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Related Concept Videos

DNA Isolation01:24

DNA Isolation

DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...

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The MPLEx Protocol for Multi-omic Analyses of Soil Samples
10:12

The MPLEx Protocol for Multi-omic Analyses of Soil Samples

Published on: May 30, 2018

Direct cellular lysis/protein extraction protocol for soil metaproteomics.

Karuna Chourey1, Janet Jansson, Nathan VerBerkmoes

  • 1Oak Ridge National Laboratory, Tennessee 37831-6131, United States.

Journal of Proteome Research
|October 20, 2010
PubMed
Summary

We developed a new direct method for deep soil microbe proteome analysis using sodium dodecyl sulfate (SDS) and trichloroacetic acid (TCA) precipitation. This technique allows for the most comprehensive soil microbial proteome characterization to date.

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Extraction of High Molecular Weight Genomic DNA from Soils and Sediments
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Extraction of High Molecular Weight Genomic DNA from Soils and Sediments

Published on: November 10, 2009

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Last Updated: Jun 8, 2026

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10:12

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Published on: May 30, 2018

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis
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Extraction of High Molecular Weight Genomic DNA from Soils and Sediments
11:24

Extraction of High Molecular Weight Genomic DNA from Soils and Sediments

Published on: November 10, 2009

Area of Science:

  • Environmental microbiology
  • Proteomics
  • Soil science

Background:

  • Soil microbial communities are crucial for ecosystem functioning.
  • Characterizing soil microbial proteomes is challenging due to complex matrices.
  • Existing methods may introduce biases in protein recovery.

Purpose of the Study:

  • To develop and validate a novel direct protocol for deep soil microbial proteome characterization.
  • To compare the direct method with an indirect approach for protein extraction.
  • To assess potential biases in protein size, localization, and functional categories.

Main Methods:

  • Thermally assisted detergent-based cellular lysis (SDS) of soil samples.
  • Trichloroacetic acid (TCA) precipitation for proteome extraction and cleanup.
  • Liquid chromatography-mass spectrometry (LC-MS) for protein identification.
  • Optimization using soils inoculated with Pseudomonas putida and Arthrobacter chlorophenolicus.

Main Results:

  • The direct SDS-TCA protocol identified over 500 unique proteins per sample.
  • The method achieved deep proteome characterization without significant bias.
  • Protein identification covered a wide range of molecular masses and functional categories.
  • Comparison with an indirect method showed comparable protein identification depth.

Conclusions:

  • The novel SDS-TCA protocol enables unprecedented depth in soil microbial proteome analysis.
  • This method provides a powerful, unbiased tool for ecological studies of soil microbial communities.
  • The protocol facilitates comprehensive understanding of microbial functions in soil ecosystems.