Research cooperations

Research cooperations

<strong>Collaborative Research Center SFB987: Microbial Diversity in Environmental Signal Response</strong>
Microorganisms are omnipresent in the biosphere and provide the greatest diversity of life on our planet. They successfully colonize almost every possible ecological niche, regardless of welcoming or hostile conditions, either as highly specialized individual cells, as microbial communities or by forming complex multi-cellular structures. A key factor for their success in colonizing varying habitats is the enormous biochemical, physiological and cellular adaptation potential of microorganisms in response to countless environmental conditions and cues. By generating microbial species with unique metabolic and cellular attributes, microbial diversity is the answer to the demands of evolution. This sets the stage for their ability to adapt to changing conditions within a given ecosystem and to explore new opportunities in novel environmental settings. For most microorganisms there is only one certainty: change! 
Period: 01.07.2012 - 30.06.2020
<strong>The Collaborative Research Center TRR174: Spatiotemporal dynamics of bacterial cells</strong>
This DFG-funded collaborative research center comprises 16 research groups from the Marburg and Munich areas. Its goals are to (i) elucidate the molecular mechanisms that regulate the spatiotemporal dynamics of cellular components in bacteria; (ii) extract from the experimental data conserved design principles for spatiotemporally organized systems; and, (iii) mathematically model, design, and synthesize modules that spatially organize minimal cells or cell-free systems.
Period of funding: 01.01.2017 – 31.12.2020
Coordinator: Prof. Dr. Martin Thanbichler, Philipps-Universität Marburg
<div style="text-align: justify;"><strong>The Priority Programme SPP 1879: Nucleotide Second Messenger Signaling in Bacteria</strong></div>
his DFG-funded priority programme centers on establishing the first systematic and comprehensive strategy ever to understand all fundamental aspects of second messenger signaling in bacteria at the molecular level. Biosynthesis, turnover and functions of c-di-GMP, the “classics” cAMP and ppGpp, as well as “newcomers” such as c-di-AMP will be studied from molecular, cellular, physiological, systems-level and ecological perspectives. The research groups in the programme, in particular, focus on understanding (i) sensory inputs into second messenger signaling; (ii) specific functions and “local” signaling of second messenger-producing and degrading enzymes in bacterial species that have multiples of these enzymes; (iii) second messenger effector mechanisms and molecular targets; and, (iv) novel physiological and ecological contexts as well as evolutionary aspects reflected in the molecular biology of second messenger signaling.
Period of funding: 09.2016 – 09.2020
Coordinator: Prof. Dr. Regine Hengge, Humboldt Universität zu Berlin
<div style="text-align: left;"><strong>DFG Priority Programm SPP 1927: "Iron-Sulfur for Life"</strong></div>
Subtitle: [Fe]-hydrogenase: Role of iron-sulfur bonding in holoenzyme assembly and in FeGP-cofactor biosynthesis 
[Fe]-hydrogenase catalyzes the reversible transfer of a hydride from H2to methenyl-tetrahydromethanopterin which is an intermediary step in methanogenesis from H2 and CO2. The enzyme contains one iron per active site. The iron is associated with a unique iron-guanylylpyridinol (FeGP) cofactor. In many methanogens, the [Fe]-hydrogenase structural gene (hmd) is clustered with hmd-co-occurring genes (hcgA-G), which have been shown to be involved in FeGP cofactor biosynthesis. In previous studies, we have already identified the function of five of the hcg gene-products (HcgB, HcgC, HcgD, HcgE and HcgF) using structure to function strategies and biochemical assays. HcgB catalyzed guanylyl-transfer from GTP to the 4-hydroxypyridinol. HcgC is a SAM-dependent methyltransferase; HcgD is a putative iron chaperone. HcgE catalyzes the adenylylation of the carboxy group of a 6-carboxymethyl-guanylylpyridinol precursor. Subsequently the product of HcgE reacts with Cys9 of HcgF yielding a thioester and AMP. Based on chemical precedents, we propose that the thioester reacts with an iron species forming the acyl and thiolate ligands. In the next three years, we would like to identify the function of the two remaining Hcg proteins (HcgA and HcgG), both of which are predicted to be iron-sulfur proteins. For this purpose, we will - as before - employ structure to function strategies, in vitro biosynthesis and metabolite analysis of hcg knock-out mutants. 
Period: 01.09.2016 - 31.08.2019
<div style="text-align: justify;"><strong>DFG Research Group FOR1680 CRISPR/Cas: "Unraveling<br />the prokaryotic immune system"</strong></div>
The FOR1680 consortium teams up scientists with expertise in microbiology, bioinformatics, structural biology and mass spectrometry. Their common goal is the elucidation of a recently discovered prokaryotic immune system based on "Clustered Regularly Interspaced Short Palindromic Repeats" (CRISPR). CRISPR elements are found in the genomes of many Bacteria and nearly all Archaea and present small RNA-based mechanisms to defend the host cell against the attack of mobile genetic elements. 
Period: 01.01.2012 - 31.12.2017
<strong>DIP project "Spatial and temporal regulation of macromolecular complex formation in bacteria"</strong>
Research in this project focuses on unraveling the spatial distribution of macromolecular complexes in bacterial cells and its underlying mechanisms, as well as to explore the physiological roles of this subcellular spatiotemporal organization. Specifically, we want to elucidate strategies for spatial regulation of bacterial. DIP is an excellence program that aims to strengthen excellence in German-Israeli research cooperation and give substantial support to joint projects of outstanding quality. 
Period: 01.02.2015 - 14.11.2018
<strong>Synthetic Biology Community Science Project - DOE Joint Genome Institute: "COFIX GENOMICS"</strong>

Synthetic Biology Community Science Project - DOE Joint Genome Institute: "COFIX GENOMICS"

Carbon dioxide (CO2) is a potent greenhouse gas that is a critical factor in global warming. At the same time CO2 is a cheap and readily available carbon source. Because chemistry lacks suitable catalysts to functionalize the CO2 molecule, there is an increasing need to understand and exploit CO2 fixing enzymes and pathways offered by Nature. The project "COFIX-GENOMICS" within the framework of the Synthetic Biology Community Science Program of the US Department of Energy (DOE) - Joint Genome Institute aims at identifying and characterizing novel CO2 fixing enzymes in microbial genomes. 
Period: 02.02.2016 - 02.01.2019
<strong>Synthetic Biology Community Science Project - DOE Joint Genome Institute: "SYNCO(2)PE"</strong>
The project aims at the implementation of the CETCH cycle, an artificial pathway for the conversion of CO2 into bacteria and unicellular algae. The project will be performed together with the synthetic biology laboratory at the Joint Genome Institute of the US Department of Energy (DOE) and includes the development of novel genetic tools for alphaproteobacteria and unicellular algae.
Period: 01.12.2016 - 30.11.2020
<strong>National Institutes of Health (NIH) project "History dependence of chemosensing strategy in <em>Escherichia coli</em>"</strong>

National Institutes of Health (NIH) project "History dependence of chemosensing strategy in Escherichia coli"

The aim of this collaborative research project is to investigate dependence of the signal processing within the chemotaxis network of E. coli on the history of cells' exposure to temperature, nutrient abundance and other environmental factors. Other participating groups: Ned Wingreen (Princeton University, USA; coordinator); Yigal Meir (Ben-Gurion University, Israel); William Ryu (University of Toronto, Canada) 
Period: 01.01.2014 - 31.08.2016
<strong>FET OPEN Project “FutureAgriculture”</strong>
The FutureAgriculture project aims at improving the yield and rate of carbon fixation in cyanobacteria and plants, which is often the limiting part of photosynthesis. To that end synthetic pathways for photorespiration will be designed in silico, reconstructed in vitro and transplanted in vivo
Period: 01.01.2016 - 31.12.2020
<strong>BMBF Research Initiative: FormatPlant</strong>
The FormatPlant project aims at establishing an alternative pathway for CO2 fixation through directly converting CO2 into formate with the photosynthetic apparatus. The goal is to develop this alternative photosynthesis from microbial enzymes in photosynthetic bacteria and chloroplasts. The project is funded by the PLANT 2030 program of the 
Period: 01.10.2016 - 30.09.2019
<strong>Max Planck Research Network in Synthetic Biology "MaxSynBio"</strong>
The goal of this Max Planck Society consortium is to pursue bottom-up synthetic biology, reconstituting functional cell-like systems or modules from well-characterized components. 
Period: 01.08.2014 - 31.07.2020
<div style="text-align: justify;"><strong>LOEWE research cluster FACE2FACE - Effects of climate change, adjusting to climate change and reducing greenhouse gas emissions by 2050</strong></div>
Elevated atmospheric CO2 concentrations lead to increased above-ground plant growth and increased production of fine roots, as well as to changes in C and N fluxes in soils and soil aggregates. Effects of global climate change on the phylogenetic and functional diversity of rhizosphere microbial communities were repeatedly analyzed, but with inconsistent results. Reasons may be differences in the experimental conditions (e.g., related to soil type, composition of plant communities, climate), but also in the sensitivity of the methods used for analysis. This workpackage of FACE2FACE aims to assess the effects of an increase in atmospheric CO2 concentration and air temperature on the diversity and activity of microbial communities in agricultural soils pertaining to pastureland, viticulture and horticulture. The research will be performed using cultivation-independent molecular ecology techniques, in particular next-generation sequencing of total RNA. 
Period: 01.01.2014 - 31.12.2017
<strong>LOEWE Research Cluster: MegaSyn</strong>
MegaSyn is a Hesse-wide research initiative funded by the Hessen State Ministry of higher Education, Research and the Arts, which focuses on the understanding, and manipulation of the biosynthetic machineries of microorganisms that produce pharmacetuically and biotechnologically interesting biomolecules, such as biofuels, immunosuppressives and antibiotics.
Period: 01.12.2016 - 30.11.2020
<strong>LOEWE Center for Synthetic Microbiology (SYNMIKRO)</strong>
The Philipps-Universität and the Max Planck Institute for Terrestrial Microbiology have been granted more than 50 million Euro in funding from 2010 to 2018 to establish the LOEWE Research Center for Synthetic Microbiology (SYNMIKRO). The LOEWE Program is an excellence initiative of the state of Hessen to support excellent research at universities and other research institutions in Hessen.
<div><strong>International Max Planck Research School for Environmental, Cellular and Molecular Microbiology.</strong></div>
Research in the graduate school aims at understanding how microorganisms compete, adapt, and differentiate in response to changes in the environment. To reach this aim, microbial ecology is tightly integrated with molecular and cellular microbiology and microbial physiology and biochemistry. The faculty members of the graduate school are from the Max Planck Institute or the Philipps-Universität.
<strong>MIT International Science and Technology Initiatives: Spatial Order and Collective Cell Behavior in Bacterial Biofilms</strong>

MIT International Science and Technology Initiatives: Spatial Order and Collective Cell Behavior in Bacterial Biofilms

Biofilms exist on almost every wet terrestrial surface and are believed to be the most abundant form of bacterial life outside the oceans. The control and suppression of biofilm-mediated infections is difficult because conventional antibiotics become inefficient or even fail completely when bacteria organize in a biofilm community, where they are protected by an extracellular gel-like matrix. Yet, in spite of intense research efforts and considerable progress over the past decades, cellular organization and communication in biofilms remain poorly understood theoretically due to a lack of quantitative models that capture the complex interplay between physical, biological and chemical processes. The proposed research aims to contribute towards a better understanding of bacterial biofilms by combining detailed mathematical and numerical modeling, performed in the Dunkel group (MIT Mathematics), with state-of-the-art microscopy data produced by the Drescher lab (Max Planck Institute for Terrestrial Microbiology).
Period: 31.12.2015-01.02.2018

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