Investigations

Short Name: 01_LabTrials Title: Laboratory trials Description: Selection of targets and their validation in trials performed in the laboratories and greenhouse at NIB Phenodata: ./phenodata_20210113.txt pISA Investigation creation date: 2021-01-13 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 02_FieldTrials Title: Field trials Description: Field trials - spraying CPB larvae on potato field with the insecticidal dsRNA validated for effectiveness in the laboratory trials Phenodata: ./phenodata_20210115.txt pISA Investigation creation date: 2021-01-15 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 03_Omics Title: Omics analysis of RNAi response in CPB Description: Transcriptomics and metagenome changes upon feeding CPB larvae with dsRNA Phenodata: ./phenodata_20210115.txt pISA Investigation creation date: 2021-01-15 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Investigation: _I_STRT Short Name: STRT Title: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Phenodata: ./phenodata_20191022.txt pISA Investigation creation date: 2019-10-22 pISA Investigation creator: Maja Zagorscak, Ziva Ramsak, Marko Petek Principal investigator: Kristina Gruden License: MIT Sharing permission: Public Upload to FAIRDOMHub: Yes

RELATED ...

Short Name: T11_dCas9SynProm Title: Development of synthetic promoters inducible by dCasEV2.1 system Description: The aim of this work is to design a range of synthetic promoters with negligible basal expression that are activated by using the "dead" Cas9 activation system developed in our lab (dCasEV2.1, Selma et al., 2019). Such tool will then be used for creating synthetic regulatory cascades where the expression of the genes for the pheromone biosynthesis can be controlled by a single dCas9 ...

Short Name: T12_CuInducible Title: Production and testing of copper inducible dCas9EV system for moth pheromone production Description: dCas9EV system used to activate the synthetic promoters made in T11 was coupled to a copper-inducible promoter made of CBS repeats and a minimal DFR promoter. Such system will be induced via CUP2 protein, which binds to CBS motif in presence of copper. This cascade-like system was tested for production of the moth pheromone pathway. Phenodata: ./phenodata_20210107.txt ...

Short Name: T21_SXPsysbio Title: Use a systems biology approach to identify regulatory bottlenecks in SxPv1 Description: Samples from SXPv1.0 plants as well as sister nulls (progeny from the original transgenic event in which the transgene has segregated) and wild type will be grown and leaf samples taken for RNA extraction and profiling of primary metabolites and volatiles (target pheromones as well as potential derivatives) (P1, P5). Phenotypic and GC-MS data will be obtained and analysed from ...

Short Name: T22_SxPv2 Title: Sexy Plant version 2: inducible and regulable SxP versions Description: The purpose of this investigation is to optimize the SxP version 1, with a switchable expression and increased compound release. Phenodata: ./phenodata_20210920.txt Principal investigator: Diego Orzaez License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes Institutions involved: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Spain; Institute ...

Short Name: T23_SxF Title: Moth pheromone production in filamentous fungi SxF Description: Demonstration of moth pheromone production in filamentous fungi by solvent extractions of liquid cultures and mycelial biomass and GC-MS/MS analysis. Constitutive and inducible expression of moth pheromones in filamentous fungi Penicillium species will be developed using a dCas9-based copper inducible system. An initial proof of concept will also be performed in P. digitatum using constitutive promoters. ...

Short Name: T24_phero Title: Pheromone Content and EAG response Description: Investigate pheromone content and electrophysiological response of target insects to extracts of plants and fungi expressing Lepidoptera pheromones Phenodata: ./phenodata_21Sep21.txt pISA Investigation creation date: 21-Sep-21 pISA Investigation creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: T31_mealybug Title: Mealybug genome and transcriptome analyses Description: Searching for enzymes involved in the mealybug pheromone biosynthesis pathways. These pheromones are known to be released by virgin females. Phenodata: ./phenodata_20190523.txt Featuredata: Principal investigator: Heribert Warzecha, Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: T32_CandidateGeneExpressionTesting Title: Candidate gene expression and testing Description: The purpose of this investigation is to express transiently candidate genes for Pcitri sex pheromone biosynthesis. This genes could act either as genes catalyzing steps related to the biosynthesis of precursors of the pheromone itself, either for the final steps of the biosynthesis. After expression, the monoterpenoid production function of those genes is checked by GCMS. Phenodata: ...

Short Name: T33_MonoterpenoidsFungi Title: Detection of Coccoidea pheromones or precursors in engineered fungi Description: Detection of lavandulol or lavandulyl acetate in different engineered fungi (SxF) lines by GC-MS-MS Phenodata: ./phenodata_20211223.txt pISA Investigation creation date: 2021-12-23 pISA Investigation creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

The aim of this project is to develop a detailed kinetic model of the CcpA-dependent regulatory network, the key regulon of flux regulation in B. subtilis. Thereby involved are more than 300 genes e.g. catabolism, overflow metabolism, the TCA cycle and amino acid anabolism which are regulated via carbon catabolite regulation (CCR)

The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work will be published as Urquiza-Garcia, Molina, Halliday and Millar, title "Abundant clock proteins point to missing molecular regulation in the plant circadian clock", in Molecular Systems Biology, 2025 doi 10.1038/s44320-025-00086-5.

Starting from the U2019.3 and U2020.3 models, this project rescales parameters to match protein levels that were predicted ...

The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work is published in Urquiza-Garcia and Millar, Testing the inferred transcription rates of a dynamic, gene network model in absolute units, In Silico Plants, 2021.

Starting from the P2011 model, this project corrects theoretical issues (EC steady state binding assumption) to form an intermediate model (first version U2017.1; published as U2019.1) model, rescales ...

Collection of models submitted to PLaSMo by Richard Adams and automatically transferred to FAIRDOM Hub.

Protein abundance of AKT and ERK pathway components governs cell-type- specific regulation of proliferation

Cyanobacterial PFKs were thought to be ATP dependent, but isolation and characterisation of 2 PFK isoenzymes from Synechocystis revealed that they belong to the PFK-A family, use ADP as phosphate donor and form a separate phylogenetic class. Their allosteric regulation via 3-PG and ATP respectively allow for flexible switching between aactive and inactive enzymes dependent on the light and carbon status.

Integrated systems biology approach including transcriptome, metabolome, proteome analyses and modelling to elucidate amino acid degradation in S. solfataricus P2.

Basically extending SYSMO-LAB 1st phase into second with addition of fourth species, Lb. plantarum. The main focus is amino acid metabolism. primary metabolisms, like glycolysis is also interest.

The Sulfolobus systems biology (‘‘SulfoSYS’’)-project represented the first (hyper-)thermophilic Systems Biology project, funded within the European trans-national research initiative ‘‘Systems Biology of Microorganisms’’. Within the SulfoSYS-project, focus lies on studying the effect of temperature variation on the central carbohydrate metabolism (CCM) of S. solfataricus that is characterized by the branched Entner–Doudoroff (ED)-like pathway for sugar (glucose, galactose) degradation and the ...

The electron transport chain of E. coli is branched. Different NAD Dehydrogenases and terminal oxidases are known to be expressed at different oxygen availabilities. By deleting multiple genes mutant strains were constructed that posses a linear electron transport chain. These mutants were investigated in continous bioreactor experiments with limiting glucose and varying oxygen supply.

Cultures grown under standard SUMO conditions were analyzed with respect to heterogeneity in gene expression. To this end GFP reporter strains were constructed and GFP expression at single cell level was monitored by flow cytometry.

In Escherichia coli several systems are known to transport glucose into the cytoplasm. A series of mutant strains were constructed, which lack one or more of these uptake systems. These were analyzed in aerobic and anaerobic batch cultures, as well as glucose limited continuous cultivations.

Design, synthesis, computational studies and biological evaluation of antiparasitic dinitroaniline-ether phospholipid hybrids

Project to test effects of natural compared to growth chamber 16:8 LD cycles, on expression of Arabidopsis flowering-time genes, and to define the genetic mechanisms and environmental triggers involved. Led by Young-Hun Song and Akane Kubota in the Imaizumi lab, with collaborators testing plants in parallel in Zurich and Edinburgh.

Data, models and simulations for the Chew et al. 2014 paper (PNAS, https://doi.org/10.1073/pnas.1410238111), using wild-type Arabidopsis ecotype Col-0 in standard 12hL:12hD growth conditions, compared to La(er) or Fei-0 accessions, or to plants overexpressing a micro RNA (miR156).

Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range