Crystallographic snapshots of ternary complexes of thermophilic secondary alcohol dehydrogenase from
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Dinh, Tung↗
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Structural complexity of snapshots of two-dimensional Fermi-Hubbard systems
The development of quantum gas microscopy for two-dimensional optical lattices has provided an unparalleled tool to study the Fermi-Hubbard model (FHM) with ultracold atoms. Spin-resolved projective measurements, or snapshots, have played a significant role in quantifying correlation functions, theory verification, and thus the uncovering of underlying physical phenomena such as antiferromagnetism at commensurate filling on bipartite lattices and other charge and spin correlations, as well as dynamical properties at various densities. Here we employ a recent concept, the multiscale structural complexity, and show that when computed for the snapshots (of single spin species, local moments, or total density) it can provide a theory-free property, immediately accessible to experiments. Specifically, after benchmarking results for Ising and $XY$ models, we study the structural complexity of snapshots of the repulsive FHM in the two-dimensional square lattice as a function of doping and temperature. We generate projective measurements using determinant quantum Monte Carlo and compare their complexities against those from the experiment. We demonstrate that these complexities are linked to relevant physical observables such as the entropy and double occupancy. Their behaviors capture the development of correlations and relevant length scales in the system. Furthermore, we provide an open-source code in python which can be implemented into data analysis routines in experimental settings for the square lattice.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
SNAPSHOT USA 2020: A second coordinated national camera trap survey of the United States during the COVID-19 pandemic
Managing wildlife populations in the face of global change requires regular data on the abundance and distribution of wild animals, but acquiring these over appropriate spatial scales in a sustainable way has proven challenging. Here, in this study, we present the data from Snapshot USA 2020, a second annual national mammal survey of the USA. This project involved 152 scientists setting camera traps in a standardized protocol at 1485 locations across 103 arrays in 43 states for a total of 52,710 trap-nights of survey effort. Most (58) of these arrays were also sampled during the same months (September and October) in 2019, providing a direct comparison of animal populations in 2 years that includes data from both during and before the COVID-19 pandemic. All data were managed by the eMammal system, with all species identifications checked by at least two reviewers. In total, we recorded 117,415 detections of 78 species of wild mammals, 9236 detections of at least 43 species of birds, 15,851 detections of six domestic animals and 23,825 detections of humans or their vehicles. Spatial differences across arrays explained more variation in the relative abundance than temporal variation across years for all 38 species modeled, although there are examples of significant site-level differences among years for many species. Temporal results show how species allocate their time and can be used to study species interactions, including between humans and wildlife. These data provide a snapshot of the mammal community of the USA for 2020 and will be useful for exploring the drivers of spatial and temporal changes in relative abundance and distribution, and the impacts of species interactions on daily activity patterns. There are no copyright restrictions, and please cite this paper when using these data, or a subset of these data, for publication.
54 ENVIRONMENTAL SCIENCES↗
Inferring Stochastic Rates from Heterogeneous Snapshots of Particle Positions
Many imaging techniques for biological systems—like fixation of cells coupled with fluorescence microscopy—provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics they intend to capture. In this study, these snapshot observations contain no information about individual trajectories, but still encode information about movement and demographic dynamics, especially when combined with a well-motivated biophysical model. The relationship between spatially evolving populations and single-moment representations of their collective locations is well-established with partial differential equations (PDEs) and their inverse problems. However, experimental data is commonly a set of locations whose number is insufficient to approximate a continuous-in-space PDE solution. Here, motivated by popular subcellular imaging data of gene expression, we embrace the stochastic nature of the data and investigate the mathematical foundations of parametrically inferring demographic rates from snapshots of particles undergoing birth, diffusion, and death in a nuclear or cellular domain. Toward inference, we rigorously derive a connection between individual particle paths and their presentation as a Poisson spatial process. Using this framework, we investigate the properties of the resulting inverse problem and study factors that affect quality of inference. One pervasive feature of this experimental regime is the presence of cell-to-cell heterogeneity. Rather than being a hindrance, we show that cell-to-cell geometric heterogeneity can increase the quality of inference on dynamics for certain parameter regimes. Altogether, the results serve as a basis for more detailed investigations of subcellular spatial patterns of RNA molecules and other stochastically evolving populations that can only be observed for single instants in their time evolution.
59 BASIC BIOLOGICAL SCIENCES↗
Energy Snapshot - Trinidad and Tobago
This profile provides a snapshot of the energy landscape of Trinidad and Tobago, a two-island nation located off the coast of Venezuela. Trinidad and Tobago's electricity rates are some of the lowest in the Caribbean at approximately $0.05 per kilowatt-hour (kWh), well below the regional average of $0.34/kWh.
Caribbean islands↗
Energy Snapshot - Guadeloupe
This profile provides a snapshot of the energy landscape of Guadeloupe, an overseas region of France located in the eastern Caribbean Sea. Guadeloupe has set a target to achieve 100% energy independence by 2030. As of 2018, 21% of Guadeloupe's electricity was generated by renewable energy.
44 EE - Strategic Programs, Energy Transition Init↗
Signaling snapshots of a serotonin receptor activated by the prototypical psychedelic LSD
Serotonin (5-hydroxytryptamine [5-HT]) 5-HT2-family receptors represent essential targets for lysergic acid diethylamide (LSD) and all other psychedelic drugs. Although the primary psychedelic drug effects are mediated by the 5-HT 2A serotonin receptor (HTR2A), the 5-HT 2B serotonin receptor (HTR2B) has been used as a model receptor to study the activation mechanisms of psychedelic drugs due to its high expression and similarity to HTR2A. Here, in this study, we determined the cryo-EM structures of LSD-bound HTR2B in the transducer-free, Gq-protein-coupled, and β-arrestin-1-coupled states. These structures provide distinct signaling snapshots of LSD’s action, ranging from the transducer-free, partially active state to the transducer-coupled, fully active states. Insights from this study will both provide comprehensive molecular insights into the signaling mechanisms of the prototypical psychedelic LSD and accelerate the discovery of novel psychedelic drugs.
60 APPLIED LIFE SCIENCES↗
Crystallographic Snapshots of Pre- and Post-Lanthanide Halide Hydrolysis─Reaction Products Captured by the 4-Amino-1,2,4-triazole Ligand
Reactions of lanthanide(III) chloride salts with 4-amino-1,2,4-triazole (4-NH 2 -1,2,4-Triaz) in azole melts have led to the isolation of both hydrolysis and non-hydrolysis products in the same synthesis with the inclusion of a variety of ligands, anions, and water, allowing us to capture crystallographic snapshots of different forms and intermediate hydrolysis fragments. The structural studies reported here include anhydrous and hydrated nonhydrolyzed complexes which were isolated alongside hydrolysis products giving oxide/hydroxide lanthanide(III) dimers, tetramers, and ultimately hexamers. The compounds isolated include [Nd 2 Cl 6 (μ 2 -4-NH 2 -1,2,4-Triaz) 4 (4-NH 2 -1,2,4-Triaz) 2 ], [Ce 2 Cl 4 (μ 2 -Cl) 2 (μ 2 -4-NH 2 -1,2,4-Triaz) 4 ] n , [Ce 2 (µ 2 -Cl) 4 (µ 2 -OH) 2 (µ 2 -4-NH 2 -1,2,4-Triaz) 2 ] n , [Ln 4 Cl 4 (µ 2 -Cl) 4 (µ 3 -OH) 4 (µ 2 -4-NH 2 -1,2,4-Triaz) 4 ] n •2nH 2 O (Ln = Ce, Nd), and [Ce 6 Cl 6 (µ 6 -O 0.5 )(µ 3 -Cl 0.5 ) 4 (µ 3 -Cl 0.75 ) 3 (µ 3 -OH) 0.75 (µ 2 -4-NH 2 -1,2,4-Triaz) 12 ((OH 2 ) 0.25 ) 2 ] 2 [CeCl 6 ][Cl 9 ]•xH 2 O. In all complexes all lanthanide atoms are pairwise connected via one or more 4-NH2-1,2,4-Triaz ligands and sometimes additional Cl - anions.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Snapshot multispectral imaging using a diffractive optical network
Abstract Multispectral imaging has been used for numerous applications in e.g., environmental monitoring, aerospace, defense, and biomedicine. Here, we present a diffractive optical network-based multispectral imaging system trained using deep learning to create a virtual spectral filter array at the output image field-of-view. This diffractive multispectral imager performs spatially-coherent imaging over a large spectrum, and at the same time, routes a pre-determined set of spectral channels onto an array of pixels at the output plane, converting a monochrome focal-plane array or image sensor into a multispectral imaging device without any spectral filters or image recovery algorithms. Furthermore, the spectral responsivity of this diffractive multispectral imager is not sensitive to input polarization states. Through numerical simulations, we present different diffractive network designs that achieve snapshot multispectral imaging with 4, 9 and 16 unique spectral bands within the visible spectrum, based on passive spatially-structured diffractive surfaces, with a compact design that axially spans ~72 λ m , where λ m is the mean wavelength of the spectral band of interest. Moreover, we experimentally demonstrate a diffractive multispectral imager based on a 3D-printed diffractive network that creates at its output image plane a spatially repeating virtual spectral filter array with 2 × 2 = 4 unique bands at terahertz spectrum. Due to their compact form factor and computation-free, power-efficient and polarization-insensitive forward operation, diffractive multispectral imagers can be transformative for various imaging and sensing applications and be used at different parts of the electromagnetic spectrum where high-density and wide-area multispectral pixel arrays are not widely available.
36 MATERIALS SCIENCE↗
Retrieving functional pathways of biomolecules from single-particle snapshots
Abstract A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands. The functional motions differ substantially from those inferred from static structures in the nature of conformationally active structural domains, the sequence and extent of conformational motions, and the way allosteric signals are transduced within and between domains. Our approach highlights the importance of combining experiment, advanced data analysis, and molecular simulations.
59 BASIC BIOLOGICAL SCIENCES↗
Energy landscapes from cryo-EM snapshots: a benchmarking study
Abstract Biomolecules undergo continuous conformational motions, a subset of which are functionally relevant. Understanding, and ultimately controlling biomolecular function are predicated on the ability to map continuous conformational motions, and identify the functionally relevant conformational trajectories. For equilibrium and near-equilibrium processes, function proceeds along minimum-energy pathways on one or more energy landscapes, because higher-energy conformations are only weakly occupied. With the growing interest in identifying functional trajectories, the need for reliable mapping of energy landscapes has become paramount. In response, various data-analytical tools for determining structural variability are emerging. A key question concerns the veracity with which each data-analytical tool can extract functionally relevant conformational trajectories from a collection of single-particle cryo-EM snapshots. Using synthetic data as an independently known ground truth, we benchmark the ability of four leading algorithms to determine biomolecular energy landscapes and identify the functionally relevant conformational paths on these landscapes. Such benchmarking is essential for systematic progress toward atomic-level movies of continuous biomolecular function.
59 BASIC BIOLOGICAL SCIENCES↗
Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism
Abstract DNA glycosylase MutY plays a critical role in suppression of mutations resulted from oxidative damage, as highlighted by cancer-association of the human enzyme. MutY requires a highly conserved catalytic Asp residue for excision of adenines misinserted opposite 8-oxo-7,8-dihydroguanine (OG). A nearby Asn residue hydrogen bonds to the catalytic Asp in structures of MutY and its mutation to Ser is an inherited variant in human MUTYH associated with colorectal cancer. We captured structural snapshots of N146S Geobacillus stearothermophilus MutY bound to DNA containing a substrate, a transition state analog and enzyme-catalyzed abasic site products to provide insight into the base excision mechanism of MutY and the role of Asn. Surprisingly, despite the ability of N146S to excise adenine and purine (P) in vitro, albeit at slow rates, N146S-OG:P complex showed a calcium coordinated to the purine base altering its conformation to inhibit hydrolysis. We obtained crystal structures of N146S Gs MutY bound to its abasic site product by removing the calcium from crystals of N146S-OG:P complex to initiate catalysis in crystallo or by crystallization in the absence of calcium. The product structures of N146S feature enzyme-generated β-anomer abasic sites that support a retaining mechanism for MutY-catalyzed base excision.
59 BASIC BIOLOGICAL SCIENCES↗
Modulating ion-binding at macromolecular interfaces during (bio)mineralization: A snapshot review for calcium carbonate and calcium phosphate systems
Abstract Local environments have strict influence over (bio)mineralization in calcifying systems. This snapshot review discusses recent insights into the roles of Ca 2+ -macromolecule interactions on the nucleation of calcium carbonate and calcium phosphate minerals. Experimental findings combined with simulations/modeling are providing breakthrough information and raising important questions for future studies. The emerging picture is that both nucleation and growth are driven by local ordering of ions and water about the macromolecule interface, rather than broader properties or molecular class. Tuning macromolecular properties at the atomic scale thus provides opportunities for highly specific controls on mineralization; however, many limitations and challenges remain. We highlight studies employing in-situ atomic force microscopy (AFM) and transmission electron microscopy (TEM) to observe crystallization processes on or near macromolecular substrates. As the distribution and ability of these techniques increases, fundamental studies integrating experimental and computational methods will be crucial to inform a broad range of applications. Graphical abstract
Knight, Brenna M. (ORCID:0000000244000067)↗
HAMscope: a snapshot Hyperspectral Autofluorescence Miniscope for real-time molecular imaging
We introduce HAMscope, a compact, snapshot hyperspectral autofluorescence miniscope that enables real-time, label-free molecular imaging in a wide range of biological systems. By integrating a thin polymer diffuser into a widefield miniscope, HAMscope spectrally encodes each frame and employs a probabilistic deep learning framework to reconstruct 30-channel hyperspectral stacks (452-703 nm) or directly infer molecular composition maps from single images. A scalable multi-pass U-Net architecture with transformer-based attention and per pixel uncertainty estimation enables high spatio-spectral fidelity (mean absolute error ∼0.0048) at video rates. While initially demonstrated in plant systems, including lignin, chlorophyll, and suberin imaging in intact poplar and cork tissues, the platform is readily adaptable to other applications such as neural activity mapping, metabolic profiling, and histopathology. We show that the system generalizes to out-of-distribution tissue types and supports direct molecular mapping without the need for spectral unmixing. HAMscope establishes a general framework for compact, uncertainty-aware spectral imaging that combines minimal optics with advanced deep learning, offering broad utility for real-time biochemical imaging across neuroscience, environmental monitoring, and biomedicine.
59 BASIC BIOLOGICAL SCIENCES↗
System and method for x-ray compatible 2D streak camera for a snapshot multiframe imager
The present disclosure is directed to a snapshot multiframe imager having an aperture element having at least one aperture, an adjacently positioned random mask, an imaging element and a computer. The random mask has a plurality of micron scale apertures and receives light passing through the aperture element, which represents the spatial information from the scene being imaged, and generates a plurality of image frames encoded in a spatial domain. The imaging element may operate in a drift-scan mode receives the encoded image frames and generates a streaked pattern of electrons representing a plurality of images of the scene at a plurality of different times. The computer analyzes the streaked pattern of electrons and mathematically reconstructs the plurality of images.
Dayton, Matthew S.↗
Anguilla Energy Snapshot 2020
This fact sheet is an update of Energy Transitions Initiative Islands series energy profile for Anguilla.
ETI, Energy Transitions Initiative, Anguilla, Snap↗
Grenada Energy Snapshot 2020
This fact sheet is an update of Energy Transitions Initiative Islands series energy profile for Grenada.
ETI, Energy Transitions Initiative, Islands, Snaps↗
Guadeloupe Energy Snapshot 2020
This fact sheet is an update of Energy Transitions Initiative Islands series energy profile for Guadeloupe.
ETI, Energy Transitions Initiative, Islands, Snaps↗