Research Projectshttps://www.uni-giessen.de/de/fbz/fb08/Inst/bioinformatik/Research/research_projectshttps://www.uni-giessen.de/@@site-logo/logo.png
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Research Projects
DFG „RTG 2355: Regulatory networks in the mRNA life cycle: from coding to non-coding RNAs” RNA is a central molecule of gene expression that is not only a target of regulation, but also a regulatory agent itself, and we are only beginning to appreciate how versatile the hitherto identified noncoding RNAs are used in cells: as scaffolds and recruiting platforms, protein and RNA sponges, allosteric regulators of protein activity, or molecular sensors. Functioning of these regulatory RNAs can in turn be regulated by mechanisms affecting base-pairing abilities and RNA folding such as RNA editing, base modification or RNA structure remodeling. Within our Research Training Group, we aim to establish how these multiple RNA-based mechanisms contribute to the plasticity of gene-regulatory networks. As regulation of gene expression underpins all cellular processes, this research has the potential to improve our understanding of many topics of medical relevance, such as bacterial biofilm formation, diet-induced changes to metabolism, virus infection, and disease.
LOEWE Priority Program “Tree-M: Mechanisms of resilience and environmental impact of the tree leaf microbiome“ Forests play an essential role in global climate. They host an immense variety of microorganisms, exhibiting enormous biochemical and physiological diversity, which in turn can affect health and resilience of trees. The research cluster Tree-M – mechanisms of resilience and environmental impact of the leaf microbiome of trees – focuses on these microorganisms and their complex interactions with the biotic and abiotic environment of their leaf habitat (the phyllosphere). With an interdisciplinary research cluster joining forces from the fields of microbiology, biochemistry, ecology, geography, and bioinformatics, research activities will for the first time investigate these microorganisms and their interaction networks on various scales. This knowledge can help in the development of sustainable strategies that reduce the impact of global change on this interaction network and can thus help sustain forest health and functions into the future.
Period of funding: 01.01.2023 - 31.12.2026 Homepage:Tree-M
BMBF “de.KCD - German Competence Center Cloud Technologies for Data Management and Processing” The de.KCD (Deutsches Kompetenzzentrum Cloud-Technologien für Datenmanagement und -verarbeitung) is a cross-location and cross-domain hub that provides skills in handling data using cloud-based technologies, resources and methods for institutions and interconnected centers as well as for researchers at all career levels. In the current phase of digital transformation, scientific and economic success as well as the connectivity of future-oriented projects depend on (i) the systematic and structured collection of relevant raw and metadata through expertise-based data management, (ii) the development and provision of innovative cloud offerings and automated workflows, (iii) the development and transfer of expertise in the field of cloud-based data processing, and (iv) the availability of a powerful and independent cloud infrastructure. The de.KCD specifically addresses these challenges in order to bundle expertise in cloud computing and data management, as well as to provide and expand the necessary hardware capacities and cloud services.
Period of funding: 01.12.2023 – 30.11.2026 Homepage:de.KCD
DFG Research Unit 5098 “ICIPS - Innovation and Coevolution in Plant Sexual Reproduction” Early land plants faced the challenge of extending their range further and further away from water and were always in danger of dehydration. Consequently, also the sexual reproduction of land plants is geared towards independency of water. Several key innovations in sexual reproduction originated in the land plant lineage, such as spores with a rigid outer surface, ovules harboring reduced female gametophytes and a multicellular embryo that is dispersed within seeds in a dehydrated state. The evolution of sexual reproduction in land plants thus provides stunning examples for the crucial biological concepts of „innovation“ and „coevolution“. However, the evolutionary dynamics and molecular mechanisms underlying these processes are poorly understood. The ICIPS aims to shed light the evolutionary dynamics and molecular mechanisms underlying the evolution of sexual reproduction in plants.
Period of funding: 01.01.2022 – 31.12.2025 Homepage:ICIPS
BMBF „Deep Legion - Detection of virulence factor protein domains in Legionella using deep autoencoders” Legionella pneumophila is a gram-negative bacterium and an important intracellular pathogen. It causes Legionnaires' disease, a specific form of pneumonia in humans. L. pneumophila is highly adapted to intracellular replication and manipulates vital host cell functions such as vesicle transport and gene expression by utilizing over 300 specific virulence factors. Many of them contain eukaryote-like protein motifs acquired during co-evolution with their hosts and inserted into bacterial virulence factors, which are important for understanding the pathophysiology of the disease and potential therapeutic targets. The aim of this joint research project of the Philipps University Marburg and the Justus Liebig University Giessen is to use deep learning approaches to identify the virulence factors based on our current data, predict their origin and function and validate these predictions in vitro. Our new deep learning approach will pave the way for new applications in precision medicine for infectious diseases.
DFG Research Grand “RanOmics - Evolution of Gene Networks: The Ranunculales Order as a Model Lineage for Evolutionary Innovations” A central goal of evolutionary research is to understand how evolutionary novelties arise. In RanOmics, we investigate the molecular genetic origin of novel traits emerging in the order Ranunculales. Within this order, several morphological traits have developed repeatedly, e.g. spurred floral organs, zygomorphy or the reduction of perianth, and many species within the Ranunculales can be treated with virus-induced gene silencing, which allows targeted gene silencing to investigate their function. We are sequencing and analyzing transcriptomes of different plant organs of several Ranunculales species and their genomes to uncover these evolutionary innovations. Co-expression networks will be identified and correlate with the corresponding evolutionary innovations. The aim of this project is to provide the necessary resources to carry out comparative transcriptome and genome analyses in Ranunculales as a prerequisite to unravel the genetic base of novel morphological traits origin.
Period of funding: 01.01.2021 – 31.12.2025 Homepage:RanOmics
LOEWE Research Cluster Diffusible Signals – Impact of diffusible signals at human cell-microbe interfaces Infectious diseases are among the most common causes of death worldwide. The research cluster "Diffusible Signals" aims to investigate and change a central basis of infection processes, the communication between bacteria and human cells. In an interdisciplinary team involving physicists, biologists and computer scientists, we are investigating the exchange of soluble (diffusible) signals at the interfaces between clinically important bacteria and immune cells and want to use this approach for the development of new therapeutic approaches.
NFDI4Biodiversity combines scientific and technical expertise to provide a broad service portfolio to handle and further develop biodiversity and environmental data in close cooperation with users from research and practice. The consortium consists of 50 scientific institutions, museums, natural history societies, state offices, and other institutes and expert groups. They are guided by the knowledge that stakeholders in science, politics, nature conservation and landscape management need reliable data to develop better contributions to the conservation of biodiversity. To this end, the consortium offers added value to the community, specifically (1) access to modern technologies and a comprehensive stock of biodiversity and environmental data, (2) methods and tools for archiving, publishing, searching and analyzing data that are suitable for everyday use and have been tried and tested in practice and (3) an expert forum for the safe and competent handling of data for diverse and responsible use.
DFG “NFDI4Microbiota - National Research Data Infrastructure for Microbiota Research Microbes play an important role in human and environmental health. The growing awareness of this fact has led to an enormous increase in research activities that contribute, e.g., to address global health threats such as antibiotic resistance and viral pandemics, but they are also used in agriculture or in the restoration of ecosystems. Although these studies are usually run independently of each other, many projects are closely linked and it makes sense to combine their results. The aim of the NFDI4Microbiota consortium is to serve and connect the broad and heterogeneous research community by improving the availability and quality of research results through specialized training and by facilitating the generation, management, interpretation, sharing and reuse of microbial data. Thus, a German microbial research network will be created and a cloud-based system will be developed to make the storage, integration and analysis of microbial data, especially omics data, consistent, reproducible and accessible in all areas of life sciences.
BMBF „FAIR Data Spaces“ Data spaces are open structures and organized decentrally. By using matching and mapping techniques, data can be made available regardless of the degree of integration in the system. Data spaces enable digital sovereignty, as the data remains the property of the company or research institution until it is retrieved. FAIR Data Spaces offer organizational, legal, technical and practical building blocks for a shared, cloud-based data space for industry and research in compliance with the FAIR principles. The main objectives of the project are (1) to create a roadmap for cooperation between the European federated and secure data infrastructure Gaia-X and the National Research Data Infrastructure (NFDI), (2) to create the ethical and legal framework for data exchange between research and industry and (3) to demonstrate the benefits of Gaia-X technology for the use of FAIR research data in various areas of science and industry. The NFDI association and numerous universities organized in NFDI consortia represent the research application area. The industry-oriented Gaia-X side is represented by the Fraunhofer-Gesellschaft and Atos as representatives of the companies involved in Gaia-X.
Period of funding: 01.05.2021 – 31.12.2024 Homepage: FairDS
DFG Research Unit 5116 “exRNA - Plant-microbe communication through extracellular RNA - Systems-level approaches to explore molecular mechanisms and agronomic applications" As a further increase in agricultural land is not acceptable, there is no other option than to increase global yield efficiency and reduce the yield gap in order to ensure global food security. Therefore, a new understanding of plant disease mechanisms and technological developments in crop protection are needed. The main objective of FOR5116 is to create a dynamic, internationally leading and collaborative consortium with the common goal of developing a mechanistic understanding of RNA-mediated cross-kingdom communication between plant hosts and their pathogens. Our central hypothesis is that exRNAs (RNA effectors) play a conserved key role in pathogen infection and plant health and therefore also have a high potential to improve plant health. We anticipate that the knowledge gained in this consortium can be used to improve agronomic RNA applications in the future, e.g. through the use of novel formulations, RNA types and/or the use of RNA-binding proteins and vesicle-based delivery.
Period of funding: 01/01/2021 – 12/31/2024 Homepage: exRNA
