Studies

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 ...

Short Name: P4_Pcitri_tr1tr2combo Title: Combining tr1 and tr2 P. citri de novo transcriptomes into one transcriptome set Description: Production of one set of transcripts that will be easier for the readers of the planned publication Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_Pcitri_tr2 Description: Study of P. citri transcriptome data from SUSPHIRE and mealybug.org RNA-Seq datasets Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_genomes Title: Mealybug genome queries for pheromone biosynthesis genes Description: Survey of the available mealybug genomes for potential sex pheromone biosynthesis genes Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_Pcitri_genome Title: P. citri SUSPHIRE samples mapping to genome and differential gene expression analysis Description: Illumina reads from virgin and mated female Pcitri samples were mapped to P. citri genome available at mealybug.org (ensembl) Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_Pcitri_genome_extSamples Title: P. citri all available samples mapping to genome and differential gene expression analysis Description: Illumina reads from all available P. citri samples (SUSPHIRE, Edinburgh and SRA) were mapped to P. citri genome available at mealybug.org (ensembl) Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_Pcitri_IsoSeq Title: P citri Iso-Seq transcriptome generation and search for new sex pheromone biosynthesis genes Description: PacBio IsoSeq transcriptome sequencing and data analysis Raw Data: SRR15093694 Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Investigation: _I_T3.1_mealybug project: _p_SUSPHIRE Short Name: P4_Pcitri_tr Title: P. citri transcriptome study Description: We are interested in certain mealybugs both because they are important pests and very difficult to control but because their sex pheromones are irregular terpenoids, which are (a) very cool molecules and (b) extremely difficult and expensive to make using chemistry.In our project, we will be doing comparative transcriptomics of virgin and mated females to attempt to ...

Investigation files _I_T31_mealybug

Short Name: P3_expressionEcoli Title: Expression of IDS candidates in E. coli Description: IDS candidate sequences are expressed in E. coli and tested for enzyme activities Raw Data: Principal investigator: Heribert Warzecha License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_AdPathGenes Title: Additional search for genes involved in P citri sex pheromone production pathway Description: Search for additional pathway genes using coexpression etc Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: P4_IDScandidates Title: Generation of the candidate list for cis and trans IDS enzymes from P. citri Description: From the P. citri genome and both de novo transcriptome assembly versions we mined homologues of trans(PF00348, IPR000092) and cis (PF01255, IPR001441) IDS enzymes Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Glucose-6-phosphate dehydrogenase (G6PDH), the enzyme that catalyzes the first step of the oxidative pentose phosphate (OPP) pathway, plays a key role in this process. G6PDH is produced at the onset of nitrogen starvation but remains inactive in dormant cells, only to be rapidly reactivated when nitrogen is restored. In this study, we investigated the mechanisms underlying this enzymatic regulation and found that G6PDH inactivation is primarily due to the accumulation of inhibitory metabolites. ...

In a well with a total volume of 250 µL, the following components are added: 219 µL of 0.1 M TEA buffer, pH 7.5 1 µL of L-LDH (550 U.mL-1) 10 µL of NADH (10 mg.mL-1) 20 µL of the sample to be assayed

The initial absorbance (Ainitial) was measured at 340 nm, followed by the introduction of the Li-HPA sample solution, whether diluted or not. After stabilization, the final absorbance (Afinal) was measured. The concentration of Li-HPA was determined using the equation: ...

Michelle Chen, Elliot I. Corless, Bevin P. Engelward, Timothy M. Swager

Link to Paper: https://pubs.acs.org/doi/full/10.1021/acsomega.4c03959

Agglutination of liquid Janus emulsions creates optical signals that can be detected and quantified. This study reports the detection and quantitation of Interleukin-6 (IL-6) using emulsions functionalized at the water-organic interface with engineered hyperthermophilic affinity proteins (rcSso7d) derived from ...

Jessica C. Beard, Chi-Hsien Wang, Arun Sridharan, Robert G. Croy, John M. Essigmann, Timothy M. Swager

Link to Paper: https://doi.org/10.1021/acssensors.4c00927

N-Nitrosamines are contaminants found throughout the environment, including in drinking water, and many nitrosamines are likely potent carcinogens. Correspondingly, there is need for rapid and cost-effective in-field detection methods that can provide timely information about their contamination ...

Shu Wang, Amy J Myers, Edward B Irvine, Chuangqi Wang, Pauline Maiello, Mark A Rodgers, Jaime Tomko, Kara Kracinovsky, H. Jacob Borish, Michael C Chao, Douaa Mugahid, Patricia A. Darrah, Robert A. Seder, Mario Roederer, Charles A Scanga, Philana Ling Lin, Galit Alter, Sarah M Fortune, JoAnne L Flynn, Douglas A Lauffenburger

Paper Link: https://doi.org/10.1101/2024.04.13.589359

Link to Model Validation Datasets: https://fairdomhub.org/studies/1198

Abstract: ...

Utilization of enzyme assays to investigate PGM variants from Synechocystis