Biophysics at the coffee shop: lessons learned working with George Oster

Over the past 50 years, the use of mathematical models, derived from physical reasoning, to describe molecular and cellular systems has evolved from an art of the few to a cornerstone of biological inquiry. George Oster stood out as a pioneer of this paradigm shift from descriptive to quantitative biology not only through his numerous research accomplishments, but also through the many students and postdocs he mentored over his long career. Those of us fortunate enough to have worked with George agree that his sharp intellect, physical intuition and passion for scientific inquiry not only inspired us as scientists but also greatly influenced the way we conduct research. We would like to share a few important lessons we learned from George in honor of his memory and with the hope that they may inspire future generations of scientists.Comment: 22 pages, 3 figures, accepted in Molecular Biology of the Cel

An active poroelastic model for mechanochemical patterns in protoplasmic droplets of Physarum polycephalum

Motivated by recent experimental studies, we derive and analyze a twodimensional model for the contraction patterns observed in protoplasmic droplets of Physarum polycephalum. The model couples a model of an active poroelastic two-phase medium with equations describing the spatiotemporal dynamics of the intracellular free calcium concentration. The poroelastic medium is assumed to consist of an active viscoelastic solid representing the cytoskeleton and a viscous fluid describing the cytosol. The model equations for the poroelastic medium are obtained from continuum force-balance equations that include the relevant mechanical fields and an incompressibility relation for the two-phase medium. The reaction-diffusion equations for the calcium dynamics in the protoplasm of Physarum are extended by advective transport due to the flow of the cytosol generated by mechanical stresses. Moreover, we assume that the active tension in the solid cytoskeleton is regulated by the calcium concentration in the fluid phase at the same location, which introduces a chemomechanical feedback. A linear stability analysis of the homogeneous state without deformation and cytosolic flows exhibits an oscillatory Turing instability for a large enough mechanochemical coupling strength. Numerical simulations of the model equations reproduce a large variety of wave patterns, including traveling and standing waves, turbulent patterns, rotating spirals and antiphase oscillations in line with experimental observations of contraction patterns in the protoplasmic droplets.Comment: Additional supplemental material is supplie

Transport of ER Vesicles on Actin Filaments in Neurons by Myosin V

Axoplasmic organelles in the giant axon of the squid have been shown to move on both actin filaments and microtubules and to switch between actin filaments and microtubules during fast axonal transport. The objectives of this investigation were to identify the specific classes of axoplasmic organelles that move on actin filaments and the myosin motors involved. We developed a procedure to isolate endoplasmic reticulum (ER) from extruded axoplasm and to reconstitute its movement in vitro. The isolated ER vesicles moved on exogenous actin filaments adsorbed to coverslips in an ATP-dependent manner without the addition of soluble factors. Therefore myosin was tightly bound and not extracted during isolation. These vesicles were identified as smooth ER by use of an antibody to an ER-resident protein, ERcalcistorin/protein disulfide isomerase (EcaSt/PDI). Furthermore, an antibody to squid myosin V was used in immunogold EM studies to show that myosin V localized to these vesicles. The antibody was generated to a squid brain myosin (p196) that was classified as myosin V based on comparisons of amino acid sequences of tryptic peptides of this myosin with those of other known members of the myosin V family. Dual labeling with the squid myosin V antibody and a kinesin heavy chain antibody showed that the two motors colocalized on the same vesicles. Finally, antibody inhibition experiments were performed with two myosin V-specific antibodies to show that myosin V motor activity is required for transport of vesicles on actin filaments in axoplasm. One antibody was made to a peptide in the globular tail domain and the other to the globular head fragment of myosin V. Both antibodies inhibited vesicle transport on actin filaments by greater than 90% compared to controls. These studies provide the first direct evidence that ER vesicles are transported on actin filaments by myosin V. These data confirm the role of actin filaments in fast axonal transport and provide support for the dual filament model of vesicle transport

Dynamic Analysis of Vascular Morphogenesis Using Transgenic Quail Embryos

Background: One of the least understood and most central questions confronting biologists is how initially simple clusters or sheet-like cell collectives can assemble into highly complex three-dimensional functional tissues and organs. Due to the limits of oxygen diffusion, blood vessels are an essential and ubiquitous presence in all amniote tissues and organs. Vasculogenesis, the de novo self-assembly of endothelial cell (EC) precursors into endothelial tubes, is the first step in blood vessel formation [1]. Static imaging and in vitro models are wholly inadequate to capture many aspects of vascular pattern formation in vivo, because vasculogenesis involves dynamic changes of the endothelial cells and of the forming blood vessels, in an embryo that is changing size and shape. Methodology/Principal Findings: We have generated Tie1 transgenic quail lines Tg(tie1:H2B-eYFP) that express H2B-eYFP in all of their endothelial cells which permit investigations into early embryonic vascular morphogenesis with unprecedented clarity and insight. By combining the power of molecular genetics with the elegance of dynamic imaging, we follow the precise patterning of endothelial cells in space and time. We show that during vasculogenesis within the vascular plexus, ECs move independently to form the rudiments of blood vessels, all while collectively moving with gastrulating tissues that flow toward the embryo midline. The aortae are a composite of somatic derived ECs forming its dorsal regions and the splanchnic derived ECs forming its ventral region. The ECs in the dorsal regions of the forming aortae exhibit variable mediolateral motions as they move rostrally; those in more ventral regions show significant lateral-to-medial movement as they course rostrally. Conclusions/Significance: The present results offer a powerful approach to the major challenge of studying the relative role(s) of the mechanical, molecular, and cellular mechanisms of vascular development. In past studies, the advantages of the molecular genetic tools available in mouse were counterbalanced by the limited experimental accessibility needed for imaging and perturbation studies. Avian embryos provide the needed accessibility, but few genetic resources. The creation of transgenic quail with labeled endothelia builds upon the important roles that avian embryos have played in previous studies of vascular development

Enzyme Powered Nanomotors Towards Biomedical Applications

[eng] The advancements in nanotechnology enabled the development of new diagnostic tools and drug delivery systems based on nanosystems, which offer unique features such as large surface area to volume ratio, cargo loading capabilities, increased circulation times, as well as versatility and multifunctionality. Despite this, the majority of nanomedicines do not translate into clinics, in part due to the biological barriers present in the body. Synthetic nano- and micromotors could be an alternative tool in nanomedicine, as the continuous propulsion force and potential to modulate the medium may aid tissue penetration and drug diffusion across biological barriers. Enzyme-powered motors are especially interesting for biomedical applications, owing to their biocompatibility and use of bioavailable substrates as fuel for propulsion. This thesis aims at exploring the potential applications of urease-powered nanomotors in nanomedicine. In the first work, we evaluated these motors as drug delivery systems. We found that active urease- powered nanomotors showed active motion in phosphate buffer solutions, and enhanced in vitro drug release profiles in comparison to passive nanoparticles. In addition, we observed that the motors were more efficient in delivering drug to cancer cells and caused higher toxicity levels, due to the combination of boosted drug release and local increase of pH produced by urea breakdown into ammonia and carbon dioxide. One of the major goals in nanomedicine is to achieve localized drug action, thus reducing side-effects. A commonly strategy to attain this is the use moieties to target specific diseases. In our second work, we assessed the ability of urease-powered nanomotors to improve the targeting and penetration of spheroids, using an antibody with therapeutic potential. We showed that the combination of active propulsion with targeting led to a significant increase in spheroid penetration, and that this effect caused a decrease in cell proliferation due to the antibody’s therapeutic action. Considering that high concentrations of nanomedicines are required to achieve therapeutic efficiency; in the third work we investigated the collective behavior of urease-powered nanomotors. Apart from optical microscopy, we evaluated the tracked the swarming behavior of the nanomotors using positron emission tomography, which is a technique widely used in clinics, due to its noninvasiveness and ability to provide quantitative information. We showed that the nanomotors were able to overcome hurdles while swimming in confined geometries. We observed that the nanomotors swarming behavior led to enhanced fluid convection and mixing both in vitro, and in vivo within mice’s bladders. Aiming at conferring protecting abilities to the enzyme-powered nanomotors, in the fourth work, we investigated the use of liposomes as chassis for nanomotors, encapsulating urease within their inner compartment. We demonstrated that the lipidic bilayer provides the enzymatic engines with protection from harsh acidic environments, and that the motility of liposome-based motors can be activated with bile salts. Altogether, these results demonstrate the potential of enzyme-powered nanomotors as nanomedicine tools, with versatile chassis, as well as capability to enhance drug delivery and tumor penetration. Moreover, their collective dynamics in vivo, tracked using medical imaging techniques, represent a step-forward in the journey towards clinical translation.[spa] Recientes avances en nanotecnología han permitido el desarrollo de nuevas herramientas para el diagnóstico de enfermedades y el transporte dirigido de fármacos, ofreciendo propiedades únicas como encapsulación de fármacos, el control sobre la biodistribución de estos, versatilidad y multifuncionalidad. A pesar de estos avances, la mayoría de nanomedicinas no consiguen llegar a aplicaciones médicas reales, lo cual es en parte debido a la presencia de barreras biológicas en el organismo que limitan su transporte hacia los tejidos de interés. En este sentido, el desarrollo de nuevos micro- y nanomotores sintéticos, capaces de autopropulsarse y causar cambios locales en el ambiente, podrían ofrecer una alternativa para la nanomedicina, promoviendo una mayor penetración en tejidos de interés y un mejor transporte de fármacos a través de las barreras biológicas. En concreto, los nanomotores enzimáticos poseen un alto potencial para aplicaciones biomédicas gracias a su biocompatibilidad y a la posibilidad de usar sustancias presentes en el organismo como combustible. Los trabajos presentados en esta tesis exploran el potenical de nanomotores, autopropulsados mediante la enzima ureasa, para aplicaciones biomédicas, y investigan su uso como vehículos para transporte de fármacos, su capacidad para mejorar penetración de tejidos diana, su versatilidad y movimiento colectivo. En conjunto, los resultados presentados en esta tesis doctoral demuestran el potencial del uso de nanomotores autopropulsados mediante enzimas como herramientas biomédicas, ofreciendo versatilidad en su diseño y una alta capacidad para promover el transporte de fármacos y la penetración en tumores. Por último, su movimiento colectivo observado in vivo mediante técnicas de imagen médicas representan un significativo avance en el viaje hacia su aplicación en medicina

Active poroelastic two-phase model for the motion of physarum microplasmodia

The onset of self-organized motion is studied in a poroelastic two-phase model with free boundaries for Physarum microplasmodia (MP). In the model, an active gel phase is assumed to be interpenetrated by a passive fluid phase on small length scales. A feedback loop between calcium kinetics, mechanical deformations, and induced fluid flow gives rise to pattern formation and the establishment of an axis of polarity. Altogether, we find that the calcium kinetics that breaks the conservation of the total calcium concentration in the model and a nonlinear friction between MP and substrate are both necessary ingredients to obtain an oscillatory movement with net motion of the MP. By numerical simulations in one spatial dimension, we find two different types of oscillations with net motion as well as modes with time-periodic or irregular switching of the axis of polarity. The more frequent type of net motion is characterized by mechano-chemical waves traveling from the front towards the rear. The second type is characterized by mechano-chemical waves that appear alternating from the front and the back. While both types exhibit oscillatory forward and backward movement with net motion in each cycle, the trajectory and gel flow pattern of the second type are also similar to recent experimental measurements of peristaltic MP motion. We found moving MPs in extended regions of experimentally accessible parameters, such as length, period and substrate friction strength. Simulations of the model show that the net speed increases with the length, provided that MPs are longer than a critical length of ≈ 120 μm. Both predictions are in line with recent experimental observations.DFG, 163436311, SFB 910: Kontrolle selbstorganisierender nichtlinearer Systeme: Theoretische Methoden und AnwendungskonzepteDFG, 87159868, GRK 1558: Kollektive Dynamik im Nichtgleichgewicht: in kondensierter Materie und biologischen SystemenDFG, 414044773, Open Access Publizieren 2019 - 2020 / Technische Universität Berli

Towards an understanding of peroxisome dynamics in mammalian cells

Peroxisomes are ubiquitous subcellular organelles involved in a variety of important metabolic processes. Recently, it became obvious that many of those functions are carried out in co-operation with mitochondria. The essential role of peroxisomes for human health is exemplified by the severe phenotype of peroxisomal disorders. Furthermore, peroxisomes are highly dynamic, adjusting their protein content, morphology and number in response to cellular needs. In recent years, peroxisome dynamics and their proper regulation were closely linked to organelle function and thus, human well-being. In line with this, a patient with a lethal defect in mitochondrial and peroxisomal fission was identified. Peroxisome dynamics are regulated by growth and division of the organelle, however, peroxisomes can also arise de novo from the ER under special conditions. In mammalian cells, peroxisomal growth and division follows a well-defined sequence of morphological alterations. Initial membrane elongation is carried out by the key peroxisomal membrane protein Pex11pβ, while final scission into smaller organelles is achieved by the combined action of the membrane adaptors Mff and Fis1 as well as the large GTPase DLP1. Interestingly, the key components of the peroxisomal fission machinery are shared with mitochondria; however the occurrence of peroxisomal fusion analogous to mitochondria remains a matter of debate. Although several external stimuli were identified to alter peroxisome dynamics, detailed information on their reception and transduction onto the peroxisomal level is limited. Thus, the aim of this study was to gain a deeper understanding of the processes contributing to and regulating peroxisome dynamics in mammalian cells. This thesis contains three parts: in the first section, the contribution of peroxisomal fusion, analogous to mitochondria, to organelle dynamics was addressed. In the second part, the regulation of peroxisome dynamics at the organelle itself was investigated by characterizing post-translational mechanisms modulating the action of Pex11pβ, the key mediator of peroxisome elongation/proliferation in mammalian cells. In the final part, different groups of external stimuli were characterized in regard to their capacity to alter peroxisome dynamics in order to study the regulation of peroxisome dynamics on a transcriptional level in mammalian cell culture. To investigate fusion of mature peroxisomes in mammalian CHO cells, an in vivo fusion assay was established based on hybridoma formation by cell fusion using cell lines stably expressing GFP- or DsRed-derived peroxisomal matrix and membrane markers. Fluorescence microscopy in time course experiments of fixed cells revealed a merge of different peroxisomal markers in fused cells, pointing to a certain degree of peroxisomal fusion. Although subsequent live cell imaging indicated that peroxisomes did not exchange matrix or membrane markers, the existence of transient, vivid interactions between individual peroxisomes was characterized for the first time. Interacting peroxisomes were shown to be tightly associated, accounting for the marker overlay observed in fixed cells. Using computational modelling and mathematical analysis, transient peroxisome interactions were shown to follow a complex, non-random behaviour that has the potential to facilitate the homogenization of the heterogeneous peroxisomal compartment. Pre-treatment with peroxisomal substrates indicated that transient, peroxisomal interactions do not contribute to the exchange of fatty acids or H2O2, but might facilitate the exchange of other peroxisomal metabolites or be part of a signaling system to sense the state and/or distribution of the peroxisomal population in the cell. Furthermore, for the first time, computational analysis provided an explanation why only 15 % of the peroxisome population is engaged in long-range microtubule-dependent movement. Additionally, evidence was provided that mitochondrial fusion proteins do not localize to peroxisomes, indicating that peroxisome dynamics in mammalian cells are regulated in a distinct manner. To gain insight into the modulation of peroxisome dynamics at the organelle itself, Pex11pβ was characterized biochemically. Differential permeabilization and protease-protection assays in combination with a newly available commercial antibody localized the position of its first transmembrane domain to the amino acid positions 90 – 110. Subsequently, the contribution of the N-terminal domain to the regulation of human Pex11pβ activity was addressed. Deletion of the first 40 amino acids abolished Pex11pβ-membrane elongation, although the essential amphipathic helix within the protein remained intact. Biochemical cross-linking and enrichment of Pex11pβ in time-course experiments linked its homo-dimerization to its activity which was diminished upon N-terminal deletion. In vivo phospho-labelling did not indicate phosphorylation of Pex11pβ in a manner similar to its S. cerevisiae orthologue. Thus, Pex11 proteins in yeast and mammals appear to be regulated in an opposite manner. Furthermore, overexpression of Pex11pβ in peroxisome-deficient patient fibroblasts resulted in its mistargeting to mitochondria where an excessive fragmentation was induced. This further emphasizes that mitochondria, but not the ER, serve a default membrane for peroxisomal membrane proteins in the absence of peroxisomes in mammals. Potential disturbances of mitochondrial function might thus contribute to the clinical severity of peroxisome disorders. In the final part of this thesis, external stimuli altering peroxisomal dynamics were characterized to establish a more physiological and amenable cell culture model to investigate the transcriptional regulation of peroxisome dynamics in mammalian cells. Application of the neurotoxin 6-OHDA in SH-S5Y5 neuroblastoma cells did not affect peroxisome dynamics, but led to a profound DLP1-dependent fragmentation of mitochondria. Though DLP1 is a shared component of both organelles, mitochondrial and peroxisomal dynamics further appear to be regulated in a distinct manner. Using a variety of compounds inducing cytosolic and mitochondrial oxidative stress, no morphological alterations of peroxisomes were observed. KillerRed-based induction of ROS in different compartments produced similar results in living cells. Thus, other factors besides the induction of oxidative stress, such as e.g. the intracellular or extracellular origin of the signal, alterations of cellular redox-state or yet unidentified signalling pathways might contribute to induce the alterations of peroxisome dynamics observed before. Addition of the glucocorticoid dexamethasone to rat pancreatic AR42J cells resulted in a profound, continuous elongation of peroxisomes. Notably, peroxisomes maintained their tubular morphology even after removal of the stimulus. Continuous peroxisome tubulation might be linked to cell differentiation or a metabolic function. Dexamethasone application induced Pex11β (and Pex11α) on a transcriptional level by a potentially PPARα-independent mechanism. Thus, dexamethasone-induced peroxisome elongation in AR42J cells has a high potential to serve as a more physiological model to study the regulation of peroxisome dynamics in mammalian cells. Future studies using expression profiling after dexamethasone stimulation in order to identify novel components and/or molecular mechanisms regulating peroxisome dynamics have been initiated

Active Stimuli-Responsive Polymer Surfaces and Thin Films: Design, Properties and Applications: Active Stimuli-Responsive Polymer Surfaces and Thin Films: Design, Properties and Applications

Design of 2D and 3D micropatterned materials is highly important for printing technology, microfluidics, microanalytics, information storage, microelectronics and biotechnology. Biotechnology deserves particular interest among the diversity of possible applications because its opens perspectives for regeneration of tissues and organs that can considerably improve our life. In fact, biotechnology is in constant need for development of microstructured materials with controlled architecture. Such materials can serve either as scaffolds or as microanalytical platforms, where cells are able to self-organize in a programmed manner. Microstructured materials, for example, allow in vitro investigation of complex cell-cell interactions, interactions between cells and engineered materials. With the help of patterned surfaces it was demonstrated that cell adhesion and viability as well as differentiation of stem cells1 depend of on the character of nano- and micro- structures 2 as well as their size. There are number of methods based on optical lithography, atomic force microscopy, printing techniques, chemical vapor deposition, which have been developed and successfully applied for 2D patterning. While each of these methods provides particular advantages, a general trade-off between spatial resolution, throughput, “biocompatibility of method” and usability of fabricated patterned surfaces exists. For example, AFM-based techniques allow very high nanometer resolution and can be used to place small numbers of functional proteins with nanometer lateral resolution, but are limited to low writing speeds and small pattern sizes. Albeit, the resolution of photolithography is lower, while it is much faster and cheaper. Therefore, it is highly desirable to develop methods for high-resolution patterning at reasonably low cost and high throughput. Although many approaches to fabricate sophisticated surface patterns exist, they are almost entirely limited to producing fixed patterns that cannot be intentionally modified or switched on the fly in physiologic environment. This limits the usability of a patterned surface to a single specific application and new microstructures have to be fabricated for new applications. Therefore, it is desirable to develop methods for design of switchable and rewritable patterns. Next, the high-energy of the ultraviolet radiation, which is typically used for photolithography, can be harmful for biological species. It is also highly important to develop an approach for photopatterning where visible light is used instead of UV light. Therefore, it is very important for biotechnological applications to achieve good resolution at low costs, create surface with switchable and reconfigurable patterns, perform patterning in mild physiologic conditions and avoid use of harmful UV light. 3D patterning is experimentally more complicated than 2D one and the applicability of available techniques is substantially limited. For example, interference photolithography allows fabrication of 3D structures with limited thickness. Two-photon photolithography, which allows nanoscale resolution, is very slow and highly expensive. Assembling of 3D structures by stacking of 2D ones is time consuming and does not allow fabrication of fine hollow structures. At the same time, nature offers an enormous arsenal of ideas for the design of novel materials with superior properties. In particular, self-assembly and self-organization being the driving principles of structure formation in nature attract significant interest as promising concepts for the design of intelligent materials 3. Self-folding films are the examples of biomimetic materials4. Such films mimic movement mechanisms of plants 5-7 and are able to self-organize and form complex 3D structures. The self-folding films consist of two materials with different properties. At least one of these materials, active one, can change its volume. Because of non-equal expansion of the materials, the self-folding films are able to form a tubes, capsules or more complex structure. Similar to origami, the self-folding films provide unique possibilities for the straightforward fabrication of highly complex 3D micro-structures with patterned inner and outer walls that cannot be achieved using other currently available technologies. The self-folded micro-objects can be assembled into sophisticated, hierarchically-organized 3D super-constructs with structural anisotropy and highly complex surface patterns. Till now most of the research in the field of self-folding films was focused on inorganic materials. Due to their rigidity, limited biocompatibility and non-biodegradability, application of inorganic self-folding materials for biomedical purposes is limited. Polymers are more suitable for these purposes. There are many factors, which make polymer-based self-folding films particularly attractive. There is a variety of polymers sensitive to different stimuli that allows design of self-folding films, which are able to fold in response to various external signals. There are many polymers changing their properties in physiological ranges of pH and temperature as well as polymers sensitive to biochemical processes. There is a variety of biocompatible and biodegradable polymers. These properties make self-folding polymer highly attractive for biological applications. Polymers undergo considerable and reversible changes of volume that allows design of systems with reversible folding. Fabrication of 3D structures with the size ranging from hundreds of nanometers to centimeters is possible. In spite of their attractive properties, the polymer-based systems remained almost out of focus – ca 15 papers including own ones were published on this topic (see own review 8, state October 2011). Thereby the development of biomimetic materials based on self-folding polymer films is highly desired and can open new horizons for the design of unique 3D materials with advanced properties for lab-on-chip applications, smart materials for everyday life and regenerative medicine