On July 28 Ulrike (Uli) Pfreundt has defended her doctoral thesis on „The non-coding paradox of Trichodesmium – Lifestyles and strategies in the oligotrophic marine environment“ with the highest possible rating summa cum laude. Big congratulations to this phantastic outcome!
Cyanolab is located at the interface of bioinformatics, synthetic biology, experimental RNA biology and microbial systems biology. We participate in the Research Training Group “MeInBio – BioInMe: Exploration of spatio-temporal dynamics of gene regulation using high-throughput and high-resolution methods“,, the Research Group FOR 2816 “The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layers (SCyCode)” the DFG Priority Programs SPP 2002 “Small Proteins in Prokaryotes, an Unexplored World“, SPP 2141 “Much more than Defence: the Multiple Functions and Facets of CRISPR-Cas“, SPP 2237 „MAdLand – Molecular Adaptation to Land: plant evolution to change“ and SPP 2389 „Emergent Functions of Bacterial Multicellularity“.
We have a long-standing interest in cyanobacteria and other photosynthetic organisms and their functions in the environment and their biotechnology. Current research activities are centered around the analysis of transcriptomic and epigenomic datasets to characterize regulatory RNAs and epigenetic modifications (see, for instance, our publications Hagemann et al., 2018; Hess et al., 2014; Klähn et al., 2015; Kopf et al., 2014; Kopf and Hess, 2015; Lott et al., 2015; Mitschke et al., 2011; Pfreundt et al., 2015; Riediger et al., 2019 and 2021; Rübsam et al., 2018; Walworth et al., 2015).
We study CRISPR systems with the aim to understand their functions in antiviral defense and also beyond defense (see, for instance, the publications Behler et al., 2018a and 2018b; Hein et al., 2013; Kieper et al., 2018; Mitrofanov et al., 2022; Reimann et al., 2017 and 2020; Scholz et al., 2013; Shah et al., 2018; Ziemann et al., 2023).
On the basis of comparative genomic information, computational and experimental tools have been developed and applied to systematically investigate the „genetic dark matter“. This includes the identification of novel regulatory RNAs (antisense and non-coding RNAs) in diverse pro- and eukaryotic organisms and to understand their functions (Barshishat et al., 2018; Georg et al., 2009, 2014 and 2017; Georg and Hess, 2018; Lott et al., 2018; Voß et al., 2009; Wright et al., 2013 and 2014; Zhan et al., 2021; Zhang et al., 2022). Further in this field, we have discovered two small proteins, which function as novel players in the regulation of the primary energy metabolism (Krauspe et al., 2021; Song et al. 2022).
Particular research has been conducted on marine microorganisms and the marine microbiome (Hou et al., 2018; Lott et al., 2020; Teikari et al., 2018a, 2018b; Voigt et al., 2014). In the characterization of the marine microbiome we have been studying the microbial metatranscriptome and community composition (Pfreundt et al., 2016a,b; Spungin et al., 2016; van Wambeke, 2016).
Dr. Matthias Kopf (Matze) has been awarded the Hans-Grisebach price for his outstanding summa cum laude dissertation in the field of comparative transcriptomics! Congratulations!!