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Related Concept Videos

Subcellular Fractionation01:32

Subcellular Fractionation

The homogenate obtained after cell lysis contains various membrane-bound organelles that can be further separated into pure fractions by subcellular fractionation. These isolates are used to study specific cellular components, analyze localized protein activity, and are even employed in diagnostics. Fractionation is typically achieved using centrifugation methods, the most common being density-gradient and differential centrifugation.
Differential Centrifugation
Differential centrifugation is...
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Extraction: Partition and Distribution Coefficients

The distribution law or Nernst's distribution law is the law that governs the distribution of a solute between two immiscible solvents. This law, also known as the partition law, states that if a solute is added to the mixture of two immiscible solvents at a constant temperature, the solute is distributed between the two solvents in such a way that the ratio of solute concentrations in the solvents remains constant at equilibrium.
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Partial Fractions01:28

Partial Fractions

A partial fraction is a component of a rational expression represented as the sum of simpler fractions. When a rational function is expressed as a ratio of two polynomials, it can often be decomposed into a sum of fractions whose denominators are simpler polynomials, typically linear or irreducible quadratic factors. This process is called partial fraction decomposition, and it is used to simplify complex expressions for integration, solving equations, or analysis.Partial fraction decomposition...
Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
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Mass Spectrometry: Alcohol Fragmentation01:03

Mass Spectrometry: Alcohol Fragmentation

Alcohols (R-OH) ionize to lose one non-bonded electron from the oxygen atom, forming molecular ions. Due to their tendency to fragment rapidly, the intensity of the molecular ion peak in the mass spectrum is weak or sometimes absent. The fragmentation patterns for alcohols occur in two ways, i.e. ⍺-cleavage and dehydration. During ⍺-cleavage, the bond at the ⍺-position adjacent to the hydroxyl group cleaves to give a resonance-stabilized cation and a radical. However, intramolecular dehydration...
Mass Spectrometry: Long-Chain Alkane Fragmentation01:18

Mass Spectrometry: Long-Chain Alkane Fragmentation

The molecular ions of linear alkanes prefer to fragment at the carbon-carbon bond away from the end of the chain since the cleavage of an inner bond creates a stable carbocation and a stable radical. Consequently, the mass signals of linear alkanes feature intense peaks in the middle of the mass-to-charge ratio plot with weaker peaks on either end. The fragmentation of each carbon-carbon bond with the release of a methyl group in each splitting leads to prominent peaks in the mass spectra...

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A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample
11:17

A Simple Fractionated Extraction Method for the Comprehensive Analysis of Metabolites, Lipids, and Proteins from a Single Sample

Published on: June 1, 2017

Fractionation statistics.

Baoyong Wang1, Chunfang Zheng, David Sankoff

  • 1Department of Mathematics and Statistics, University of Ottawa Ottawa, Canada K1N 6N5.

BMC Bioinformatics
|December 14, 2011
PubMed
Summary
This summary is machine-generated.

Gene loss after whole genome duplication (WGD) can occur gene by gene or in larger segments. This study develops a model to estimate the rate of gene deletion (µ), suggesting it

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Whole genome duplication (WGD) leads to paralog reduction, the loss of duplicate genes.
  • The mechanism of gene loss (individual genes vs. multi-gene segments) and fractionation bias remain debated.

Purpose of the Study:

  • To develop a statistical model for estimating the rate of gene deletion (µ) after WGD.
  • To investigate whether gene loss occurs predominantly gene by gene or in larger segments.
  • To correct for biases in run length analysis caused by genome rearrangements.

Main Methods:

  • Developed a null model assuming geometrically distributed gene deletions on one homeolog.
  • Introduced a more realistic model with truncated geometric distributions for deletion events on both homeologs.
  • Simulated run length distributions and developed a deterministic recurrence to calculate underlying parameters.
  • Applied the model to 15 genomes from 6 distinct WGD events.

Main Results:

  • The model allows estimation of the gene deletion rate (µ) from run lengths of single-copy regions.
  • Simulations explored the relationship between deletion rate (µ) and run length distributions.
  • Bias correction for genome rearrangements was implemented.

Conclusions:

  • Estimates of µ from real genomic data are consistent with gene-by-gene deletion.
  • The possibility of occasional multi-gene segment deletions cannot be excluded.