Studies

Files required for reproducibility of computational results. This include Docker file and python packages

Clock mutants for lhy-1/cca1-11, prr9/7, toc1, lux-4, elf3-1 were transformed with the genomic regions of the associated clock genes tagged with NanoLUC-3FLAG-10His. The tagged genomic constructs were transformed in the mutants using Agrobcterium ABI strain (kindly donated by Prof. Seth Davis University of York). T3 plants resistant to homozygous for BASTA resistance were phenotyped by luciferase imaging asessing period phenotype or plant architecture. Rescuing lines were then used for performing ...

Huu Tuan Nguyen, Nadia Gurvich, Mark Robert Gillrie, Giovanni Offeddu, Mouhita Humayun, Ellen L. Kan, Zhengpeng Wan, Mark Frederick Coughlin, Christie Zhang, Vivian Vu, Sharon Wei Ling Lee, Seng-Lai Tan, David Barbie, Jonathan Hsu, Roger D. Kamm

Link to Paper: https://www.sciencedirect.com/science/article/abs/pii/S0142961224002655

Abstract: Tumor-associated inflammation drives cancer progression and therapy resistance, often linked to the infiltration of ...

Leela RL Davies, Chuangqi Wang, Pia Steigler, Kathryn A Bowman, Stephanie Fischinger, Mark Hatherill, Michelle Fisher, Staney Kimbung Mbandi, Miguel Rodo, Tom HM Ottenhoff, Hazel M Dockrell, Jayne S Sutherland, Harriet Mayanja-Kizza, W Henry Boom, Gerhard Walzl, Stefan H.E. Kaufmann, Elisa Nemes, Thomas J Scriba, Douglas Lauffenburger, Galit Alter, Sarah M. Fortune.

Link to Paper: https://doi.org/10.1038/s41564-024-01678-x

Abstract: Antibody features vary ...

Joshua D. Bromley, Sharie Keanne C. Ganchua, Sarah K. Nyquist, Pauline Maiello, Michael Chao, H. Jacob Borish, Mark Rodgers, Jaime Tomko, Kara Kracinovsky, Douaa Mugahid, Son Nguyen, Dennis Wang, Jacob M. Rosenberg, Edwin C. Klein, Hannah P. Gideon, Roisin Floyd-O’Sullivan, Bonnie Berger, Charles A Scanga, Philana Ling Lin, Sarah M. Fortune, Alex K. Shalek, JoAnne L. Flynn

Link to Paper: https://www.cell.com/immunity/fulltext/S1074-7613(24)00375-3

Immunological ...

Joshua M. Peters, Edward B. Irvine, Jacob M. Rosenberg, Marc H. Wadsworth II, Travis K. Hughes, Matthew Sutton, Sarah K. Nyquist, Joshua D. Bromley, Rajib Mondal, Mario Roederer, Robert A. Seder, Patricia A. Darrah, Galit Alter, JoAnne L. Flynn, Alex K. Shalek, Sarah M. Fortune, Bryan D. Bryson

DOI:

Intradermal (ID) Bacillus Calmette–Guérin (BCG) is the most widely administered vaccine in the world. However, ID-BCG fails to achieve the level of protection ...

Short Name: P5_SxF_lav_ac Title: Detection of lavandulyl acetate in extracts of engineered fungi Description: Detection of lavandulyl acetate in extracts of engineered fungi (SxF) by GC-MS-MS Raw Data: pISA Study creation date: 2021-12-23 pISA Study creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P5_SxF_lavandulol Title: Detection of lavandulol in SxF extracts Description: Detection of lavandulol in extracts of engineered fungi by GC-MS-MS Raw Data: pISA Study creation date: 2021-12-23 pISA Study creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Investigation files _I_T33_MonoterpenoidsFungi

Investigation files _I_T32_CandidateGeneExpressionTesting

Short Name: TransientLPPSCPPS Title: Transient expression of lavandulyl pirophosphate synthase (LPPS) and chrysanthemyl pirophhosphate synthase (CPPS) Description: The purpose of this study is to perform the transient expression of LPPS and CPPS gene for the production of lavandulol and chrysanthemol, respectively. Production is measured by GCMS of samples. Raw Data: pISA Study creation date: 2021-12-03 pISA Study creator: RMF Principal investigator: Diego Orzaez License: Creative Commons Attribution ...

Short Name: P5_PhContentPlants Title: Quantification of total moth pheromone contents in SxP Description: Quantification of the total pheromone content in SxPv1.2 plants Raw Data: pISA Study creation date: 21-Sep-21 pISA Study creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P5_PhEmissionPlants Title: Quantification of the pheromone emitted by SxP plants Description: Quantification of the quantity of pheromone emitted by SxPv1.2 plants by volatile collection and GC-MS/MS analysis Raw Data: pISA Study creation date: 21-Sep-21 pISA Study creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Investigation files _I_T24_phero

Short Name: P5_EAGresponse Title: Electrophysiological response of moths to SxP extracts Description: Electrophysiological response of Sesamia nonagrioides males to selected fractions of the SxPv1.2 extracts Raw Data: pISA Study creation date: 21-Sep-21 pISA Study creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P1_ConstExp_Pdigitatum Title: Constitutive expression of moth pheromone pathway in Penicillium digitatum. Description: For this Proof of Concept, the three enzymes of the moth pheromones route were assembled in TUs using fungal promoters and terminators, and transformed into Penicillium digitatum. Pheromone production of the selected transformants will be assessed via GC-MS. Raw Data: pISA Study creation date: 2020-18-04 pISA Study creator: ElenaMG Principal investigator: Diego Orzaez ...

Short Name: P5_SxFliquids Title: Pheromone detection in liquid extracts of SxF Description: Pheromone detection in liquid extracts of modified filamentous fungi (SxF) by liquid-liquid solvent extraction and GC-MS/MS analysis Raw Data: pISA Study creation date: 21-Sep-22 pISA Study creator: Sandra Vacas Principal investigator: * License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P5_SxFmycelia Title: Pheromone detection in SxF mycelial biomass Description: Pheromone detection in the mycelial biomass of modified filamentous fungi by solid-liquid solvent extraction and GC-MS/MS analysis Raw Data: pISA Study creation date: 21-Sep-22 pISA Study creator: Sandra Vacas Principal investigator: * License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Investigation files _I_T23_SxF

Investigation files _I_T22_SxPv2

Short Name: P1_TransgenicStableSxPv2 Title: Generation of Sexy Plant version 2: transgenic plants with the moth sex pheromones biosynthetic pathway genes regulated by synthetic promotors. Description: The purpose of this study is to generate transgenic stable lines of Nicotiana benthamiana plants ready to express the moth sex pheromone biosynthetic pathway in a regulable way. The moth sex pheromones biosynthetic pathway genes are regulated by synthetic promotors, so in a basal state, the plants ...

Investigation files _I_T12_CuInducible

Short Name: P1_TransientExp_Nb Title: Agroinfiltration of copper inducible system in Nicotiana benthamiana Description: The copper inducible dCasEV was tested transiently in Nicotiana benthamiana leaves together with the moth pheromone pathway under the regulation of the synthetic promoters created in T11 Raw Data: https://zenodo.org/communities/susphire/search?page=1&size=20 pISA Study creation date: 2020-10-28 pISA Study creator: ElenaMG Principal investigator: Diego Orzaez License: Creative ...

Investigation files _I_T11_dCas9SynProm

Short Name: P1_SynProm_Nbenthamiana Title: Transient expression in Nicotiana benthamiana of the synthetic promoters developed Description: Different A1 and A2 Different A1 and A2 promoter pieces were designed containing as much random sequence as possible, and the target sequence for the guideRNA 1 of SlDFR promoter. In the same way, some minimal promoters containing only the TATA-Box signal and the 5'UTR region were designed as "core promoter" pieces. Different synthetic promoters were then ...