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ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion

Analysis of rewired upstream subnetworks impacting downstream differential gene expression aids the delineation of evolving molecular mechanisms. Cumulative statistics based on conventional differential correlation are limited for subnetwork rewiring analysis since rewiring is not necessarily equivalent to change in correlation coefficients. Here we present a computational method...

Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae

Menggen Ma 0 Z Lewis Liu 0 0 Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS , Peoria, IL USA Background: The yeast Saccharomyces cerevisiae is able to

Furfural induces reactive oxygen species accumulation and cellular damage in Saccharomyces cerevisiae

Background Biofuels offer a viable alternative to petroleum-based fuel. However, current methods are not sufficient and the technology required in order to use lignocellulosic biomass as a fermentation substrate faces several challenges. One challenge is the need for a robust fermentative microorganism that can tolerate the inhibitors present during lignocellulosic fermentation...

Signature pathway expression of xylose utilization in the genetically engineered industrial yeast Saccharomyces cerevisiae

recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer. Author Contributions Conceptualization: Z. Lewis Liu. Data curation: Quanzhou Feng ... . Formal analysis: Z. Lewis Liu. Investigation: Quanzhou Feng, Scott A. Weber. Methodology: Z. Lewis Liu. Resources: Z. Lewis Liu, Shizhong Li. Supervision: Shizhong Li. Validation: Z. Lewis Liu

Two New Native β-Glucosidases from Clavispora NRRL Y-50464 Confer Its Dual Function as Cellobiose Fermenting Ethanologenic Yeast

Yeast strain Clavispora NRRL Y-50464 is able to produce cellulosic ethanol from lignocellulosic materials without addition of external β-glucosidase by simultaneous saccharification and fermentation. A β-glucosidase BGL1 protein from this strain was recently reported supporting its cellobiose utilization capability. Here, we report two additional new β-glucosidase genes encoding...

Virulence Structure of Blumeria graminis f. sp. tritici and Its Genetic Diversity by ISSR and SRAP Profiling Analyses

Blumeria graminis f. sp. tritici, which causes wheat powdery mildew, is an obligate biotrophic pathogen that can easily genetically adapt to its host plant. Understanding the virulence structure of and genetic variations in this pathogen is essential for disease control and for breeding resistance to wheat powdery mildew. This study investigated 17 pathogenic populations in...