Extraordinary research ideas attracts VILLUM Experiment grants

Head of Department, professor Niels Kroer says: “The Department of Biology received 1/3 of all Villum Experiment grants going to the University of Copenhagen and, together with DTU Physics, is the department that has received the highest number of grants of all. That is pretty astonishing!”

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Mette Burmølle, Associate Professor 
Section of Microbiology

Project: Printing nature to study nature - artificial 3D-leaves for ecologically relevant studies of bacterial biofilm communities

Grant: DKK 2 million

Bacteria in nature live in complex communities, where they communicate and collaborate. These communities often form on surfaces offering favorable growth conditions, and to enhance attachment and protection, the bacteria produce an extracellular polymeric matrix. Such matrix encased communities are known as biofilms. In the laboratory, biofilms are studied under simplified conditions, and, therefore, we face a severe knowledge gap concerning interactions and organization in multispecies biofilms. In BioPrint, I will 3D print artificial, degradable leaves that serve as surface and substrate for model soil biofilms. The 3D leaves are easily manipulated and compatible with microscopy. The developed methodology will be used to unravel interspecies bacterial interactions in biofilms under ecologically relevant conditions, specifically aiming at identification of metabolic interactions and how these depend on the distance between bacteria.

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Anders Løbner-Olesen, Professor
Section for Functional Genomics

Project: Engineering biological memory in bacteria

Grant: DKK 2 million

The goal is to develop a new tool for information storage in bacteria using DNA methylation as an epigenetic switch. We will develop an artificial gene promoter regulated by methylation to create specific DNA methylation profiles. The novel DNA methylation patterns generated will be used to memorize inputs in living bacteria. Here we wish to design a DNA methylation system to track and record DNA replication to identify and study metabolically dormant bacteria. This system will be usable for studying bacterial phenotypic heterogeneity.

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Jakob Frimodt-Møller, Postdoc
Section for Functional Genomics

Project: Insane in the membrane; how to avoid crowding of the Escherichia coli inner membrane?

Grant: DKK 2 million

Escherichia coli is one of - if not - the most well studied organism on earth, however it keeps coming up with surprises. Recently, we added to this by observing loss of viability (to ex. aminoglycosides) if the inner membrane (IM) was crowded with proteins. Thus, E. coli possess the ability to avoid crowding of the IM without compromising its function in uptake of metabolites, efflux of toxins, and its essential role in envelope integrity. We will investigate this ability of E. coli to avoid crowding from multiple different angels to cover everything from IM protein composition to changes in fluidity. This exploration will add to our basic understanding of E. coli, influence several biological fields, and provide a blueprint for investigating this phenome in higher organism.

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Joseph Nesme, Postdoc
Section of Microbiology

Catch me if you conjugate. Plasmid recovery from complex ecosystems using secreted pilus machinery as a hook

Grant: DKK 2 million

Microbes engages in promiscuous but very permissive sex allowing them to acquire new competences from their neighbors such as antibiotic resistance obtained by many pathogens from environmental microbes. Plasmid conjugation notably involves the secretion of a filament-like appendage – the conjugative pilus – that will bring into contact bacterial cells and funnel plasmid DNA transfer. Yet, we do not know much about the true diversity of conjugative plasmids in Nature and definitely very little on their transfer dynamic, despites their proven implication in bacterial adaptation. Current assays of plasmid transfer are limited by the cultivability of environmental microbes and the relatively low abundance of plasmids in total environmental DNA. I propose here a method to target directly the transfer mechanism proteins and recover cells containing a conjugative plasmid. This holistic approach will be applied on complex hot-spots of plasmid transfers environmental samples, such as wastewaters. I expect here not only to uncover novel plasmid sequences but also their dynamic in-situ using comparative plasmid-targeted metagenomics.

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Maria Herranz Matesanz, Postdoc

Tiny dragons (Kinorhyncha) answering big questions - insights into metazoan segmentation

Grant: DKK 2 million

Segmentation is one of the most successful body plans in metazoans and thus, it has played a central role in our understanding of animal evolution. Kinorhynchs, commonly known as mud dragons, are one of the four existing segmented animal groups together with arthropods, annelids and chordates. While arthropod, annelid and chordate segmentation has been intensively studied, segmentation machinery is completely unknown in kinorhynchs. What are the mechanisms underlying segmentation in mud dragons? How are segments formed? What are the responsible genes? Is kinorhynch and arthropod segmentation homologous or do kinorhynchs represent a novel type of segmentation in metazoans?
We aim to fill the big gap of knowledge generating: (i) novel morphological evidence (gene expression, cell proliferation and immunohistochemistry studies) and (ii) molecular evidence (de novo transcriptomics, phylogenomics). Results will not only shed light on the origin of segmentation within Ecdysozoa (molting animals), but also broaden our knowledge on segmentation patterns, their deviations and evolutionary transformations throughout ancient history.

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