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An extracellular vesicle targeting ligand that binds to Arc proteins and facilitates Arc transport in vivo
No full textCommunication between distant cells can be mediated by extracellular vesicles (EVs) that deliver proteins and RNAs to recipient cells. Little is known about how EVs are targeted to specific cell types. Here we identify the Drosophila cell-surface protein Stranded at second (Sas) as a targeting ligand for EVs. Full-length Sas is present in EV preparations from transfected Drosophila Schneider 2 (S2 cells). Sas is a binding partner for the Ptp10D receptor tyrosine phosphatase, and Sas-bearing EVs preferentially target to cells expressing Ptp10D. We used co-immunoprecipitation and peptide binding to show that the cytoplasmic domain (ICD) of Sas binds to dArc1. dArc1 and mammalian Arc are related to retrotransposon Gag proteins. They form virus-like capsids which encapsulate Arc and other mRNAs and are transported between cells via EVs. The Sas ICD contains a motif required for dArc1 binding that is shared by the mammalian and Drosophila amyloid precursor protein (APP) orthologs, and the Sas and APP ICDs also bind to mammalian Arc. Sas facilitates delivery of dArc1 capsids bearing dArc1 mRNA into distant Ptp10D-expressing recipient cells in vivo
A cryogenic, coincident fluorescence, electron, and ion beam microscope
No full textCryogenic electron tomography (cryo-ET) combined with subtomogram averaging, allows in situ visualization and structure determination of macromolecular complexes at subnanometre resolution. Cryogenic focused ion beam (cryo-FIB) micromachining is used to prepare a thin lamella-shaped sample out of a frozen-hydrated cell for cryo-ET imaging, but standard cryo-FIB fabrication is blind to the precise location of the structure or proteins of interest. Fluorescence-guided focused ion beam (FIB) milling at target locations requires multiple sample transfers prone to contamination, and relocation and registration accuracy is often insufficient for 3D targeting. Here, we present in situ fluorescence microscopy-guided FIB fabrication of a frozen-hydrated lamella to address this problem: we built a coincident three-beam cryogenic correlative microscope by retrofitting a compact cryogenic microcooler, custom positioning stage, and an inverted widefield fluorescence microscope (FM) on an existing FIB scanning electron microscope. We show FM controlled targeting at every milling step in the lamella fabrication process, validated with transmission electron microscope tomogram reconstructions of the target regions. The ability to check the lamella during and after the milling process results in a higher success rate in the fabrication process and will increase the throughput of fabrication for lamellae suitable for high-resolution imaging
NUPACK: Analysis and Design of Nucleic Acid Structures, Devices, and Systems
No full textNUPACK is a growing software suite for the analysis and design of nucleic acid structures, devices, and systems serving the needs of researchers in the fields of nucleic acid nanotechnology, molecular programming, synthetic biology, and across the life sciences. NUPACK algorithms are unique in treating complex and test tube ensembles containing arbitrary numbers of interacting strand species, providing crucial tools for capturing concentration effects essential to analyzing and designing the intermolecular interactions that are a hallmark of these fields. The all-new NUPACK web app (nupack.org) has been re-architected for the cloud, leveraging a cluster that scales dynamically in response to user demand to enable rapid job submission and result inspection even at times of peak user demand. The web app exploits the all-new NUPACK 4 scientific code base as its backend, offering enhanced physical models (coaxial and dangle stacking subensembles), dramatic speedups (20-120x for test tube analysis), and increased scalability for large complexes. NUPACK 4 algorithms can also be run locally using the all-new NUPACK Python module
Wavelet-based resolvent analysis for statistically-stationary and temporally-evolving flows
No full textThis work introduces a formulation of resolvent analysis that uses wavelet transforms rather than Fourier transforms in time. This allows resolvent analysis to be extended to turbulent flows with non-stationary means in addition to statistically-stationary flows. The optimal resolvent modes for this formulation correspond to the potentially time-transient structures that are most amplified by the linearized Navier-Stokes operator. We validate this methodology for turbulent channel flow and show that the wavelet-based and Fourier-based resolvent analyses are equivalent for statistically-stationary flows. We then apply the wavelet-based resolvent analysis to study the transient growth mechanism in the buffer layer of a turbulent channel flow by windowing the resolvent operator in time and frequency. The method is also applied to temporally-evolving parallel shear flows such as an oscillating boundary layer and three-dimensional channel flow, in which a lateral pressure gradient perturbs a fully-developed turbulent flow in a channel
Control of protein activity by photoinduced spin polarized charge reorganization
No full textConsiderable electric fields are present within living cells, and the role of bioelectricity has been well established at the organismal level. Yet much remains to be learned about electric-field effects on protein function. Here, we use phototriggered charge injection from a site-specifically attached ruthenium photosensitizer to directly demonstrate the effect of dynamic charge redistribution within a protein. We find that binding of an antibody to phosphoglycerate kinase (PGK) is increased twofold under illumination. Remarkably, illumination is found to suppress the enzymatic activity of PGK by a factor as large as three. These responses are sensitive to the photosensitizer position on the protein. Surprisingly, left (but not right) circularly polarized light elicits these responses, indicating that the electrons involved in the observed dynamics are spin polarized, due to spin filtration by protein chiral structures. Our results directly establish the contribution of electrical polarization as an allosteric signal within proteins. Future experiments with phototriggered charge injection will allow delineation of charge rearrangement pathways within proteins and will further depict their effects on protein function
Improved Heralded Single-Photon Source with a Photon-Number-Resolving Superconducting Nanowire Detector
No full textDeterministic generation of single photons is essential for many quantum information technologies. A bulk optical nonlinearity emitting a photon pair, where the measurement of one of the photons heralds the presence of the other, is commonly used with the caveat that the single-photon emission rate is constrained due to a trade-off between multiphoton events and pair emission rate. Using an efficient and low noise photon-number-resolving superconducting nanowire detector we herald, in real time, a single photon at telecommunication wavelength. We perform a second-order photon correlation g²(0) measurement of the signal mode conditioned on the measured photon number of the idler mode for various pump powers and demonstrate an improvement of a heralded single-photon source. We develop an analytical model using a phase-space formalism that encompasses all multiphoton effects and relevant imperfections, such as loss and multiple Schmidt modes. We perform a maximum-likelihood fit to test the agreement of the model to the data and extract the best-fit mean photon number μ of the pair source for each pump power. A maximum reduction of 0.118 ± 0.012 in the photon g²(0) correlation function at μ = 0.327 ± 0.007 is obtained, indicating a strong suppression of multiphoton emissions. For a fixed g²(0) = 7 × 10⁻³, we increase the single pair generation probability by 25%. Our experiment, built using fiber-coupled and off-the-shelf components, delineates a path to engineering ideal sources of single photons
Calibrating a thermometer for Earth's interior over time
No full textNew high-pressure, high-temperature experiments refine our ability to trace the thermal evolution of the Earth’s interior using the geological record of intermittent, large-volume volcanic episodes
Bongard-HOI: Benchmarking Few-Shot Visual Reasoning for Human-Object Interactions
No full textA significant gap remains between today's visual pattern recognition models and humanlevel visual cognition especially when it comes to fewshot learning and compositional reasoning of novel concepts. We introduce Bongard-HOI, a new visual reasoning benchmark that focuses on compositional learning of humanobject interactions (HOIs) from natural images. It is inspired by two desirable characteristics from the classical Bongard problems (BPs): 1) fewshot concept learning, and 2) contextdependent reasoning. We carefully curate the fewshot instances with hard negatives, where positive and negative images only disagree on action labels, making mere recognition of object categories insufficient to complete our benchmarks. We also design multiple test sets to systematically study the generalization of visual learning models, where we vary the overlap of the HOI concepts between the training and test sets of fewshot instances, from partial to no overlaps. Bongard-HOI presents a substantial challenge to today's visual recognition models. The state-of-the-art HOI detection model achieves only 62% accuracy on fewshot binary prediction while even amateur human testers on MTurk have 91% accuracy. With the Bongard-HOI benchmark, we hope to further advance research efforts in visual reasoning, especially in holistic perception-reasoning systems and better representation learning
OSCAR: Data-Driven Operational Space Control for Adaptive and Robust Robot Manipulation
No full textLearning performant robot manipulation policies can be challenging due to high-dimensional continuous actions and complex physics-based dynamics. This can be alleviated through intelligent choice of action space. Operational Space Control (OSC) has been used as an effective task-space controller for manipulation. Nonetheless, its strength depends on the underlying modeling fidelity, and is prone to failure when there are modeling errors. In this work, we propose OSC for Adaptation and Robustness (OSCAR), a data-driven variant of OSC that compensates for modeling errors by inferring relevant dynamics parameters from online trajectories. OSCAR decomposes dynamics learning into task-agnostic and task-specific phases, decoupling the dynamics dependencies of the robot and the extrinsics due to its environment. This structure enables robust zero-shot performance under out-of-distribution and rapid adaptation to significant domain shifts through additional finetuning. We evaluate our method on a variety of simulated manipulation problems, and find substantial improvements over an array of controller baselines. For more results and information, please visit https://cremebrule.github.io/oscar-web/
Assessment of clinical continuity strategies offered by dual-degree training programs in the USA
No full textBackground:
Integration of clinical skills during graduate training in dual-degree programs remains a challenge. The present study investigated the availability and self-perceived efficacy of clinical continuity strategies for dual-degree trainees preparing for clinical training.
Methods:
Survey participants were MD/DO-PhD students enrolled in dual-degree-granting institutions in the USA. The response rate was 95% of 73 unique institutions surveyed, representing 56% of the 124 MD-PhD and 7 DO-PhD recognized training programs. Respondents were asked to indicate the availability and self-perceived efficacy of each strategy.
Results:
Reported available clinical continuity strategies included clinical volunteering (95.6%), medical grand rounds (86.9%), mentored clinical experiences (84.2%), standardized patients/ practice Objective Structured Clinical Examinations (OSCEs) (70.3%), clinical case reviews (45.9%), clinical journal clubs (38.3%), and preclinical courses/review sessions (37.2%). Trainees rated standardized patients (µ = 6.98 ± 0.356), mentored clinical experiences (µ = 6.94 ± 0.301), clinical skills review sessions (µ = 6.89 ± 0.384), preclinical courses/review sessions (µ = 6.74 ± 0.482), and clinical volunteering (µ = 6.60 ± 0.369), significantly (p < 0.050) higher than clinical case review (µ = 5.34 ± 0.412), clinical journal club (µ = 4.75 ± 0.498), and medicine grand rounds (µ = 4.45 ± 0.377). Further, 84.4% of respondents stated they would be willing to devote at least 0.5–1 hour per week to clinical continuity opportunities during graduate training.
Conclusion:
Less than half of the institutions surveyed offered strategies perceived as the most efficacious in preparing trainees for clinical reentry, such as clinical skills review sessions. Broader implementation of these strategies could help better prepare dual-degree students for their return to clinical training