Genome editing and bioinformatics

K Nakamae, H Bono - Gene and Genome Editing, 2022 - Elsevier
Bioinformatics has become an indispensable technology in molecular biology for genome
editing. In this review, we outline various bioinformatic techniques necessary for genome …

Microbial cell factories in the bioeconomy era: from discovery to creation

X Yan, Q He, B Geng, S Yang - BioDesign Research, 2024 - spj.science.org
Microbial cell factories (MCFs) are extensively used to produce a wide array of bioproducts,
such as bioenergy, biochemical, food, nutrients, and pharmaceuticals, and have been …

Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae

SB Lee, M Tremaine, M Place, L Liu, A Pier… - Metabolic …, 2021 - Elsevier
Bottlenecks in the efficient conversion of xylose into cost-effective biofuels have limited the
widespread use of plant lignocellulose as a renewable feedstock. The yeast Saccharomyces …

Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces

KO Barros, M Mader, DJ Krause, J Pangilinan… - … for Biofuels and …, 2024 - Springer
Background Cost-effective production of biofuels from lignocellulose requires the
fermentation of d-xylose. Many yeast species within and closely related to the genera …

Ploidy evolution in a wild yeast is linked to an interaction between cell type and metabolism

JG Crandall, KJ Fisher, TK Sato, CT Hittinger - PLoS Biology, 2023 - journals.plos.org
Ploidy is an evolutionarily labile trait, and its variation across the tree of life has profound
impacts on evolutionary trajectories and life histories. The immediate consequences and …

Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway

FV Gambacorta, ER Wagner, TB Jacobson… - Synthetic and Systems …, 2022 - Elsevier
Metabolic engineering strategies have been successfully implemented to improve the
production of isobutanol, a next-generation biofuel, in Saccharomyces cerevisiae. Here, we …

Combinatorial library design for improving isobutanol production in Saccharomyces cerevisiae

FV Gambacorta, JJ Dietrich, JJ Baerwald… - … in Bioengineering and …, 2022 - frontiersin.org
Saccharomyces cerevisiae is the dominant fermentative producer of ethanol in industry and
a preferred host for production of other biofuels. That said, rewiring the metabolism of S …

Revitalizing the ethanologenic bacterium Zymomonas mobilis for sugar reduction in high-sugar-content fruits and commercial products

M Hu, X Chen, J Huang, J Du, M Li, S Yang - Bioresources and …, 2021 - Springer
The excessive consumption of sugars can cause health issues. Different strategies have
been developed to reduce sugars in the diets. However, sugars in fruits and commercial …

The Evolution of Nucleic Acid–Based Diagnosis Methods from the (pre-) CRISPR to CRISPR era and the Associated Machine/Deep Learning Approaches in Relevant …

SS Chakraborty, J Ray Dutta, R Ganesan… - RNA Design: Methods …, 2024 - Springer
Nucleic acid tests (NATs) are considered as gold standard in molecular diagnosis. To meet
the demand for onsite, point-of-care, specific and sensitive, trace and genotype detection of …

[HTML][HTML] Improved vectors for retron-mediated CRISPR-Cas9 genome editing in Saccharomyces cerevisiae

TN Stuecker, SE Hood, JM Pineda, S Lenaduwe… - …, 2024 - pmc.ncbi.nlm.nih.gov
In vivo site-directed mutagenesis is a powerful genetic tool for testing the effects of specific
alleles in their normal genomic context. While the budding yeast Saccharomyces cerevisiae …