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Related Concept Videos

Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Crossing over is the exchange of genetic information between homologous chromosomes during prophase I of meiosis I. Genetic recombination gives rise to allelic diversity in the newly formed daughter cells. In humans, crossing over produces genetically distinct haploid egg and sperm cells that undergo fertilization to produce unique offspring. Before cell division starts, the germ cell’s chromosome(s) undergo duplication in the S phase of the cell cycle. As the cells enter prophase I, duplicated...
Exon Recombination02:32

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

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Recombineering Homologous Recombination Constructs in Drosophila
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Recombineering Homologous Recombination Constructs in Drosophila

Published on: July 13, 2013

Ancestral recombinations graph: a reconstructability perspective using random-graphs framework.

Laxmi Parida1

  • 1Computational Biology Center, IBM T J Watson Research, Yorktown, New York, USA. parida@us.ibm.com

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|October 27, 2010
PubMed
Summary
This summary is machine-generated.

We introduce a unified random graphs framework to analyze pedigree history. This framework offers a novel topological definition for the Ancestral Recombinations Graph (ARG) and a new sampling algorithm for ARG instances.

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Design and Synthesis of a Reconfigurable DNA Accordion Rack
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Area of Science:

  • Population Genetics
  • Computational Biology
  • Graph Theory

Background:

  • Pedigree history and genetic transmission are crucial for understanding evolutionary processes.
  • Existing models for studying genetic history, such as the Ancestral Recombinations Graph (ARG), have limitations in parametrization and sampling.
  • Unifying diverse mathematical objects related to genetic history into a single framework is needed.

Purpose of the Study:

  • To develop a unified random graphs framework for studying pedigree history in ideal populations.
  • To provide a novel, topology-based definition of the Ancestral Recombinations Graph (ARG).
  • To introduce a new parameter (M) for ARG parametrization, independent of recombination rate.
  • To define the Grand Multiple Coalescent Root Ancestor (GMRCA) topologically.
  • To present a novel, uniformly sampling algorithm for constructing ARG instances.
  • To assess the reconstructability of past historical events from extant genetic sequences.

Main Methods:

  • Development of a random graphs framework to unify mathematical objects like pedigree graphs, mtDNA/NRY trees, ARGs, and Hidden Unilineal Descent (HUD).
  • Topological definition of the ARG based on graph structure, independent of recombination rate (q), using a parameter M related to non-mixing segments.
  • Topological definition of GMRCA.
  • Extension of random graph concepts to create a sampling algorithm for ARG/unilinear transmission graphs, ensuring uniform sampling.
  • Development of a measure to quantify the reconstructability of historical genetic events from extant sequences.

Main Results:

  • A unified random graphs framework encompassing various genetic history models.
  • A natural, topology-based definition of the ARG.
  • An alternative ARG parametrization using parameter M instead of recombination rate q.
  • A purely topological definition of GMRCA.
  • The first algorithm guaranteeing uniform sampling of ARG instances under an ideal population model.
  • Demonstration that joint history of local chromosomal segments is reconstructible from extant sequences.

Conclusions:

  • The random graphs framework provides a cohesive approach to studying genetic history.
  • The new ARG definition and parametrization offer insights into population dynamics separate from biological recombination.
  • The uniform sampling algorithm enables accurate simulation of genetic histories.
  • Reconstructing past evolutionary events from current genetic data is feasible.