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:Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes.
Authors:Najeh S,  Zandi K,  Djerroud S,  Kharma N,  Perreault J
Link:https://www.ncbi.nlm.nih.gov/pubmed/32712917
DOI:10.1007/978-1-0716-0716-9_7
Category:Methods Mol Biol
PMID:32712917
Dept Affiliation: ENCS
1 Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, QC, Canada.
2 Software Engineering and Computer Science Department, Concordia University, Montreal, QC, Canada.
3 Electrical and Computer Engineering Department, Concordia University, Montreal, QC, Canada. kharma@ece.concordia.ca.
4 Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, QC, Canada. jonathan.perreault@iaf.inrs.ca.

Description:

Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes.

Methods Mol Biol. 2021;2167:91-111

Authors: Najeh S, Zandi K, Djerroud S, Kharma N, Perreault J

Abstract

Pseudoknots are important motifs for stabilizing the structure of functional RNAs. As an example, pseudoknotted hammerhead ribozymes are highly active compared to minimal ribozymes. The design of new RNA sequences that retain the function of a model RNA structure includes taking in account pseudoknots presence in the structure, which is usually a challenge for bioinformatics tools. Our method includes using "Enzymer," a software for designing RNA sequences with desired secondary structures that may include pseudoknots. Enzymer implements an efficient stochastic search and optimization algorithm to sample RNA sequences from low ensemble defect mutational landscape of an initial design template to generate an RNA sequence that is predicted to fold into the desired target structure.

PMID: 32712917 [PubMed - in process]