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Combinatorial Gene Control02:33

Combinatorial Gene Control

Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
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Circadian Rhythms and Gene Regulation

The biological clock is involved in many aspects of regulating complex physiology in all animals. It was in 1935 when German zoologists, Hans Kalmus and Erwin Bünning, discovered the existence of circadian rhythm in Drosophila melanogaster. However, the internal molecular mechanisms behind the circadian clock remained a mystery until 1984, when Jeffrey C. Hall, Michael Rosbash, and Michael W. Young discovered the expression of the Per gene oscillating over a 24-hour cycle. In subsequent years,...
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The circadian—or biological—clock is an intrinsic, timekeeping, molecular mechanism that allows plants to coordinate physiological activities over 24-hour cycles called circadian rhythms. Photoperiodism is a collective term for the biological responses of plants to variations in the relative lengths of dark and light periods. The period of light-exposure is called the photoperiod.
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Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
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Reliably Engineering and Controlling Stable Optogenetic Gene Circuits in Mammalian Cells
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Published on: July 6, 2021

Robust network clocks: design of genetic oscillators as a complex combinatorial optimization problem.

Yasuaki Kobayashi1, Tatsuo Shibata, Yoshiki Kuramoto

  • 1Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society, Berlin, Germany. yasuaki@fhi-berlin.mpg.de

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|July 30, 2011
PubMed
Summary

Researchers designed robust genetic clocks with specific oscillation periods. These networks are resilient to damage and noise, enabling the creation of reliable biological timing mechanisms.

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Area of Science:

  • Systems biology
  • Computational biology
  • Network science

Background:

  • Designing biological networks with specific dynamic properties is challenging.
  • Network robustness against perturbations is crucial for reliable function.

Purpose of the Study:

  • To construct genetic networks exhibiting limit-cycle oscillations with prescribed periods.
  • To ensure these networks are robust against structural perturbations like link/node deletion and noise.

Main Methods:

  • Utilized complex combinatorial optimization techniques.
  • Designed genetic networks with inherent robustness features.

Main Results:

  • Successfully constructed genetic clocks with controllable oscillation periods.
  • Demonstrated robustness against link deletion, node deletion, and applied noise.
  • Obtained large ensembles of these robust genetic clocks.

Conclusions:

  • Complex combinatorial optimization is effective for designing robust network systems with desired dynamics.
  • The developed methods can be applied to create robust network oscillators across various origins.