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Elements and Compounds01:27

Elements and Compounds

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Pure substances consist of only one type of matter. A pure substance can be an element or a compound. An element consists of only one type of atom, while a compound consists of two or more types of atoms held together by a chemical bond.
Elements
Elements are classified as atomic or molecular based on the nature of their basic units. They are unique forms of matter with specific chemical and physical properties that cannot break down into smaller substances by ordinary chemical reactions. There...
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Periodic Classification of the Elements04:00

Periodic Classification of the Elements

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The periodic table arranges atoms based on increasing atomic number so that elements with the same chemical properties recur periodically. When their electron configurations are added to the table, a periodic recurrence of similar electron configurations in the outer shells of these elements is observed. Because they are in the outer shells of an atom, valence electrons play the most important role in chemical reactions. The outer electrons have the highest energy of the electrons in an atom...
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Classification of Elements and Compounds02:54

Classification of Elements and Compounds

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Pure substances consist of only one type of matter. A pure substance can be an element or a compound. An element consists of only one type of atom, while a compound consists of two or more types of atoms held together by a chemical bond. Elements are classified as atomic or molecular based on the nature of their basic units.
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Key Elements for Plant Nutrition02:35

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Like all living organisms, plants require organic and inorganic nutrients to survive, reproduce, grow and maintain homeostasis. To identify nutrients that are essential for plant functioning, researchers have leveraged a technique called hydroponics. In hydroponic culture systems, plants are grown—without soil—in water-based solutions containing nutrients. At least 17 nutrients have been identified as essential elements required by plants. Plants acquire these elements from the...
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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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The Periodic Table and Organismal Elements00:57

The Periodic Table and Organismal Elements

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Overview
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Author Spotlight: Decoding RNA Methylation's Role in Pancreatic Cancer - A Single-Base Resolution Study
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High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS).

Arundhati Bakshi1, Muhammad B Ekram1, Joomyeong Kim2

  • 1Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|January 17, 2019
PubMed
Summary
This summary is machine-generated.

High-throughput targeted repeat element bisulfite sequencing (HT-TREBS) offers a genome-wide method to measure retrotransposon methylation at specific locations. This technique enables detailed analysis of epigenetic modifications across the genome.

Keywords:
AluDNA methylationERVEndogenous retrovirusHT-TREBSLINELong interspersed elementLong terminal repeatRepeat elementsRetrotransposonsSINEShort interspersed element

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Area of Science:

  • Epigenetics
  • Genomics
  • Molecular Biology

Background:

  • Retrotransposons are mobile genetic elements that can influence genome stability and function.
  • Understanding retrotransposon methylation is crucial for studying gene regulation and disease.
  • Existing methods may lack the specificity or scale required for comprehensive analysis.

Purpose of the Study:

  • To introduce and describe High-throughput targeted repeat element bisulfite sequencing (HT-TREBS).
  • To provide a detailed protocol for library construction and bioinformatics analysis for HT-TREBS.
  • To enable locus-specific, genome-wide assessment of retrotransposon methylation levels.

Main Methods:

  • Genomic DNA is sheared and ligated to Ion Torrent adaptors.
  • Bisulfite conversion followed by amplification using targeted retrotransposon primers with adaptor extensions.
  • Library preparation includes size selection and sequencing on a next-generation platform.
  • Retrotransposon loci are mapped using unique flanking sequences, and methylation levels are calculated with BiQ Analyzer HT.

Main Results:

  • HT-TREBS successfully assays methylation levels of individual retrotransposon loci.
  • The method provides locus-specific and genome-wide coverage.
  • A complete protocol and bioinformatics pipeline are established for the technique.

Conclusions:

  • HT-TREBS is an effective method for detailed retrotransposon methylation analysis.
  • The described protocol facilitates the application of HT-TREBS in various research settings.
  • This technique advances the study of epigenetic regulation by mobile elements.