Toward Imaging Defect-Mediated Energy Transfer between Single Nanocrystal Donors and Single Molecule Acceptors
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
SEARCH · Engineering Papers
Results for “Super-resolution”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Biased localization of actin binding proteins by actin filament conformation
The assembly of actin filaments into distinct cytoskeletal structures plays a critical role in cell physiology, but how proteins localize differentially to these structures within a shared cytoplasm remains unclear. Here, we show that the actin-binding domains of accessory proteins can be sensitive to filament conformational changes. Using a combination of live cell imaging and in vitro single molecule binding measurements, we show that tandem calponin homology domains (CH1–CH2) can be mutated to preferentially bind actin networks at the front or rear of motile cells. We demonstrate that the binding kinetics of CH1–CH2 domain mutants varies as actin filament conformation is altered by perturbations that include stabilizing drugs and other binding proteins. These findings suggest that conformational changes of actin filaments in cells could help to direct accessory binding proteins to different actin cytoskeletal structures through a biophysical feedback loop.
42 ENGINEERING↗
Imaging a terahertz superfluid plasmon in a two-dimensional superconductor
The superconducting gap defines the fundamental energy scale for the emergence of dissipationless transport and collective phenomena in a superconductor. In layered high-temperature cuprate superconductors, in which the Cooper pairs are confined to weakly coupled two-dimensional (2D) copper–oxygen (CuO 2 ) planes, terahertz (THz) spectroscopy at subgap millielectronvolt (meV) energies has provided crucial insights into the collective superfluid response perpendicular to the superconducting layers. However, within the CuO 2 planes, the collective superfluid response manifests as plasmonic charge oscillations at energies far exceeding the superconducting gap, obscured by strong dissipation. Here, in this study, we present spectroscopic evidence of a below-gap, 2D superfluid plasmon in few-layer Bi 2 Sr 2 CaCu 2 O 8+x and spatially resolve its deeply subdiffractive THz electrodynamics. By placing the superconductor in the near field of a spintronic THz emitter, we reveal this distinct resonance—absent in bulk samples and observed only in the superconducting phase—and determine its plasmonic nature by mapping the geometric anisotropy and dispersion. Crucially, these measurements offer a direct view of the momentum-dependent and frequency-dependent superconducting transition in two dimensions.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Label-free nanoscopy of cell metabolism by ultrasensitive reweighted visible stimulated Raman scattering
Nanoscopic imaging of cell metabolism is hindered by the incompatibility of small metabolites with fluorescent dyes and the limited resolution of imaging mass spectrometry. We present ultrasensitive reweighted visible stimulated Raman scattering (URV-SRS), a label-free vibrational nanoscopy technique that enables multiplexed detection of metabolic nanostructures within cells. We developed an extensively chirped spectral focusing visible SRS microscope that achieves a detection limit of 4,000 molecules and introduced a self-supervised learning-based denoiser to robustly suppress non-independent SRS noise by over 7.2 dB. The instrumentation-based signal enhancement and computation-based noise suppression synergistically improved the detection sensitivity by 50 times over near-infrared SRS. Leveraging this enhanced sensitivity, we further pushed the resolution to nanoscopic levels by introducing Fourier reweighting to amplify sub-100 nm spatial frequencies previously overwhelmed by noise. Validated by Fourier ring correlation, URV-SRS achieves a lateral resolution of 86 nm in cellular imaging. Here, we applied URV-SRS to elucidate the reprogramming of metabolic nanostructures associated with virus replication in Vero E6 host cells and to compositionally delineate subcellular fatty acid synthesis in engineered Escherichia coli, demonstrating its capability towards nanoscopic spatial metabolomics.
59 BASIC BIOLOGICAL SCIENCES↗
Sneaking in SpyCatcher using cell penetrating peptides for in vivo imaging
Abstract In vivo imaging of protein complexes is a powerful method for understanding the underlying biological function of these key biomolecules. Though the engineering of small, high affinity nanobodies have become more prevalent, the off-rates of these tags may result in incomplete or partial labeling of proteins in live cells. The SpyCatcher003 and SpyTag split protein system allow for irreversible, covalent binding to a short target peptide unlike nanobody-affinity based probes. However, delivering these tags into a cell without disrupting its normal function is a key challenge. Cell penetrating peptides (CPPs) are short peptide sequences that facilitate the transduction of otherwise membrane-impermeable ‘cargo’ , such as proteins, into cells. Here we report on our efforts to engineer and characterize CPP-SpyCatcher003 fusions as modular imaging probes. We selected three CPPs, CUPID, Pentratin, and pVEC, to engineer fusion protein probes for superresolution microscopy, with the aim to eliminate prior permeabilization treatments that could introduce imaging artifacts. We find that fusing the CPP sequences to SpyCatcher003 resulted in dimer and multimer formation as determined by size exclusion chromatography, dynamic light scattering, and SDS resistant dimers on SDS-PAGE gels. By isolating and labeling the monomeric forms of the engineered protein, we show these constructs retained their ability to bind SpyTag and all three CPP sequences remain membrane active, as assessed by CD spectroscopy in the presence of SDS detergent. Using fluorescence and super resolution Lattice structured illumination microscopy (Lattice SIM) imaging we show that the CPPs did not enhance uptake of SpyCatcher by E. coli, however with Caulobacter crescentus cells, we show that Penetratin, and to a lesser degree CUPID, does enhance uptake. Our results demonstrate the ability of the CPP-SpyCatcher003 to label targets within living cells, providing the groundwork for using split protein systems for targeted in vivo imaging.
59 BASIC BIOLOGICAL SCIENCES↗
Ferrimagnetic spin waves in honeycomb and triangular layers of Mn{sub 3}Si{sub 2}Te{sub 6}.
A detailed analysis of the ferrimagnetic ground state of Mn 3 Si 2 Te 6 has been performed using inelastic neutron scattering. Although the proposed valence of the nominal Mn 2+ ions would have quenched orbital angular momentum, a significant exchange anisotropy exists in Mn 3 Si 2 Te 6 . This apparent exchange anisotropy is a manifestation of a weak spin-orbit coupling in the layered material. We employ a detailed simulation of the spin-wave spectrum coupling traditional refinement of dispersion parameters to image analysis techniques, while including Monte Carlo simulations of the instrumental resolution to accurately identify the exchange couplings to the third nearest neighbor. An independent validation of our results is made by comparing our final Hamiltonian to heat capacity measurements.
Sala, G.↗
Deep Hierarchical Super Resolution for Scientific Data
We present a novel technique for hierarchical super resolution (SR) with neural networks (NNs), which upscales volumetric data represented with an octree data structure to a high-resolution uniform gridwith minimal seam artifacts on octree node boundaries. Our method uses existing state-of-the-art SR models and adds flexibility to upscale input data with varying levels of detail across the domain, instead of only uniform grid data that are supported in previous approaches.The key is to use a hierarchy of SR NNs, each trained to perform 2x SR between two levels of detail, with a hierarchical SR algorithm that minimizes seam artifacts by starting from the coarsest level of detail and working up.We show that our hierarchical approach outperforms baseline interpolation and hierarchical upscaling methods, and demonstrate the usefulness of our proposed approach across three use cases including data reduction using hierarchical downsampling+SR instead of uniform downsampling+SR, computation savings for hierarchical finite-time Lyapunov exponent field calculation, and super-resolving low-resolution simulation results for a high-resolution approximation visualization.
97 MATHEMATICS AND COMPUTING↗
Development of Strong Anaerobic Fluorescent Reporters for Clostridium acetobutylicum and Clostridium ljungdahlii Using HaloTag and SNAP-tag Proteins
One of the biggest limitations in the study and engineering of anaerobic Clostridium organisms is the lack of strong fluorescent reporters capable of strong and real-time fluorescence. Recently, we developed a strong fluorescent reporter system for Clostridium organisms based on the FAST protein. Here, we report the development of two new strong fluorescent reporter systems for Clostridium organisms based on the HaloTag and SNAP-tag proteins, which produce strong fluorescent signals when covalently bound to fluorogenic ligands. These new fluorescent reporters are orthogonal to the FAST ligands and to each other, allowing for simultaneous labeling and visualization. We used HaloTag and SNAP-tag to label the strictly anaerobic organisms Clostridium acetobutylicum and Clostridium ljungdahlii. We have also identified a new strong promoter for protein expression in C. acetobutylicum, based on the phosphotransacetylase gene (pta) from C. ljungdahlii. Furthermore, the HaloTag and the SNAP-tag, in combination with the previously described FAST system, were successfully used to measure cell populations in bacterial mixed cultures and showed the simultaneous orthogonal labeling of HaloTag and SNAP-tag together with the FAST protein reporter. Finally, we show the expression of recombinant fusion protein of FAST and the ZapA division protein (from C. acetobutylicum) in C. ljungdahlii. The availability of multiple strong fluorescent reporters is a major addition to the genetic toolkit of Here, Clostridium and other anaerobes that will lead to better understanding of these unique organisms.
59 BASIC BIOLOGICAL SCIENCES↗
Optimality of Gradient-MUSIC for Spectral Estimation
We introduce the Gradient-MUSIC algorithm for estimating the unknown frequencies and amplitudes of a nonharmonic signal from noisy time samples. While the classical MUSIC algorithm performs a computationally expensive search over a fine grid, Gradient-MUSIC is significantly more efficient and eliminates the need for discretization over a fine grid by using optimization techniques. It coarsely scans the 1D landscape to find initialization simultaneously for all frequencies followed by parallelizable local refinement via gradient descent. We also analyze its performance when the noise level is sufficiently small and the signal frequencies are separated by at least 8π/m, where π/m is the standard resolution of this problem. Even though the 1D landscape is nonconvex, we prove a global convergence result for Gradient-MUSIC: coarse scanning provably finds suitable initialization and gradient descent converges at a linear rate. In addition to convergence results, we also upper bound the error between the true signal frequencies and amplitudes with those found by Gradient-MUSIC. For example, if the noise has $\ell^\infty$ norm at most ϵ, then the frequencies and amplitudes are recovered up to error at most Cϵ/m and Cϵ respectively, which are minimax optimal in m and ϵ. Our theory can also handle stochastic noise with performance guarantees under nonstationary independent Gaussian noise. Our main approach is a comprehensive geometric analysis of the landscape, a perspective that has not been explored before.
97 MATHEMATICS AND COMPUTING↗