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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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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.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...
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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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DNA Base Pairing02:27

DNA Base Pairing

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Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,
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DNA Base Pairing02:27

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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.
An isotope containing...
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DNA Stable-Isotope Probing DNA-SIP
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DNA-Based Stable Isotope Probing.

Zhongjun Jia1, Weiwei Cao2, Marcela Hernández García3

  • 1State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, People's Republic of China. jia@issas.ac.cn.

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

DNA-based stable isotope probing (DNA-SIP) links microbial activity to biogeochemical cycles. This method identifies active microbes by tracking 13C-labeled DNA, crucial for understanding microbial functions in diverse environments.

Keywords:
13C-DNADNA-SIPMicrobial ecophysiologyNext-generation sequencing

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Area of Science:

  • Microbiology
  • Environmental Science
  • Biogeochemistry

Background:

  • Microbial communities drive global biogeochemical cycles, but identifying active members remains challenging.
  • DNA-based stable isotope probing (DNA-SIP) is a key technique for linking microbial taxa to specific functions.
  • Understanding active microbial roles is vital for comprehending ecosystem processes.

Purpose of the Study:

  • To present a protocol for DNA-SIP to identify active microorganisms involved in biogeochemical processes.
  • To demonstrate the utility of DNA-SIP in linking microbial identity to function within complex environments.
  • To showcase the application of DNA-SIP using diazotrophic methanotrophs in paddy soil.

Main Methods:

  • Utilizing 13C-labeled substrates to enrich DNA of actively growing microorganisms.
  • Employing high-throughput sequencing of 16S rRNA genes to identify labeled microbes without prior knowledge.
  • Quantifying functional genes within fractionated DNA to confirm isotopic enrichment.

Main Results:

  • Successful enrichment of 13C-DNA from targeted microbial communities.
  • Identification of active microorganisms and their functional roles through DNA-SIP.
  • Demonstration of the protocol's effectiveness in a paddy soil ecosystem.

Conclusions:

  • DNA-SIP is a powerful tool for deciphering microbial community functions and their roles in biogeochemical cycles.
  • The presented protocol enables robust identification of active microbes by analyzing 13C-labeled DNA.
  • This method advances our understanding of microbial ecophysiology in environmental settings.