The cell nucleus is a compartment in which essential processes such as gene transcription and DNA replication occur. Although the large amount of chromatin confined in the finite nuclear space could ...install the picture of a particularly dense organelle surrounded by less dense cytoplasm, recent studies have begun to report the opposite. However, the generality of this newly emerging, opposite picture has so far not been tested. Here, we used combined optical diffraction tomography and epi-fluorescence microscopy to systematically quantify the mass densities of cytoplasm, nucleoplasm, and nucleoli of human cell lines, challenged by various perturbations. We found that the nucleoplasm maintains a lower mass density than cytoplasm during cell cycle progression by scaling its volume to match the increase of dry mass during cell growth. At the same time, nucleoli exhibited a significantly higher mass density than the cytoplasm. Moreover, actin and microtubule depolymerization and changing chromatin condensation altered volume, shape, and dry mass of those compartments, whereas the relative distribution of mass densities was generally unchanged. Our findings suggest that the relative mass densities across membrane-bound and membraneless compartments are robustly conserved, likely by different as-of-yet unknown mechanisms, which hints at an underlying functional relevance. This surprising robustness of mass densities contributes to an increasing recognition of the importance of physico-chemical properties in determining cellular characteristics and compartments.
A variety of communication networks, such as industrial communication systems, have to provide strict delay guarantees to the carried flows. Fast and close to optimal quality of service (QoS) routing ...algorithms, e.g., delay-constrained leastcost (DCLC) routing algorithms, are required for routing flows in such networks with strict delay requirements. The emerging software-defined networking (SDN) paradigm centralizes the network control in SDN controllers that can centrally execute QoS routing algorithms. A wide range of QoS routing algorithms have been proposed in the literature and examined in individual studies. However, a comprehensive evaluation framework and quantitative comparison of QoS routing algorithms that can serve as a basis for selecting and further advancing QoS routing in SDN networks is missing in the literature. This makes it difficult to select the most appropriate QoS routing algorithm for a particular use case, e.g., for SDN controlled industrial communications. We close this gap in the literature by conducting a comprehensive up-to-date survey of centralized QoS routing algorithms. We introduce a novel four-dimensional (4D) evaluation framework for QoS routing algorithms, whereby the 4D correspond to the type of topology, two forms of scalability of a topology, and the tightness of the delay constraint. We implemented 26 selected DCLC algorithms and compared their runtime and cost inefficiency within the 4D evaluation framework. While the main conclusion of this evaluation is that the best algorithm depends on the specific sub-space of the 4D space that is targeted, we identify two algorithms, namely Lagrange relaxation-based aggregated cost (LARAC) and search space reduction delay-cost-constrained routing (SSR+DCCR), that perform very well in most of the 4D evaluation space.
The mechanical phenotype of a cell is an inherent biophysical marker of its state and function, with many applications in basic and applied biological research. Microfluidics-based methods have ...enabled single-cell mechanophenotyping at throughputs comparable to those of flow cytometry. Here, we present a standardized cross-laboratory study comparing three microfluidics-based approaches for measuring cell mechanical phenotype: constriction-based deformability cytometry (cDC), shear flow deformability cytometry (sDC) and extensional flow deformability cytometry (xDC). All three methods detect cell deformability changes induced by exposure to altered osmolarity. However, a dose-dependent deformability increase upon latrunculin B-induced actin disassembly was detected only with cDC and sDC, which suggests that when exposing cells to the higher strain rate imposed by xDC, cellular components other than the actin cytoskeleton dominate the response. The direct comparison presented here furthers our understanding of the applicability of the different deformability cytometry methods and provides context for the interpretation of deformability measurements performed using different platforms.
Industrial networks demand centrally controlled quality of service (QoS), often in the form of hard real-time guarantees. Software-defined networking (SDN) provides a convenient paradigm for central ...QoS control. However, existing SDN-based solutions cannot guarantee hard real-time QoS as they rely on a control loop over the forwarding (data) and control planes. We propose a novel SDN-based QoS control framework that maintains an accurate network model through network calculus to avoid a control loop over forwarding and control planes, allocates resources to and routes flows over a network of "queue links," whereby each physical network link houses multiple queue links (with different QoS levels), and manages QoS through a function split between delay-constrained least-cost routing on the network of queue links and the resource allocation to the queue links. This function split greatly reduces the computational complexity while achieving hard real-time QoS with high bandwidth utilization. Our evaluation results indicate that our function split approach allows for online runtime admission control and can achieve bandwidth utilization above 80% while meeting deterministic real-time QoS requirements.
Cells can enter into a dormant state when faced with unfavorable conditions. However, how cells enter into and recover from this state is still poorly understood. Here, we study dormancy in different ...eukaryotic organisms and find it to be associated with a significant decrease in the mobility of organelles and foreign tracer particles. We show that this reduced mobility is caused by an influx of protons and a marked acidification of the cytoplasm, which leads to widespread macromolecular assembly of proteins and triggers a transition of the cytoplasm to a solid-like state with increased mechanical stability. We further demonstrate that this transition is required for cellular survival under conditions of starvation. Our findings have broad implications for understanding alternative physiological states, such as quiescence and dormancy, and create a new view of the cytoplasm as an adaptable fluid that can reversibly transition into a protective solid-like state.
Implantable neuroprostheses are engineered systems designed to restore or substitute function for individuals with neurological deficits or disabilities. These systems involve at least one uni- or ...bidirectional interface between a living neural tissue and a synthetic structure, through which information in the form of electrons, ions or photons flows. Despite a few notable exceptions, the clinical dissemination of implantable neuroprostheses remains limited, because many implants display inconsistent long-term stability and performance, and are ultimately rejected by the body. Intensive research is currently being conducted to untangle the complex interplay of failure mechanisms. In this Review, we emphasize the importance of minimizing the physical and mechanical mismatch between neural tissues and implantable interfaces. We explore possible materials solutions to design and manufacture neurointegrated prostheses, and outline their immense therapeutic potential.Implantable neuroprostheses communicate with the nervous system to provide diagnosis or therapy to the injured body. In this review, we discuss materials-based approaches to overcome the physical and mechanical mismatch at the tissue–implant interface and to design long-term neurointegrated prostheses.
Stressed cells shut down translation, release mRNA molecules from polysomes, and form stress granules (SGs) via a network of interactions that involve G3BP. Here we focus on the mechanistic ...underpinnings of SG assembly. We show that, under non-stress conditions, G3BP adopts a compact auto-inhibited state stabilized by electrostatic intramolecular interactions between the intrinsically disordered acidic tracts and the positively charged arginine-rich region. Upon release from polysomes, unfolded mRNAs outcompete G3BP auto-inhibitory interactions, engendering a conformational transition that facilitates clustering of G3BP through protein-RNA interactions. Subsequent physical crosslinking of G3BP clusters drives RNA molecules into networked RNA/protein condensates. We show that G3BP condensates impede RNA entanglement and recruit additional client proteins that promote SG maturation or induce a liquid-to-solid transition that may underlie disease. We propose that condensation coupled to conformational rearrangements and heterotypic multivalent interactions may be a general principle underlying RNP granule assembly.
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•Under non-stressed conditions, G3BP adopts a compact auto-inhibited state•Conformational expansion of G3BP increases the interaction valences•G3BP clusters crosslink RNA to assemble stress granules upon cellular stress•G3BP condensates prevent RNA entanglement
Reconstitution of stress granule assembly reveals an autoinhibitory conformation of G3BP that is alleviated by RNA binding, demonstrating how this central node of the stress granule network phase-separates in response to rising cellular RNA concentrations.
We introduce real-time deformability cytometry (RT-DC) for continuous cell mechanical characterization of large populations (>100,000 cells) with analysis rates greater than 100 cells/s. RT-DC is ...sensitive to cytoskeletal alterations and can distinguish cell-cycle phases, track stem cell differentiation into distinct lineages and identify cell populations in whole blood by their mechanical fingerprints. This technique adds a new marker-free dimension to flow cytometry with diverse applications in biology, biotechnology and medicine.
During nervous system development, neurons extend axons along well-defined pathways. The current understanding of axon pathfinding is based mainly on chemical signaling. However, growing neurons ...interact not only chemically but also mechanically with their environment. Here we identify mechanical signals as important regulators of axon pathfinding. In vitro, substrate stiffness determined growth patterns of Xenopus retinal ganglion cell axons. In vivo atomic force microscopy revealed a noticeable pattern of stiffness gradients in the embryonic brain. Retinal ganglion cell axons grew toward softer tissue, which was reproduced in vitro in the absence of chemical gradients. To test the importance of mechanical signals for axon growth in vivo, we altered brain stiffness, blocked mechanotransduction pharmacologically and knocked down the mechanosensitive ion channel piezo1. All treatments resulted in aberrant axonal growth and pathfinding errors, suggesting that local tissue stiffness, read out by mechanosensitive ion channels, is critically involved in instructing neuronal growth in vivo.
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