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graduation
Congratulations on your PhD!


Samira Parhizkar
Loss of TREM2 function increases amyloid seeding but reduces plaque associated ApoE
RG: Christian Haass



 

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Hergenhan S, Holtkamp S, and Scheiermann C.
J Mol Biol. 2020;S0022-2836(20)30028-0.
(*IMPRS-LS students are in bold)
doi:10.1016/j.jmb.2019.12.044

Molecular interactions between components of the circadian clock and the immune system

The immune system is under control of the circadian clock. Many of the circadian rhythms observed in the immune system originate in direct interactions between components of the circadian clock and components of the immune system. The main means of circadian control over the immune system is by direct control of circadian clock proteins acting as transcription factors driving the expression or repression of immune genes. A second circadian control of immunity lies in the acetylation or methylation of histones to regulate gene transcription or inflammatory proteins. Furthermore, circadian clock proteins can engage in direct physical interactions with components of key inflammatory pathways such as members of the NFκB protein family. This regulation is transcription independent and allows the immune system to also reciprocally exert control over circadian clock function. Thus, the molecular interactions between the circadian clock and the immune system are manifold. We highlight and discuss here the recent findings with respect to the molecular mechanisms that control time-of-day dependent immunity. This review provides a structured overview focusing on the key circadian clock proteins and discusses their reciprocal interactions with the immune system.


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Kuo TT, and Ladurner AG.
Front Genet. 2019;10:1210.
doi:10.3389/fgene.2019.01210

Exploiting the Circadian Clock for Improved Cancer Therapy: Perspective From a Cell Biologist

Since the discovery of the biological clock, the concept of treating cancer according to biological rhythms, here termed cancer chronotherapy, has rapidly evolved. Its fundamental aim is to improve the efficacy of drugs and to minimize adverse effects by administering chemotherapeutic drugs at the appropriate time-of-day. In the last two decades, several experimental and clinical studies have reported positive associations between the circadian clock and drug response in cancer patients. However, the lack of mechanistic insights into critical, deterministic clock-controlled genetic, and metabolic variations between and within individual cancer patients continue to cast a shadow on the potential benefits cancer chronotherapy may provide. Here, we provide first a simplified overview on our biological clocks and how our life-style induces complex biochemical reactions and genetic interactions. Next, we summarize how these reactions directly and indirectly modulate the effectiveness and toxicity of oncological drug treatments. Since cytotoxic chemotherapy represents the most common and affordable of cancer treatments, a case should be made that we need to ensure these treatments are used in the best possible manner. Thus, we list current challenges and future directions toward that goal.


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Swietlik JJ, Sinha A, and Meissner F.
Curr Opin Cell Biol. 2020; 63:20–30.
doi:10.1016/j.ceb.2019.12.002

Dissecting intercellular signaling with mass spectrometry-based proteomics

Physiological functions depend on a coordinated interplay of numerous different cell types. Proteins serve as major signaling molecules between cells; however, their comprehensive investigation in physiologically relevant settings has remained challenging. Mass spectrometry (MS)-based shotgun proteomics is emerging as a powerful technology for the systematic analysis of protein-mediated intercellular signaling and regulated post-translational modifications. Here, we discuss recent advancements in cell biological, chemical, and biochemical MS-based approaches for the profiling of cellular messengers released by sending cells, receptors expressed on the cell surface, and their interactions. We highlight methods tailored toward the mapping of dynamic signal transduction mechanisms at cellular interfaces and approaches to dissect communication cell specifically in heterocellular systems. Thereby, MS-based proteomics contributes a unique systems biology perspective for the identification of intercellular signaling pathways deregulated in disease.


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Bartnik, K., Barth, A., Pilo-Pais, M., Crevenna, A.H., Liedl, T., and Lamb, D.C.
J Am Chem Soc, 2019, [Epub ahead of print].
doi: 10.1021/jacs.9b09093

A DNA origami platform for single-pair Forster Resonance Energy Transfer investigation of DNA-DNA interactions and ligation

DNA double-strand breaks (DSBs) pose an everyday threat to the conservation of genetic information and therefore life itself. Several pathways have evolved to repair these cytotoxic lesions by re-joining broken ends, among them the non-homologous end-joining (NHEJ) mechanism that utilizes a DNA ligase. Here, we use a custom-designed DNA origami nanostructure as a model system to specifically mimic a DNA DSB, enabling us to study the end-joining of two fluorescently-labeled DNA double-strands with the T4 DNA ligase on the single-molecule level. The ligation reaction is monitored by Förster Resonance Energy Transfer (FRET) experiments both in solution and on surface-anchored origamis. Due to the modularity of DNA nanotechnology, DNA double-strands with different complementary overhang lengths can be studied using the same DNA origami design. We show that the T4 DNA ligase repairs sticky ends more efficiently than blunt ends and that the ligation efficiency is both influenced by DNA sequence and the incubation conditions. Before ligation, dynamic fluctuations of the FRET signal are observed due to transient binding of the sticky overhangs. After ligation, the FRET signal becomes static. Thus, we can directly monitor the ligation reaction through the transition from dynamic to static FRET signals. Finally, we revert the ligation process using a restriction enzyme digestion and re-ligate the resulting blunt ends. The here presented DNA origami platform is thus suited to study complex multi-step reactions occurring over several cycles of enzymatic treatment.


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Yim, A., Koti, P., Bonnard, A., Marchiano, F., Durrbaum, M., Garcia-Perez, C., Villaveces, J., Gamal, S., Cardone, G., Perocchi, F., Storchova Z., and Habermann, B.
(IMPRS-LS students are in bold)
Nucleic Acids Res, 2019, [Epub ahead of print].
doi: 10.1093/nar/gkz1128

mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations

Mitochondria participate in metabolism and signaling. They adapt to the requirements of various cell types. Publicly available expression data permit to study expression dynamics of genes with mitochondrial function (mito-genes) in various cell types, conditions and organisms. Yet, we lack an easy way of extracting these data for mito-genes. Here, we introduce the visual data mining platform mitoXplorer, which integrates expression and mutation data of mito-genes with a manually curated mitochondrial interactome containing ∼1200 genes grouped in 38 mitochondrial processes. User-friendly analysis and visualization tools allow to mine mitochondrial expression dynamics and mutations across various datasets from four model species including human. To test the predictive power of mitoXplorer, we quantify mito-gene expression dynamics in trisomy 21 cells, as mitochondrial defects are frequent in trisomy 21. We uncover remarkable differences in the regulation of the mitochondrial transcriptome and proteome in one of the trisomy 21 cell lines, caused by dysregulation of the mitochondrial ribosome and resulting in severe defects in oxidative phosphorylation. With the newly developed Fiji plugin mitoMorph, we identify mild changes in mitochondrial morphology in trisomy 21. Taken together, mitoXplorer (http://mitoxplorer.ibdm.univ-mrs.fr) is a user-friendly, web-based and freely accessible software, aiding experimental scientists to quantify mitochondrial expression dynamics.


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Baek, K., and Schulman, B.A.
Nat Chem Biol, 2019, [Epub ahead of print].
doi: 10.1038/s41589-019-0414-3

Molecular glue concept solidifies

Molecular-glue-mediated proximity-induced degradation now allows unprecedented therapeutic targeting of previously undruggable proteins. Structures showing how aryl-sulfonamides mediate recruitment of the splicing factor RBM39 to the E3 CRL4DCAF15 broaden the mechanistic principles by which molecular glues target ubiquitylation.


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Glock, P., Brauns, F., Halatek, J., Frey, E., and Schwille, P.
Elife 8, 2019.
doi: 10.7554/eLife.48646

Design of biochemical pattern forming systems from minimal motifs

Although molecular self-organization and pattern formation are key features of life, only very few pattern-forming biochemical systems have been identified that can be reconstituted and studied in vitro under defined conditions. A systematic understanding of the underlying mechanisms is often hampered by multiple interactions, conformational flexibility and other complex features of the pattern forming proteins. Because of its compositional simplicity of only two proteins and a membrane, the MinDE system from Escherichia coli has in the past years been invaluable for deciphering the mechanisms of spatiotemporal self-organization in cells. Here we explored the potential of reducing the complexity of this system even further, by identifying key functional motifs in the effector MinE that could be used to design pattern formation from scratch. In a combined approach of experiment and quantitative modeling, we show that starting from a minimal MinE-MinD interaction motif, pattern formation can be obtained by adding either dimerization or membrane-binding motifs. Moreover, we show that the pathways underlying pattern formation are recruitment-driven cytosolic cycling of MinE and recombination of membrane-bound MinE, and that these differ in their in vivo phenomenology.


graduationCongratulations on your PhD!

Silvia Martinelli
Effect of stress on protein homeostasis mediated by FKBP51 as a possible mechanism underlying stress-related psychiatric disorders
RG: Mathias V. Schmidt / Elisabeth Binder

Andrea Cosolo
Patterning of tissue stress responses by JNK and JAK/STAT
RG: Anne-Kathrin Classen


 

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Kist, A.M., and Portugues, R.
Cell Rep, 2019, 29, 659-670.e653.
doi: 10.1016/j.celrep.2019.09.024

Optomotor Swimming in Larval Zebrafish Is Driven by Global Whole-Field Visual Motion and Local Light-Dark Transitions

Stabilizing gaze and position within an environment constitutes an important task for the nervous system of many animals. The optomotor response (OMR) is a reflexive behavior, present across many species, in which animals move in the direction of perceived whole-field visual motion, therefore stabilizing themselves with respect to the visual environment. Although the OMR has been extensively used to probe visuomotor neuronal circuitry, the exact visual cues that elicit the behavior remain unidentified. In this study, we use larval zebrafish to identify spatiotemporal visual features that robustly elicit forward OMR swimming. These cues consist of a local, forward-moving, off edge together with on/off symmetric, similarly directed, global motion. Imaging experiments reveal neural units specifically activated by the forward-moving light-dark transition. We conclude that the OMR is driven not just by whole-field motion but by the interplay between global and local visual stimuli, where the latter exhibits a strong light-dark asymmetry.