, Methylomonas, Methylocystis and Methylocella were actively expressing genes involved in methane and methanol oxidation. Transcripts of pmoA but not mmoX were readily detected by reverse transcription polymerase chain reaction (RT-PCR), indicating that particulate methane monooxygenase may be largely responsible for methane oxidation in situ.

  5. Plant-fed versus chemicals-fed rhizobacteria of Lucerne: Plant-only teabags culture media not only increase culturability of rhizobacteria but also recover a previously uncultured Lysobacter sp., Novosphingobium sp. and Pedobacter sp.

    Science.gov (United States)

    Hegazi, Nabil A; Sarhan, Mohamed S; Fayez, Mohamed; Patz, Sascha; Murphy, Brian R; Ruppel, Silke

    2017-01-01

    In an effort to axenically culture the previously uncultivable populations of the rhizobacteria of Lucerne (Medicago sativa L.), we propose plant-only teabags culture media to mimic the nutritional matrix available in the rhizosphere. Here, we show that culture media prepared from Lucerne powder teabags substantially increased the cultivability of Lucerne rhizobacteria compared with a standard nutrient agar, where we found that the cultivable populations significantly increased by up to 60% of the total bacterial numbers as estimated by Quantitative Real-time Polymerase Chain Reaction (qRT-PCR). Cluster analysis of 16S rDNA Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) of cultivable Colony-Forming Units (CFUs) revealed a more distinct composition and separation of bacterial populations recovered on the plant-only teabags culture media than those developed on a standard nutrient agar. Further, the new plant medium gave preference to the micro-symbiont Sinorhizobium meliloti, and succeeded in isolating a number of not-yet-cultured bacteria, most closely matched to Novosphingobium sp., Lysobacter sp. and Pedobacter sp. The present study may encourage other researchers to consider moving from the well-established standard culture media to the challenging new plant-only culture media. Such a move may reveal previously hidden members of rhizobacteria, and help to further explore their potential environmental impacts.

  6. A new sol–gel synthesis of 45S5 bioactive glass using an organic acid as catalyst

    Energy Technology Data Exchange (ETDEWEB)

    Faure, J., E-mail: joel.faure@univ-reims.fr [Université de Reims Champagne-Ardenne, Laboratoire Ingénierie et Sciences des Matériaux, LISM EA 4695, 21 rue Clément ADER, 51685 REIMS Cedex 2 (France); Drevet, R., E-mail: richard.drevet@univ-reims.fr [Université de Reims Champagne-Ardenne, Laboratoire Ingénierie et Sciences des Matériaux, LISM EA 4695, 21 rue Clément ADER, 51685 REIMS Cedex 2 (France); Lemelle, A.; Ben Jaber, N.; Tara, A. [Université de Reims Champagne-Ardenne, Laboratoire Ingénierie et Sciences des Matériaux, LISM EA 4695, 21 rue Clément ADER, 51685 REIMS Cedex 2 (France); El Btaouri, H. [Université de Reims Champagne-Ardenne UMR CNRS MEDyC, EA 7369, Campus Moulin de la Housse, 51687 REIMS Cedex 2 (France); Benhayoune, H. [Université de Reims Champagne-Ardenne, Laboratoire Ingénierie et Sciences des Matériaux, LISM EA 4695, 21 rue Clément ADER, 51685 REIMS Cedex 2 (France)

    2015-02-01

    In this paper a new sol–gel approach was explored for the synthesis of the 45S5 bioactive glass. We demonstrate that citric acid can be used instead of the usual nitric acid to catalyze the sol–gel reactions. The substitution of nitric acid by citric acid allows to reduce strongly the concentration of the acid solution necessary to catalyze the hydrolysis of silicon and phosphorus alkoxides. Two sol–gel powders with chemical compositions very close to that of the 45S5 were obtained by using either a 2 M nitric acid solution or either a 5 mM citric acid solution. These powders were characterized and compared to the commercial Bioglass®. The surface properties of the two bioglass powders were assessed by scanning electron microscopy (SEM) and by Brunauer–Emmett–Teller method (BET). The Fourier transformed infrared spectroscopy (FTIR) and the X-ray diffraction (XRD) revealed a partial crystallization associated to the formation of crystalline phases on the two sol–gel powders. The in vitro bioactivity was then studied at the key times during the first hours of immersion into acellular Simulated Body Fluid (SBF). After 4 h immersion into SBF we clearly demonstrate that the bioactivity level of the two sol–gel powders is similar and much higher than that of the commercial Bioglass®. This bioactivity improvement is associated to the increase of the porosity and the specific surface area of the powders synthesized by the sol–gel process. Moreover, the nitric acid is efficiently substituted by the citric acid to catalyze the sol–gel reactions without alteration of the bioactivity of the 45S5 bioactive glass. - Highlights: • Citric acid is employed as a catalyzer of the sol–gel process. • This catalyzer is used at a very low concentration for the hydrolysis reaction. • The chemical composition of the bioglass synthesized by the sol–gel process is optimized. • The properties of two sol–gel bioglasses are compared with those of the commercial

  7. A new sol–gel synthesis of 45S5 bioactive glass using an organic acid as catalyst

    International Nuclear Information System (INIS)

    Faure, J.; Drevet, R.; Lemelle, A.; Ben Jaber, N.; Tara, A.; El Btaouri, H.; Benhayoune, H.

    2015-01-01

    In this paper a new sol–gel approach was explored for the synthesis of the 45S5 bioactive glass. We demonstrate that citric acid can be used instead of the usual nitric acid to catalyze the sol–gel reactions. The substitution of nitric acid by citric acid allows to reduce strongly the concentration of the acid solution necessary to catalyze the hydrolysis of silicon and phosphorus alkoxides. Two sol–gel powders with chemical compositions very close to that of the 45S5 were obtained by using either a 2 M nitric acid solution or either a 5 mM citric acid solution. These powders were characterized and compared to the commercial Bioglass®. The surface properties of the two bioglass powders were assessed by scanning electron microscopy (SEM) and by Brunauer–Emmett–Teller method (BET). The Fourier transformed infrared spectroscopy (FTIR) and the X-ray diffraction (XRD) revealed a partial crystallization associated to the formation of crystalline phases on the two sol–gel powders. The in vitro bioactivity was then studied at the key times during the first hours of immersion into acellular Simulated Body Fluid (SBF). After 4 h immersion into SBF we clearly demonstrate that the bioactivity level of the two sol–gel powders is similar and much higher than that of the commercial Bioglass®. This bioactivity improvement is associated to the increase of the porosity and the specific surface area of the powders synthesized by the sol–gel process. Moreover, the nitric acid is efficiently substituted by the citric acid to catalyze the sol–gel reactions without alteration of the bioactivity of the 45S5 bioactive glass. - Highlights: • Citric acid is employed as a catalyzer of the sol–gel process. • This catalyzer is used at a very low concentration for the hydrolysis reaction. • The chemical composition of the bioglass synthesized by the sol–gel process is optimized. • The properties of two sol–gel bioglasses are compared with those of the commercial

  8. Reversible thermal denaturation of immobilized rhodanese

    International Nuclear Information System (INIS)

    Horowitz, P.; Bowman, S.

    1987-01-01

    For the first time, the enzyme rhodanese had been refolded after thermal denaturation. This was previously not possible because of the strong tendency for the soluble enzyme to aggregate at temperatures above 37 degrees C. The present work used rhodanese that was covalently coupled to a solid support under conditions that were found to preserve enzyme activity. Rhodanese was immobilized using an N-hydroxymalonimidyl derivative of Sepharose containing a 6-carbon spacer. The number of immobilized competent active sites was measured by using [ 35 S]SO 3 (2-) to form an active site persulfide that is the obligatory catalytic intermediate. Soluble enzyme was irreversibly inactivated in 10 min at 52 degrees C. The immobilized enzyme regained at least 30% of its original activity even after boiling for 20 min. The immobilized enzyme had a Km and Vmax that were each approximately 3 times higher than the corresponding values for the native enzyme. After preincubation at high temperatures, progress curves for the immobilized enzyme showed induction periods of up to 5 min before attaining apparently linear steady states. The pH dependence of the activity was the same for both the soluble and the immobilized enzyme. These results indicate significant stabilization of rhodanese after immobilization, and instabilities caused by adventitious solution components are not the sole reasons for irreversibility of thermal denaturation seen with the soluble enzyme. The results are consistent with models for rhodanese that invoke protein association as a major cause of inactivation of the enzyme. Furthermore, the induction period in the progress curves is consistent with studies which show that rhodanese refolding proceeds through intermediate states

  9. Whey protein isolate modified by transglutaminase aggregation and emulsion gel properties

    Science.gov (United States)

    Qi, Weiwei; Chen, Chong; Liu, Mujun; Yu, Guoping; Cai, Xinghang; Guo, Peipei; Yao, Yuxiu; Mei, Sijie

    2015-07-01

    Whey protein isolate and commercial soybean salad oil were used to produce the WPI emulsion dispersions. The properties of TG-catalyzed emulsion gelation produced from WPI emulsion dispersions were investigated by the amount of TG, temperature, pH and reaction time. Specifically, the texture properties (hardness and springiness), water-holding capacity and rheological properties (G' and G") were assessed. The result of Orthogonal tests showed WPI emulsion can form better hardness and springiness gel when the ratio of TG and WPI was 20U/g, pH 7.5, treatment temperature and time were 50°C and 3 h, respectively. The microstructure of TG emulsion gels was more compact, gel pore is smaller, distribution more uniform, the oil droplets size smaller compared with untreated emulsion gels. Compared to the control of rheological properties, G' and G" were significantly increased and G' > G", results showed that the gel was solid state, and TG speeded up the process of gelation.

  10. Sequential Events in the Irreversible Thermal Denaturation of Human Brain-Type Creatine Kinase by Spectroscopic Methods

    Directory of Open Access Journals (Sweden)

    Yan-Song Gao

    2010-06-01

    Full Text Available The non-cooperative or sequential events which occur during protein thermal denaturation are closely correlated with protein folding, stability, and physiological functions. In this research, the sequential events of human brain-type creatine kinase (hBBCK thermal denaturation were studied by differential scanning calorimetry (DSC, CD, and intrinsic fluorescence spectroscopy. DSC experiments revealed that the thermal denaturation of hBBCK was calorimetrically irreversible. The existence of several endothermic peaks suggested that the denaturation involved stepwise conformational changes, which were further verified by the discrepancy in the transition curves obtained from various spectroscopic probes. During heating, the disruption of the active site structure occurred prior to the secondary and tertiary structural changes. The thermal unfolding and aggregation of hBBCK was found to occur through sequential events. This is quite different from that of muscle-type CK (MMCK. The results herein suggest that BBCK and MMCK undergo quite dissimilar thermal unfolding pathways, although they are highly conserved in the primary and tertiary structures. A minor difference in structure might endow the isoenzymes dissimilar local stabilities in structure, which further contribute to isoenzyme-specific thermal stabilities.

  11. How do monomeric components of a polymer gel dosimeter respond to ionising radiation: A steady-state radiolysis towards preparation of a 3D polymer gel dosimeter

    International Nuclear Information System (INIS)

    Kozicki, Marek

    2011-01-01

    Ionising radiation-induced reactions of aqueous single monomer solutions and mixtures of poly(ethylene glycol) diacrylate (PEGDA) and N,N'-methylenebisacrylamide (Bis) in a steady-state condition are presented below and above gelation doses in order to highlight reactions in irradiated 3D polymer gel dosimeters, which are assigned for radiotherapy dosimetry. Both monomers are shown to undergo radical polymerisation and cross-linking, which result in the measured increase in molecular weight and radius of gyration of the formed polydisperse polymer coils. The formation of nanogels was also observed for Bis solutions at a low concentration. In the case of PEGDA-Bis mixtures, co-polymerisation is suggested as well. At a sufficiently high radiation dose, the formation of a polymer network was observed for both monomers and their mixture. For this reason a sol-gel analysis for PEGDA and Bis was performed gravimetrically and a proposition of an alternative to this method employing a nuclear magnetic resonance technique is made. The two monomers were used for preparation of 3D polymer gel dosimeters having the acronyms PABIG and PABIG nx . The latter is presented for the first time in this work and is a type of the formerly established PABIG polymer gel dosimeter. The elementary characteristics of the new composition are presented, underlining the ease of its preparation, low dose threshold, and slightly increased sensitivity but lower quasi-linear range of dose response in comparison to PABIG. - Highlights: → Steady-state radiolysis of Bis, PEGDA and Bis-PEGDA is examined. → High Mw products are formed at low absorbed doses. → Formation of Bis nanogels is likely; PEGDA solutions form hydrogels. → NMR technique can be used for sol-gel analysis. → Features of 3D polymer gel dosimeters made from PEGDA and Bis are shown.

  12. Hemichrome formation during hemoglobin Zurich denaturation

    International Nuclear Information System (INIS)

    Zago, M.A.; Costa, F.F.; Botura, C.; Baffa, O.

    1988-01-01

    Electron paramagnetic resonance (EPR)spectrum of hemoglobin Zurich, after oxidation, storage and heating, showed several absorption derives in the high field region (g ≅ 2) which are indicative of hemichrome formation. Characteristic visible spectra of hemichromes were observed for oxidized Hb Zurich and for its spontaneous precipitate. The proportional increase of EPR signals at g ≅ 2 and decrease at g = 6.37, the constant ratio of absorbance at 540 nm to 280 nm during heating, and the similarity of this ratio for spontaneously precipitated HbA and for Hb Zurich indicate that heme is not lost during the first steps of Hb Zurich denaturation. (author) [pt

  13. The characterisation of a genipin-gelatin gel dosimeter

    International Nuclear Information System (INIS)

    Davies, J B; Bosi, S; Baldock, C

    2010-01-01

    Genipin cross links gelatin to slowly form a blue colour that bleaches upon irradiation. Spectrophotometric measurements of the absorbance change following irradiation to doses up to 100 Gy gives a linear dose response for certain concentrations of the gel ingredients; genipin, gelatin and sulphuric acid. Dose sensitivity increases with increasing concentrations of sulphuric acid and genipin and is also strongly dependent on the time allowed for the genipin-gelatin cross linking reaction (referred to here as blending) to take place. The optimum formulation of this gel was found for genipin concentration between 0.3 - 0.5 mM and blending time of at least 4 h.

  14. Chemical denaturation of globular proteins at the air/water interface: an x-ray and neutron reflectometry study

    International Nuclear Information System (INIS)

    Perriman, A.W.; Henderson, M.J.; White, J.W.

    2003-01-01

    Full text: X-ray and neutron reflectometry has been used to probe the equilibrium surface structure of hen egg white lysozyme (lysozyme) and bovine β -lactoglobulin (β -lactoglobulin) under denaturing conditions at the air-water interface. This was achieved by performing experiments on 10 mg mL -1 protein solutions containing increasing concentrations of the chemical denaturant guanidinium hydrochloride (G.HCl). For solutions containing no G.HCl, the surface structure of the proteins was represented by a two-layer model with total thicknesses of 48 Angstroms and 38 Angstroms for lysozyme and β -lactoglobulin, respectively. The total volume of a single protein molecule and the associated water molecules was evaluated to be approximately 45 (0.3) nm 3 for lysozyme, and 60 (0.3) nm 3 for β-lactoglobulin. The thickness dimensions and the total volumes compared favourably with the crystal dimensions of 45 x 30 x 30 Angstroms (40.5 nm 3 ),1 and 36 x 36 x 36 Angstroms (47 nm 3 ) 2 for lysozyme and β -lactoglobulin, respectively. This comparison suggests that when no denaturant was present, the structures of lysozyme and β -lactoglobulin were near to their native conformations at the air-water interface. The response to the presence of the chemical denaturant was different for each protein. The surface layer of β-lactoglobulin expanded at very low concentrations (0.2 mol dm -3 ) of G.HCl. In contrast, the lysozyme layer contracted. At higher concentrations, unfolding of both the proteins led to the formation of a third diffuse layer. In general, lysozyme appeared to be less responsive to the chemical denaturant, which is most likely a result of the higher disulfide content of lysozyme. A protocol allowing quantitative thermodynamic analysis of the contribution from the air-water interface to the chemical denaturation of a protein was developed

  15. Effect of DCCA on synthesis of inorganic mesoporous gels

    International Nuclear Information System (INIS)

    Nemancha, A.R.

    2004-01-01

    Full text.The porous texture of the monolith inorganic gels plays an important role in the utilization of porous material by control of several properties such as gas diffusion, thermal stability, mechanical strength. the sol gel process provides many possibilities to manufacture porous material with extremely low concentration of impurities at low sinter temperature. The serious problem in the production of the monolith gels is fracture and crack formation which may occur in the conversion of the wet gels to dry gels. This phenomenon is probably due to the capillary forces which appear during the drying steps. in order to reduce the effect of capillary forces a number of methods were applied (hyper critic drying, organic DCCAs). The purpose of the present work, is to understand the chemical changes that result from adding formamide as drying control chemical additives DCCA to the colloidal silica sols in the presence of acid catalyst. Fourier Transformed Infrared spectroscopy and Raman spectroscopy were used to investigate the influence of formamide on gel formation. The Nitrogen adsorption-desorption technique is used to investigate the effect of formamide on gel texture. The results show that the gels with formamide are monolith and obtained during a short time of gelling reaction, the silica particles link formation depend strongly on the formamide concentration. the BET and BJH results show that the presence of formamide promotes the creation of meso porous texture depending on formamide/silica molar ratio in the starting sol. The maximum average diameter of the obtained gel reaches a value close to 25 nm with a bulk density equal to 1.1 g/cm 3

  16. A colourimetric method for the determination of the degree of chemical cross-linking in aspartic acid-based polymer gels

    Directory of Open Access Journals (Sweden)

    B. Gyarmati

    2015-02-01

    Full Text Available A 2,4,6-trinitrobenzenesulphonic acid (TNBS-based assay is developed to determine the degree of chemical cross-linking in aspartic acid-based polymer gels. The conventional colourimetric method for the quantitative determination of amine groups is difficult to use in polymer networks; thus, an improved method is developed to analyse polymer gels swollen in dimethyl sulfoxide (DMSO. Reaction products of the derivatizing reaction are examined by NMR. The chemical stability of the reagent is increased in DMSO, and the method shows satisfactory linearity and accuracy. The degree of chemical cross-linking in the investigated gels is close to its theoretical maximum, but the conversion of the pendant amine groups to cross-linking points is strongly dependent on the feed composition of the gels.

  17. Transdermal delivery of paeonol using cubic gel and microemulsion gel

    Science.gov (United States)

    Luo, Maofu; Shen, Qi; Chen, Jinjin

    2011-01-01

    Background The aim of this study was to develop new systems for transdermal delivery of paeonol, in particular microemulsion gel and cubic gel formulations. Methods Various microemulsion vehicles were prepared using isopropyl myristate as an oil phase, polyoxyethylated castor oil (Cremophor® EL) as a surfactant, and polyethylene glycol 400 as a cosurfactant. In the optimum microemulsion gel formulation, carbomer 940 was selected as the gel matrix, and consisted of 1% paeonol, 4% isopropyl myristate, 28% Cremophor EL/polyethylene glycol 400 (1:1), and 67% water. The cubic gel was prepared containing 3% paeonol, 30% water, and 67% glyceryl monooleate. Results A skin permeability test using excised rat skins indicated that both the cubic gel and microemulsion gel formulations had higher permeability than did the paeonol solution. An in vivo pharmacokinetic study done in rats showed that the relative bioavailability of the cubic gel and microemulsion gel was enhanced by about 1.51-fold and 1.28-fold, respectively, compared with orally administered paeonol suspension. Conclusion Both the cubic gel and microemulsion gel formulations are promising delivery systems to enhance the skin permeability of paeonol, in particular the cubic gel. PMID:21904450

  18. Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA

    International Nuclear Information System (INIS)

    Fye, R.M.; Benham, C.J.

    1999-01-01

    Local denaturation, the separation at specific sites of the two strands comprising the DNA double helix, is one of the most fundamental processes in biology, required to allow the base sequence to be read both in DNA transcription and in replication. In living organisms this process can be mediated by enzymes which regulate the amount of superhelical stress imposed on the DNA. We present a numerically exact technique for analyzing a model of denaturation in superhelically stressed DNA. This approach is capable of predicting the locations and extents of transition in circular superhelical DNA molecules of kilobase lengths and specified base pair sequences. It can also be used for closed loops of DNA which are typically found in vivo to be kilobases long. The analytic method consists of an integration over the DNA twist degrees of freedom followed by the introduction of auxiliary variables to decouple the remaining degrees of freedom, which allows the use of the transfer matrix method. The algorithm implementing our technique requires O(N 2 ) operations and O(N) memory to analyze a DNA domain containing N base pairs. However, to analyze kilobase length DNA molecules it must be implemented in high precision floating point arithmetic. An accelerated algorithm is constructed by imposing an upper bound M on the number of base pairs that can simultaneously denature in a state. This accelerated algorithm requires O(MN) operations, and has an analytically bounded error. Sample calculations show that it achieves high accuracy (greater than 15 decimal digits) with relatively small values of M (M<0.05N) for kilobase length molecules under physiologically relevant conditions. Calculations are performed on the superhelical pBR322 DNA sequence to test the accuracy of the method. With no free parameters in the model, the locations and extents of local denaturation predicted by this analysis are in quantitatively precise agreement with in vitro experimental measurements

  19. Zr alkoxide chain effect on the sol-gel synthesis of lithium metazirconate

    International Nuclear Information System (INIS)

    Pfeiffer, Heriberto; Bosch, Pedro; Bulbulian, Silvia

    2003-01-01

    Lithium metazirconate (Li 2 ZrO 3 ) was synthesized by the sol-gel method, using four different Zr alkoxides: zirconium ethoxide, zirconium iso-propoxide, zirconium propoxide and zirconium butoxide. The syntheses were made under two different catalytic regimes, acid and basic. The resulting powders were mixtures of Li 2 ZrO 3 and ZrO 2 . The best yield of Li 2 ZrO 3 (100%) was obtained when the sol-gel reaction was developed with lithium methoxide and zirconium ethoxide under acid catalysis regime. This study establishes that, for base-catalyzed reactions the ZrO 2 formation decreases when the alkyl-chain increases in the alkoxides. By contrast, for acid-catalyzed reactions the ZrO 2 formation increases as the alkyl-chain increases. Finally, when Zr propoxide and Zr iso-propoxide were used, the Li 2 ZrO 3 amounts were different due to steric effects

  20. pH dependence of cyanide binding to the ferric heme domain of the direct oxygen sensor from Escherichia coli and the effect of alkaline denaturation.

    Science.gov (United States)

    Bidwai, Anil K; Ok, Esther Y; Erman, James E

    2008-09-30

    The spectrum of the ferric heme domain of the direct oxygen sensor protein from Escherichia coli ( EcDosH) has been measured between pH 3.0 and 12.6. EcDosH undergoes acid denaturation with an apparent p K a of 4.24 +/- 0.05 and a Hill coefficient of 3.1 +/- 0.6 and reversible alkaline denaturation with a p K a of 9.86 +/- 0.04 and a Hill coefficient of 1.1 +/- 0.1. Cyanide binding to EcDosH has been investigated between pH 4 and 11. The EcDosH-cyanide complex is most stable at pH 9 with a K D of 0.29 +/- 0.06 microM. The kinetics of cyanide binding are monophasic between pH 4 and 8. At pH >or=8.5, the reaction is biphasic with the fast phase dependent upon the cyanide concentration and the slow phase independent of cyanide. The slow phase is attributed to conversion of denatured EcDosH to the native state, with a pH-independent rate of 0.052 +/- 0.006 s (-1). The apparent association rate constant for cyanide binding to EcDosH increases from 3.6 +/- 0.1 M (-1) s (-1) at pH 4 to 520 +/- 20 M (-1) s (-1) at pH 11. The dissociation rate constant averages (8.6 +/- 1.3) x 10 (-5) s (-1) between pH 5 and 9, increasing to (1.4 +/- 0.1) x 10 (-3) s (-1) at pH 4 and (2.5 +/- 0.1) x 10 (-3) s (-1) at pH 12.2. The mechanism of cyanide binding is consistent with preferential binding of the cyanide anion to native EcDosH. The reactions of imidazole and H 2O 2 with ferric EcDosH were also investigated and show little reactivity.

  1. Two-dimensional salt and temperature DNA denaturation analysis using a magnetoresistive sensor

    DEFF Research Database (Denmark)

    Rizzi, Giovanni; Dufva, Martin; Hansen, Mikkel Fougt

    2017-01-01

    We present a microfluidic system and its use to measure DNA denaturation curves by varying the temperature or salt (Na+) concentration. The readout is based on real-time measurements of DNA hybridization using magnetoresistive sensors and magnetic nanoparticles (MNPs) as labels. We report the first...... melting curves of DNA hybrids measured as a function of continuously decreasing salt concentration at fixed temperature and compare them to the corresponding curves obtained vs. temperature at fixed salt concentration. The magnetoresistive sensor platform provided reliable results under varying....... The results demonstrate that concentration melting provides an attractive alternative to temperature melting in on-chip DNA denaturation experiments and further show that the magnetoresistive platform is attractive due to its low cross-sensitivity to temperature and liquid composition....

  2. A comprehensive collection of experimentally validated primers for Polymerase Chain Reaction quantitation of murine transcript abundance

    Directory of Open Access Journals (Sweden)

    Wang Xiaowei

    2008-12-01

    Full Text Available Abstract Background Quantitative polymerase chain reaction (QPCR is a widely applied analytical method for the accurate determination of transcript abundance. Primers for QPCR have been designed on a genomic scale but non-specific amplification of non-target genes has frequently been a problem. Although several online databases have been created for the storage and retrieval of experimentally validated primers, only a few thousand primer pairs are currently present in existing databases and the primers are not designed for use under a common PCR thermal profile. Results We previously reported the implementation of an algorithm to predict PCR primers for most known human and mouse genes. We now report the use of that resource to identify 17483 pairs of primers that have been experimentally verified to amplify unique sequences corresponding to distinct murine transcripts. The primer pairs have been validated by gel electrophoresis, DNA sequence analysis and thermal denaturation profile. In addition to the validation studies, we have determined the uniformity of amplification using the primers and the technical reproducibility of the QPCR reaction using the popular and inexpensive SYBR Green I detection method. Conclusion We have identified an experimentally validated collection of murine primer pairs for PCR and QPCR which can be used under a common PCR thermal profile, allowing the evaluation of transcript abundance of a large number of genes in parallel. This feature is increasingly attractive for confirming and/or making more precise data trends observed from experiments performed with DNA microarrays.

  3. Two-dimensional polyacrylamide gel analysis of Plodia interpunctella granulosis virus

    International Nuclear Information System (INIS)

    Russell, D.L.; Consigli, R.A.

    1986-01-01

    The structural polypeptides of purified Plodia interpunctella granulosis virus were analyzed by three different two-dimensional gel systems. Isoelectric focusing followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed resolution of 53 acidic polypeptides in the enveloped nucleocapsid of the virus ranging in molecular weight from 97,300 to 8000. Nine of these polypeptides were shown to be glycoproteins by the technique of radiolabeled lectin blotting. Separation of the granulin in this system allowed resolution of five species, all of which have identical tryptic peptide maps. This matrix protein was demonstrated to be a phosphoglycoprotein by radiolabeled lectin blotting and acid phosphatase dephosphorylation. Nonequilibrium pH gel electrophoresis followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed resolution of the major basic protein of the virus, VP12, from a more acidic protein of the same molecular weight. Tryptic peptide analysis demonstrated that these two proteins were indeed different and acid urea gels followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed localization of the acidic protein to the envelope and the basic protein to the nucleocapsid of the virus. Finally, probing of the separated envelope nucleocapsid proteins in both the isoelectric focusing and nonequilibrium pH gel electrophoresis two-dimensional systems after transfer to nitrocellulose with iodinated, purified viral proteins allowed further insight into reactions which may be important in the maintenance of the virion structure

  4. User`s guide and documentation manual for ``PC-Gel`` simulator

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Ming-Ming; Gao, Hong W.

    1993-10-01

    PC-GEL is a three-dimensional, three-phase (oil, water, and gas) permeability modification simulator developed by incorporating an in-situ gelation model into a black oil simulator (BOAST) for personal computer application. The features included in the simulator are: transport of each chemical species of the polymer/crosslinker system in porous media, gelation reaction kinetics of the polymer with crosslinking agents, rheology of the polymer and gel, inaccessible pore volume to macromolecules, adsorption of chemical species on rock surfaces, retention of gel on the rock matrix, and permeability reduction caused by the adsorption of polymer and gel. The in-situ gelation model and simulator were validated against data reported in the literature. The simulator PC-GEL is useful for simulating and optimizing any combination of primary production, waterflooding, polymer flooding, and permeability modification treatments. A general background of permeability modification using crosslinked polymer gels is given in Section I and the governing equations, mechanisms, and numerical solutions of PC-GEL are given in Section II. Steps for preparing an input data file with reservoir and gel-chemical transport data, and recurrent data are described in Sections III and IV, respectively. Example data inputs are enclosed after explanations of each input line to help the user prepare data files. Major items of the output files are reviewed in Section V. Finally, three sample problems for running PC-GEL are described in Section VI, and input files and part of the output files of these problems are listed in the appendices. For the user`s reference a copy of the source code of PC-GEL computer program is attached in Appendix A.

  5. Topical Niosome Gel of Zingiber cassumunar Roxb. Extract for Anti-inflammatory Activity Enhanced Skin Permeation and Stability of Compound D.

    Science.gov (United States)

    Priprem, Aroonsri; Janpim, Khwanhatai; Nualkaew, Somsak; Mahakunakorn, Pramote

    2016-06-01

    An extract of Zingiber cassumunar Roxb. (ZC) was encapsulated in niosomes of which a topical gel was formed. (E)-4-(3',4'-dimethoxyphenyl)but-3-en-1-ol or compound D detected by a gradient HPLC was employed as the marker and its degradation determined to follow zero-order kinetics. Niosomes significantly retarded thermal-accelerated decomposition of compound D in the gel (p D. Niosomes enhanced in vitro permeation rate of compound D from the gel. Topical applications of ZC noisome gel gave a faster change in tail flick latency than piroxicam gel and hydrocortisone cream (p anti-inflammatory activity up to 6 h using croton oil-induced ear edema model in mice (p > 0.05). Thus, encapsulation of ZC extract in niosomes enhanced chemical stability and skin permeation with comparable topical anti-inflammatory effects to steroid and NSAID.

  6. Ultrapure glass optical waveguide development in microgravity by the sol-gel process

    Science.gov (United States)

    1982-01-01

    Containerless melting of glasses in space for the preparation of ultrapure homogeneous glass for optical waveguides is discussed. The homogenization of the glass using conventional raw materials is normally achieved on Earth either by the gravity induced convection currents or by the mechanical stirring of the melt. Because of the absence of gravity induced convection currents, the homogenization of glass using convectional raw materials is difficult in the space environment. Multicomponent, homogeneous, noncrystalline oxide gels can be prepared by the sol-gel process and these gels are promising starting materials for melting glasses in the space environment. The sol-gel process is based on the polymerization reaction of alkoxysilane with other metal alkoxy compounds or suitable metal salts. Many of the alkoxysilanes or other metal alkoxides are liquids and thus can be purified by distillation.

  7. Intrinsic alterations in the partial molar volume on the protein denaturation: surficial Kirkwood-Buff approach.

    Science.gov (United States)

    Yu, Isseki; Takayanagi, Masayoshi; Nagaoka, Masataka

    2009-03-19

    The partial molar volume (PMV) of the protein chymotrypsin inhibitor 2 (CI2) was calculated by all-atom MD simulation. Denatured CI2 showed almost the same average PMV value as that of native CI2. This is consistent with the phenomenological question of the protein volume paradox. Furthermore, using the surficial Kirkwood-Buff approach, spatial distributions of PMV were analyzed as a function of the distance from the CI2 surface. The profiles of the new R-dependent PMV indicate that, in denatured CI2, the reduction in the solvent electrostatic interaction volume is canceled out mainly by an increment in thermal volume in the vicinity of its surface. In addition, the PMV of the denatured CI2 was found to increase in the region in which the number density of water atoms is minimum. These results provide a direct and detailed picture of the mechanism of the protein volume paradox suggested by Chalikian et al.

  8. Polymer gel dosimetry for synchrotron stereotactic radiotherapy and iodine dose-enhancement measurements

    International Nuclear Information System (INIS)

    Boudou, C; Tropres, I; Rousseau, J; Lamalle, L; Adam, J F; Esteve, F; Elleaume, H

    2007-01-01

    Synchrotron stereotactic radiotherapy (SSR) is a radiotherapy technique that makes use of the interactions of monochromatic low energy x-rays with high atomic number (Z) elements. An important dose-enhancement can be obtained if the target volume has been loaded with a sufficient amount of a high-Z element, such as iodine. In this study, we compare experimental dose measurements, obtained with normoxic polymer gel (nPAG), with Monte Carlo computations. Gels were irradiated within an anthropomorphic head phantom and were read out by magnetic resonance imaging. The dose-enhancement due to the presence of iodine in the gel (iodine concentration: 5 and 10 mg ml -1 ) was measured at two radiation energies (35 and 80 keV) and was compared to the calculated factors. nPAG dosimetry was shown to be efficient for measuring the sharp dose gradients produced by SSR. The agreement between 3D gel dosimetry and calculated dose distributions was found to be within 4% of the dose difference criterion and a distance to agreement of 2.1 mm for 80% of the voxels. Polymer gel doped with iodine exhibited higher sensitivity, in good agreement with the calculated iodine-dose enhancement. We demonstrate in this preliminary study that iodine-doped nPAG could be used for measuring in situ dose distributions for iodine-enhanced SSR treatment

  9. Analysis of the response of PVA-GTA Fricke-gel dosimeters with clinical magnetic resonance imaging

    Science.gov (United States)

    Collura, Giorgio; Gallo, Salvatore; Tranchina, Luigi; Abbate, Boris Federico; Bartolotta, Antonio; d'Errico, Francesco; Marrale, Maurizio

    2018-01-01

    Fricke gel dosimeters produced with a matrix of Poly-vinyl alcohol (PVA) cross-linked with glutaraldehyde (GTA) were analyzed with magnetic resonance imaging (MRI). Previous studies based on spectrophotometry showed valuable dosimetric features of these gels in terms of X-ray sensitivity and diffusion of the ferric ions produced after irradiation. In this study, MRI was performed on the gels at 1.5 T with a clinical scanner in order to optimize the acquisition parameters and obtain high contrast between irradiated and non-irradiated samples. The PVA gels were found to offer good linearity in the range of 0-10 Gy and a stable signal for several hours after irradiation. The sensitivity was about 40% higher compared to gels produced with agarose as gelling agent. The effect of xylenol orange (XO) on the MRI signal was also investigated: gel dosimeters made without XO show higher sensitivity to x-rays than those made with XO. The dosimetric accuracy of the 3D gels was investigated by comparing their MRI response to percentage depth dose and transversal dose profile measurements made with an ionization chamber in a water phantom. The comparison of PVA-GTA gels with and without XO showed that the chelating agent reduces the MRI sensitivity of the gels. Depth-dose and transversal dose profiles acquired by PVA-GTA gels without XO are more accurate and consistent with the ionization chamber data. However, diffusion effects hinder accurate measurements in the steep dose gradient regions and they should be further reduced by modifying the gel matrix and/or by minimizing the delay between irradiation and imaging.

  10. Co3O4/TiO2 films obtained by laser ablation and sol-gel for the reaction of oxygen liberation in alkaline medium

    International Nuclear Information System (INIS)

    Perez A, J.; Fernandez V, S. M.; Escobar A, L.; Jimenez B, J.

    2008-01-01

    The laser ablation technique known as Pulsed Laser Deposition (PLD) is used for obtaining thin films of TiO 2 /SnO 2 , which was later modified with Co 3 O 4 by PLD or by sol-gel technique. The films were characterized by X-ray diffraction, ultraviolet Vis and Raman spectroscopies, scanning electron microscopy and energy analysis of the dispersed X-rays produced by Auger decay. The anatase phase with particles of nano metric size was obtained by depositing the titanium dioxide in argon atmosphere. The Co 3 O 4 films obtained by PLD on the TiO 2 showed the same morphology. The electrocatalytic activity of the films that were used as photo anodes for the reaction of oxygen liberation was carried out in the darkness, with environment light and the light emitted by a xenon lamp. The current density was higher for films of Co 3 O 4 /TiO 2 /SnO 2 obtained by PLD that for cobalt dioxide of mixed valence obtained by sol-gel. (Author)

  11. Dynamic covalent gels assembled from small molecules:from discrete gelators to dynamic covalent polymers

    Institute of Scientific and Technical Information of China (English)

    Jian-Yong Zhang; Li-Hua Zeng; Juan Feng

    2017-01-01

    Dynamic covalent chemistry has emerged recently to be a powerful tool to construct functional materials.This article reviews the progress in the research and development of dynamic covalent chemistry in gels assembled from small molecules.First dynamic covalent reactions used in gels are reviewed to understand the dynamic covalent bonding.Afterwards the catalogues of dynamic covalent gels are reviewed according to the nature of gelators and the interactions between gelators.Dynamic covalent bonding can be involved to form low molecular weight gelators.Low molecular weight molecules with multiple functional groups react to form dynamic covalent cross-linked polymers and act as gelators.Two catalogues of gels show different properties arising from their different structures.This review aims to illustrate the structure-property relationships of these dynamic covalent gels.

  12. Pressure-assisted cold denaturation of hen egg white lysozyme: the influence of co-solvents probed by hydrogen exchange nuclear magnetic resonance.

    Science.gov (United States)

    Vogtt, K; Winter, R

    2005-08-01

    COSY proton nuclear magnetic resonance was used to measure the exchange rates of amide protons of hen egg white lysozyme (HEWL) in the pressure-assisted cold-denatured state and in the heat-denatured state. After dissolving lysozyme in deuterium oxide buffer, labile protons exchange for deuterons in such a way that exposed protons are substituted rapidly, whereas "protected" protons within structured parts of the protein are substituted slowly. The exchange rates k obs were determined for HEWL under heat treatment (80 degrees C) and under high pressure conditions at low temperature (3.75 kbar, -13 degrees C). Moreover, the influence of co-solvents (sorbitol, urea) on the exchange rate was examined under pressure-assisted cold denaturation conditions, and the corresponding protection factors, P, were determined. The exchange kinetics upon heat treatment was found to be a two-step process with initial slow exchange followed by a fast one, showing residual protection in the slow-exchange state and P-factors in the random-coil-like range for the final temperature-denatured state. Addition of sorbitol (500 mM) led to an increase of P-factors for the pressure-assisted cold denatured state, but not for the heat-denatured state. The presence of 2 M urea resulted in a drastic decrease of the P-factors of the pressure-assisted cold denatured state. For both types of co-solvents, the effect they exert appears to be cooperative, i.e., no particular regions within the protein can be identified with significantly diverse changes of P-factors.

  13. Pressure-assisted cold denaturation of hen egg white lysozyme: the influence of co-solvents probed by hydrogen exchange nuclear magnetic resonance

    Directory of Open Access Journals (Sweden)

    K. Vogtt

    2005-08-01

    Full Text Available COSY proton nuclear magnetic resonance was used to measure the exchange rates of amide protons of hen egg white lysozyme (HEWL in the pressure-assisted cold-denatured state and in the heat-denatured state. After dissolving lysozyme in deuterium oxide buffer, labile protons exchange for deuterons in such a way that exposed protons are substituted rapidly, whereas "protected" protons within structured parts of the protein are substituted slowly. The exchange rates k obs were determined for HEWL under heat treatment (80ºC and under high pressure conditions at low temperature (3.75 kbar, -13ºC. Moreover, the influence of co-solvents (sorbitol, urea on the exchange rate was examined under pressure-assisted cold denaturation conditions, and the corresponding protection factors, P, were determined. The exchange kinetics upon heat treatment was found to be a two-step process with initial slow exchange followed by a fast one, showing residual protection in the slow-exchange state and P-factors in the random-coil-like range for the final temperature-denatured state. Addition of sorbitol (500 mM led to an increase of P-factors for the pressure-assisted cold denatured state, but not for the heat-denatured state. The presence of 2 M urea resulted in a drastic decrease of the P-factors of the pressure-assisted cold denatured state. For both types of co-solvents, the effect they exert appears to be cooperative, i.e., no particular regions within the protein can be identified with significantly diverse changes of P-factors.

  14. Structure and amphoteric properties of titanium dioxide gels

    International Nuclear Information System (INIS)

    Kertesz, C.

    1991-01-01

    Mechanisms responsible for the in-solution ion retention by titanium dioxide are studied. Mineral oxide gel formation and structure are described and various titanium dioxide gel synthesis modes are presented. A two-phase model, taking into account the porous nature of the solid and allowing for the application of the mass action law, is adopted. The oxide amphoteric properties are studied with the potentiometric titration technique. Hysteresis loops are imputed to the slowness of the acid-basic neutralization reaction. The main characteristics are determined: isoelectric point, cation and anion retention capacity. Depending on the suspension agitation, the speed limiting factor may be the diffusion in the film or the diffusion in the particle. 60 fig., 128 ref

  15. Urea and Guanidinium Induced Denaturation of a Trp-Cage Miniprotein

    Czech Academy of Sciences Publication Activity Database

    Heyda, Jan; Kožíšek, Milan; Bednárová, Lucie; Thompson, G.; Konvalinka, Jan; Vondrášek, Jiří; Jungwirth, Pavel

    2011-01-01

    Roč. 115, č. 28 (2011), s. 8910-8924 ISSN 1520-6106 R&D Projects: GA MŠk LC512; GA ČR GA203/08/0114 Institutional research plan: CEZ:AV0Z40550506 Keywords : trp-cage denaturation * urea * guanidinium * molecular dynamics Subject RIV: CC - Organic Chemistry Impact factor: 3.696, year: 2011

  16. Ion transport properties of lithium ionic liquids and their ion gels

    International Nuclear Information System (INIS)

    Shobukawa, Hitoshi; Tokuda, Hiroyuki; Susan, Md. Abu Bin Hasan; Watanabe, Masayoshi

    2005-01-01

    A new series of lithium ionic liquids were prepared by introducing of two electron-withdrawing trifluoroacetyl groups in borate salts containing two methoxy-oligo(ethylene oxide) groups in the structures. Successive substitution reactions of oligo-ethylene glycol monomethyl ether and trifluroacetic acid from LiBH 4 yielded the lithium salts, which were clear and colorless liquids at room temperature. The fundamental physicochemical properties, such as density, thermal property, viscosity, ionic conductivity, self-diffusion coefficients, and electrochemical stability, were measured. The lithium ionic liquids had self-dissociation ability and conducted ions even in the absence of organic solvents. New polymer electrolytes, named 'ion gels', were prepared by radical cross-linking reactions of a poly(ethylene oxide-co-propylene oxide)tri-acrylate macromonomer in the presence the lithium ionic liquid. An increase in the glass transition temperatures (T g ) of the ion gels was very small even with increasing lithium ionic liquid concentration, and the T g 's were lower than that of the ionic liquid itself. The ionic conductivity of the ion gels surpassed that of the lithium ionic liquid in the bulk at certain compositions

  17. Immobilization of Beauveria bassiana Lipase on Silica Gel by Physical Adsorption

    Directory of Open Access Journals (Sweden)

    Vanessa Hitomi Sugahara

    2014-12-01

    Full Text Available Extracellular lipase from Beauveria bassianastrain CG481 was immobilized by using thirteen different immobilization protocols. Silica gel was chosen as the most suitable adsorbent with 94.8% of activity yield. The adsorption on silica gel did not change the optimum pH (8.5 and temperature (45ºC values of the free lipase (FL for lipolytic activity, and it showed higher activities in extreme conditions (pH 9.0 to 10.5, 60ºC. The lipase immobilized on silica gel (ILS showed enhanced stability at pH 7.0 after 120 h incubation (69.0% when compared to FL (33.3%. The thermal stability was also enhanced by immobilization at 60ºC in aqueous (64.6% and organic medium (95.1%, while FL showed only 40.6% of residual activity in aqueous medium and exhibited no activity for esterification reaction in n-heptane. The treatment of ILS with 0.8 M NaCl prevented lipase desorption while Triton X-100 (0.1% resulted the enzyme leakage. The ILS was reused for four times for esterification reaction with 80.8% of initial activity.

  18. A calorimetric study of the interactions in the aqueous solutions of lysozyme in the presence of denaturing cosolvents

    Energy Technology Data Exchange (ETDEWEB)

    Castronuovo, Giuseppina, E-mail: giuseppina.castronuovo@unina.it [Department of Chemistry, University Federico II of Naples, Complesso Universitario Monte S. Angelo, via Cintia, 80126 Naples (Italy); Niccoli, Marcella [Department of Chemistry, University Federico II of Naples, Complesso Universitario Monte S. Angelo, via Cintia, 80126 Naples (Italy)

    2012-09-10

    Highlights: Black-Right-Pointing-Pointer A thermodynamic method is reported to monitor the chemical denaturation of lysozyme. Black-Right-Pointing-Pointer The enthalpic interaction coefficients are very useful parameters to gain information about the mechanism through which two hydrated molecules interact in solution. Black-Right-Pointing-Pointer Hypotheses are proposed about the mechanism underlying the denaturation of lysozyme induced by high concentrations of urea or ethanol. - Abstract: A thermodynamic method is reported to monitor the chemical denaturation of lysozyme. Heats of dilution of the protein in concentrated aqueous solutions of urea or ethanol have been determined at 298.15 K by flow microcalorimetry. The pairwise enthalpic interaction coefficients of the protein in the different solvent media are derived. These parameters allow to gain information about the influence of the cosolvents on the interactions acting between two interacting hydrated molecules of lysozyme, hence on the denaturation process. At increasing urea concentration, up to about 6 mol kg{sup -1}, the values of the interaction coefficients are large and negative and remain almost unaltered. The invariance of the coefficients underlines that, even in highly concentrated urea, the hydration shell of the protein is such to maintain essentially unaltered the native conformation. At higher urea concentrations, a sudden change in the sign of the coefficients monitors the variation in the interactions between two hydrated denatured protein molecules. The same trend is found when ethanol is the cosolvent. At increasing concentration of the cosolvent, coefficients are, at first, almost invariant. After that, denaturation occurs, detected as a jump toward much more negative values. The results obtained are rationalized on the basis of those previously found for small model molecules in concentrated solutions of urea or ethanol. The thermodynamic framework allows useful comments to be made on

  19. A calorimetric study of the interactions in the aqueous solutions of lysozyme in the presence of denaturing cosolvents

    International Nuclear Information System (INIS)

    Castronuovo, Giuseppina; Niccoli, Marcella

    2012-01-01

    Highlights: ► A thermodynamic method is reported to monitor the chemical denaturation of lysozyme. ► The enthalpic interaction coefficients are very useful parameters to gain information about the mechanism through which two hydrated molecules interact in solution. ► Hypotheses are proposed about the mechanism underlying the denaturation of lysozyme induced by high concentrations of urea or ethanol. - Abstract: A thermodynamic method is reported to monitor the chemical denaturation of lysozyme. Heats of dilution of the protein in concentrated aqueous solutions of urea or ethanol have been determined at 298.15 K by flow microcalorimetry. The pairwise enthalpic interaction coefficients of the protein in the different solvent media are derived. These parameters allow to gain information about the influence of the cosolvents on the interactions acting between two interacting hydrated molecules of lysozyme, hence on the denaturation process. At increasing urea concentration, up to about 6 mol kg −1 , the values of the interaction coefficients are large and negative and remain almost unaltered. The invariance of the coefficients underlines that, even in highly concentrated urea, the hydration shell of the protein is such to maintain essentially unaltered the native conformation. At higher urea concentrations, a sudden change in the sign of the coefficients monitors the variation in the interactions between two hydrated denatured protein molecules. The same trend is found when ethanol is the cosolvent. At increasing concentration of the cosolvent, coefficients are, at first, almost invariant. After that, denaturation occurs, detected as a jump toward much more negative values. The results obtained are rationalized on the basis of those previously found for small model molecules in concentrated solutions of urea or ethanol. The thermodynamic framework allows useful comments to be made on the possible mode of action of the two cosolvents on the stability of proteins

  20. Characterization of biomimetically synthesized Hap-Gel nanocomposites as bone substitute

    International Nuclear Information System (INIS)

    Bera, Tanmay; Vivek, A N; Saraf, S K; Ramachandrarao, P

    2008-01-01

    There is an increasing demand for an affordable and easy-to-fabricate material to help patients having a long bone gap. In this paper, we describe the biomimetic synthesis of Hap-Gel in situ nanocomposite powders with varied proportions. Their biocompatibility and bone regeneration abilities were assessed on a rabbit model. The use of Hap crystals and Gel molecule, the soluble form of bone protein, makes the nanocomposites comparable to natural bone in constituents. The application of biomimetic principles improves crystal morphology and the interaction of Hap crystals with the Gel molecules as seen through in vitro characterizations. Out of the various compositions studied, one with 80:20 proportions of Hap to Gel proved to be closest to the characteristics of natural bone. The immunological response to this composite, assessed through intradermal inoculation, did not reveal any reaction. The in vivo implantation studies in the femoral condyle of the animals, as assessed by serial post-operative follow-up radiography and the histological evaluation, revealed a good biocompatibility and bone-regeneration ability of the material. Thus, nanocomposites of Hap-Gel have a great potential for serving as an effective and affordable biomaterial for bone grafting applications

  1. Dip coating of sol-gels

    Science.gov (United States)

    Schunk, P. R.; Hurd, A. J.; Brinker, C. J.

    Dip coating is the primary means of depositing sol-gel films for precision optical coatings. Sols are typically multicomponent systems consisting of an inorganic phase dispersed in a solvent mixture, with each component differing in volatility and surface tension. This, together with slow coating speeds (less than 1cm/s), makes analysis of the coating process complicated; unlike most high-speed coating methods, solvent evaporation, evolving rheology, and surface tension gradients alter significantly the fluid mechanics of the deposition stage. These phenomena were studied with computer-aided predictions of the flow and species transport fields. The underlying theory involves mass, momentum, and species transport on a domain of unknown shape, with models and constitutive equations for vapor-liquid equilibria and surface tension. Due accounting is made for the unknown position of the free surface, which locates according to the capillary hydrodynamic forces and solvent loss by evaporation. Predictions of the effects of mass transfer, hydrodynamics, and surface tension gradients on final film thickness are compared with ellipsometry measurements of film thickness on a laboratory pilot coater. Although quantitative agreement is still lacking, both experiment and theory reveal that the film profile near the drying line takes on a parabolic shape.

  2. An estimation of applicable thermodynamic data for C-S-H gel to PHREEQC

    International Nuclear Information System (INIS)

    Kato, Hiroshige; Honda, Akira

    2004-07-01

    Cementitious materials will be used extensively in the TRU waste repository. The dissolution/precipitation of cementitious materials will affect the chemical condition of pore waster of TRU waste repository. Thus, it is important for estimation of chemical condition of pore water to apply the dissolution/precipitation of cementitious materials appropriately. A C-S-H gel (poorly crystallized calcium silicate hydrate) is a major component in cementitious materials which determined the mechanical characteristics of cementitious materials. The hydraulic condition of cementitious materials is strongly affected by the dissolution/precipitation of C-S-H gel due to the change of porosity accompanied with the dissolution/precipitation processes. Further, the chemical condition of pore water will be dominated by the dissolution/ precipitation of C-S-H gel for a long period. Therefore, an importance of the dissolution/precipitation of C-S-H gel has been recognized internationally, and several dissolution/precipitation models of C-S-H gel have been proposed. The principal scopes of the C-S-H gel models are description of an incongruent dissolution/precipitation behavior of C-S-H gel. On the other hand, PHREEQC is a compute program, which has been used generally for the geochemical calculation. PHREEQC can provide the state of chemical equilibrium of system defined by chemical equations and equilibrium constants (log K). In JNC, reference model groundwater determined by calculation using PHREEQC in HLW study will be also used in TRU waste study. In addition, PHREEQC will be used for calculation of the cement-water reaction. Therefore, applicability of the presented dissolution/precipitation models of C-S-H gel to PHREEQC was estimated. As a result of estimation of the applicability, Atkinson model and Reardon model were selected as suitable models to the PHREEQC. The chemical equations and log K values of C-S-H gel were derived from these models and tested using PHREEQC. The

  3. Use of a ring chromosome and pulsed-field gels to study recombinational repair

    International Nuclear Information System (INIS)

    Game, J.C.; Arabi, S.; Mortimer, R.K.

    1989-01-01

    In wild type yeast, it is known that x-ray induced DNA double-strand breaks (dsb) are repaired, leading to recovery of high molecular-weight molecules on gradients or pulsed-field gels. There is genetic evidence that some or all of this repair occurs via recombinational mechanisms involving sister-chromatid exchange (SCE) and (in diploids) inter-homologue recombination. However, this evidence is indirect and qualitative. The authors of this paper are attempting to use pulsed-field gels to detect and measure recombinational repair at the physical level in yeast strains with a circular homologue of Chr. III. The authors have previously used such strains to study meiotic recombination. The authors have shown that double-size circular molecules can be detected in log-phase haploid yeast cells carrying a ring chromosome, when such cells are exposed to x-rays and allowed time for subsequent repair. Large circular molecules will not enter our pulsed-field gels, but treatment of the DNA samples with radiation prior to running the gels will linearize a fraction of such molecules with a single dsb. Such linearized molecules will run as a band whose position indicates the size of the original unbroken circles

  4. Corrosion of ferritic steels by molten lithium: Influence of competing thermal gradient mass transfer and surface product reactions

    International Nuclear Information System (INIS)

    Tortorelli, P.F.

    1987-10-01

    An Fe-12Cr-1MoVW steel was exposed to thermally convective lithium for 6962 h. Results showed that the weight change profile of Fe-12Cr-1MoVW steel changed substantially as the maximum loop temperature was raised from 500 to 600 0 C. Furthermore, for a particular loop experiment, changes in the structure and composition of the exposed surfaces did not reflect typical thermal gradient mass transfer effects for all elements: the surface concentration of chromium was often a maximum at intermediate temperatures, while nickel (present at low concentrations in the starting material) tended to be transported to the coldest part of the loop. Such data were interpreted in terms of a qualitative model in which there are different dominant reactions or the various constituents of the ferritic steels (surface product formation involving nitrogen and/or carbon and solubility-driven elemental transport). This competition among different reactions is important in evaluating overall corrosion behavior and the effects of temperature. The overall corrosion rate of the 12Cr-1MoVW steel was relatively low when compared to that for austenitic stainless steel exposed under similar conditions

  5. Modulation of the Extent of Cooperative Structural Change During Protein Folding by Chemical Denaturant.

    Science.gov (United States)

    Jethva, Prashant N; Udgaonkar, Jayant B

    2017-09-07

    Protein folding and unfolding reactions invariably appear to be highly cooperative reactions, but the structural and sequence determinants of cooperativity are poorly understood. Importantly, it is not known whether cooperative structural change occurs throughout the protein, or whether some parts change cooperatively and other parts change noncooperatively. In the current study, hydrogen exchange mass spectrometry has been used to show that the mechanism of unfolding of the PI3K SH3 domain is similar in the absence and presence of 5 M urea. The data are well described by a four state N ↔ I N ↔ I 2 ↔ U model, in which structural changes occur noncooperatively during the N ↔ I N and I N ↔ I 2 transitions, and occur cooperatively during the I 2 ↔ U transition. The nSrc-loop and RT-loop, as well as β strands 4 and 5 undergo noncooperative unfolding, while β strands 1, 2, and 3 unfold cooperatively in the absence of urea. However, in the presence of 5 M urea, the unfolding of β strand 4 switches to become cooperative, leading to an increase in the extent of cooperative structural change. The current study highlights the relationship between protein stability and cooperativity, by showing how the extent of cooperativity can be varied, using chemical denaturant to alter protein stability.

  6. Lipophilic polyelectrolyte gel derived from phosphonium borate can absorb a wide range of organic solvents.

    Science.gov (United States)

    Sunaga, Sokuro; Kokado, Kenta; Sada, Kazuki

    2018-01-24

    Herein, we demonstrate a polyelectrolyte gel which can absorb a wide range of organic solvents from dimethylsulfoxide (DMSO, permittivity: ε = 47.0) to tetrahydrofuran (ε = 5.6). The gel consists of polystyrene chains with small amounts (∼5 mol%) of lipophilic electrolytes derived from triphenylphosphonium tetraaryl borate. The swelling ability of the polyelectrolyte gel was higher than that of the alkyl ammonium tetraaryl borate previously reported by us, and this is attributed to the higher compatibility with organic solvents, as well as the higher dissociating ability, of the triphenyl phosphonium salt. The role of the ionic moieties was additionally confirmed by post modification of the polyelectrolyte gel via a conventional Wittig reaction, resulting in a nonionic gel. Our findings introduced here will lead to a clear-cut molecular design for polyelectrolyte gels which absorb all solvents.

  7. A Pendulum-Like Motion of Nanofiber Gel Actuator Synchronized with External Periodic pH Oscillation

    Directory of Open Access Journals (Sweden)

    Shuji Hasimoto

    2011-02-01

    Full Text Available In this study, we succeeded in manufacturing a novel nanofiber hydrogel actuator that caused a bending and stretching motion synchronized with external pH oscillation, based on a bromate/sulfite/ferrocyanide reaction. The novel nanofiber gel actuator was composed of electrospun nanofibers synthesized by copolymerizing acrylic acid and hydrophobic butyl methacrylate as a solubility control site. By changing the electrospinning flow rate, the nanofiber gel actuator introduced an anisotropic internal structure into the gel. Therefore, the unsymmetrical motion of the nanofiber actuator was generated.

  8. Polymeric reaction of polymer-monomer system for pressure sensitive adhesives by low energy electron beam

    International Nuclear Information System (INIS)

    Takiguchi, R.; Uryu, T.

    1985-01-01

    Application of low-energy electron beam to non-solvent type pressure sensitive adhesives is investigated. The adhesive properties such as peel strength and holding time (dead-load strength) were closely related to the reaction of acrylate polymer-monomer systems. The reaction behavior is elucidated by combining the measurement of gel fraction, infrared spectrum of gel, and the molecular weight distribution detected by gel permeation chromatography. It was important for the production of pressure sensitive adhesives by electron beam that the adhesive with high peel strength and long holding time is composed of a proper combination of three factors, that is, about 35% gel fraction, 25% monomer units in gel, and 15% graft efficiency by irradiating the polymer-monomer system containing low molecular weight poly (butyl acrylate). (author)

  9. Equilibrium unfolding of A. niger RNase: pH dependence of chemical and thermal denaturation.

    Science.gov (United States)

    Kumar, Gundampati Ravi; Sharma, Anurag; Kumari, Moni; Jagannadham, Medicherla V; Debnath, Mira

    2011-08-01

    Equilibrium unfolding of A. niger RNase with chemical denaturants, for example GuHCl and urea, and thermal unfolding have been studied as a function of pH using fluorescence, far-UV, near-UV, and absorbance spectroscopy. Because of their ability to affect electrostatic interactions, pH and chemical denaturants have a marked effect on the stability, structure, and function of many globular proteins. ANS binding studies have been conducted to enable understanding of the folding mechanism of the protein in the presence of the denaturants. Spectroscopic studies by absorbance, fluorescence, and circular dichroism and use of K2D software revealed that the enzyme has α + β type secondary structure with approximately 29% α-helix, 24% β-sheet, and 47% random coil. Under neutral conditions the enzyme is stable in urea whereas GuHCl-induced equilibrium unfolding was cooperative. A. niger RNase has little ANS binding even under neutral conditions. Multiple intermediates were populated during the pH-induced unfolding of A. niger RNase. Urea and temperature-induced unfolding of A. niger RNase into the molten globule-like state is non-cooperative, in contrast to the cooperativity seen with the native protein, suggesting the presence of two parts/domains, in the molecular structure of A. niger RNase, with different stability that unfolds in steps. Interestingly, the GuHCl-induced unfolding of the A state (molten globule state) of A. niger RNase is unique, because a low concentration of denaturant not only induces structural change but also facilitates transition from one molten globule like state (A(MG1)) into another (I(MG2)).

  10. Synthesis and Characterization of Silicotungstic Acid Nanoparticles Via Sol Gel Technique as a Catalyst in Esterification Reaction

    International Nuclear Information System (INIS)

    Wan Nor Roslam Wan Ishak; Manal Ismail

    2011-01-01

    The purpose of this work is to study the synthesis, characterization and catalytic performance of silicotungstic acid-silica sol gel (STA-SG) as acid catalyst in esterification reaction. The activity and selectivity of STA-SG have been investigated and compared to the STA bulk (STAB) and sulphuric acid (H 2 SO 4 ). The synthesized catalysts were characterized by various techniques shown that the STA-SG catalyst is relatively high in surface area compared to STAB of 460.11 m 2 /g and 0.98 m 2 /g, respectively. From the XPS analyses, there was a significant formation of W-O-Si, W-O-W and Si-O-Si bonding in STA-SG compared to that in STAB. Both the H 2 SO 4 and the STAB gave high conversion of 100 % and 98 %, while lower selectivity of glycerol monooleate (GMO) with 81.6 % and 89.9 %, respectively. On the contrary, the STA-SG enabled a conversion of 94 %, while significantly higher GMO selectivity of 95 % rendering it the more efficient acid catalyst. (author)

  11. Sol-Gel Glasses

    Science.gov (United States)

    Mukherjee, S. P.

    1985-01-01

    Multicomponent homogeneous, ultrapure noncrystalline gels/gel derived glasses are promising batch materials for the containerless glass melting experiments in microgravity. Hence, ultrapure, homogeneous gel precursors could be used to: (1) investigate the effect of the container induced nucleation on the glass forming ability of marginally glass forming compositions; and (2) investigate the influence of gravity on the phase separation and coarsening behavior of gel derived glasses in the liquid-liquid immiscibility zone of the nonsilicate systems having a high density phase. The structure and crystallization behavior of gels in the SiO2-GeO2 as a function of gel chemistry and thermal treatment were investigated. As are the chemical principles involved in the distribution of a second network former in silica gel matrix being investigated. The procedures for synthesizing noncrystalline gels/gel-monoliths in the SiO2-GeO2, GeO2-PbO systems were developed. Preliminary investigations on the levitation and thermal treatment of germania silicate gel-monoliths in the Pressure Facility Acoustic Levitator were done.

  12. Structural analysis of protein complexes with sodium alkyl sulfates by small-angle scattering and polyacrylamide gel electrophoresis.

    Science.gov (United States)

    Ospinal-Jiménez, Mónica; Pozzo, Danilo C

    2011-02-01

    Small-angle X-ray (SAXS) and neutron (SANS) scattering is used to probe the structure of protein-surfactant complexes in solution and to correlate this information with their performance in gel electrophoresis. Proteins with sizes between 6.5 to 116 kDa are denatured with sodium alkyl sulfates (SC(x)S) of variable tail lengths. Several combinations of proteins and surfactants are analyzed to measure micelle radii, the distance between micelles, the extension of the complex, the radius of gyration, and the electrophoretic mobility. The structural characterization shows that most protein-surfactant complexes can be accurately described as pearl-necklace structures with spherical micelles. However, protein complexes with short surfactants (SC(8)S) bind with micelles that deviate significantly from spherical shape. Sodium decyl (SC(10)S) and dodecyl (SC(12)S, more commonly abbreviated as SDS) sulfates result in the best protein separations in standard gel electrophoresis. Particularly, SC(10)S shows higher resolutions for complexes of low molecular weight. The systematic characterization of alkyl sulfate surfactants demonstrates that changes in the chain architecture can significantly affect electrophoretic migration so that protein-surfactant structures could be optimized for high resolution protein separations.

  13. Introduction of a deformable x-ray CT polymer gel dosimetry system

    Science.gov (United States)

    Maynard, E.; Heath, E.; Hilts, M.; Jirasek, A.

    2018-04-01

    This study introduces the first 3D deformable dosimetry system based on x-ray computed tomography (CT) polymer gel dosimetry and establishes the setup reproducibility, deformation characteristics and dose response of the system. A N-isopropylacrylamide (NIPAM)-based gel formulation optimized for x-ray CT gel dosimetry was used, with a latex balloon serving as the deformable container and low-density polyethylene and polyvinyl alcohol providing additional oxygen barrier. Deformable gels were irradiated with a 6 MV calibration pattern to determine dosimetric response and a dosimetrically uniform plan to determine the spatial uniformity of the response. Wax beads were added to each gel as fiducial markers to track the deformation and setup of the gel dosimeters. From positions of the beads on CT images the setup reproducibility and the limits and reproducibility of gel deformation were determined. Comparison of gel measurements with Monte Carlo dose calculations found excellent dosimetric accuracy, comparable to that of an established non-deformable dosimetry system, with a mean dose discrepancy of 1.5% in the low-dose gradient region and a gamma pass rate of 97.9% using a 3%/3 mm criterion. The deformable dosimeter also showed good overall spatial dose uniformity throughout the dosimeter with some discrepancies within 20 mm of the edge of the container. Tracking of the beads within the dosimeter found that sub-millimetre setup accuracy is achievable with this system. The dosimeter was able to deform and relax when externally compressed by up to 30 mm without sustaining any permanent damage. Internal deformations in 3D produced average marker movements of up to 12 mm along the direction of compression. These deformations were also shown to be reproducible over 100 consecutive deformations. This work has established several important characteristics of a new deformable dosimetry system which shows promise for future clinical applications, including the

  14. Preparasi Katalis Cu/Silika Gel dari Kristobalit Alam Sabang serta Uji Aktivitasnya pada Reaksi Dehidrogenasi Etanol

    Directory of Open Access Journals (Sweden)

    Surya Lubis

    2009-06-01

    Full Text Available Cu/Silica gel catalyst preparation by using silica content which is obtained from Sabang natural crystobalit has been done. Isolated silica from crystobalit is reacted with natrium hidroxide to produce silicate natrium that reacted further with sulphate acid to produce silica gel. Silica gel is characterized by infra red spektroscopy dan BET test. BET test result showed that silica gel obtained has specific surface area 260,04 m2/gram and ion Cu  impregnation into silica gel pores produce Cu/silica gel catalyst with spesific surace area 158,53 m/gram ith Cu2+ metal content = 193 ppm. Catalyst activation test Cu/silica gel at dehidrogenation reaction of etanol to produce asetaldehide was done at temperature 100oC – 300oC. Reseach showed that the highest asetaldehide consentration (20,24% is obtained at temperature 300oC.   Keywords: asetaldehide, crystobalit, Cu/silica gel, dehidrogenation, ethanol

  15. Development of Polymer Gel Systems to Improve Volumetric Sweep and Reduce Producing Water/Oil Ratios

    Energy Technology Data Exchange (ETDEWEB)

    G. Paul Willhite; Stan McCool; Don W. Green; Min Cheng; Feiyan Chen

    2005-12-31

    Gelled polymer treatments are applied to oil reservoirs to increase oil production and to reduce water production by altering the fluid movement within the reservoir. This report describes the results of a 42-month research program that focused on the understanding of gelation chemistry and the fundamental mechanisms that alter the flows of oil and water in reservoir rocks after a gel treatment. Work was conducted on a widely applied system in the field, the partially hydrolyzed polyacrylamide-chromium acetate gel. Gelation occurs by network formation through the crosslinking of polyacrylamide molecules as a result of reaction with chromium acetate. Pre-gel aggregates form and grow as reactions between chromium acetate and polyacrylamide proceed. A rate equation that describes the reaction between chromium acetate and polymer molecules was regressed from experimental data. A mathematical model that describes the crosslinking reaction between two polymer molecules as a function of time was derived. The model was based on probability concepts and provides molecular-weight averages and molecular-weight distributions of the pre-gel aggregates as a function of time and initial system conditions. Average molecular weights of pre-gel aggregates were measured as a function of time and were comparable to model simulations. Experimental methods to determine molecular weight distributions of pre-gel aggregates were unsuccessful. Dissolution of carbonate minerals during the injection of gelants causes the pH of the gelant to increase. Chromium precipitates from solution at the higher pH values robbing the gelant of crosslinker. Experimental data on the transport of chromium acetate solutions through dolomite cores were obtained. A mathematical model that describes the transport of brine and chromium acetate solutions through rocks containing carbonate minerals was used to simulate the experimental results and data from literature. Gel treatments usually reduce the permeability

  16. Chemical Denaturants Smoothen Ruggedness on the Free Energy Landscape of Protein Folding.

    Science.gov (United States)

    Malhotra, Pooja; Jethva, Prashant N; Udgaonkar, Jayant B

    2017-08-08

    To characterize experimentally the ruggedness of the free energy landscape of protein folding is challenging, because the distributed small free energy barriers are usually dominated by one, or a few, large activation free energy barriers. This study delineates changes in the roughness of the free energy landscape by making use of the observation that a decrease in ruggedness is accompanied invariably by an increase in folding cooperativity. Hydrogen exchange (HX) coupled to mass spectrometry was used to detect transient sampling of local energy minima and the global unfolded state on the free energy landscape of the small protein single-chain monellin. Under native conditions, local noncooperative openings result in interconversions between Boltzmann-distributed intermediate states, populated on an extremely rugged "uphill" energy landscape. The cooperativity of these interconversions was increased by selectively destabilizing the native state via mutations, and further by the addition of a chemical denaturant. The perturbation of stability alone resulted in seven backbone amide sites exchanging cooperatively. The size of the cooperatively exchanging and/or unfolding unit did not depend on the extent of protein destabilization. Only upon the addition of a denaturant to a destabilized mutant variant did seven additional backbone amide sites exchange cooperatively. Segmentwise analysis of the HX kinetics of the mutant variants further confirmed that the observed increase in cooperativity was due to the smoothing of the ruggedness of the free energy landscape of folding of the protein by the chemical denaturant.

  17. Comparative mutagenesis of human cells in vivo and in vitro

    International Nuclear Information System (INIS)

    Thilly, W.G.

    1990-01-01

    Our goal is to develop the tools of mutational spectrometry in order to discover the cause(s) of genetic change in somatic and germinal cells in humans. Our study of the spectrum of point mutations in human mitochrondrial DNA sequences has revealed that there are multiple point mutation hotspots in each of four separate sequences in the mitochrondrial genome. These spectra were revealed by a combination of high fidelity PCR (modified T 7 polymerase) and denaturing gradient gel electrophoresis which has a limit of detection of about 10 -3 . There appear to be identical hotspot mutations in both cultured B cell and fresh human blood T cell samples

  18. Effects of a Campylobacter jejuni infection on the development of the intestinal microflora of broiler chickens.

    Science.gov (United States)

    Johansen, C H; Bjerrum, L; Finster, K; Pedersen, K

    2006-04-01

    The effect of a Campylobacter jejuni colonization on the development of the microflora of the cecum and the ileum of broiler chickens was studied using molecular methods. The infection did affect the development and complexity of the microbial communities of the ceca, but we found no permanent effect of a C. jejuni infection on the ileal microflora of the broilers. In addition, denaturant gradient gel electrophoresis (DGGE) profiles generated from cecal and ileal contents revealed several DGGE bands that were present in the control chickens, but not in the chickens colonized with C. jejuni. Some of these DGGE bands could be affiliated with Lactobacillus reuteri, Clostridium perfringens, and the genus Klebsiella.

  19. Radioimmunoassay and heat denaturation enzyme assay for the detection of Tay-Sachs heterozygotes during pregnancy

    International Nuclear Information System (INIS)

    Nguyen, C.; Gold, R.J.M.; Mahuran, D.; Lowden, J.A.

    1981-01-01

    Tay-Sachs disease results from a loss of activity of hexosaminidase A (HEX A) in body tissues and fluids. Heterozygotes for the disease are usually identified by their relatively low ratio of heat-labile HEX A to total hexosaminidase. During pregnancy an intermediate isoenzyme (HEX I) increases in activity in serum and obscures the heterozygote status. HEX I does not increase in leucocytes, tears and other body tissues but because of technical difficulties in these assays the authors examined the feasibility of using a radioimmunoassay for HEX A. By univariate analysis, the heat denaturation assay gave a lower cost of misclassification for non-pregnant normals while RIA did so for pregnant normals. A combination of both tests led to reduced cost of misclassification compared to either alone. Bayesian analysis of bivariate gaussian density functions for heat denaturation and for radioimmunoassays of HEX isoenzymes was employed to calculate misclassification frequencies. Among the parameters examined, HEX A measured by RIA and % HEX A by heat-denaturation assay were the two having the best discriminatory power. (Auth.)

  20. Formation and rupture of Ca(2+) induced pectin biopolymer gels.

    Science.gov (United States)

    Basak, Rajib; Bandyopadhyay, Ranjini

    2014-10-07

    When calcium salts are added to an aqueous solution of polysaccharide pectin, ionic cross-links form between pectin chains, giving rise to a gel network in dilute solution. In this work, dynamic light scattering (DLS) is employed to study the microscopic dynamics of the fractal aggregates (flocs) that constitute the gels, while rheological measurements are carried out to study the process of gel rupture. As the calcium salt concentration is increased, DLS experiments reveal that the polydispersity of the flocs increase simultaneously with the characteristic relaxation times of the gel network. Above a critical salt concentration, the flocs become interlinked to form a reaction-limited fractal gel network. Rheological studies demonstrate that the limits of the linear rheological response and the critical stresses required to rupture these networks both decrease with the increase in salt concentration. These features indicate that the ion-mediated pectin gels studied here lie in a 'strong link' regime that is characterised by inter-floc links that are stronger than intra-floc links. A scaling analysis of the experimental data presented here demonstrates that the elasticities of the individual fractal flocs exhibit power-law dependences on the added salt concentration. We conclude that when both pectin and salt concentrations are increased, the number of fractal flocs of pectin increases simultaneously with the density of crosslinks, giving rise to very large values of the bulk elastic modulus.

  1. The phenotypic variance gradient - a novel concept.

    Science.gov (United States)

    Pertoldi, Cino; Bundgaard, Jørgen; Loeschcke, Volker; Barker, James Stuart Flinton

    2014-11-01

    Evolutionary ecologists commonly use reaction norms, which show the range of phenotypes produced by a set of genotypes exposed to different environments, to quantify the degree of phenotypic variance and the magnitude of plasticity of morphometric and life-history traits. Significant differences among the values of the slopes of the reaction norms are interpreted as significant differences in phenotypic plasticity, whereas significant differences among phenotypic variances (variance or coefficient of variation) are interpreted as differences in the degree of developmental instability or canalization. We highlight some potential problems with this approach to quantifying phenotypic variance and suggest a novel and more informative way to plot reaction norms: namely "a plot of log (variance) on the y-axis versus log (mean) on the x-axis, with a reference line added". This approach gives an immediate impression of how the degree of phenotypic variance varies across an environmental gradient, taking into account the consequences of the scaling effect of the variance with the mean. The evolutionary implications of the variation in the degree of phenotypic variance, which we call a "phenotypic variance gradient", are discussed together with its potential interactions with variation in the degree of phenotypic plasticity and canalization.

  2. T1ρ is superior to T2 mapping for the evaluation of articular cartilage denaturalization with osteoarthritis: radiological-pathological correlation after total knee arthroplasty.

    Science.gov (United States)

    Takayama, Yukihisa; Hatakenaka, Masamitsu; Tsushima, Hidetoshi; Okazaki, Ken; Yoshiura, Takashi; Yonezawa, Masato; Nishikawa, Kei; Iwamoto, Yukihide; Honda, Hiroshi

    2013-04-01

    We compared the diagnostic performance of T1ρ and T2 mappings in the evaluation of denatured articular cartilage with osteoarthritis of the knee. 2D-Sagittal T1ρ and T2 mappings of the knee were obtained from 16 patients before total knee arthroplasty. After surgery, specimens of the femur and tibia were regionally segmented according to a 5-point scale of the severity of denaturalization. The T1ρ and T2 values in the full thickness of the articular cartilage in each region were measured by two observers. The two mappings were compared for their ability to differentiate between normal and denatured articular cartilage and also for their usefulness in grading the severity of the denaturalization using the area under receiver operating characteristic curves (Az). A pT2 mapping for the differentiation between normal and denatured articular cartilage (pT2 mapping could not. However, there were no significant differences between the two mappings in the discrimination of mild versus moderate denaturalization or of moderate versus severe denaturalization. The two observers showed good agreement in the results (intraclass correlation coefficient=0.81 for T1ρ and 0.92 for T2). T1ρ mapping is superior to T2 mapping for the evaluation of denatured articular cartilage with osteoarthritis of the knee. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  3. Analyses of Dynamics in Dairy Products and Identification of Lactic Acid Bacteria Population by Molecular Methods

    Directory of Open Access Journals (Sweden)

    Aytül Sofu

    2017-01-01

    Full Text Available Lactic acid bacteria (LAB with different ecological niches are widely seen in fermented meat, vegetables, dairy products and cereals as well as in fermented beverages. Lactic acid bacteria are the most important group of bacteria in dairy industry due to their probiotic characteristics and fermentation agents as starter culture. In the taxonomy of the lactic acid bacteria; by means of rep-PCR, which is the analysis of repetitive sequences that are based on 16S ribosomal RNA (rRNA gene sequence, it is possible to conduct structural microbial community analyses such as Restriction Fragment Length Polymorphism (RFLP analysis of DNA fragments of different sizes cut with enzymes, Random Amplified Polymorphic DNA (RAPD polymorphic DNA amplified randomly at low temperatures and Amplified Fragment-Length Polymorphism (AFLP-PCR of cut genomic DNA. Besides, in the recent years, non-culture-based molecular methods such as Pulse Field Gel Electrophoresis (PFGE, Denaturing Gradient Gel Electrophoresis (DGGE, Thermal Gradient Gel Electrophoresis (TGGE, and Fluorescence In-situ Hybridization (FISH have replaced classical methods once used for the identification of LAB. Identification of lactic acid bacteria culture independent regardless of the method will be one of the most important methods used in the future pyrosequencing as a Next Generation Sequencing (NGS techniques. This paper reviews molecular-method based studies conducted on the identification of LAB species in dairy products.

  4. Biofilm formation and microbial community analysis of the simulated river bioreactor for contaminated source water remediation.

    Science.gov (United States)

    Xu, Xiang-Yang; Feng, Li-Juan; Zhu, Liang; Xu, Jing; Ding, Wei; Qi, Han-Ying

    2012-06-01

    The start-up pattern of biofilm remediation system affects the biofilm characteristics and operating performances. The objective of this study was to evaluate the performances of the contaminated source water remediation systems with different start-up patterns in view of the pollutants removal performances and microbial community succession. The operating performances of four lab-scale simulated river biofilm reactors were examined which employed different start-up methods (natural enrichment and artificial enhancement via discharging sediment with influent velocity gradient increase) and different bio-fillers (Elastic filler and AquaMats® ecobase). At the same time, the microbial communities of the bioreactors in different phases were analyzed by polymerase chain reaction, denaturing gradient gel electrophoresis, and sequencing. The pollutants removal performances became stable in the four reactors after 2 months' operation, with ammonia nitrogen and permanganate index (COD(Mn)) removal efficiencies of 84.41-94.21% and 69.66-76.60%, respectively. The biomass of mature biofilm was higher in the bioreactors by artificial enhancement than that by natural enrichment. Microbial community analysis indicated that elastic filler could enrich mature biofilm faster than AquaMats®. The heterotrophic bacteria diversity of biofilm decreased by artificial enhancement, which favored the ammonia-oxidizing bacteria (AOB) developing on the bio-fillers. Furthermore, Nitrosomonas- and Nitrosospira-like AOB coexisted in the biofilm, and Pseudomonas sp., Sphaerotilus sp., Janthinobacterium sp., Corynebacterium aurimucosum were dominant in the oligotrophic niche. Artificial enhancement via the combination of sediment discharging and influent velocity gradient increasing could enhance the biofilm formation and autotrophic AOB enrichment in oligotrophic niche.

  5. Effects of Shear Fracture on In-depth Profile Modification of Weak Gels

    Institute of Scientific and Technical Information of China (English)

    Li Xianjie; Song Xinwang; Yue Xiang'an; Hou Jirui; Fang Lichun; Zhang Huazhen

    2007-01-01

    Two sand packs were filled with fine glass beads and quartz sand respectively. The characteristics of crosslinked polymer flowing through the sand packs as well as the influence of shear fracture of porous media on the in-depth profile modification of the weak gel generated from the crosslinked polymer were investigated. The results indicated that under the dynamic condition crosslinking reaction happened in both sand packs,and the weak gels in these two cases became small gel particles after water flooding. The differences were:the dynamic gelation time in the quartz sand pack was longer than that in the glass bead pack. Residual resistance factor (FRR) caused by the weak gel in the quartz sand pack was smaller than that in the glass bead pack. The weak gel became gel particles after being scoured by subsequent flood water. A weak gel with uniform apparent viscosity and sealing characteristics was generated in every part of the glass bead pack,which could not only move deeply into the sand pack but also seal the high capacity channels again when it reached the deep part. The weak gel performed in-depth profile modification in the glass bead pack,while in the quartz sand pack,the weak gel was concentrated with 100 cm from the entrance of the sand pack. When propelled by the subsequent flood water,the weak gel could move towards the deep part of the sand pack but then became tiny gel particles and could not effectively seal the high capacity channels there. The in-depth profile modification of the weak gel was very weak in the quartz sand pack. It was the shear fracture of porous media that mainly affected the properties and weakened the in-depth profile modification of the weak gel.

  6. Sucralfate gel as a radioprotector against radiation induced dermatitis in a hypo-fractionated schedule: a non-randomized study.

    Science.gov (United States)

    Kouloulias, V; Asimakopoulos, C; Tolia, M; Filippou, G; Platoni, K; Dilvoi, M; Beli, I; Georgakopoulos, J; Patatoukas, G; Kelekis, N

    2013-04-01

    External beam radiotherapy with high doses provokes many acute skin reactions, such as erythema and moist desquamation. Many topical preparations are used in radiation oncology departments in the skin care. Sucralfate humid gel, a colloidal physical form of the anti-ulcer drug sucralfate, promotes epithelial regeneration and activates cell proliferation. Based on this knowledge, we performed a non-randomized clinical trial to evaluate the efficacy of topical sucralfate gel in 30 breast cancer patients receiving postoperative accelerated hypofractionated photon beam therapy. The comparison was performed with 30 patients as historical controls. The acute reaction of the skin was significantly lower in the group receiving the sucralfate gel (p<0.05, Mann Whitney test), while 90% of the patients had no evidence of radiation induced skin toxicity. There was no sucralfate gel related toxicity reported by any patient in this study. More patients in a randomized way are needed for more definite results.

  7. Densification and crystallization behaviour of colloidal cordierite-type gels

    Directory of Open Access Journals (Sweden)

    LJILJANA KOSTIC-GVOZDENOVIC

    2001-05-01

    Full Text Available Three cordierite-type gels were prepared from an aqueous solution of Mg(NO32, a boehmite sol and silica sols of very small particle sizes. The effect of varying the silica particle size on the crystallization and densification behaviour was studied. Phase development was examined by thermal analysis and X-ray diffraction, while the densification behaviour was characterized by measuring the linear shrinkage of pellets. The activation energy of densification by viscous flow was determined using the Franckel model for non-isothermal conditions and a constant heating rate. The results show that spinel crystallizes from the colloidal gels prior to cristobalite, and their reaction gives a-cordierite, which is specific for three-phase gels. Decreasing the silica particles size lowers the cristobalite crystallization temperature and the a-cordierite formation temperature. The activation energy of densification by viscous flow is lower and the densification more efficient, the smaller the silica particles are.

  8. GelTouch

    DEFF Research Database (Denmark)

    Miruchna, Viktor; Walter, Robert; Lindlbauer, David

    2015-01-01

    We present GelTouch, a gel-based layer that can selectively transition between soft and stiff to provide tactile multi-touch feedback. It is flexible, transparent when not activated, and contains no mechanical, electromagnetic, or hydraulic components, resulting in a compact form factor (a 2mm thin...... touchscreen layer for our prototype). The activated areas can be morphed freely and continuously, without being limited to fixed, predefined shapes. GelTouch consists of a poly(N-isopropylacrylamide) gel layer which alters its viscoelasticity when activated by applying heat (>32 C). We present three different...

  9. Theoretical aspects of pressure and solute denaturation of proteins: A Kirkwood-buff-theory approach

    Science.gov (United States)

    Ben-Naim, Arieh

    2012-12-01

    A new approach to the problem of pressure-denaturation (PD) and solute-denaturation (SD) of proteins is presented. The problem is formulated in terms of Le Chatelier principle, and a solution is sought in terms of the Kirkwood-Buff theory of solutions. It is found that both problems have one factor in common; the excluded volumes of the folded and the unfolded forms with respect to the solvent molecules. It is shown that solvent-induced effects operating on hydrophilic groups along the protein are probably the main reason for PD. On the other hand, the SD depends on the preferential solvation of the folded and the unfolded forms with respect to solvent and co-solvent molecules.

  10. Resistance to DNA denaturation in irradiated Chinese hamster V79 fibroblasts is linked to cell shape

    International Nuclear Information System (INIS)

    Olive, P.L.; Vanderbyl, S.; MacPhail, S.H.

    1991-01-01

    Exponentially growing Chinese hamster V79-171b lung fibroblasts seeded at high density on plastic (approximately 7 x 10(3) cells/cm2) flatten, elongate, and produce significant amounts of extracellular fibronectin. When lysed in weak alkali/high salt, the rate of DNA denaturation following exposure to ionizing radiation is exponential. Conversely, cells plated at low density (approximately 7 x 10(2) cells/cm2) on plastic are more rounded 24 h later, produce little extracellular fibronectin, and display unusual DNA denaturation kinetics after X-irradiation. DNA in these cells resists denaturation, as though constraints to DNA unwinding have developed. Cell doubling time and distribution of cells in the growth cycle are identical for both high and low density cultures as is cell survival in response to radiation damage. The connection between DNA conformation and cell shape was examined further in low density cultures grown in conditioned medium. Under these conditions, cells at low density were able to elongate, and DNA denaturation of low density cultures was identical to that of high density cultures. Conversely, cytochalasin D, which interferes with actin polymerization causing cells to round up and release fibronectin, allowed development of constraints in high density cultures. These results suggest that DNA conformation is sensitive to changes in cell shape which result when cells are grown in different environments. However, these changes in DNA conformation detected by the DNA unwinding assay do not appear to play a direct role in radiation-induced cell killing

  11. The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.

    Science.gov (United States)

    Gibson, Frank; Hoogland, Christine; Martinez-Bartolomé, Salvador; Medina-Aunon, J Alberto; Albar, Juan Pablo; Babnigg, Gyorgy; Wipat, Anil; Hermjakob, Henning; Almeida, Jonas S; Stanislaus, Romesh; Paton, Norman W; Jones, Andrew R

    2010-09-01

    The Human Proteome Organisation's Proteomics Standards Initiative has developed the GelML (gel electrophoresis markup language) data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for MS data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications.

  12. Thermodynamic analysis of sol-gel transition of gelatin in terms of water activity in various solutions.

    Science.gov (United States)

    Miyawaki, Osato; Omote, Chiaki; Matsuhira, Keiko

    2015-12-01

    Sol-gel transition of gelatin was analyzed as a multisite stoichiometric reaction of a gelatin molecule with water and solute molecules. The equilibrium sol-gel transition temperature, Tt , was estimated from the average of gelation and melting temperature measured by differential scanning calorimetry. From Tt and the melting enthalpy, ΔHsol , the equilibrium sol-to-gel ratio was estimated by the van't Hoff equation. The reciprocal form of the Wyman-Tanford equation, which describes the sol-to-gel ratio as a function of water activity, was successfully applied to obtain a good linear relationship. From this analysis, the role of water activity on the sol-gel transition of gelatin was clearly explained and the contributions of hydration and solute binding to gelatin molecules were separately discussed in sol-gel transition. The general solution for the free energy for gel-stabilization in various solutions was obtained as a simple function of solute concentration. © 2015 Wiley Periodicals, Inc.

  13. Stacking gels: A method for maximising output for pulsed-field gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Heng See

    2009-01-01

    Full Text Available Pulsed field gel electrophoresis (PFGE, the gold standard of molecular typing methods, has a major disadvantage of an unusually long electrophoretic time. From the original protocol of 6 days, it was modified to 3 days and subsequently to a single day. We describe the procedure of stacking five to six gels one on top of another in order to increase and maximize the output in a shorter time without compromising the resolution and reproducibility. All the variables that affect pulsed field gels during electrophoresis were taken into consideration. We firstly optimized the parameters to be used and secondly determined whether stacking of five to six gels had any effect on the molecular separation during electrophoresis in comparison with a single gel run. DNA preparation, restriction, electrophoresis, staining and gel documentation was carried out based on previously published methods. Gels were analysed using BioNumerics and dice coefficient and unweighted pair group methods were used to generate dendrograms based on 1.5% tolerance values. Identical band profiles and band resolution-separation were seen in the PFGE patterns with single gel and multiple stacking gels. Cluster analysis further strengthened the fact that results from stacking gels were reproducible and comparable with a single gel run. This method of stacking gels saves time and maximizes the output at the same time. The run time for a single gel was about 28 hours, but with six stacked gels the run time was 54 hours compared with 28 x 6 = 168 hours if they were run separately as single gels thus saving time of 67.86%. Beside the big factor of saving time, stacking gels save resources (electricity, reagents, water, chemicals and working time by increasing the sample throughput in a shorter time without compromising on quality of data. But optimization of working parameters is vital depending on the PFGE system used.

  14. Genetic diversity analysis of some exotic, Indian and mutant ...

    African Journals Online (AJOL)

    USER

    2010-06-28

    Jun 28, 2010 ... 25 µl reaction mixture (reagents of a single PCR reaction given in. Table 3). Finally, the PCR tubes were subjected to the thermal profile given above. The reaction was carried out in a gradient. Mastercycler for amplification program. A 1.5% agarose gel in 1 X TAE buffer (Tris-base, glacial acetic acid, EDTA) ...

  15. Washing of gel particles in wet chemical manufacture of reactor fuel particles

    International Nuclear Information System (INIS)

    Ringel, H.

    1980-07-01

    In the manufacture of HTR fuel particles and particles of fertile material by wet chemical methods, the ammonium nitrate formed during the precipitation reaction must be washed out of the gel particles. This washing process has been investigated theoretically and experimentally. A counter-current washer has been developed which in particular takes account of the aspects of refabrication - such as compact construction and minimum waste. A counter-current washing column of 17 mm internal diameter and 640 mm length gives to gel particle throughput of 0.65 1/h. The volume ratio of wash water to gel particles is 5, and the residual nitrate concentration in the particles is 7 x 10 -3 mols of NO - 3 /1. (orig.) [de

  16. Novel sol–gel methodology to produce LaCoO3 by acrylamide polymerization assisted by γ-irradiation

    International Nuclear Information System (INIS)

    Carabalí, G.; Chavira, E.; Castro, I.; Bucio, E.; Huerta, L.; Jiménez-Mier, J.

    2012-01-01

    In this paper we report the synthesis of LaCoO 3 (LCO) nano-particles with two methodologies: the conventional sol–gel reaction of acrylamide (AA) polymerization using a cross-linking agent (methylenebisacrylamide or MBA) with the activation of the polymerization reaction by thermo-chemical initiator (azobisisobutyrnitrile or AIBN). The second was a novel sol–gel methodology in which the polymerization of AA monomers was done without MBA and the initiation was achieved by gamma radiation. With thermochemical initiator a xerogel with a foam and porous structure was obtained, while the gamma-irradiation of the mixture leads to the formation of a compact resin with entrapped cations. X-ray diffraction (XRD) shows that formation of the product begins around 500 °C and according to analysis of microscopy images of powders calcined in 700 °C the average sizes of particles are 20 nm and 42 nm for samples obtained using γ-irradiation and AIBN as initiators, respectively. TEM images also show differences in particle morphology. Those synthesized using AIBN as initiator are dispersed, while those with γ-irradiation are in aggregates. - Highlights: ► LaCoO 3 nano-crystallites were synthesized by two different polyacrylamide sol–gel processes. ► Acrylamide polymerization reaction initiated by gamma irradiation and by thermo-chemical agent. ► Polymerization reaction with thermo-chemical initiator produces a porous gel. ► Xerogel obtained using gamma radiation is compact resin. ► LaCoO 3 powders produced by both methods differ in the size and morphology of particles.

  17. Controlled release of vancomycin from thin sol-gel films on implant surfaces successfully controls osteomyelitis.

    Science.gov (United States)

    Adams, Christopher S; Antoci, Valentin; Harrison, Gerald; Patal, Payal; Freeman, Terry A; Shapiro, Irving M; Parvizi, Javad; Hickok, Noreen J; Radin, Shula; Ducheyne, Paul

    2009-06-01

    Peri-prosthetic infection remains a serious complication of joint replacement surgery. Herein, we demonstrate that a vancomycin-containing sol-gel film on Ti alloy rods can successfully treat bacterial infections in an animal model. The vancomycin-containing sol-gel films exhibited predictable release kinetics, while significantly inhibiting S. aureus adhesion. When evaluated in a rat osteomyelitis model, microbiological analysis indicated that the vancomycin-containing sol-gel film caused a profound decrease in S. aureus number. Radiologically, while the control side showed extensive bone degradation, including abscesses and an extensive periosteal reaction, rods coated with the vancomycin-containing sol-gel film resulted in minimal signs of infection. MicroCT analysis confirmed the radiological results, while demonstrating that the vancomycin-containing sol-gel film significantly protected dense bone from resorption and minimized remodeling. These results clearly demonstrate that this novel thin sol-gel technology can be used for the targeted delivery of antibiotics for the treatment of periprosthetic as well as other bone infections. Copyright 2008 Orthopaedic Research Society

  18. Effect of saccharide additives on response of ferrous-agarose-xylenol orange radiotherapy gel dosimeters

    International Nuclear Information System (INIS)

    Healy, B.J.; Zahmatkesh, M.H.; Nitschke, K.N.; Baldock, C.

    2003-01-01

    Glucose, sucrose, starch, and locust bean gum have been used as additives to the ferrous-agarose-xylenol orange (FAX) gel dosimeter. The saccharide enhanced dosimeters were found to have a higher dose sensitivity over a standard FAX gel as measured by both optical density change and magnetic resonance imaging (MRI). With optical density measurement, OD-dose sensitivity increases were up to 55% for glucose, 122% for sucrose and 43% for starch, while locust bean gum did not give a consistent response. With MRI, R 1 -dose sensitivity increases were up to 178% with sucrose addition. The FAX gel with sucrose was studied in greatest detail. The OD-dose sensitivity dependence on cooling rate was reduced for the sucrose FAX gel over the standard FAX gel, which has significant implications for uniform dose sensitivity in large gel phantoms. The thermal oxidation rate in the sucrose FAX gel was up to 2.3 times higher than in the standard gel. The OD-dose sensitivity of oxygenated sucrose FAX gels was 4.3 times greater than standard FAX gels, while continued enhancement in OD-dose sensitivity with increased sucrose concentrations beyond 2.0 g/l was found only for the oxygenated sucrose FAX gels. Both the molar absorption coefficient of the ferric ion-xylenol orange complex at 543 nm and gel pH were not affected by the presence of sucrose, with the implication that the higher OD-dose sensitivity of gels with saccharides is due to increased chain reaction production of ferric ions

  19. Application of the denaturing gradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliate communities in soil

    OpenAIRE

    Jousset, Alexandre; Lara, Enrique; Nikolausz, Marcell; Harms, Hauke; Chatzinotasa, Antonis

    2010-01-01

    Ciliates (or Ciliophora) are ubiquitous organisms which can be widely used as bioindicators in ecosystems exposed to anthropogenic and industrial influences. The evaluation of the environmental impact on soil ciliate communities with methods relying on morphology-based identification may be hampered by the large number of samples usually required for a statistically supported, reliable conclusion. Cultivation-independent molecular-biological diagnostic tools are a promising alternative to gre...

  20. Isoenergic modification of whey protein structure by denaturation and crosslinking using transglutaminase

    DEFF Research Database (Denmark)

    Stender, Emil G. P.; Koutina, Glykeria; Almdal, Kristoffer

    2018-01-01

    Transglutaminase (TG) catalyzes formation of covalent bonds between lysine and glutamine side chains and has applications in manipulation of food structure. Physical properties of a whey protein mixture (SPC) denatured either at elevated pH or by heat-treatment and followed by TG catalyzed...