Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications [PDF]
Nature CommunicationsLack of standardization in biofoundries limits the scalability and efficiency of synthetic biology research. Here, we propose an abstraction hierarchy that organizes biofoundry activities into four interoperable levels: Project, Service/Capability ...
Haseong Kim +2 more
exaly +3 more sources
Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts [PDF]
Microbial Cell Factories, 2023 Efficient conversion of pentose sugars remains a significant barrier to the replacement of petroleum-derived chemicals with plant biomass-derived bioproducts. While the oleaginous yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) has
Samuel T. Coradetti +11 more
doaj +2 more sources
Non-canonical d-xylose and l-arabinose metabolism via d-arabitol in the oleaginous yeast Rhodosporidium toruloides [PDF]
Microbial Cell Factories, 2023 R. toruloides is an oleaginous yeast, with diverse metabolic capacities and high tolerance for inhibitory compounds abundant in plant biomass hydrolysates. While R.
Paul A. Adamczyk +2 more
doaj +2 more sources
Metabolic engineering to improve production of 3-hydroxypropionic acid from corn-stover hydrolysate in Aspergillus species [PDF]
Biotechnology for Biofuels and Bioproducts, 2023 Background Fuels and chemicals derived from non-fossil sources are needed to lessen human impacts on the environment while providing a healthy and growing economy.
Ziyu Dai +14 more
doaj +2 more sources
Prediction of non-intuitive metabolic targets with bayesian metabolic control analysis to improve 3-hydroxypropionic acid production in Aspergillus niger [PDF]
Frontiers in Bioengineering and BiotechnologyDevelopment of efficient bioconversion processes is limited by the ability to predictably improve metabolic flux. Here we deployed Bayesian Metabolic Control Analysis as a platform to integrate multi-omics data with metabolic modeling and evaluated its ...
Ziyu Dai +26 more
doaj +2 more sources
Production of triacetic acid lactone from oleic acid by engineering the yeast Candida viswanathii [PDF]
Microbial Cell FactoriesTriacetic acid lactone (TAL) is a promising platform chemical to produce valuable compounds. The development of engineered microbial hosts to efficiently produce TAL from lipid-containing waste streams could be a cost-effective, sustainable and ...
Saptarshi Ghosh +8 more
doaj +2 more sources
The Future of a Myriad of Accelerated Biodiscoveries Lies in AI-Powered Mass Spectrometry and Multiomics Integration. [PDF]
J Mass SpectromABSTRACT The intersection of modern artificial intelligence (AI) and mass spectrometry (MS) is set to transform the MS‐based “omics” research fields, particularly proteomics, metabolomics, lipidomics, and glycomics, enabling advancements across a wide range of domains, from health to environment and industrial biotechnology.
Bilbao A.
europepmc +2 more sources
Muconic acid production from glucose and xylose in Pseudomonas putida via evolution and metabolic engineering [PDF]
Nature Communications, 2022 Muconic acid is a platform chemical with wide industrial applicability. Here, the authors report efficient muconate production from glucose and xylose by engineered Pseudomonas putida strain using adaptive laboratory evolution, metabolic modeling, and ...
Chen Ling +16 more
doaj +2 more sources
PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements [PDF]
Nature Communications, 2023 Multidimensional measurements using state-of-the-art separations and mass spectrometry provide advantages in untargeted metabolomics analyses for studying biological and environmental bio-chemical processes.
Aivett Bilbao +27 more
doaj +2 more sources
Enabling malic acid production from corn-stover hydrolysate in Lipomyces starkeyi via metabolic engineering and bioprocess optimization [PDF]
Microbial Cell FactoriesBackground Lipomyces starkeyi is an oleaginous yeast with a native metabolism well-suited for production of lipids and biofuels from complex lignocellulosic and waste feedstocks.
Jeffrey J. Czajka +15 more
doaj +2 more sources