Keyword search (3,619 papers available)


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:Evolutionary Adaptation to Generate Mutants.
Authors:de Vries RP,  Lubbers R,  Patyshakuliyeva A,  Wiebenga A,  Benoit-Gelber I
Link:https://www.ncbi.nlm.nih.gov/pubmed/29876815?dopt=Abstract
DOI:10.1007/978-1-4939-7804-5_12
Category:Methods Mol Biol
PMID:29876815
Dept Affiliation: BIOLOGY
1 Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands. r.devries@westerdijkinstitute.nl.
2 Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.
3 Centre for Structural and Functional Genomics, Department of Biology, Concordia University, Montreal, QC, Canada.

Description:

Evolutionary Adaptation to Generate Mutants.

Methods Mol Biol. 2018;1775:133-137

Authors: de Vries RP, Lubbers R, Patyshakuliyeva A, Wiebenga A, Benoit-Gelber I

Abstract

In this chapter we describe a method to generate mutants of filamentous fungi using their genomic plasticity and rapid adaptability to their environment. This method is based on spontaneous mutations occurring in relation to improved growth of fungi on media by repeated inoculation resulting in adaptation of the strain to the condition. The critical aspect of this method is the design of the selective media, which will depend strongly on the phenomenon that will be studied. This method is advantageous over UV or chemical random mutagenesis as it results in a lower frequency of undesired mutations and can result in strains that combined with (post)genomic approaches can enhance our understanding of the mechanisms driving various biological processes. In addition, it can be used to obtain better strains for various industrial applications. The method described here is specific for sporulating fungi and has so far not yet been tested for nonsporulating fungi.

PMID: 29876815 [PubMed - indexed for MEDLINE]