AMOLF Institutional Repository
Not a member yet
1351 research outputs found
Sort by
Editorial: From reconstituting minimal cell-cell signaling systems to bioinspired synthetic communication networks
Get PDFDirect observation of Hsp90-induced compaction in a protein chain
Get PDFThe chaperone heat shock protein 90 (Hsp90) is well known to undergo important conformational changes, which depend on nucleotide and substrate interactions. Conversely, how the conformations of its unstable and disordered substrates are affected by Hsp90 is difficult to address experimentally yet is central to its function. Here, using optical tweezers, we find that Hsp90 promotes local contractions in unfolded chains that drive their global compaction down to dimensions of folded states. This compaction has a gradual nature while showing small steps, is stimulated by ATP, and performs mechanical work against counteracting forces that expand the chain dimensions. The Hsp90 interactions suppress the formation of larger-scale folded, misfolded, and aggregated structures. The observations support a model in which Hsp90 alters client conformations directly by promoting local intra-chain interactions while suppressing distant ones. We conjecture that chain compaction may be central to how Hsp90 protects unstable clients and cooperates with Hsp70
Robust replication initiation from coupled homeostatic mechanisms
Get PDFThe bacterium Escherichia coli initiates replication once per cell cycle at a precise volume per origin and adds an on average constant volume between successive initiation events, independent of the initiation size. Yet, a molecular model that can explain these observations has been lacking. Experiments indicate that E. coli controls replication initiation via titration and activation of the initiator protein DnaA. Here, we study by mathematical modelling how these two mechanisms interact to generate robust replication-initiation cycles. We first show that a mechanism solely based on titration generates stable replication cycles at low growth rates, but inevitably causes premature reinitiation events at higher growth rates. In this regime, the DnaA activation switch becomes essential for stable replication initiation. Conversely, while the activation switch alone yields robust rhythms at high growth rates, titration can strongly enhance the stability of the switch at low growth rates. Our analysis thus predicts that both mechanisms together drive robust replication cycles at all growth rates. In addition, it reveals how an origin-density sensor yields adder correlations
Reply to Zhang et al.: The critical temperature dependence of developmental rates is in search of a mechanism
Get PDFThe observation that the rate of development scales with temperature T as (T−TC) for a broad range of animals is very interesting as it strongly suggests a common mechanism, yet an explanation for it is currently lacking. Zhang et al. (1), in their letter responding to our recent study on developmental timing in Caenorhabditis elegans (2), suggest this temperature dependence is due to development taking place near a critical point, with TC the critical temperature. If correct, it would imply that similar conceptual mechanisms underlie processes as diverse as phase transitions in inanimate matter and development in complex multicellular organisms
Extreme-Ultraviolet Shaping and Imaging by High-Harmonic Generation from Nanostructured Silica
Get PDFCoherent extreme-ultraviolet pulses from high-harmonic generation have ample applications in attosecond science, lensless imaging, and industrial metrology. However, tailoring complex spatial amplitude, phase, and polarization properties of extreme-ultraviolet pulses is made nontrivial by the lack of efficient optical elements. Here, we have overcome this limitation through nanoengineered solid samples, which enable direct control over amplitude and phase patterns of nonlinearly generated extreme-ultraviolet pulses. We demonstrate experimental configurations and emitting structures that yield spatially patterned beam profiles, increased conversion efficiencies, and tailored polarization states. Furthermore, we use the emitted patterns to reconstruct height profiles, probe the near-field confinement in nanostructures below the diffraction limit of the fundamental radiation, and to image complex structures through coherent diffractive emission from these structures. Our results pave the way for introducing sub-fundamental-wavelength resolution imaging, direct manipulation of beams through nanoengineered samples, and metrology of nanostructures into the extreme-ultraviolet spectral range
Plasma Focused Ion Beam Tomography for Accurate Characterization of Black Silicon Validated by Full Wave Optical Simulation
Get PDFBlack silicon (BSi) is a branch of silicon material whose surface is specially processed to a micro/nanoscale structure, which can achieve ultra-low reflectance or ultra-high electrochemical reactivity. The diversity and complex surface structures of BSi make it challenging to commercialize BSi devices. Modeling and simulation are commonly used in the semiconductor industry to help in better understanding the material properties, predict the device performance, and provide guidelines for fabrication parameters’ optimization. The biggest challenge for BSi device modeling and simulation is obtaining accurate input surface morphological data. In this work, the 3D models of challenging BSi textures are compared as obtained by atomic force microscopy (AFM) and plasma focused ion beam (PFIB) tomography techniques. In previous work, the PFIB tomography workflow toward the application of surface topography is optimized. In this work, the 3D models obtained from both AFM and PFIB are comprehensively compared, by using the surface models as inputs for finite-difference time-domain-based optical simulation. The results provide strong evidence that PFIB tomography is a better choice for characterizing highly roughened surface such as BSi and provides surface 3D models with better reliability and consistency
Quantification of the Helical Morphology of Chiral Gold Nanorods
Get PDFChirality in inorganic nanoparticles and nanostructures has gained increasing scientific interest, because of the possibility to tune their ability to interact differently with left- and right-handed circularly polarized light. In some cases, the optical activity is hypothesized to originate from a chiral morphology of the nanomaterial. However, quantifying the degree of chirality in objects with sizes of tens of nanometers is far from straightforward. Electron tomography offers the possibility to faithfully retrieve the three-dimensional morphology of nanomaterials, but only a qualitative interpretation of the morphology of chiral nanoparticles has been possible so far. We introduce herein a methodology that enables us to quantify the helicity of complex chiral nanomaterials, based on the geometrical properties of a helix. We demonstrate that an analysis at the single particle level can provide significant insights into the origin of chiroptical properties
Cross-linkers at growing microtubule ends generate forces that drive actin transport
Get PDFThe actin and microtubule cytoskeletons form active networks in the cell that can contract and remodel, resulting in vital cellular processes such as cell division and motility. Motor proteins play an important role in generating the forces required for these processes, but more recently the concept of passive cross-linkers being able to generate forces has emerged. So far, these passive cross-linkers have been studied in the context of separate actin and microtubule systems. Here, we show that cross-linkers also allow actin and microtubules to exert forces on each other. More specifically, we study single actin filaments that are cross-linked to growing microtubule ends, using in vitro reconstitution, computer simulations, and a minimal theoretical model. We show that microtubules can transport actin filaments over large (micrometer-range) distances and find that this transport results from two antagonistic forces arising from the binding of cross-linkers to the overlap between the actin and microtubule filaments. The cross-linkers attempt to maximize the overlap between the actin and the tip of the growing microtubules, creating an affinity-driven forward condensation force, and simultaneously create a competing friction force along the microtubule lattice. We predict and verify experimentally how the average transport time depends on the actin filament length and the microtubule growth velocity, confirming the competition between a forward condensation force and a backward friction force. In addition, we theoretically predict and experimentally verify that the condensation force is of the order of 0.1 pN. Thus, our results reveal an active mechanism for local actin remodeling by growing microtubules that relies on passive cross-linkers
A Lab-in-a-Fiber optofluidic device using droplet microfluidics and laser-induced fluorescence for virus detection
Get PDFMicrofluidics has emerged rapidly over the past 20 years and has been investigated for a variety of applications from life sciences to environmental monitoring. Although continuous-flow microfluidics is ubiquitous, segmented-flow or droplet microfluidics offers several attractive features. Droplets can be independently manipulated and analyzed with very high throughput. Typically, microfluidics is carried out within planar networks of microchannels, namely, microfluidic chips. We propose that fibers offer an interesting alternative format with key advantages for enhanced optical coupling. Herein, we demonstrate the generation of monodisperse droplets within a uniaxial optofluidic Lab-in-a-Fiber scheme. We combine droplet microfluidics with laser-induced fluorescence (LIF) detection achieved through the development of an optical side-coupling fiber, which we term a periscope fiber. This arrangement provides stable and compact alignment. Laser-induced fluorescence offers high sensitivity and low detection limits with a rapid response time making it an attractive detection method for in situ real-time measurements. We use the well-established fluorophore, fluorescein, to characterize the Lab-in-a-Fiber device and determine the generation of [Formula: see text] 0.9 nL droplets. We present characterization data of a range of fluorescein concentrations, establishing a limit of detection (LOD) of 10 nM fluorescein. Finally, we show that the device operates within a realistic and relevant fluorescence regime by detecting reverse-transcription loop-mediated isothermal amplification (RT-LAMP) products in the context of COVID-19 diagnostics. The device represents a step towards the development of a point-of-care droplet digital RT-LAMP platform
Mother cells control daughter cell proliferation in intestinal organoids to minimize proliferation fluctuations
Get PDFDuring renewal of the intestine, cells are continuously generated by proliferation. Proliferation and differentiation must be tightly balanced, as any bias toward proliferation results in uncontrolled exponential growth. Yet, the inherently stochastic nature of cells raises the question how such fluctuations are limited. We used time-lapse microscopy to track all cells in crypts of growing mouse intestinal organoids for multiple generations, allowing full reconstruction of the underlying lineage dynamics in space and time. Proliferative behavior was highly symmetric between sister cells, with both sisters either jointly ceasing or continuing proliferation. Simulations revealed that such symmetric proliferative behavior minimizes cell number fluctuations, explaining our observation that proliferating cell number remained constant even as crypts increased in size considerably. Proliferative symmetry did not reflect positional symmetry but rather lineage control through the mother cell. Our results indicate a concrete mechanism to balance proliferation and differentiation with minimal fluctuations that may be broadly relevant for other tissues.The vast majority of cells lining our intestine die within three to five days. They are replaced by a small group of stem cells which divide to produce either more stem cells, or cells that stop dividing and transform, or ‘differentiate’, in to mature cells in the intestine. Stem cells must generate the same number of dividing and differentiated cells. If there is even a slight bias and too many stem cells are produced, this can lead to uncontrolled growth, which is the root cause of cancer. In principal, the best way to achieve this balance is for stem cells to always asymmetrically divide in to two distinct cells: one that will continue to divide, and another that will mature in to an adult cell. However, recent research suggests that this process is much more random, with stem cells also dividing symmetrically, either in to two stem cells or two differentiated cells. So, how does the random nature of stem cell divisions not cause the number of dividing cells to fluctuate unpredictably in the intestine? To investigate, Huelsz-Prince et al. studied stem cells in a miniature model of the mouse intestine, known as an organoid, which can be grown outside of the body in a laboratory. All stem cells and their progeny were tracked for over 65 hours using a microscope to see how many dividing and differentiated cells they formed. This revealed that almost all stem cells in the organoid split symmetrically rather than asymmetrically. Huelsz-Prince et al. then developed a computer model of stem cells in the model intestine and tested the impact of changing the proportion of symmetric and asymmetric divisions. The results showed that having more symmetric divisions reduced fluctuations in the number of dividing cells better than high levels of asymmetric divisions. Other organs rely on a similar system to the intestine to replenish their mature cells. Consequently, the finding that symmetric divisions control fluctuations in the number of stem cells may be applicable to other parts of the body. Further testing with human disease samples, such as cells from cancer patients, using the organoid model system may also shed light on how division is disrupted in these conditions