cscl centrifugation  (Beckman Coulter)


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    Structured Review

    Beckman Coulter cscl centrifugation
    SIPSim output provides data that approximates results obtained from <t>DNA-SIP</t> experiments. The <t>CsCl</t> gradient BD distributions of diverse amplicon fragments ( n = 1,147 taxa) are depicted such that the distribution of each taxon is represented by a different color. All taxa in the control had 0% atom excess 13 C, while 10% of taxa in the treatment were randomly assigned 100% atom excess 13 C. Most unlabeled amplicon fragments occur within the range of 1.69–1.72 g ml −1 , while 13 C-labeled taxa are shifted into higher BD fractions (pre-sequencing, top panels). During the process of high-throughput DNA sequencing amplicon fragments are randomly sampled from each fraction, and this sampling effect alters the shape of the fragment distributions observed in DNA-SIP experiments (post-sequencing, middle panel) relative to the actual distribution of DNA in the gradient (top panels). Typically, data from DNA-SIP experiments are transformed into relative abundance values (post-sequencing, bottom panel) prior to analysis. Identification of taxa that have incorporated isotope requires comparison of amplicon fragment relative abundance distributions in treatment relative to control gradients. The dashed vertical line is provided as a point of reference and designates the theoretical buoyant density of an unlabeled DNA fragment with 50% G + C (as modeled in Equation 1).
    Cscl Centrifugation, supplied by Beckman Coulter, used in various techniques. Bioz Stars score: 96/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/cscl centrifugation/product/Beckman Coulter
    Average 96 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    cscl centrifugation - by Bioz Stars, 2022-12
    96/100 stars

    Images

    1) Product Images from "SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments"

    Article Title: SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2018.00570

    SIPSim output provides data that approximates results obtained from DNA-SIP experiments. The CsCl gradient BD distributions of diverse amplicon fragments ( n = 1,147 taxa) are depicted such that the distribution of each taxon is represented by a different color. All taxa in the control had 0% atom excess 13 C, while 10% of taxa in the treatment were randomly assigned 100% atom excess 13 C. Most unlabeled amplicon fragments occur within the range of 1.69–1.72 g ml −1 , while 13 C-labeled taxa are shifted into higher BD fractions (pre-sequencing, top panels). During the process of high-throughput DNA sequencing amplicon fragments are randomly sampled from each fraction, and this sampling effect alters the shape of the fragment distributions observed in DNA-SIP experiments (post-sequencing, middle panel) relative to the actual distribution of DNA in the gradient (top panels). Typically, data from DNA-SIP experiments are transformed into relative abundance values (post-sequencing, bottom panel) prior to analysis. Identification of taxa that have incorporated isotope requires comparison of amplicon fragment relative abundance distributions in treatment relative to control gradients. The dashed vertical line is provided as a point of reference and designates the theoretical buoyant density of an unlabeled DNA fragment with 50% G + C (as modeled in Equation 1).
    Figure Legend Snippet: SIPSim output provides data that approximates results obtained from DNA-SIP experiments. The CsCl gradient BD distributions of diverse amplicon fragments ( n = 1,147 taxa) are depicted such that the distribution of each taxon is represented by a different color. All taxa in the control had 0% atom excess 13 C, while 10% of taxa in the treatment were randomly assigned 100% atom excess 13 C. Most unlabeled amplicon fragments occur within the range of 1.69–1.72 g ml −1 , while 13 C-labeled taxa are shifted into higher BD fractions (pre-sequencing, top panels). During the process of high-throughput DNA sequencing amplicon fragments are randomly sampled from each fraction, and this sampling effect alters the shape of the fragment distributions observed in DNA-SIP experiments (post-sequencing, middle panel) relative to the actual distribution of DNA in the gradient (top panels). Typically, data from DNA-SIP experiments are transformed into relative abundance values (post-sequencing, bottom panel) prior to analysis. Identification of taxa that have incorporated isotope requires comparison of amplicon fragment relative abundance distributions in treatment relative to control gradients. The dashed vertical line is provided as a point of reference and designates the theoretical buoyant density of an unlabeled DNA fragment with 50% G + C (as modeled in Equation 1).

    Techniques Used: Amplification, Labeling, Sequencing, High Throughput Screening Assay, DNA Sequencing, Sampling, Transformation Assay

    Empirical DNA-SIP data shows that unlabeled DNA is found widely within the gradient and that changes in beta-diversity can alter the composition of “heavy” fractions in the absence of isotopically labeled substrates. The DNA is from soil communities incubated for 1, 3, 6, 14, 30, or 48 days following the addition of an unlabeled nutrient mixture. SSU rRNA genes were amplified and sequenced from approximately 24 fractions from each gradient, these amplicons were used to identify the BD variance of amplicon fragments derived from discrete OTUs. The DNA concentration of each gradient fraction was measured using Picogreen assay (A) . These values are normalized to the maximum concentration within each gradient. The amplicon diversity within each gradient fraction was measured using the Shannon Index, showing that the diversity of heavy fractions differs between samples even in the absence of isotopic labeling (B) . The correlograms (C) reveal autocorrelation (measured with Mantel tests) between taxonomic similarity and fraction BD within each gradient. The variance in OTU BD is positively correlated with OTU pre-fractionation relative abundance, with highly abundant OTUs found throughout the CsCl gradient (D) . To improve clarity, single OTUs in (D) were binned into hexagons, with darker shading indicating more OTUs.
    Figure Legend Snippet: Empirical DNA-SIP data shows that unlabeled DNA is found widely within the gradient and that changes in beta-diversity can alter the composition of “heavy” fractions in the absence of isotopically labeled substrates. The DNA is from soil communities incubated for 1, 3, 6, 14, 30, or 48 days following the addition of an unlabeled nutrient mixture. SSU rRNA genes were amplified and sequenced from approximately 24 fractions from each gradient, these amplicons were used to identify the BD variance of amplicon fragments derived from discrete OTUs. The DNA concentration of each gradient fraction was measured using Picogreen assay (A) . These values are normalized to the maximum concentration within each gradient. The amplicon diversity within each gradient fraction was measured using the Shannon Index, showing that the diversity of heavy fractions differs between samples even in the absence of isotopic labeling (B) . The correlograms (C) reveal autocorrelation (measured with Mantel tests) between taxonomic similarity and fraction BD within each gradient. The variance in OTU BD is positively correlated with OTU pre-fractionation relative abundance, with highly abundant OTUs found throughout the CsCl gradient (D) . To improve clarity, single OTUs in (D) were binned into hexagons, with darker shading indicating more OTUs.

    Techniques Used: Labeling, Incubation, Amplification, Derivative Assay, Concentration Assay, Picogreen Assay, Isotopic Labeling, Fractionation

    2) Product Images from "SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments"

    Article Title: SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2018.00570

    SIPSim output provides data that approximates results obtained from DNA-SIP experiments. The CsCl gradient BD distributions of diverse amplicon fragments ( n = 1,147 taxa) are depicted such that the distribution of each taxon is represented by a different color. All taxa in the control had 0% atom excess 13 C, while 10% of taxa in the treatment were randomly assigned 100% atom excess 13 C. Most unlabeled amplicon fragments occur within the range of 1.69–1.72 g ml −1 , while 13 C-labeled taxa are shifted into higher BD fractions (pre-sequencing, top panels). During the process of high-throughput DNA sequencing amplicon fragments are randomly sampled from each fraction, and this sampling effect alters the shape of the fragment distributions observed in DNA-SIP experiments (post-sequencing, middle panel) relative to the actual distribution of DNA in the gradient (top panels). Typically, data from DNA-SIP experiments are transformed into relative abundance values (post-sequencing, bottom panel) prior to analysis. Identification of taxa that have incorporated isotope requires comparison of amplicon fragment relative abundance distributions in treatment relative to control gradients. The dashed vertical line is provided as a point of reference and designates the theoretical buoyant density of an unlabeled DNA fragment with 50% G + C (as modeled in Equation 1).
    Figure Legend Snippet: SIPSim output provides data that approximates results obtained from DNA-SIP experiments. The CsCl gradient BD distributions of diverse amplicon fragments ( n = 1,147 taxa) are depicted such that the distribution of each taxon is represented by a different color. All taxa in the control had 0% atom excess 13 C, while 10% of taxa in the treatment were randomly assigned 100% atom excess 13 C. Most unlabeled amplicon fragments occur within the range of 1.69–1.72 g ml −1 , while 13 C-labeled taxa are shifted into higher BD fractions (pre-sequencing, top panels). During the process of high-throughput DNA sequencing amplicon fragments are randomly sampled from each fraction, and this sampling effect alters the shape of the fragment distributions observed in DNA-SIP experiments (post-sequencing, middle panel) relative to the actual distribution of DNA in the gradient (top panels). Typically, data from DNA-SIP experiments are transformed into relative abundance values (post-sequencing, bottom panel) prior to analysis. Identification of taxa that have incorporated isotope requires comparison of amplicon fragment relative abundance distributions in treatment relative to control gradients. The dashed vertical line is provided as a point of reference and designates the theoretical buoyant density of an unlabeled DNA fragment with 50% G + C (as modeled in Equation 1).

    Techniques Used: Amplification, Labeling, Sequencing, High Throughput Screening Assay, DNA Sequencing, Sampling, Transformation Assay

    Empirical DNA-SIP data shows that unlabeled DNA is found widely within the gradient and that changes in beta-diversity can alter the composition of “heavy” fractions in the absence of isotopically labeled substrates. The DNA is from soil communities incubated for 1, 3, 6, 14, 30, or 48 days following the addition of an unlabeled nutrient mixture. SSU rRNA genes were amplified and sequenced from approximately 24 fractions from each gradient, these amplicons were used to identify the BD variance of amplicon fragments derived from discrete OTUs. The DNA concentration of each gradient fraction was measured using Picogreen assay (A) . These values are normalized to the maximum concentration within each gradient. The amplicon diversity within each gradient fraction was measured using the Shannon Index, showing that the diversity of heavy fractions differs between samples even in the absence of isotopic labeling (B) . The correlograms (C) reveal autocorrelation (measured with Mantel tests) between taxonomic similarity and fraction BD within each gradient. The variance in OTU BD is positively correlated with OTU pre-fractionation relative abundance, with highly abundant OTUs found throughout the CsCl gradient (D) . To improve clarity, single OTUs in (D) were binned into hexagons, with darker shading indicating more OTUs.
    Figure Legend Snippet: Empirical DNA-SIP data shows that unlabeled DNA is found widely within the gradient and that changes in beta-diversity can alter the composition of “heavy” fractions in the absence of isotopically labeled substrates. The DNA is from soil communities incubated for 1, 3, 6, 14, 30, or 48 days following the addition of an unlabeled nutrient mixture. SSU rRNA genes were amplified and sequenced from approximately 24 fractions from each gradient, these amplicons were used to identify the BD variance of amplicon fragments derived from discrete OTUs. The DNA concentration of each gradient fraction was measured using Picogreen assay (A) . These values are normalized to the maximum concentration within each gradient. The amplicon diversity within each gradient fraction was measured using the Shannon Index, showing that the diversity of heavy fractions differs between samples even in the absence of isotopic labeling (B) . The correlograms (C) reveal autocorrelation (measured with Mantel tests) between taxonomic similarity and fraction BD within each gradient. The variance in OTU BD is positively correlated with OTU pre-fractionation relative abundance, with highly abundant OTUs found throughout the CsCl gradient (D) . To improve clarity, single OTUs in (D) were binned into hexagons, with darker shading indicating more OTUs.

    Techniques Used: Labeling, Incubation, Amplification, Derivative Assay, Concentration Assay, Picogreen Assay, Isotopic Labeling, Fractionation

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