News

graduation

Congratulations on your PhD!

 

Hamid Hamzeiy

Advancing Computational Methods for Mass Spectrometry-Based Proteomics, Metabolomics, and Analysis of Multi-Omics Datasets

RG: Jürgen Cox

 


 

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Delgado de la Herran, H.C., Cheng, Y., and Perocchi, F.
Cell Calcium, 2021, 95, 102364.
doi: 10.1016/j.ceca.2021.102364

Towards a systems-level understanding of mitochondrial biology

Human mitochondria are complex and highly dynamic biological systems, comprised of over a thousand parts and evolved to fully integrate into the specialized intracellular signaling networks and metabolic requirements of each cell and organ. Over the last two decades, several complementary, top-down computational and experimental approaches have been developed to identify, characterize and modulate the human mitochondrial system, demonstrating the power of integrating classical reductionist and discovery-driven analyses in order to de-orphanize hitherto unknown molecular components of mitochondrial machineries and pathways. To this goal, systematic, multiomics-based surveys of proteome composition, protein networks, and phenotype-to-pathway associations at the tissue, cell and organellar level have been largely exploited to predict the full complement of mitochondrial proteins and their functional interactions, therefore catalyzing data-driven hypotheses. Collectively, these multidisciplinary and integrative research approaches hold the potential to propel our understanding of mitochondrial biology and provide a systems-level framework to unraveling mitochondria-mediated and disease-spanning pathomechanisms.

 


 

graduation

Congratulations on your PhD!

 

Stephan Holtkamp

Time-of-Day Dependent Trafficking of Leukocytes Across Lymphatics


RG: Christoph Scheiermann

 


 

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Behrens, A., Rodschinka, G., and Nedialkova, D.D.
(IMPRS-LS students in bold)
Mol Cell, 2021, online ahead of print.
doi: 10.1016/j.molcel.2021.01.028

High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq

Measurements of cellular tRNA abundance are hampered by pervasive blocks to cDNA synthesis at modified nucleosides and the extensive similarity among tRNA genes. We overcome these limitations with modification-induced misincorporation tRNA sequencing (mim-tRNAseq), which combines a workflow for full-length cDNA library construction from endogenously modified tRNA with a comprehensive and user-friendly computational analysis toolkit. Our method accurately captures tRNA abundance and modification status in yeast, fly, and human cells and is applicable to any organism with a known genome. We applied mim-tRNAseq to discover a dramatic heterogeneity of tRNA isodecoder pools among diverse human cell lines and a surprising interdependence of modifications at distinct sites within the same tRNA transcript.

 


 

graduation

Congratulations on your PhD!

 

Alexandra Klein

State-dependent regulation of fear extinction learning by the interoceptive insular cortex

RG: Nadine Gogolla

 

 


 

graduation

Congratulations on your PhD!

 

Chia-Wei Lee

Selective Autophagy Degrades Nuclear Pore Complexes

RG: Stefan Jentsch / Wolfgang Baumeister

 

 


 

Retinal ganglion cells (RGCs) are the bottleneck through which all visual impressions flow from the retina to the brain. A team from the Max Planck Institute of Neurobiology, University of California Berkeley and Harvard University created a molecular catalog that describes the different types of these neurons. In this way, individual RGC types could be systematically studied and linked to a specific connection, function and behavioral response.

When zebrafish see light, they often swim towards it. Same with prey, although the signals are entirely different. A predator, on the other hand, prompts the fish to escape. That’s good, because a mix-up would have fatal consequences. But how does the brain manage to react to a visual stimulus with the proper behavior?

Optical signals are generated by photons that bombard the retina of the eye. Neurons in the retina collect and process these impressions. While doing so, the retina focuses on the important details: Is there contrast or color? Are there small or large objects? Is something moving? Once these details are filtered out, retinal ganglion cells (RGCs) send them to the brain, where they are translated into a specific behavior.

As the only connection between the retina and the brain, RGCs play a central role in the visual system. We already knew that specific RGC types sends different details to different regions of the brain. However, it has been unclear how RGC types differ on the molecular level, what their respective functions are, and how they help to regulate context-dependent behavior.

Read more

 


 

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Klein, A.S., and Gogolla, N.
Science, 2021, 371, 122-123.
doi: 10.1126/science.abf5940

How mice feel each other's pain or fear

Empathic behaviors play crucial roles in human society by regulating social interactions, promoting cooperation toward a common goal, and providing the basis for moral decision-making (1, 2). Understanding the neural basis of empathy is crucial to understanding not only the human mind but also the neural mechanisms that give rise to social behaviors and the principles of our societies. Functional imaging studies in humans have identified essential brain regions that are engaged when people empathize with the affective experiences of others. However, human neuroimaging studies provide only limited spatial resolution and are solely correlative in nature. It has thus remained unclear how empathy with distinct affective experiences is set apart within the brain. read more

 


 

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Hansen, F.M., Tanzer, M.C., Brüning, F., Bludau, I., Stafford, C., Schulman, B.A., Robles, M.S., Karayel, O., and Mann, M.
(IMPRS-LS students are in bold)
Nat Commun, 2021, 12, 254.
doi: 10.1038/s41467-020-20509-1

Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology

Protein ubiquitination is involved in virtually all cellular processes. Enrichment strategies employing antibodies targeting ubiquitin-derived diGly remnants combined with mass spectrometry (MS) have enabled investigations of ubiquitin signaling at a large scale. However, so far the power of data independent acquisition (DIA) with regards to sensitivity in single run analysis and data completeness have not yet been explored. Here, we develop a sensitive workflow combining diGly antibody-based enrichment and optimized Orbitrap-based DIA with comprehensive spectral libraries together containing more than 90,000 diGly peptides. This approach identifies 35,000 diGly peptides in single measurements of proteasome inhibitor-treated cells - double the number and quantitative accuracy of data dependent acquisition. Applied to TNF signaling, the workflow comprehensively captures known sites while adding many novel ones. An in-depth, systems-wide investigation of ubiquitination across the circadian cycle uncovers hundreds of cycling ubiquitination sites and dozens of cycling ubiquitin clusters within individual membrane protein receptors and transporters, highlighting new connections between metabolism and circadian regulation.

 


 

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Brunner, A.-D., Thielert, M., Vasilopoulou, C., Ammar, C., Coscia, F., Mund, A., Horning, O.B., Bache, N., Apalategui, A., Lubeck, M., Raether, O., Park, M.A., Richter, S., Fischer, D.S., Theis, F.J., Meier, F., and Mann, M.
(IMPRS-LS students are in bold)
bioRxiv, 2020.2012.2022.423933.
doi: 10.1101/2020.12.22.423933

Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation

Single-cell technologies are revolutionizing biology but are today mainly limited to imaging and deep sequencing. However, proteins are the main drivers of cellular function and in-depth characterization of individual cells by mass spectrometry (MS)-based proteomics would thus be highly valuable and complementary. Chemical labeling-based single-cell approaches introduce hundreds of cells into the MS, but direct analysis of single cells has not yet reached the necessary sensitivity, robustness and quantitative accuracy to answer biological questions. Here, we develop a robust workflow combining miniaturized sample preparation, very-low flow-rate chromatography and a novel trapped ion mobility mass spectrometer, resulting in a more than ten-fold improved sensitivity. We accurately and robustly quantify proteomes and their changes in single, FACS-isolated cells. Arresting cells at defined stages of the cell cycle by drug treatment retrieves expected key regulators such as CDK2NA, E2 ubiquitin ligases such as UBE2S and highlights potential novel ones. Comparing the variability in more than 420 single-cell proteomes to transcriptome data revealed a stable core proteome despite perturbation. Our technology can readily be applied to ultra-high sensitivity analysis of tissue material, including post-translational modifications and to small molecule studies.