Projects

SAFE-Aqua (SustainAble Farming for Effective Aquaculture) is an international consortium research project, consisting of a group of multidisciplinary experts from leading research institutes in France, UK, Thailand and a private-company in Spain.

Test case for porting sampleBD to fairdom-seek

With aging comes cellular senescence, and (multi-)morbidity. Cellular senescence is a key driver of an interconnected disease network including cancer and stroke. We wish to utilize systems modeling and bioinformatics, learning from omics and other lab data, to design and develop a biomarker + software kit with a focus on measuring and interpreting senescence-related signatures for precise (and early) diagnosis, prognosis, and, ultimately, therapy, of pancreatic cancer and ischemic stroke/thromboembolism. ...

Multi-level mathematical modeling of erythropoiesis for optimized expansion of erythroid progenitor cells and improved treatment regimes

Study on the mechanism of acupuncture combined with treadmill in treating apoplexy

Systems Biology of a genetically engineered Pseudomonas fluorescens with inducible exo-polysaccharide production: analysis of the dynamics and robustness of metabolic networks

Cyanobacteria are the only prokaryotes performing oxygenic photosynthesis. Theyhad and have tremendous influence on the biogeochemical cycles on Earth. Recently,cyanobacteria are increasingly investigated as cell factories for a sustainableeconomy. Despite their global, environmental and rising economic importance, ourknowledge on the regulation of their primary metabolism is fragmented.Cyanobacteria switch between photoautotrophic and heterotrophic modes ofmetabolism during day/night cycles or ...

The purpose of this project is to exchange public and private research data that is not attached to "normal" projects together with SDBV via the FAIRDOMHub.

SDBV group using Hub

This is a sandbox where DigiSal members can learn to use the SEEK.

Tutorial document: http://tinyurl.com/seek-ds17

The SEEK is a web interface to a database of research "assets" organised in a hierarchical "ISA structure" (investigation-study-assay) [1]. These are further organised into projects and programmes.

• Programme = Overarching research theme (The Digital Salmon)
• Project = Research grant (DigiSal, GenoSysFat)
• Investigation = a particular biological process, phenomenon or thing ...

We are modelling ROS management and mitochondrial dysfunction. Mitochondria produce both energy and reactive oxygen species (ROS), and suffer from ROS. Experimental data from University Milan-Bicocca.

Cystic Fibrosis (CF)- lethal autosomic disease CFTR - Cystic Fibrosis Transmembrane Regulator

Pesticides, plastics, cosmetics, electrical transformers and many other products contain Endocrine disruptors (EDCs). EDCs interfere with natural hormone functions and may cause the disease.

The SilicoTryp project aims at the creation of a “Silicon Trypanosome”, a comprehensive, experiment-based, multi-scale mathematical model of trypanosome physiology. Trypanosomes are blood-stream parasites transmitted by tsetse flies; they cause African sleeping sickness in humans and livestock. Currently available drugs have severe side effects, and the parasites are rapidly developing resistance. In this project, we collect a wide range of new experimental data on the parasite in its various ...

The Integrated Platform for Endocrine Disruptor Risk Assessment (SNAPPER) project will propose solutions based around three core philosophies: Integrated Science: Integration of knowledge from a complete pipeline of systems biology into a holistic yet mechanistic framework that enhances the understanding both of endocrine biology and of adverse effects due to externally induced disruption of the body’s endocrine system. The pipeline includes in vivo, in vitro, and in silico data resulting both ...

Investigation regarding the impact of periportal steatosis on selected parameters of drug metabolism.

Transcription bursting and stochastics

Global metabolic switching in Streptomyces coelicolor

Antibiotics are made during the second phase of growth when there is a transition in metabolism from primary to secondary metabolism. Primary metabolism is growth related and involves all the normal cellular activities associated with cell growth and division. Whereas secondary metabolism is non-growth linked and is non-essential but many important activities occur during this phase which help the bacterium survive.

to complete

Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

Within the e:Bio - Innovationswettbewerb Systembiologie (Federal Ministry of Education and Research (BMBF)), the SulfoSYSBIOTECH consortium (10 partners), aim to unravel the complexity and regulation of the carbon metabolic network of the thermoacidophilic archaeon Sulfolobus solfataricus (optimal growth at 80°C and pH 3) in order to provide new catalysts ‘extremozymes’ for utilization in White Biotechnology.

Based on the available S. solfataricus genome scale metabolic model (Ulas et al., 2012) ...

"Systems Understanding of Microbial Oxygen responses" (SUMO) investigates how Escherichia coli senses oxygen, or the associated changes in oxidation/reduction balance, via the Fnr and ArcA proteins, how these systems interact with other regulatory systems, and how the redox response of an E. coli population is generated from the responses of single cells. There are five sub-projects to determine system properties and behaviour and three sub-projects to employ different and complementary modelling ...

This work aims to identify the biochemical pathways of THP-1 human monocytes infected by different Leishmania infantum clinical isolates from patients with either resistance or with TF outcome, using whole cell differential Mass Spectrometry proteomics. Network enrichment analysis was adopted to integrate the transcriptomics and the proteomic results of infected cells studies. Transferrin Receptor C and Nucleoside Diphosphate Kinase 3 were discovered as overexpressed proteins in THP-1 cells ...

SUSPHIRE aims to provide a sustainable, low-cost biomanufacturing platform for the commercial production of insect pheromones.

Sustainable co-production is the short form of the research project “Tobacco as sustainable production platform of the natural biopolymer cyanophycin as co-product to oil and protein”. It combines plant and industrial biotechnology to increase the value of commercially grown tobacco with products that can sustainably substitute fossil raw materials. We aim to establish a new economically feasible production system for the biopolymer cyanophycin (CGP) as a by-product of tobacco without relevant ...

The main objective of SynBio4Flav is to go further in the standardization of high complexity synthetic biological parts, and to demonstrate the development of a standardized, and systematic platform for flavonoids production based on synthetic microbial consortia (SMCs).

The main goal of this project is to create a null-CO2 foot-printing and robust biotechnological platform based on microbial consortia to produce sustainable bio-based compounds using CO2 and light as the sole sources of carbon and energy, respectively.

Biomining is a biotechnological process carried out in many parts of the world that exploits acid loving microorganisms to extract metals from sulphide minerals. One industrial biomining method is called ‘heap bioleaching’ where typically copper containing minerals are piled into very large heaps, acid and microorganisms are added to the top and the soluble metal is collected at the heap base.

The role of the different types of microbes in the process is to speed up metal solubilisation by oxidising ...

Designer microbial communities for fermented milk products: A Systems Biology Approach

The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:

• facilitates and maximises the potential for data exchange between SysMO research groups;
• maximises the ‘shelf life’ and ...

Comparative Systems Biology: Lactic Acid Bacteria

Overall, we will measure in-vitro and model in-silico the short-term biochemical network dynamics of extra cellular matrix maintenance (ECM) in populations of young, old and senescent dermal fibroblasts. We have shown in previous work that differences in network dynamics are highly informative and provide a means to identify parts of the network that could be targeted to restore healthy function.

The work will be first carried out in 2D culture of human dermal fibroblasts then extended to a novel ...

Coastal zones and oceans constitute an essential fundament for Norway’s history as well as current economy, providing ecosystem services for fisheries, aquaculture, transport, tourism, and recreation. The petroleum activities in Norwegian waters have been crucial for Norway’s financial growth and in financing the Norwegian welfare state. As the pressure on the oceans continuously increases, both the petroleum industry and the seafood industries have acknowledged that awareness and actions are ...

There is an urgent need for novel antibiotics to fight life-threatening infections and to counteract the increasing problem of propagating antibiotic resistance. Recently, new molecular genetic and biochemical tools have provided insight into the enormous unexploited genetic pool of environmental microbial biodiversity for new antibiotic compounds. New tools for more efficiently lifting this hidden treasure are needed to strengthen competitiveness of European industry, as well as for a cost-saving ...

This project provides a space for storing, annotating and publishing Systo models.

Translating Systems Virology data into broad-spectrum antiviral Drugs