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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
Discovery and characterization of family 39 glycoside hydrolases from rumen anaerobic fungi with polyspecific activity on rare arabinosyl substrates.

Author(s): Jones DR, Uddin MS, Gruninger RJ, Pham TTM, Thomas D, Boraston AB, Briggs J, Pluvinage B, McAllister TA, Forster RJ, Tsang A, Selinger LB, Abbott DW

J Biol Chem. 2017 07 28;292(30):12606-12620 Authors: Jones DR, Uddin MS, Gruninger RJ, Pham TTM, Thomas D, Boraston AB, Briggs J, Pluvinage B, McAllister TA, Forster RJ, Tsang A, Selinger LB, Abbott DW

Article GUID: 28588026
Application of Transcriptomics to Compare the Carbohydrate Active Enzymes That Are Expressed by Diverse Genera of Anaerobic Fungi to Degrade Plant Cell Wall Carbohydrates.

Author(s): Gruninger RJ, Nguyen TTM, Reid ID, Yanke JL, Wang P, Abbott DW, Tsang A, McAllister T

Front Microbiol. 2018;9:1581 Authors: Gruninger RJ, Nguyen TTM, Reid ID, Yanke JL, Wang P, Abbott DW, Tsang A, McAllister T

Article GUID: 30061875
Title:Identification of Genes Involved in the Degradation of Lignocellulose Using Comparative Transcriptomics.
Authors:Gruninger RJ,  Reid I,  Forster RJ,  Tsang A,  McAllister TA
Link:https://www.ncbi.nlm.nih.gov/pubmed/28417376?dopt=Abstract
DOI:10.1007/978-1-4939-6899-2_21
Category:Methods Mol Biol
PMID:28417376
Dept Affiliation: GENOMICS
1 Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave. South, Lethbridge, AB, Canada, T1J 4B1. robert.gruninger@agr.gc.ca.
2 Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada.
3 Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave. South, Lethbridge, AB, Canada, T1J 4B1.

Description:

Identification of Genes Involved in the Degradation of Lignocellulose Using Comparative Transcriptomics.

Methods Mol Biol. 2017;1588:279-298

Authors: Gruninger RJ, Reid I, Forster RJ, Tsang A, McAllister TA

Abstract

Lignocellulosic biomass represents an abundant, renewable resource that can be used to produce biofuels, low-cost livestock feed, and high-value chemicals. The potential of this resource has led to intensive research efforts to develop cost effective methods to breakdown lignocellulose. The efficiency with which the anaerobic fungi (phylum Neocallimastigomycota) degrade plant biomass is well recognized and in recent years has received renewed interest. Transcriptomics has been used to identify enzymes that are expressed by these fungi and are involved in the degradation of a range of lignocellulose feedstocks. The transcriptome is the entire complement of coding and noncoding RNA transcripts that are expressed by a cell under a particular set of conditions. Monitoring changes in gene expression can provide fundamental information about the biology of an organism. Here we outline a general methodology that will enable researchers to conduct comparative transcriptomic studies with the goal of identifying enzymes involved in the degradation of the plant cell wall. The method described here includes growth of fungal cultures, isolation and sequencing of RNA, and a basic description of data analysis for bioinformatic identification of differentially expressed transcripts.

PMID: 28417376 [PubMed - indexed for MEDLINE]