Samuel T. Coradetti
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View article: The “Grove-First” Framework: Starting in the Grove to Find Therapies for Huanglongbing
The “Grove-First” Framework: Starting in the Grove to Find Therapies for Huanglongbing Open
Citrus greening disease, also known as huanglongbing (HLB), is the most serious vector-borne bacterial disease of citrus world-wide 1,2 . There is an immediate global need to provide the citrus industry with relief from HLB and a return to…
View article: Methods of producing lipid-derived compounds and host cells thereof
Methods of producing lipid-derived compounds and host cells thereof Open
The present disclosure relates to genetically engineered host cells and methods of producing a lipid-derived compound by employing such host cells. In particular embodiments, the host cell includes a first mutant gene encoding a cytoplasmi…
View article: Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts
Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts Open
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 …
View article: Additional file 2 of Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts
Additional file 2 of Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts Open
Additional file 2 Strains used in this study with strain IDs and part numbers for relevant plasmids for retrieval on the Agile BioFoundry public registry ( https://public-registry.agilebiofoundry.org ) Data used for T-tests referenced in t…
View article: Additional file 1 of Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts
Additional file 1 of Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts Open
Additional file 1: Intensities and statistical analysis from global proteomics of WT IFO 0880, OE-Pnt1, ∆Pnt1 grown on xylose and xylose plus glycerol medium.
View article: Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides
Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides Open
An oleaginous yeast Rhodosporidium toruloides is a promising host for converting lignocellulosic biomass to bioproducts and biofuels. In this work, we performed multi-omics analysis of lignocellulosic carbon utilization in R. toruloides an…
View article: Exploiting nonionic surfactants to enhance fatty alcohol production in <i>Rhodosporidium toruloides</i>
Exploiting nonionic surfactants to enhance fatty alcohol production in <i>Rhodosporidium toruloides</i> Open
Fatty alcohols (FOHs) are important feedstocks in the chemical industry to produce detergents, cosmetics, and lubricants. Microbial production of FOHs has become an attractive alternative to production in plants and animals due to growing …
View article: Genomewide and Enzymatic Analysis Reveals Efficient <scp>d</scp> -Galacturonic Acid Metabolism in the Basidiomycete Yeast Rhodosporidium toruloides
Genomewide and Enzymatic Analysis Reveals Efficient <span>d</span> -Galacturonic Acid Metabolism in the Basidiomycete Yeast Rhodosporidium toruloides Open
The switch from the traditional fossil-based industry to a green and sustainable bioeconomy demands the complete utilization of renewable feedstocks. Many currently used bioconversion hosts are unable to utilize major components of plant b…
View article: Genome-wide and enzymatic analysis reveals efficient D-galacturonic acid metabolism in the basidiomycete yeast<i>Rhodosporidium toruloides</i>
Genome-wide and enzymatic analysis reveals efficient D-galacturonic acid metabolism in the basidiomycete yeast<i>Rhodosporidium toruloides</i> Open
Biorefining of renewable feedstocks is one of the most promising routes to replace fossil-based products. Since many common fermentation hosts, such as Saccharomyces cerevisiae , are naturally unable to convert many component plant cell wa…
View article: Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides
Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides Open
The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of l…
View article: Author response: Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides
Author response: Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides Open
Article Figures and data Abstract eLife digest Introduction Results Discussion Materials and methods Appendix 1 Data availability References Decision letter Author response Article and author information Metrics Abstract The basidiomycete …
View article: Network of nutrient-sensing pathways and a conserved kinase cascade integrate osmolarity and carbon sensing in <i>Neurospora crassa</i>
Network of nutrient-sensing pathways and a conserved kinase cascade integrate osmolarity and carbon sensing in <i>Neurospora crassa</i> Open
Significance Microbes have evolved complex signaling networks to identify and prioritize utilization of available energy sources. For many fungi, such as Neurospora crassa , this entails distinguishing between an array of carbon sources, i…
View article: Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa
Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa Open
Here we built a network that serves as a scaffold for integration of diverse experimental datasets. This approach led to the elucidation of regulatory design principles for plant cell wall deconstruction by filamentous fungi and a novel fu…
View article: Functional genomics of lipid metabolism in the oleaginous yeast<i>Rhodosporidium toruloides</i>
Functional genomics of lipid metabolism in the oleaginous yeast<i>Rhodosporidium toruloides</i> Open
The basidomycete yeast Rhodosporidium toruloides (a.k.a. Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid dro…
View article: Network reconstruction and systems analysis of plant cell wall deconstruction by<i>neurospora crassa</i>
Network reconstruction and systems analysis of plant cell wall deconstruction by<i>neurospora crassa</i> Open
Plant biomass degradation by fungal derived enzymes is rapidly expanding in economic importance as a clean and efficient source for biofuels. The ability to rationally engineer filamentous fungi would facilitate biotechnological applicatio…
View article: MOESM1 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa
MOESM1 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa Open
Additional file 1. List of reactions, compounds and genes in the plant cell wall degradation network (PCWDN) of N. crassa. The first, second and third sheets contain the list of reactions, genes and compounds, respectively, in the PCWDN. T…
View article: MOESM12 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa
MOESM12 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa Open
Additional file 12. Comparative analysis of the plant cell wall degradation network (PCWDN) with the genome-scale metabolic models of N. crassa and other filamentous fungi. The first and second sheets compare the list of reactions and gene…
View article: MOESM6 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa
MOESM6 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa Open
Additional file 6. Compiled dataset of experimentally validated deletion strains with growth-deficient phenotypes compared to WT for genes in the plant cell wall degradation network (PCWDN) of N. crassa.
View article: MOESM5 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa
MOESM5 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa Open
Additional file 5. Proteomics-based annotation support for genes in the plant cell wall degradation network (PCWDN) of N. crassa. The first sheet contains information on the proteomics-based annotation support for each gene in the PCWDN. T…
View article: MOESM10 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa
MOESM10 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa Open
Additional file 10. Hierarchical clustering of genes in the plant cell wall degradation network (PCWDN) of N. crassa based on RNA-seq data obtained in nine different conditions. The first sheet lists the different clusters in the same orde…
View article: MOESM7 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa
MOESM7 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa Open
Additional file 7. Biochemical characterization of genes in the plant cell wall degradation network (PCWDN) of N. crassa.
View article: MOESM3 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa
MOESM3 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa Open
Additional file 3. Functional genomics-based annotation support for genes in the plant cell wall degradation network (PCWDN) of N. crassa. The table contains information from following sources: CAZY, BROAD, TransportDB, SignalP, Phobius, W…
View article: MOESM2 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa
MOESM2 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa Open
Additional file 2. List of predicted genes coding for carbohydrate-active enzymes (CAZY) in N. crassa and the plant cell wall degradation network (PCWDN). List of CAZY genes in N. crassa was obtained from two sources: CAZY database [41] an…
View article: MOESM4 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa
MOESM4 of Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa Open
Additional file 4. Transcriptomics-based annotation support for genes in the plant cell wall degradation network (PCWDN) of N. crassa. The first sheet contains information on the transcriptomics-based annotation support for each gene in th…