The Experts below are selected from a list of 222 Experts worldwide ranked by ideXlab platform
Arturas Petronis - One of the best experts on this subject based on the ideXlab platform.
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profiling dna methylation from small amounts of genomic dna starting material efficient Sodium Bisulfite conversion and subsequent whole genome amplification
Methods of Molecular Biology, 2009Co-Authors: Jonathan Mill, Arturas PetronisAbstract:noindent Sodium Bisulfite modification-based fine mapping of methylated cytosines represents the gold standard technique for DNA methylation studies. A major problem with this approach, however, is that it results in considerable DNA degradation, and large quantities of genomic DNA material are needed if numerous genomic regions are to be profiled. This chapter describes a method for profiling DNA methylation from small amounts of genomic-DNA starting material utilizing an efficient Sodium Bisulfite conversion method followed by whole-genome amplification (WGA). WGA is a useful method to overcome the problem of low initial amount of DNA and/or severe DNA degradation during conventional Sodium Bisulfite treatment in studies investigating DNA methylation. WGA is a relatively inexpensive process that can be optimized for high-throughput application and enables the thorough investigation of methylation at numerous genomic locations on samples for which DNA availability is low. Data from our lab has demonstrated that Bisulfite-treated DNA amplified using WGA can be used for a range of downstream DNA methylation mapping procedures, including Bisulfite-primer optimization, the sequencing of cloned PCR products, MS-SNuPE, and Pyrosequencing.
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whole genome amplification of Sodium Bisulfite treated dna allows the accurate estimate of methylated cytosine density in limited dna resources
BioTechniques, 2006Co-Authors: Jonathan Mill, Simin Yazdanpanah, Eva Gückel, Sigrid Ziegler, Zachary A Kaminsky, Arturas PetronisAbstract:Sodium Bisulfite modification-based fine mapping of methylated cytosines represents the gold standard technique for DNA methylation studies. A major problem with this approach, however, is that it results in considerable DNA degradation, and large quantities of genomic DNA material are needed if numerous genomic regions are to be profiled. In this study, we examined whether whole genome amplification (WGA) techniques can be applied to Sodium Bisulfite-treated DNA and whether WGA would bias DNA methylation results. Sodium Bisulfite-treated DNA was amplified using a standard WGA method: optimized primer-extension preamplification (PEP) with degenerate primers. Following the PCR of Bisulfite-treated DNA, the DNA methylation profiles of specific DNA fragments were assessed using three approaches: (i) direct sequencing of the overall product; (ii) the sequencing of cloned PCR products; and (iii) methylation-sensitive single nucleotide primer extension (MS-SNuPE)—and compared with those obtained from Bisulfite-...
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Whole genome amplification of Sodium Bisulfite-treated DNA allows the accurate estimate of methylated cytosine density in limited DNA resources.
BioTechniques, 2006Co-Authors: Jonathan Mill, Simin Yazdanpanah, Eva Gückel, Sigrid Ziegler, Zachary Kaminsky, Arturas PetronisAbstract:Sodium Bisulfite modification-based fine mapping of methylated cytosines represents the gold standard technique for DNA methylation studies. A major problem with this approach, however is that it results in considerable DNA degradation, and large quantities of genomic DNA material are needed if numerous genomic regions are to be profiled. In this study, we examined whether whole genome amplification (WGA) techniques can be applied to Sodium Bisulfite-treated DNA and whether WGA would bias DNA methylation results. Sodium Bisulfite-treated DNA was amplified using a standard WGA method: optimized primer-extension preamplification (PEP) with degenerate primers. Following the PCR of Bisulfite-treated DNA, the DNA methylation profiles of specific DNA fragments were assessed using three approaches: (i) direct sequencing of the overall product; (ii) the sequencing of cloned PCR products; and (iii) methylation-sensitive single nucleotide primer extension (MS-SNuPE)--and compared with those obtained from Bisulfite-treated DNA not subjected to WGA. Our data indicates that the DNA methylation profiles obtained from WGA of Sodium Bisulfite-treated DNA are consistent with those obtained from non-WGA DNA. The average difference in methylation percentage calculated from the two sets of template using MS-SNuPE was 4%. If our results are replicated on other genomic loci, WGA may become a useful technique in DNA methylation studies.
Jonathan Mill - One of the best experts on this subject based on the ideXlab platform.
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profiling dna methylation from small amounts of genomic dna starting material efficient Sodium Bisulfite conversion and subsequent whole genome amplification
Methods of Molecular Biology, 2009Co-Authors: Jonathan Mill, Arturas PetronisAbstract:noindent Sodium Bisulfite modification-based fine mapping of methylated cytosines represents the gold standard technique for DNA methylation studies. A major problem with this approach, however, is that it results in considerable DNA degradation, and large quantities of genomic DNA material are needed if numerous genomic regions are to be profiled. This chapter describes a method for profiling DNA methylation from small amounts of genomic-DNA starting material utilizing an efficient Sodium Bisulfite conversion method followed by whole-genome amplification (WGA). WGA is a useful method to overcome the problem of low initial amount of DNA and/or severe DNA degradation during conventional Sodium Bisulfite treatment in studies investigating DNA methylation. WGA is a relatively inexpensive process that can be optimized for high-throughput application and enables the thorough investigation of methylation at numerous genomic locations on samples for which DNA availability is low. Data from our lab has demonstrated that Bisulfite-treated DNA amplified using WGA can be used for a range of downstream DNA methylation mapping procedures, including Bisulfite-primer optimization, the sequencing of cloned PCR products, MS-SNuPE, and Pyrosequencing.
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whole genome amplification of Sodium Bisulfite treated dna allows the accurate estimate of methylated cytosine density in limited dna resources
BioTechniques, 2006Co-Authors: Jonathan Mill, Simin Yazdanpanah, Eva Gückel, Sigrid Ziegler, Zachary A Kaminsky, Arturas PetronisAbstract:Sodium Bisulfite modification-based fine mapping of methylated cytosines represents the gold standard technique for DNA methylation studies. A major problem with this approach, however, is that it results in considerable DNA degradation, and large quantities of genomic DNA material are needed if numerous genomic regions are to be profiled. In this study, we examined whether whole genome amplification (WGA) techniques can be applied to Sodium Bisulfite-treated DNA and whether WGA would bias DNA methylation results. Sodium Bisulfite-treated DNA was amplified using a standard WGA method: optimized primer-extension preamplification (PEP) with degenerate primers. Following the PCR of Bisulfite-treated DNA, the DNA methylation profiles of specific DNA fragments were assessed using three approaches: (i) direct sequencing of the overall product; (ii) the sequencing of cloned PCR products; and (iii) methylation-sensitive single nucleotide primer extension (MS-SNuPE)—and compared with those obtained from Bisulfite-...
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Whole genome amplification of Sodium Bisulfite-treated DNA allows the accurate estimate of methylated cytosine density in limited DNA resources.
BioTechniques, 2006Co-Authors: Jonathan Mill, Simin Yazdanpanah, Eva Gückel, Sigrid Ziegler, Zachary Kaminsky, Arturas PetronisAbstract:Sodium Bisulfite modification-based fine mapping of methylated cytosines represents the gold standard technique for DNA methylation studies. A major problem with this approach, however is that it results in considerable DNA degradation, and large quantities of genomic DNA material are needed if numerous genomic regions are to be profiled. In this study, we examined whether whole genome amplification (WGA) techniques can be applied to Sodium Bisulfite-treated DNA and whether WGA would bias DNA methylation results. Sodium Bisulfite-treated DNA was amplified using a standard WGA method: optimized primer-extension preamplification (PEP) with degenerate primers. Following the PCR of Bisulfite-treated DNA, the DNA methylation profiles of specific DNA fragments were assessed using three approaches: (i) direct sequencing of the overall product; (ii) the sequencing of cloned PCR products; and (iii) methylation-sensitive single nucleotide primer extension (MS-SNuPE)--and compared with those obtained from Bisulfite-treated DNA not subjected to WGA. Our data indicates that the DNA methylation profiles obtained from WGA of Sodium Bisulfite-treated DNA are consistent with those obtained from non-WGA DNA. The average difference in methylation percentage calculated from the two sets of template using MS-SNuPE was 4%. If our results are replicated on other genomic loci, WGA may become a useful technique in DNA methylation studies.
Moacir Cardoso Elias - One of the best experts on this subject based on the ideXlab platform.
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Thiamine content and technological quality properties of parboiled rice treated with Sodium Bisulfite: Benefits and food safety risk
Journal of Food Composition and Analysis, 2015Co-Authors: Nathan Levien Vanier, Jose De J Berrios, Leandro da Conceição Oliveira, Ricardo Tadeu Paraginski, Moacir Cardoso EliasAbstract:Rice is a staple food for more than half of the world's population. The parboiling process is known to increase the nutritional value of milled rice, but the process darkens the grains, with a corresponding negative effect on consumer acceptability. The aim of this study was to evaluate the effects of using different concentrations of Sodium Bisulfite (0, 0.2, 0.4, 0.6, 0.8, 1.0%) during the soaking step of rice parboiling process on the thiamine content and technological properties of parboiled rice. Moreover, the residual sulfite content in parboiled grains was also evaluated. The lowest concentration of 0.2% Sodium Bisulfite was able to significantly (p
Xiuzhi Susan Sun - One of the best experts on this subject based on the ideXlab platform.
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Sodium Bisulfite-Induced Changes in the Physicochemical, Surface and Adhesive Properties of Soy β-Conglycinin
Journal of the American Oil Chemists' Society, 2010Co-Authors: Lu Zhang, Xiuzhi Susan SunAbstract:The effects of Sodium Bisulfite on the electrophoresis profile; turbidity; and thermal, surface, and adhesive properties of soy β-conglycinin protein were studied. Sodium Bisulfite dissociated high-molecular-weight aggregates in the protein, and the aggregate percentage decreased with increasing Sodium Bisulfite concentration. Denaturation temperature of Sodium-Bisulfite-treated β-conglycinin increased as Sodium Bisulfite increased. However, at high Sodium Bisulfite concentration (i.e. 36 g/L), denaturation enthalpy decreased significantly. Sodium Bisulfite caused changes in the β-conglycinin secondary structure and promoted ionization of lysine residues as indicated by FT-IR results. A sudden drop in turbidity at pH 4.8 was observed at the same salt level. The contact angle of β-conglycinin on cherry wood reached its minimum at 6 g/L Sodium Bisulfite and 24 g/L on glass. Water resistance of β-conglycinin was improved but not significantly by 6 g/L Sodium Bisulfite at pH 9.5. An obvious increase in adhesion strength of the protein occurred at 3 and 6 g/L Sodium Bisulfite at pH 4.8. A high Sodium Bisulfite concentration at 36 g/L sharply reduced the adhesive performance of β-conglycinin.
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Effect of Sodium Bisulfite on properties of soybean glycinin
Journal of Agricultural and Food Chemistry, 2008Co-Authors: Lu Zhang, Xiuzhi Susan SunAbstract:The objective of this work is to understand the function of glycinin in soy protein adhesive formation. Glycinin protein was treated with Sodium Bisulfite, and physicochemical, morphological, and adhesion properties of the modified soy glycinin were characterized. More disulfide bonds that associated acidic and basic polypeptides of glycinin broke as the Sodium Bisulfite concentration increased. The reduction of disulfide bonds did not decrease the thermal stability of glycinin. Instead, the denaturation temperature of modified glycinin increased as Sodium Bisulfite increased. Sodium Bisulfite-induced disulfide bond cleavage increased the surface hydrophobicity of modified glycinin. Hydrophobic force is the main driving force for glycinin aggregation, and the balance between hydrophobic and electrostatic forces makes glycinin form chainlike aggregates. The adhesive strength and water resistance of glycinin dropped significantly at lower levels of Sodium Bisulfite and then increased as the amount of Sodium Bisulfite increased up to 24 g/L. The adhesive performance decreased again with further addition of Sodium Bisulfite. The adhesive strength of glycinin was not improved by Sodium Bisulfite modification in the studied range.
Nathan Levien Vanier - One of the best experts on this subject based on the ideXlab platform.
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Thiamine content and technological quality properties of parboiled rice treated with Sodium Bisulfite: Benefits and food safety risk
Journal of Food Composition and Analysis, 2015Co-Authors: Nathan Levien Vanier, Jose De J Berrios, Leandro da Conceição Oliveira, Ricardo Tadeu Paraginski, Moacir Cardoso EliasAbstract:Rice is a staple food for more than half of the world's population. The parboiling process is known to increase the nutritional value of milled rice, but the process darkens the grains, with a corresponding negative effect on consumer acceptability. The aim of this study was to evaluate the effects of using different concentrations of Sodium Bisulfite (0, 0.2, 0.4, 0.6, 0.8, 1.0%) during the soaking step of rice parboiling process on the thiamine content and technological properties of parboiled rice. Moreover, the residual sulfite content in parboiled grains was also evaluated. The lowest concentration of 0.2% Sodium Bisulfite was able to significantly (p
