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Using Models to (Re-)Design Synthetic Circuits.

Author(s): McCallum G, Potvin-Trottier L

Mathematical models play an important role in the design of synthetic gene circuits, by guiding the choice of biological components and their assembly into novel gene networks. Here, we present a guide for biologists to build and utilize models of gene netw...

Article GUID: 33405217
Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes.

Author(s): Najeh S, Zandi K, Djerroud S, Kharma N, Perreault J

Methods Mol Biol. 2021;2167:91-111 Authors: Najeh S, Zandi K, Djerroud S, Kharma N, Perreault J

Article GUID: 32712917
Metabolomic and lipidomic analyses of chronologically aging yeast.

Author(s): Richard VR, Bourque SD, Titorenko VI

Methods Mol Biol. 2014;1205:359-73 Authors: Richard VR, Bourque SD, Titorenko VI

Article GUID: 25213255
A Cell-Free Content Mixing Assay for SNARE-Mediated Multivesicular Body-Vacuole Membrane Fusion.

Author(s): Karim MA, Samyn DR, Brett CL

Methods Mol Biol. 2019;1860:289-301 Authors: Karim MA, Samyn DR, Brett CL

Article GUID: 30317513
Visualization of SNARE-Mediated Organelle Membrane Hemifusion by Electron Microscopy.

Author(s): Mattie S, Kazmirchuk T, Mui J, Vali H, Brett CL

Methods Mol Biol. 2019;1860:361-377 Authors: Mattie S, Kazmirchuk T, Mui J, Vali H, Brett CL

Article GUID: 30317518
Identification of Genes Involved in the Degradation of Lignocellulose Using Comparative Transcriptomics.

Author(s): Gruninger RJ, Reid I, Forster RJ, Tsang A, McAllister TA

Methods Mol Biol. 2017;1588:279-298 Authors: Gruninger RJ, Reid I, Forster RJ, Tsang A, McAllister TA

Article GUID: 28417376
Isolation and Preparation of Extracellular Proteins from Lignocellulose Degrading Fungi for Comparative Proteomic Studies Using Mass Spectrometry

Author(s): Robert J Gruninger

Fungi utilize a unique mechanism of nutrient acquisition involving extracellular digestion. To understand the biology of these microbes, it is important to identify and characterize the function of proteins that are secreted and involved in this process. Ma...

Article GUID: 28417377
Introduction: Overview of Fungal Genomics.

Author(s): de Vries RP, Grigoriev IV, Tsang A

Methods Mol Biol. 2018;1775:1-7 Authors: de Vries RP, Grigoriev IV, Tsang A

Article GUID: 29876804
Fungal Genomic DNA Extraction Methods for Rapid Genotyping and Genome Sequencing.

Author(s): Bellemare A, John T, Marqueteau S

Methods Mol Biol. 2018;1775:11-20 Authors: Bellemare A, John T, Marqueteau S

Article GUID: 29876805
Mass Spectrometry-Based Proteomics

Author(s): Marcos Rafael Di Falco

Proteomics is the large-scale analysis of proteins rendered possible by modern mass spectrometry analysis methods capable of identifying thousands of peptides/proteins in a fast high-throughput manner. Here I describe protocols for the preparation of fungal...

Article GUID: 29876812
Evolutionary Adaptation to Generate Mutants.

Author(s): de Vries RP, Lubbers R, Patyshakuliyeva A, Wiebenga A, Benoit-Gelber I

Methods Mol Biol. 2018;1775:133-137 Authors: de Vries RP, Lubbers R, Patyshakuliyeva A, Wiebenga A, Benoit-Gelber I

Article GUID: 29876815
Manual Gene Curation and Functional Annotation.

Author(s): McDonnell E, Strasser K, Tsang A

Methods Mol Biol. 2018;1775:185-208 Authors: McDonnell E, Strasser K, Tsang A

Article GUID: 29876819
Evaluating Programs for Predicting Genes and Transcripts with RNA-Seq Support in Fungal Genomes.

Author(s): Reid I

Methods Mol Biol. 2018;1775:209-227 Authors: Reid I

Article GUID: 29876820
Phylogenetic Analysis of Protein Family.

Author(s): Song L, Wu S, Tsang A

Phylogenetic Analysis of Protein Family.

Methods Mol Biol. 2018;1775:267-275

Authors: Song L, Wu S, Tsang A

Abstract
With the number of sequenced genomes increasing rapidly, it is impractical to perform functional and stru...

Article GUID: 29876824
Title:Using Models to (Re-)Design Synthetic Circuits.
Authors:McCallum G,  Potvin-Trottier L
Link:https://www.ncbi.nlm.nih.gov/pubmed/33405217
DOI:10.1007/978-1-0716-1032-9_3
Category:Methods Mol Biol
PMID:33405217
Dept Affiliation: BIOLOGY
1 Department of Biology, Concordia University, Montreal, QC, Canada.
2 Department of Biology, Concordia University, Montreal, QC, Canada. laurent.potvin@concordia.ca.
3 Center for Applied Synthetic Biology, Concordia University, Montreal, QC, Canada. laurent.potvin@concordia.ca.
4 Department of Physics, Concordia University, Montreal, QC, Canada. laurent.potvin@concordia.ca.

Description:

Using Models to (Re-)Design Synthetic Circuits.

Methods Mol Biol. 2021; 2229:91-118

Authors: McCallum G, Potvin-Trottier L

Abstract

Mathematical models play an important role in the design of synthetic gene circuits, by guiding the choice of biological components and their assembly into novel gene networks. Here, we present a guide for biologists to build and utilize models of gene networks (synthetic or natural) to analyze dynamical properties of these networks while considering the low numbers of molecules inside cells that results in stochastic gene expression. We start by describing how to write down a model and discussing the level of details to include. We then briefly demonstrate how to simulate a network's dynamics using deterministic differential equations that assume high numbers of molecules. To consider the role of stochastic gene expression in single cells, we provide a detailed tutorial on running stochastic Gillespie simulations of a network, including instructions on coding the Gillespie algorithm with example code. Finally, we illustrate how using a combination of quantitative experimental characterization of a synthetic circuit and mathematical modeling can guide the iterative redesign of a synthetic circuit to achieve the desired properties. This is shown using a classic synthetic oscillator, the repressilator, which we recently redesigned into the most precise and robust synthetic oscillator to date. We thus provide a toolkit for synthetic biologists to build more precise and robust synthetic circuits, which should lead to a deeper understanding of the dynamics of gene regulatory networks.

PMID: 33405217 [PubMed - in process]