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Biological systems are dynamic and three-dimensional but many techniques allow only static and two-dimensional observation of cells. We used three-dimensional (3D) lattice light-sheet single-molecule localization microscopy (dSTORM) to investigate the complex interactions and distribution of single molecules in the plasma membrane of whole cells. Different receptor densities of the adhesion receptor CD56 at different parts of the cell highlight the importance and need of three-dimensional observation and analysis techniques.
Neisseria meningitidis (meningococcus) is a Gram-negative bacterium responsible for epidemic meningitis and sepsis worldwide. A critical step in the development of meningitis is the interaction of bacteria with cells forming the blood-cerebrospinal fluid barrier, which requires tight adhesion of the pathogen to highly specialized brain endothelial cells. Two endothelial receptors, CD147 and the β2-adrenergic receptor, have been found to be sequentially recruited by meningococci involving the interaction with type IV pilus. Despite the identification of cellular key players in bacterial adhesion the detailed mechanism of invasion is still poorly understood. Here, we investigated cellular dynamics and mobility of the type IV pilus receptor CD147 upon treatment with pili enriched fractions and specific antibodies directed against two extracellular Ig-like domains in living human brain microvascular endothelial cells. Modulation of CD147 mobility after ligand binding revealed by single-molecule tracking experiments demonstrates receptor activation and indicates plasma membrane rearrangements. Exploiting the binding of Shiga (STxB) and Cholera toxin B (CTxB) subunits to the two native plasma membrane sphingolipids globotriaosylceramide (Gb3) and raft-associated monosialotetrahexosylganglioside GM1, respectively, we investigated their involvement in bacterial invasion by super-resolution microscopy. Structured illumination microscopy (SIM) and direct stochastic optical reconstruction microscopy (dSTORM) unraveled accumulation and coating of meningococci with GM1 upon cellular uptake. Blocking of CTxB binding sites did not impair bacterial adhesion but dramatically reduced bacterial invasion efficiency. In addition, cell cycle arrest in G1 phase induced by serum starvation led to an overall increase of GM1 molecules in the plasma membrane and consequently also in bacterial invasion efficiency. Our results will help to understand downstream signaling events after initial type IV pilus-host cell interactions and thus have general impact on the development of new therapeutics targeting key molecules involved in infection.
Translation efficiency can be affected by mRNA stability and secondary structures, including G-quadruplex structures (G4s). The highly conserved DEAH-box helicase DHX36/RHAU resolves G4s on DNA and RNA in vitro, however a systems-wide analysis of DHX36 targets and function is lacking. We map globally DHX36 binding to RNA in human cell lines and find it preferentially interacting with G-rich and G4-forming sequences on more than 4500 mRNAs. While DHX36 knockout (KO) results in a significant increase in target mRNA abundance, ribosome occupancy and protein output from these targets decrease, suggesting that they were rendered translationally incompetent. Considering that DHX36 targets, harboring G4s, preferentially localize in stress granules, and that DHX36 KO results in increased SG formation and protein kinase R (PKR/EIF2AK2) phosphorylation, we speculate that DHX36 is involved in resolution of rG4 induced cellular stress.
With the progress in robotics research the human machine interfaces reach more and more the status of being the major limiting factor for the overall system performance of a system for remote navigation and coordination of robots. In this monograph it is elaborated how mixed reality technologies can be applied for the user interfaces in order to increase the overall system performance. Concepts, technologies, and frameworks are developed and evaluated in user studies which enable for novel user-centered approaches to the design of mixed-reality user interfaces for remote robot operation. Both the technological requirements and the human factors are considered to achieve a consistent system design. Novel technologies like 3D time-of-flight cameras are investigated for the application in the navigation tasks and for the application in the developed concept of a generic mixed reality user interface. In addition it is shown how the network traffic of a video stream can be shaped on application layer in order to reach a stable frame rate in dynamic networks. The elaborated generic mixed reality framework enables an integrated 3D graphical user interface. The realized spatial integration and visualization of available information reduces the demand for mental transformations for the human operator and supports the use of immersive stereo devices. The developed concepts make also use of the fact that local robust autonomy components can be realized and thus can be incorporated as assistance systems for the human operators. A sliding autonomy concept is introduced combining force and visual augmented reality feedback. The force feedback component allows rendering the robot's current navigation intention to the human operator, such that a real sliding autonomy with seamless transitions is achieved. The user-studies prove the significant increase in navigation performance by application of this concept. The generic mixed reality user interface together with robust local autonomy enables a further extension of the teleoperation system to a short-term predictive mixed reality user interface. With the presented concept of operation, it is possible to significantly reduce the visibility of system delays for the human operator. In addition, both advantageous characteristics of a 3D graphical user interface for robot teleoperation- an exocentric view and an augmented reality view – can be combined.
Ein sehr wichtiger Tumorsuppressor ist der Transkriptionsfaktor p53, der Zellschicksals-Entscheidungen wie Zellzyklus-Arrest und programmierten Zelltod (Apoptose) kontrolliert. Die Wirkung von p53 und von seinen Familienmitgliedern p63 und p73 beruht überwiegend auf der Fähigkeit, als Transkriptionsfaktoren die Genexpression zu regulieren. Die DNA-Bindung an Promotoren von Zielgenen ist dabei von grundlegender Bedeutung und wird durch die hoch konservierte zentrale DNA-Bindungs-Domäne und den Carboxy-Terminus bestimmt. In dieser Arbeit wurden die DNA-Bindungseigenschaften von p53 und verschiedener Carboxy-terminalen p73 Isoformen untersucht. In „electrophoretic mobility shift assay” (EMSA) Experimenten bildeten p53 und p73gamma nur schwache Sequenz-spezifische DNA-Komplexe, wohingegen p73alpha, beta und delta die DNA deutlich stärker banden. Die schwache DNA-Bindung von p53 und p73gamma kann durch mehrfach positiv geladene Carboxy-Termini erklärt werden, die über eine Sequenz-unabhängige DNA-Bindung ein Gleiten entlang der DNA ermöglichen. Die Deletion der Carboxy-terminalen Domäne (CTD) von p53 („p53delta30“) verstärkte dementsprechend die Sequenz-spezifische DNA-Bindung in vitro und seine Übertragung auf p73alpha („p73alpha+30“) schwächte sie ab. Mittels „fluorescence recovery after photobleaching“ (FRAP) Experimenten konnte in lebenden Zellen eine Verminderung der intra-nukleären Mobilität von p53 und p73alpha+30 durch die CTD gezeigt werden, die aus der Sequenz-unabhängigen DNA-Bindung resultiert. Zusätzlich reduzierte die CTD die Sequenz-spezifische DNA-Bindung von p53 an den p21 (CDKN1A) Promotor. Das Spektrum der regulierten Zielgene wurde in einer Genom-weiten Genexpressions-Analyse nicht durch die CTD verändert, sondern maßgeblich durch das Protein-Rückgrat von p53 beziehungsweise p73 bestimmt. Allerdings verminderte die CTD das Ausmaß der Transkriptions-Regulation und hemmte die Induktion von Zellzyklus-Arrest und Apoptose. Die mehrfach positiv geladene CTD in p53 besitzt demzufolge eine negativ regulatorische Wirkung, die in den wichtigsten p73 Isoformen alpha, beta und delta fehlt. Die zentrale DNA-Bindungs-Domäne trägt durch elektrostatische Wechselwirkungen zwischen H1-Helices (Aminosäurereste 177 bis 182) unterschiedlicher p53 Monomere zu kooperativer DNA-Bindung und zu Zellschicksals-Entscheidungen bei. Anhand von Mutanten, die unterschiedlich starke H1-Helix-Interaktionen ermöglichen, konnte gezeigt werden, dass starke Interaktionen die Bindung an Promotoren von pro-apoptotischen Genen verstärkte, wohingegen die Bindung an anti-apoptotische und Zellzyklus-blockierende Gene unabhängig von der Interaktions-Stärke war. Diese Unterschiede in der Promotor-Bindung ließen sich nicht auf eine veränderte zelluläre Lokalisation der Mutanten zurückführen, da alle Mutanten überwiegend nukleär lokalisiert waren. Eine an Serin 183 Phosphorylierungs-defekte Mutante von p53 bildete stabile DNA-Komplexe, entsprechend einer Mutante mit starker H1-Helix-Interaktion, und trans-aktivierte pro-apoptotische Promotoren stärker als Mutanten, die Phosphorylierung von p53 an Serin 183 simulieren. Da zusätzlich bekannt ist, dass Serin 183 mit der H1-Helix wechselwirkt, könnte diese Phosphorylierung einen physiologischen Mechanismus zur Regulation der H1-Helix-Interaktion und damit des Zellschicksals darstellen. Zusammenfassend ließ sich zeigen, dass sowohl die Interaktions-Stärke zweier DNA-Bindungs-Domänen als auch die elektrische Ladung des Carboxy-Terminus die DNA-Bindungseigenschaften von p53 Familienmitgliedern bestimmen und so Zellschicksals-Entscheidungen der p53 Familie beeinflussen.
The expression of genetic information into proteins is a key aspect of life. The efficient and exact regulation of this process is essential for the cell to produce the correct amounts of these effector molecules to a given situation. For this purpose, eukaryotic cells have developed many different levels of transcriptional and posttranscriptional gene regulation. These mechanisms themselves heavily rely on interactions of proteins with associated nucleic acids. In the case of posttranscriptional gene regulation an orchestrated interplay between RNA-binding proteins, messenger RNAs (mRNA), and non-coding RNAs is compulsory to achieve this important function.
A pivotal factor hereby are RNA secondary structures. One of the most stable and diverse representatives is the G-quadruplex structure (G4) implicated in many cellular mechanisms, such as mRNA processing and translation. In protein biosynthesis, G4s often act as obstacles but can also assist in this process. However, their presence has to be tightly regulated, a task which is often fulfilled by helicases.
One of the best characterized G4-resolving factors is the DEAH-box protein DHX36. The in vitro function of this helicase is extensively described and individual reports aimed to address diverse cellular functions as well. Nevertheless, a comprehensive and systems-wide study on the function of this specific helicase was missing, so far.
The here-presented doctoral thesis provides a detailed view on the global cellular function of DHX36. The binding sites of this helicase were defined in a transcriptome-wide manner, a consensus binding motif was deviated, and RNA targets as well as the effect this helicase exerts on them were examined. In human embryonic kidney cells, DHX36 is a mainly cytoplasmic protein preferentially binding to G-rich and G4-forming sequence motifs on more than 4,500 mRNAs. Loss of DHX36 leads to increased target mRNA levels whereas ribosome occupancy on and protein output of these transcripts are reduced. Furthermore, DHX36 knockout leads to higher RNA G4 levels and concomitant stress reactions in the cell. I hypothesize that, upon loss of this helicase, translationally-incompetent structured DHX36 target mRNAs, prone to localize in stress granules, accumulate in the cell. The cell reacts with basal stress to avoid cytotoxic effects produced by these mis-regulated and structured transcripts.
Background
Localization-based super-resolution microscopy resolves macromolecular structures down to a few nanometers by computationally reconstructing fluorescent emitter coordinates from diffraction-limited spots. The most commonly used algorithms are based on fitting parametric models of the point spread function (PSF) to a measured photon distribution. These algorithms make assumptions about the symmetry of the PSF and thus, do not work well with irregular, non-linear PSFs that occur for example in confocal lifetime imaging, where a laser is scanned across the sample. An alternative method for reconstructing sparse emitter sets from noisy, diffraction-limited images is compressed sensing, but due to its high computational cost it has not yet been widely adopted. Deep neural network fitters have recently emerged as a new competitive method for localization microscopy. They can learn to fit arbitrary PSFs, but require extensive simulated training data and do not generalize well. A method to efficiently fit the irregular PSFs from confocal lifetime localization microscopy combining the advantages of deep learning and compressed sensing would greatly improve the acquisition speed and throughput of this method.
Results
Here we introduce ReCSAI, a compressed sensing neural network to reconstruct localizations for confocal dSTORM, together with a simulation tool to generate training data. We implemented and compared different artificial network architectures, aiming to combine the advantages of compressed sensing and deep learning. We found that a U-Net with a recursive structure inspired by iterative compressed sensing showed the best results on realistic simulated datasets with noise, as well as on real experimentally measured confocal lifetime scanning data. Adding a trainable wavelet denoising layer as prior step further improved the reconstruction quality.
Conclusions
Our deep learning approach can reach a similar reconstruction accuracy for confocal dSTORM as frame binning with traditional fitting without requiring the acquisition of multiple frames. In addition, our work offers generic insights on the reconstruction of sparse measurements from noisy experimental data by combining compressed sensing and deep learning. We provide the trained networks, the code for network training and inference as well as the simulation tool as python code and Jupyter notebooks for easy reproducibility.
In recent years three-dimensional (3D) super-resolution fluorescence imaging by single-molecule localization (localization microscopy) has gained considerable interest because of its simple implementation and high optical resolution. Astigmatic and biplane imaging are experimentally simple methods to engineer a 3D-specific point spread function (PSF), but existing evaluation methods have proven problematic in practical application. Here we introduce the use of cubic B-splines to model the relationship of axial position and PSF width in the above mentioned approaches and compare the performance with existing methods. We show that cubic B-splines are the first method that can combine precision, accuracy and simplicity.
Sphingolipids, including ceramides, are a diverse group of structurally related lipids composed of a sphingoid base backbone coupled to a fatty acid side chain and modified terminal hydroxyl group. Recently, it has been shown that sphingolipids show antimicrobial activity against a broad range of pathogenic microorganisms. The antimicrobial mechanism, however, remains so far elusive. Here, we introduce 'click-AT-CLEM', a labeling technique for correlated light and electron microscopy (CLEM) based on the super-resolution array tomography (srAT) approach and bio-orthogonal click chemistry for imaging of azido-tagged sphingolipids to directly visualize their interaction with the model Gram-negative bacterium Neisseria meningitidis at subcellular level. We observed ultrastructural damage of bacteria and disruption of the bacterial outer membrane induced by two azido-modified sphingolipids by scanning electron microscopy and transmission electron microscopy. Click-AT-CLEM imaging and mass spectrometry clearly revealed efficient incorporation of azido-tagged sphingolipids into the outer membrane of Gram-negative bacteria as underlying cause of their antimicrobial activity.
Revealing the molecular organization of anatomically precisely defined brain regions is necessary for refined understanding of synaptic plasticity. Although three-dimensional (3D) single-molecule localization microscopy can provide the required resolution, imaging more than a few micrometers deep into tissue remains challenging. To quantify presynaptic active zones (AZ) of entire, large, conditional detonator hippocampal mossy fiber (MF) boutons with diameters as large as 10 mu m, we developed a method for targeted volumetric direct stochastic optical reconstruction microscopy (dSTORM). An optimized protocol for fast repeated axial scanning and efficient sequential labeling of the AZ scaffold Bassoon and membrane bound GFP with Alexa Fluor 647 enabled 3D-dSTORM imaging of 25 mu m thick mouse brain sections and assignment of AZs to specific neuronal substructures. Quantitative data analysis revealed large differences in Bassoon cluster size and density for distinct hippocampal regions with largest clusters in MF boutons. Pauli et al. develop targeted volumetric dSTORM in order to image large hippocampal mossy fiber boutons (MFBs) in brain slices. They can identify synaptic targets of individual MFBs and measured size and density of Bassoon clusters within individual untruncated MFBs at nanoscopic resolution.