Universität Stuttgart
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Item Open Access Editorial - optical microscopic and spectroscopic techniques targeting biological applications(2021) Micó, Vicente; Pedrini, Giancarlo; Lei, Ming; Zuo, Chao; Gao, PengItem Open Access Helium-electrospray improves sample delivery in X-ray single-particle imaging experiments(2024) Yenupuri, Tej Varma; Rafie-Zinedine, Safi; Worbs, Lena; Heymann, Michael; Schulz, Joachim; Bielecki, Johan; Maia, Filipe R. N. C.Imaging the structure and observing the dynamics of isolated proteins using single-particle X-ray diffractive imaging (SPI) is one of the potential applications of X-ray free-electron lasers (XFELs). Currently, SPI experiments on isolated proteins are limited by three factors: low signal strength, limited data and high background from gas scattering. The last two factors are largely due to the shortcomings of the aerosol sample delivery methods in use. Here we present our modified electrospray ionization (ESI) source, which we dubbed helium-ESI (He-ESI). With it, we increased particle delivery into the interaction region by a factor of 10, for 26 nm-sized biological particles, and decreased the gas load in the interaction chamber corresponding to an 80% reduction in gas scattering when compared to the original ESI. These improvements have the potential to significantly increase the quality and quantity of SPI diffraction patterns in future experiments using He-ESI, resulting in higher-resolution structures.Item Open Access The natural breakup length of a steady capillary jet : application to serial femtosecond crystallography(2021) Gañán-Calvo, Alfonso M.; Chapman, Henry N.; Heymann, Michael; Wiedorn, Max O.; Knoska, Juraj; Gañán-Riesco, Braulio; López-Herrera, José M.; Cruz-Mazo, Francisco; Herrada, Miguel A.; Montanero, José M.; Bajt, SašaOne of the most successful ways to introduce samples in Serial Femtosecond Crystallography has been the use of microscopic capillary liquid jets produced by gas flow focusing, whose length-to-diameter ratio and velocity are essential to fulfill the requirements of the high pulse rates of current XFELs. In this work, we demonstrate the validity of a classical scaling law with two universal constants to calculate that length as a function of the liquid properties and operating conditions. These constants are determined by fitting the scaling law to a large set of experimental and numerical measurements, including previously published data. Both the experimental and numerical jet lengths conform remarkably well to the proposed scaling law. We show that, while a capillary jet is a globally unstable system to linear perturbations above a critical length, its actual and shorter long-term average intact length is determined by the nonlinear perturbations coming from the jet breakup itself. Therefore, this length is determined solely by the properties of the liquid, the average velocity of the liquid and the flow rate expelled. This confirms the very early observations from Smith and Moss 1917, Proc R Soc Lond A Math Phys Eng, 93, 373, to McCarthy and Molloy 1974, Chem Eng J, 7, 1, among others, while it contrasts with the classical conception of temporal stability that attributes the natural breakup length to the jet birth conditions in the ejector or small interactions with the environment.Item Open Access Dimerization and oligomerization of DNA-assembled building blocks for controlled multi-motion in high-order architectures(2021) Xin, Ling; Duan, Xiaoyang; Liu, NaIn living organisms, proteins are organized prevalently through a self-association mechanism to form dimers and oligomers, which often confer new functions at the intermolecular interfaces. Despite the progress on DNA-assembled artificial systems, endeavors have been largely paid to achieve monomeric nanostructures that mimic motor proteins for a single type of motion. Here, we demonstrate a DNA-assembled building block with rotary and walking modules, which can introduce new motion through dimerization and oligomerization. The building block is a chiral system, comprising two interacting gold nanorods to perform rotation and walking, respectively. Through dimerization, two building blocks can form a dimer to yield coordinated sliding. Further oligomerization leads to higher-order structures, containing alternating rotation and sliding dimer interfaces to impose structural twisting. Our hierarchical assembly scheme offers a design blueprint to construct DNA-assembled advanced architectures with high degrees of freedom to tailor the optical responses and regulate multi-motion on the nanoscale.Item Open Access Optimality principles in human point-to-manifold reaching accounting for muscle dynamics(2020) Wochner, Isabell; Driess, Danny; Zimmermann, Heiko; Häufle, Daniel F. B.; Toussaint, Marc; Schmitt, SynHuman arm movements are highly stereotypical under a large variety of experimental conditions. This is striking due to the high redundancy of the human musculoskeletal system, which in principle allows many possible trajectories toward a goal. Many researchers hypothesize that through evolution, learning, and adaption, the human system has developed optimal control strategies to select between these possibilities. Various optimality principles were proposed in the literature that reproduce human-like trajectories in certain conditions. However, these studies often focus on a single cost function and use simple torque-driven models of motion generation, which are not consistent with human muscle-actuated motion. The underlying structure of our human system, with the use of muscle dynamics in interaction with the control principles, might have a significant influence on what optimality principles best model human motion. To investigate this hypothesis, we consider a point-to-manifold reaching task that leaves the target underdetermined. Given hypothesized motion objectives, the control input is generated using Bayesian optimization, which is a machine learning based method that trades-off exploitation and exploration. Using numerical simulations with Hill-type muscles, we show that a combination of optimality principles best predicts human point-to-manifold reaching when accounting for the muscle dynamics.Item Open Access Giraffes and hominins: reductionist model predictions of compressive loads at the spine base for erect exponents of the animal kingdom(2021) Günther, Michael; Mörl, FalkIn humans, compressive stress on intervertebral discs is commonly deployed as a measurand for assessing the loads that act within the spine. Examining this physical quantity is crucially beneficial: the intradiscal pressure can be directly measured in vivo in humans, and is immediately related to compressive stress. Hence, measured intradiscal pressure data are utterly useful for validating such biomechanical animal models that have the spine incorporated, and can, thus, compute compressive stress values. Here, we utilise human intradiscal pressure data to verify the predictions of a reductionist spine model, which has in fact only one joint degree of freedom. We calculate the pulling force of one lumped anatomical structure that acts past this (intervertebral) joint at the base of the spine - lumbar in hominins, cervical in giraffes - to compensate the torque that is induced by the weight of all masses located cranially to the base. Given morphometric estimates of the human and australopith trunks, respectively, and the giraffe's neck, as well as the respective structures' lever arms and disc areas, we predict, for all three species, the compressive stress on the intervertebral disc at the spine base, while systematically varying the angular orientation of the species' spinal columns with respect to gravity. The comparison between these species demonstrates that hominin everyday compressive disc stresses are lower than such in big quadrupedal animals. Within each species, erecting the spine from being bent forward by, for example, thirty degrees to fully upright posture reduces the compressive disc stress roughly to a third. We conclude that erecting the spine immediately allows to carry extra loads of the order of body weight, and yet the compressive disc stress is lower than in a moderately forward-bent posture with none extra load.Item Open Access Solubilization of inclusion bodies : insights from explainable machine learning approaches(2023) Walther, Cornelia; Martinetz, Michael C.; Friedrich, Anja; Tscheließnig, Anne-Luise; Voigtmann, Martin; Jung, Alexander; Brocard, Cécile; Bluhmki, Erich; Smiatek, JensWe present explainable machine learning approaches for gaining deeper insights into the solubilization processes of inclusion bodies. The machine learning model with the highest prediction accuracy for the protein yield is further evaluated with regard to Shapley additive explanation (SHAP) values in terms of feature importance studies. Our results highlight an inverse fractional relationship between the protein yield and total protein concentration. Further correlations can also be observed for the dominant influences of the urea concentration and the underlying pH values. All findings are used to develop an analytical expression that is in reasonable agreement with experimental data. The resulting master curve highlights the benefits of explainable machine learning approaches for the detailed understanding of certain biopharmaceutical manufacturing steps.Item Open Access Optimizing NV magnetometry for magnetoneurography and magnetomyography applications(2023) Zhang, Chen; Zhang, Jixing; Widmann, Matthias; Benke, Magnus; Kübler, Michael; Dasari, Durga; Klotz, Thomas; Gizzi, Leonardo; Röhrle, Oliver; Brenner, Philipp; Wrachtrup, JörgMagnetometers based on color centers in diamond are setting new frontiers for sensing capabilities due to their combined extraordinary performances in sensitivity, bandwidth, dynamic range, and spatial resolution, with stable operability in a wide range of conditions ranging from room to low temperatures. This has allowed for its wide range of applications, from biology and chemical studies to industrial applications. Among the many, sensing of bio-magnetic fields from muscular and neurophysiology has been one of the most attractive applications for NV magnetometry due to its compact and proximal sensing capability. Although SQUID magnetometers and optically pumped magnetometers (OPM) have made huge progress in Magnetomyography (MMG) and Magnetoneurography (MNG), exploring the same with NV magnetometry is scant at best. Given the room temperature operability and gradiometric applications of the NV magnetometer, it could be highly sensitive in the pT/Hz-range even without magnetic shielding, bringing it close to industrial applications. The presented work here elaborates on the performance metrics of these magnetometers to the state-of-the-art techniques by analyzing the sensitivity, dynamic range, and bandwidth, and discusses the potential benefits of using NV magnetometers for MMG and MNG applications.Item Open Access Galvanotaxis of ciliates : spatiotemporal dynamics of Coleps hirtus under electric fields(2022) Daul, Anna; Lemloh, Marie-Louise; Hörning, MarcelGalvanotaxis describes the functional response of organisms to electric fields. In ciliates, the electric field influences the electrophysiology, and thus, the cilia beat dynamics. This leads to a change of the swimming direction toward the cathode. The dynamical response to electric fields of Coleps hirtus has not been studied since the observations of Verworn in 1890 Pflüger Arch. 46 267-303. While galvanotaxis has been studied in other ciliates, C. hirtus exhibit properties not found elsewhere, such as biomineralization processes of alveolar plates with impact on the intracellular calcium regulation and a bimodal resting membrane potential, which leads to unique electrophysiological driven bimodal swimming dynamics. Here, we statistically analyze the galvanotactic dynamics of C. hirtus by automated cell tracking routines. We found that the number of cells that show a galvanotactic response, increases with the increase of the applied electric field strength with a mean at about 2.1 V cm-1. The spatiotemporal swimming dynamics change and lead to a statistical increase of linear elongated cell trajectories that point toward the cathode. Further, the increase of the electric fields decreases the mean velocity variance for electric fields larger than about 1.3 V cm-1, while showing no significant change in the absolute velocity for any applied electric field. Fully functional galvanotactic responses were observed at a minimum extracellular calcium concentration of about 5 μM. The results add important insights to the current understanding of cellular dynamics of ciliates and suggest that the currently accepted model lacks the inclusion of the swimming dynamics and the complex calcium regulatory system of the cell. The results of this study not only extend the fundamental understanding of current physical models for galvanotaxis and C. hirtus dynamics, but also open possibilities for technical applications, such as biosensors or microrobots in the future.Item Open Access Predicting concentrations of mixed sugar solutions with a combination of resonant plasmon-enhanced SEIRA and principal component analysis(2022) Pfezer, Diana; Karst, Julian; Hentschel, Mario; Giessen, HaraldThe detection and quantification of glucose concentrations in human blood or in the ocular fluid gain importance due to the increasing number of diabetes patients. A reliable determination of these low concentrations is hindered by the complex aqueous environments in which various biomolecules are present. In this study, we push the detection limit as well as the discriminative power of plasmonic nanoantenna-based sensors towards the physiological limit. We utilize plasmonic surface-enhanced infrared absorption spectroscopy (SEIRA) to study aqueous solutions of mixtures of up to five different physiologically relevant saccharides, namely the monosaccharides glucose, fructose, and galactose, as well as the disaccharides maltose and lactose. Resonantly tuned plasmonic nanoantennas in a reflection flow cell geometry allow us to enhance the specific vibrational fingerprints of the mono- and disaccharides. The obtained spectra are analyzed via principal component analysis (PCA) using a machine learning algorithm. The high performance of the sensor together with the strength of PCA allows us to detect concentrations of aqueous mono- and disaccharides solutions down to the physiological levels of 1 g/L. Furthermore, we demonstrate the reliable discrimination of the saccharide concentrations, as well as compositions in mixed solutions, which contain all five mono- and disaccharides simultaneously. These results underline the excellent discriminative power of plasmonic SEIRA spectroscopy in combination with the PCA. This unique combination and the insights gained will improve the detection of biomolecules in different complex environments.