Investigations

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.

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

The BENEFIT project is an interdisciplinary eHealth initiative to offer long-term lifestyle support for patients with cardiovascular disease (CVD). Data collected from BENEFIT patients is heterogeneous and encompasses demographics, observational lifestyle data, self-reported motivation for lifestyle change and physical measurements. Analysing these results can provide new insights into the effects of different intervention strategies used in the cardiac rehabilitation programme on maintaining a ...

Genome-wide association studies with ampicillin resistance as phenotype were conducted on based on variant-call data. A linear regression was performed for MICs and logistic regression was performed based on clinical breakpoint concentrations.

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

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: 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: 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: 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: 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: 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: 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

The family of Desulfobacteraceae comprises mtabolically versatile, completely oxidizing, sulfate-reducing bacteria that play an important role in the global carbon- and sulfor-cycles, mainly in the marine realm. In this study, six different species of Desulfobacteraceae were studied by comparative proteogenomics, i.e. Desulfobacula toluolica Tol2, Desulfococcus multivorans 1be1, Desulfonema limicola, Desulfonema magnum, Desulfosarcina variabilis 3be13 and Desulfobacterium autotrophicum ...

Investigation of the regulation of different PGM variants from Synechocystis sp. PCC 6803

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.

The figures 2, 3, 4 and 6 in the main text of the manuscript: "Inhibition of the glucocorticoid-activating enzyme 11β-hydroxysteroid dehydrogenase type 1 drives concurrent 11-oxygenated androgen excess", submitted to FASEB by Lina Schiffer, Imken Oestlund, Jacky Snoep, Lorna C. Gilligan, Angela E. Taylor, Alexandra J. Sinclair, Rishi Singhal, Adrian Freeman, Ramzi Ajjan, Ana Tiganescu, Wiebke Arlt and Karl-Heinz Storbeck, are reproduced in Mathematica notebooks. The notebooks and the corresponding ...

Here we collect curated data to be integrated into public repositories

Current chemical concept recognition tools have demonstrated significantly lower performance for in full-text articles than in abstracts. Improving automated full-text chemical concept recognition can substantially accelerate manual indexing and curation and advance downstream NLP tasks such as relevant article retrieval. Participating in BioCreative Track NLM-Chem we focus identifying chemicals in full-text articles (i.e. named entity recognition and normalization).

In biomedical text mining, named entity recognition (NER) is an important task used to extract information from biomedical articles. Improving the NER’s performance will directly have a positive impact on extracting relations between those entities. In recent years, deep learning has become the main research direction of NER due to the development of effective models. Language transformer models like e.g. BERT are frequently used because they enable the specialisation of models by domain-specific ...

TA3 focusses on the services, service enabling tools, and software that NFDI4Health will provide to the user community. Most services and tools will be based on open source software that has already been developed by the (co-)applicants or by the broader scientific developer community. In close cooperation with TA4 and TA5, use case requirements and community feedback will help to further develop these tools and to foster interoperability of currently fragmented IT solutions for storage of metadata, ...

nfdi4health Dokumente und (interne) Daten, SOPs, etc., die relevant für das gesamte Konsortium sind

Key activities of TA1 concern the establishment of functional bodies and of the project governance for NFDI4Health.

NFDI4Health task area 2 targets core deficits in medical sciences, i.e. the lack of harmonised standards for data and data quality management in clinical trials, public health surveys, and epidemiological cohorts, as well as the lack of information on and access to relevant standards. By making standards available, TA2 will improve the findability, accessibility and interoperability of existing and novel data bodies. For this purpose, guidelines, standards and policies on data management and ...

With its focus on interaction, networking and exchange, task area 4 addresses the overall NFDI4Health Key Objective to support cooperation between clinical research, epidemiological and public health communities. It also provides training and education for the health research community and beyond, focusing on FAIR data principles.

Shared Space on OneDrive: https://onedrive.live.com/?id=4E57D2DCFD31954C%213715&cid=4E57D2DCFD31954C

The main objective of task area 5 of NFDI4Health is to implement or to at least explore the possibilities to implement these infrastructure components in specific use cases which reflect core needs of the scientific community related to health data research. The use cases will address a range of areas which will lay the ground for future expansion for full coverage of the broad range of data collected in health research.