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Related Concept Videos

Isotopes01:12

Isotopes

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Elements have a set number of protons that determines their atomic number (Z). For example, all atoms with eight protons are oxygen; however, the number of neutrons can vary for atoms of the same element. The sum of the number of protons and the number of neutrons is the mass number (A). Atoms with the same atomic number but different mass numbers are called isotopes. Elements can have multiple isotopes, for example, carbon-12, carbon-13, and carbon-14.
An element's atomic mass, or weight,...
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Data Collection by Experiments01:13

Data Collection by Experiments

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Data collection is a systematic method of obtaining, observing, measuring, and analyzing accurate information. An experimental study is a standard method of data collection that involves the manipulation of the samples by applying some form of treatment prior to data collection. It refers to manipulating one variable to determine its changes on another variable. The sample subjected to treatment is known as “experimental units.”
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Labeling DNA Probes03:31

Labeling DNA Probes

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DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
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Elements: Chemical Symbols and Isotopes02:31

Elements: Chemical Symbols and Isotopes

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A chemical symbol is an abbreviation used to indicate an element or an atom of an element. For example, the symbol for mercury is Hg. The same symbol is used to indicate one atom of mercury (microscopic domain) or to label a container of many atoms of the element mercury (macroscopic domain).
Some symbols are derived from the common English name of the element; others are abbreviations of the name in another language — Latin, Greek or German. For example, the symbol for aluminum (common name)...
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Analysis of Population Pharmacokinetic Data01:12

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Analysis of population pharmacokinetic data involves studying the behavior of drugs within diverse populations to understand their pharmacokinetic parameters. Traditional pharmacokinetic methods typically involve collecting samples from a few individuals and estimating these parameters. While these methods are commonly used, they have limitations in capturing the variability in drug response among individuals or heterogeneous populations. Population pharmacokinetics is employed to address these...
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Isotopes and Radioisotopes01:28

Isotopes and Radioisotopes

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In the early 1900s, English chemist Frederick Soddy realized that an element could have atoms with different masses that were chemically indistinguishable. These different types are called isotopes — atoms of the same element that differ in mass. Isotopes differ in mass because they have different numbers of neutrons but are chemically identical because they have the same number of protons. Soddy was awarded the Nobel Prize in Chemistry in 1921 for this discovery.
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DNA Stable-Isotope Probing DNA-SIP
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Data Analysis for DNA Stable Isotope Probing Experiments Using Multiple Window High-Resolution SIP.

Samuel E Barnett1, Nicholas D Youngblut2, Daniel H Buckley3

  • 1School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.

Methods in Molecular Biology (Clifton, N.J.)
|August 14, 2019
PubMed
Summary
This summary is machine-generated.

DNA stable isotope probing (DNA-SIP) identifies microbes that incorporate labeled substrates into their DNA. The multiple window high-resolution DNA-SIP (MW-HR-SIP) method improves accuracy and is implemented in R.

Keywords:
DNA-SIPHigh throughput sequencingRStable isotope probing

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Area of Science:

  • Microbiology
  • Molecular Biology
  • Bioinformatics

Background:

  • DNA stable isotope probing (DNA-SIP) is a powerful technique for identifying microorganisms that utilize specific substrates.
  • Accurate analysis of DNA-SIP sequencing data is crucial for understanding microbial community functions.
  • Existing methods for DNA-SIP data analysis can be complex and may lack sufficient accuracy.

Purpose of the Study:

  • To introduce and describe the multiple window high-resolution DNA-SIP (MW-HR-SIP) method for analyzing DNA-SIP sequencing data.
  • To highlight the improved accuracy and ease of implementation of MW-HR-SIP.
  • To provide guidance on experimental design parameters affecting DNA-SIP analysis accuracy.

Main Methods:

  • Development and implementation of the MW-HR-SIP method for DNA-SIP data analysis.
  • Utilizing the statistical platform R for data processing and analysis.
  • Evaluation of key experimental parameters influencing the accuracy of DNA-SIP results.

Main Results:

  • The MW-HR-SIP method demonstrates enhanced accuracy compared to other DNA-SIP analysis techniques.
  • The method is readily implementable within the R statistical environment.
  • Identification of critical experimental parameters that impact the precision of microbial identification via DNA-SIP.

Conclusions:

  • MW-HR-SIP offers a more accurate and accessible approach for analyzing DNA-SIP sequencing data.
  • Proper consideration of experimental design parameters is essential for maximizing the reliability of DNA-SIP studies.
  • This method facilitates a deeper understanding of microbial assimilation processes in various environments.