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Nir, E.

Publications and source records attributed to Nir, E..

5 recordsLinked to original sources

High-Performance, Computer-Controlled Bipedal DNA Motor

Achieving precise, repeatable motion at the molecular scale remains a central challenge in the development of synthetic molecular machines. Here we report a high-fidelity, fast bipedal DNA walker that moves bidirectionally along a DNA origami track using a fuel-before-antifuel operational scheme that suppresses trap states typical of externally powered DNA motors. Automated, computer-controlled microfluidics enables programmable trajectory execution with >98% yield per step and sustained bidirectional walking over distances of up to 360 nm, as monitored by single-molecule FRET. Kinetic analysis reveals rapid leg lifting but slower leg placement due to inhibitory fuel-antifuel heterocomplex formation, identifying a mechanistic bottleneck that can be mitigated through optimization of fuel, antifuel and foothold design. The resulting motor operates with efficiencies of up to 4 orders of magnitude higher than previous externally controlled DNA walkers, establishing a robust framework for deterministic, programmable molecular transport.

biophysics↗

A High-Performance and Recoverable DNA Origami Rotary Motor

Inspired by biological molecular machines, we developed a highly processive DNA origami rotary motor. The rotor consists of two disk-shaped DNA origamis that are connected by a single-stranded swivel that allows free rotation but prevents rotor dissociation in the event of operational error. The rotor is propelled by two bipedal walkers that stride on a circular DNA track propelled by a previously optimized DNA propulsion mechanism called fuel before antifuel. The DNA fuel and antifuel strands are delivered by a microfluidic device. The rotation is monitored by a single-molecule, light scattering, defocused imaging technique; light scattered from a gold nanorod attached to the rotor enables high angular and temporal resolution analyses of rotor orientation. Imaging movies show individual rotors performing 96 individual steps, corresponding to 8 full rotor revolutions, with direction determined by the fuel and antifuel sequence. In cases of operational errors, which result in free Brownian rotation, the rotors were able to recover and continue rotating as commanded. Our origami-based rotary motor design, microfluidics-based control system, and high-resolution monitoring of rotor orientation will facilitate the development of DNA-based machines driven by autonomous propulsion.

biophysics↗

Neurodegeneration impairs the consolidation of developmentally synchronized behavioral patterns

Animals generate predictable patterns of behavior that are robustly synchronized with the developmental clock. However, the dynamics of the long-term establishment of synchronized behaviors across the entire developmental trajectory, and the neuronal circuits that control this developmental synchronization, remain underexplored. Here, we show that in C. elegans individuals, developmental synchronization of behavior continuously consolidates throughout development time, and that this consolidation is controlled by multiple neuronal pathways. In particular, we found that the degeneration of a specific mechanosensory circuit early in development strongly impairs the developmental synchronization of behavior. Furthermore, early neuronal activity patterns in downstream motor neurons are altered following the mechanosensory circuit degeneration. Interestingly, we show that either pharmacological or genetic neuroprotection of the mechanosensory circuit from degeneration restores normal modes of developmentally synchronized behaviors. These results imply the control of time-locked behaviors across the developmental trajectory by a localized sensory circuit within the nervous system.

neuroscience↗

Hyperinflammation evokes different antiviral TMPRSS2 and ADAM17 expression responses in human gut xenograft versus host mouse gut although overall genomic responses are similar

The global spread of the newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the pandemic outbreak of coronavirus disease 2019 (COVID-19), an inflammatory disease that is primarily affecting the respiratory system. However, gastrointestinal symptoms in COVID-19 patients suggests that the gut may present another viral target organ. Disease development and severity is dependent on viral interaction with two cell surface human proteins, ACE2 and TMPRSS2, and on antiviral response which may lead to systemic hyperinflammatory syndrome and multiorgan dysfunction. Understanding the host response to SARS-CoV-2 infection and the pathology of the disease will be greatly enhanced by the development of appropriate animal models. Laboratory mice have been the mainstay of therapeutic and vaccine development, however, the virus does not grow in wild type mice and only induced mild disease in transgenic animals expressing human ACE2. As there are known differences between immune response in laboratory mice and humans we evaluated the response of human gut developed as xenografts and host mouse gut following systemic LPS injections as a hyperinflammation model system. The orthologous gene expression levels in the mouse and human gut were highly correlated (Spearmans rank correlation coefficient: 0.28-0.76) and gene set enrichment analysis of significantly upregulated human and mouse genes revealed that a number of inflammatory and immune response pathways are commonly regulated in the two species. However, species differences were also observed, most importantly, in the inflamed human gut but not in the mouse gut, there was clear upregulation of mRNAs coding for TMPRSS2, ADAM17 and for RIG-I-like receptors, which are involved in the recognition of viruses and in antiviral innate immune response. Moreover, using species-specific immunofluorescence microscopy, we demonstrated the expression and localization of human ACE2 and TMPRSS2 proteins, which are essential elements of the molecular machinery that enables SARS-CoV-2 to infect and replicate in human gut cells. Our findings demonstrate that the intestinal immune response to inflammation in humans and mice are generally very similar. However, certain human-specific diseases, such as COVID-19, can only be successfully studied in an experimental model of human tissue, such as the gut xenograft.

immunology↗

NF-kappa-B activation unveils the presence of inflammatory hotspots in human gut xenografts

The single-epithelial cell layer of the gut mucosa serves as an essential barrier between the host and luminal microflora and plays a major role in innate immunity against invading pathogens. Nuclear factor kB (NF-{kappa}B), a central component of the cellular signaling machinery, regulates immune response and inflammation. NF-{kappa}B proteins are activated by signaling pathways downstream to microbial recognition receptors and cytokines receptors. Highly regulated NF-{kappa}B activity in intestinal epithelial cells (IEC) is essential for normal gut homeostasis; dysregulated activity has been linked to a number of disease states, including inflammatory bowel diseases (IBD) such as Crohns Disease (CD). Our aim was to visualize and quantify spatial and temporal dynamics of NF-{kappa}B activity in steady state and inflamed human gut. Lentivirus technology was used to transduce the IEC of human gut xenografts in SCID mice with a NF-{kappa}B luminescence reporter system. NF-{kappa}B signaling was visualized and quantified using low resolution, intravital imaging of the whole body and high resolution, immunofluorescence microscopic imaging of the tissues. We show that NF-{kappa}B is activated in select subset of IEC with low "leaky" NF-{kappa}B activity. These unique inflammatory epithelial cells are clustered in the gut into discrete hotspots of NF-{kappa}B activity that are visible in steady state and selectively activated by systemic LPS and human TNF or luminal bacteria. The presence of inflammatory hotspots in the normal and inflamed gut might explain the patchy mucosal lesions characterizing CD and thus could have important implications for diagnosis and therapy.

immunology↗