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At least 343 records · Page 19

A global metagenomic map of urban microbiomes and antimicrobial resistance

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

59 BASIC BIOLOGICAL SCIENCES↗

Multi-fidelity Uncertainty Quantification for Homogenization Problems in Structure-Property Relationships from Crystal Plasticity Finite Elements

Crystal plasticity finite element method (CPFEM) has been an integrated computational materials engineering (ICME) workhorse to study materials behaviors and structure-property relationships for the last few decades. These relations are mappings from the microstructure space to the materials properties space. Due to the stochastic and random nature of microstructures, there is always some uncertainty associated with materials properties, for example, in homogenized stress-strain curves. For critical applications with strong reliability needs, it is often desirable to quantify the microstructure-induced uncertainty in the context of structure-property relationships. However, this uncertainty quantification (UQ) problem often incurs a large computational cost because many statistically equivalent representative volume elements (SERVEs) are needed. In this article, we apply a multi-level Monte Carlo (MLMC) method to CPFEM to study the uncertainty in stress-strain curves, given an ensemble of SERVEs at multiple mesh resolutions. By using the information at coarse meshes, we show that it is possible to approximate the response at fine meshes with a much reduced computational cost. We focus on problems where the model output is multi-dimensional, which requires us to track multiple quantities of interest (QoIs) at the same time. In conclusion, our numerical results show that MLMC can accelerate UQ tasks around 2.23x, compared to the classical Monte Carlo (MC) method, which is widely known as ensemble average in the CPFEM literature.

36 MATERIALS SCIENCE↗

Species- and site-specific genome editing in complex bacterial communities

Knowledge of microbial gene functions comes from manipulating the DNA of individual strains in isolation from their natural communities. While this approach to microbial genetics has been foundational, its requirement for culturable microorganisms has left the majority of microbes and their interactions genetically unexplored. Here, we describe a generalizable strategy for editing the genomes of specific organisms within microbial communities. We identified genetically tractable bacteria within a community using Environmental Transformation Sequencing (ET-Seq), an approach in which non-targeted transposon integrations are mapped and quantified following community delivery. We next developed and used DNA-editing All-in-one RNA-guided CRISPR-Cas Transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-Seq, enabling organism- and locus-specific genetic manipulation within the community context. To illustrate the utility of our approach, we selectively edited closely related strains, measured gene fitness, and enriched targeted members within soil and infant gut microbiota. These results establish a new paradigm for targeted community editing relevant to research and applications on medical, agricultural, and industrial microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

Integrated lipidomic and proteomic profiling reveals metabolic network disruption by SARS-CoV-2 variants

The rapid evolution of SARS-CoV-2 has produced myriad viral strains with increasing transmissibility and capacity for immune evasion. While effective vaccination campaigns have reduced the fatalities associated with SARS-CoV-2, infections continue, and a detailed understanding of how this virus manipulates host biochemical pathways remains elusive. We asked both whether the patterns of host lipid rewiring remained consistent across variants and whether the changes in the abundance of lipid classes are related to changes in the expression of the enzymes involved in their biosynthesis. We compared global nontargeted lipidomics on A549-ACE2 cells infected with the delta variant (B.1.617.2), or the omicron (B.1.1.529) variant to our previous results of global nontargeted lipidomics on A549-ACE2 cells infected with the original WA1 strain and further performed quantitative proteomics to assess changes in the host proteome. We found that metabolic rewiring, both on the lipid and the enzymatic level, is remarkably consistent across all three variants. We further mapped changes in the expression of host metabolic enzymes, linking enzyme expression to alterations in the abundance of specific lipids during infection. This analysis identified key proteins related to virus-mediated changes in lipid abundance, including fatty acid synthase (FASN), lysosomal acid lipase (LIPA), and ORMDL, a regulator of sphingolipid biosynthesis. These integrated lipidomic and proteomic experiments shed light on the importance of the complex network of host metabolism networks that support SARS-CoV-2 infection and suggest that lipid metabolism may be a promising avenue for uncovering conserved therapeutic targets.

SARS-CoV-2↗

PVDF-based backsheet cracking: Mapping in situ phase evolution by X-ray scattering

One of the most common polymers used in commercial photovoltaic backsheets is polyvinylidene fluoride (PVDF). However, recent reports have shown the potential for PVDF-based backsheets to crack and fail prematurely. Previous work has suggested that polymer phase changes play a role in the failure mechanism. Here, in situ wide-angle X-ray scattering maps are used to show that α- to β-phase transformations occur at crack tips in aged PVDF-based backsheets under stretching. Substantial β-phase formation is shown to be associated with strain hardening. In addition, our work demonstrates that β-phase formation is not required for crack growth and only occurs at crack tips when plastic deformation of the PVDF polymer has occurred. In conclusion, the anisotropy in the strength of aged PVDF-based backsheets is linked to the lack of β-phase formation when strain is applied to aged backsheets in the transverse direction.

14 SOLAR ENERGY↗

Interface-driven magnetic anisotropy in relaxed La 0.7 Sr 0.3 CrO 3 /La 0.7 Sr 0.3 MnO 3 heterostructures on MgO

We investigate the structural and magnetic properties of La 0.7 Sr 0.3 CrO 3 /La 0.7 Sr 0.3 MnO 3 (LSMO) heterostructures grown on (001)-oriented MgO by molecular beam epitaxy. Due to the large film-substrate lattice mismatch, strain relaxation is found to occur within the first 2–3 unit cells (uc) of the film as evidenced by reflection high energy electron diffraction and high-resolution synchrotron x-ray reciprocal space mapping. Furthermore, we find that the presence of the LSCO spacer and capping layers leads to ferromagnetism in ultra-thin LSMO layers with thicknesses of the order of 2 uc with the magnetic easy axis oriented in the film plane. Net magnetic moments of 1.4 and 2.4 μ B /Mn are measured for (2 uc LSCO/2 uc LSMO) and (2 uc LSCO/4 uc LSMO) superlattices, respectively, by superconducting quantum interference device magnetometry. The effective magnetic anisotropy of the relaxed (2 uc LSCO/4 uc LSMO) heterostructure is found to be an order of magnitude higher than bulk LSMO highlighting the critical role of interfacial interactions in tuning magnetic anisotropy at complex oxide interfaces.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Report of the panel on plate motion and deformation, section 2

Given here is a panel report on the goals and objectives, requirements and recommendations for the investigation of plate motion and deformation. The goals are to refine our knowledge of plate motions, study regional and local deformation, and contribute to the solution of important societal problems. The requirements include basic space-positioning measurements, the use of global and regional data sets obtained with space-based techniques, topographic and geoid data to help characterize the internal processes that shape the planet, gravity data to study the density structure at depth and help determine the driving mechanisms for plate tectonics, and satellite images to map lithology, structure and morphology. The most important recommendation of the panel is for the implementation of a world-wide space-geodetic fiducial network to provide a systematic and uniform measure of global strain.

Bock, Yehuda↗

Engineering regulatory networks for complex phenotypes in E. coli

Regulatory networks describe the hierarchical relationship between transcription factors, associated proteins, and their target genes. Regulatory networks respond to environmental and genetic perturbations by reprogramming cellular metabolism. Here we design, construct, and map a comprehensive regulatory network library containing 110,120 specific mutations in 82 regulators expected to perturb metabolism. We screen the library for different targeted phenotypes, and identify mutants that confer strong resistance to various inhibitors, and/or enhanced production of target compounds. These improvements are identified in a single round of selection, showing that the regulatory network library is universally applicable and is convenient and effective for engineering targeted phenotypes. The facile construction and mapping of the regulatory network library provides a path for developing a more detailed understanding of global regulation in E. coli , with potential for adaptation and use in less-understood organisms, expanding toolkits for future strain engineering, synthetic biology, and broader efforts.

59 BASIC BIOLOGICAL SCIENCES↗

Deformation of Polycrystalline MgO Up to 8.3 GPa and 1270 K: Microstructures, Dominant Slip-Systems, and Transition to Grain Boundary Sliding

Ferropericlase is the second most abundant mineral in the Earth’s lower mantle and its mechanical properties have a strong influence on the rheology of this region. Here, we deform polycrystalline MgO, the magnesium end-member of ferropericlase, at conditions ranging from 1.6 to 8.3 GPa and 875–1,270 K. We analyse the flow laws and microstructures of the recovered samples using electron microscopy and compare our observations with predictions from the literature. We identify a first mechanism for samples deformed at 1,270 K, attributed to a regime controlled by grain boundary sliding accommodated by diffusion, and characterized by a small grain size, an absence of texture, and no intracrystalline deformation. At 1,070 K and below, the deformation regime is controlled by dislocations. The samples show a more homogeneous grain size distribution, significant texture, and intracrystalline strains. In this regime, deformation is controlled by the ⟨110⟩{110} slip system and a combined ⟨110⟩{110} and ⟨110⟩{100} slip, depending on pressure and temperature. Based on these results, we propose an updated deformation map for polycrystalline MgO at mantle conditions. The implications for ferropericlase and seismic observations in the Earth’s lower mantle are discussed.

Ledoux, Estelle Elisa↗

Measuring Shock Stage of ltokawa Regolith Grains by Electron Back-Scattered Diffraction and Synchrotron X-Ray Diffraction

We have been analyzing Itokawa samples in order to definitively establish the degree of shock experienced by the regolith of asteroid Itokawa, and to devise a bridge between shock determinations by standard light optical petrography, crystal structures as determined by electron and X-ray diffraction techniques. We are making measurements of olivine crystal structures and using these to elucidate critical regolith impact processes. We use electron back-scattered diffraction (EBSD) and synchrotron X-ray diffraction (SXRD). We are comparing the Itokawa samples to L and LL chondrite meteorites chosen to span the shock scale experienced by Itokawa, specifically Chainpur (LL3.4, Shock Stage 1), Semarkona (LL3.00, S2), Kilabo (LL6, S3), NWA100 (L6, S4) and Chelyabinsk (LL5, S4). In SXRD we measure the line broadening of olivine reflections as a measure of shock stage. In this presentation we concentrate on the EBSD work. We employed JSC's Supra 55 variable pressure FEG-SEM and Bruker EBSD system. We are not seeking actual strain values, but rather indirect strain-related measurements such as extent of intra-grain lattice rotation, and determining whether shock state "standards" (meteorite samples of accepted shock state, and appropriate small grain size) show strain measurements that may be statistically differentiated, using a sampling of particles (number and size range) typical of asteroid regoliths. Using our system we determined that a column pressure of 9 Pa and no C-coating on the sample was optimal. We varied camera exposure time and gain to optimize mapping performance, concluding that 320x240 pattern pixilation, frame averaging of 3, 15 kV, and low extractor voltage yielded an acceptable balance of hit rate (>90%), speed (11 fps) and map quality using an exposure time of 30 ms (gain 650). We found that there was no strong effect of step size on Grain Orientation Spread (GOS) and Grain Reference Orientation Deviation angle (GROD-a) distribution; there was some effect on grain average Kernel Average Misorientation (KAM) (reduced with smaller step size for the same grain), as expected. We monitored GOS, Maximum Orientation Spread (MOS) and GROD-a differences between whole olivine grains and sub-sampled areas, and found that there were significant differences between the whole grain dataset and subsets, as well as between subsets, likely due to sampling-related "noise". Also, in general (and logically) whole grains exhibit greater degrees of cumulative lattice rotation. Sampling size affects the apparent strain character of the grain, at least as measured by GOS, MOS and GROD-a. There were differences in the distribution frequencies of GOS and MOS between shock stages, and in plots of MOS and GOS vs. grain diameter. These results are generally consistent with those reported this year. However, it is unknown whether the differences between samples of different shock states exceeds the clustering of these values to the extent that shock stage determinations can still be made with confidence. We are investigating this by examination of meteorites with higher shock stage 4 to 5. Our research will improve our understanding of how small, primitive solar system bodies formed and evolved, and improve understanding of the processes that determine the history and future of habitability of environments on other solar system bodies. The results will directly enrich the ongoing asteroid and comet exploration missions by NASA and JAXA, and broaden our understanding of the origin and evolution of small bodies in the early solar system, and elucidate the nature of asteroid and comet regolith.

Zolensky, Michael↗

Elemental segregation to lattice defects in the CrMnFeCoNi high-entropy alloy during high temperature exposures

The influence of small plastic pre-strains on the elevated-temperature stability and microstructure of the equiatomic CrMnFeCoNi FCC solid solution is investigated. Particular attention is given to whether any of the alloy elements segregate to individual dislocations. To that end, CrMnFeCoNi samples were first deformed in tension at room temperature to plastic strains of 0.2 and 2.3%, and subsequently annealed at 973 K for 800 hours. The pre-strains activated planar slip of 1/2<110>-type dislocations on {111}-type glide planes. Interactions of this planar slip with special Σ3 grain boundaries formed a large number of dislocation segments with a <110>-type crystallographic orientation suitable for a credible end-on analysis of dislocation cores in HR-STEM. The cores of the 1/2<110> dislocations pushed up against the investigated grain boundaries were found to be close to the compact configuration. Within the sensitivity of the Super-X EDS mapping, no concentration gradient was detected near dislocations that would indicate enrichment at dislocation cores of any of the elemental constituents of the alloy after the pre-deformation and annealing. However, a Cr-rich tetragonal sigma phase nucleated and grew at grain boundary triple junctions during this anneal, processes that were not accelerated by the enhanced dislocation density present after pre-strain. A clear chromium gradient was observed in the Cr-depleted zones near grain boundaries suggesting that Cr transport occurred by relatively slow diffusion from the bulk to the grain boundaries and then by relatively fast diffusion along the grain boundaries to the precipitates. Accompanying the Cr depletion near grain boundaries is a simultaneous Ni and Mn enrichment, which promotes formation of the L1 0 NiMn phase that is observed on the grain boundaries after prolonged annealing.

36 MATERIALS SCIENCE↗

Rational Selection of Transition-Metal Oxide Electrocatalysts from Structure Electronic Structure-Activity Relations: The Role of Defects, Strain, and Sub-Surface Layering

This BES research investigates the physicochemical properties of metal oxides and how they affect electrocatalytic functionalities. The goal is to develop a predictive framework for realizing top-performing electrocatalytic materials for energy-critical reactions. The hypothesis is that well-defined thin films allow detailed mapping of structural-activity relationships because flat surfaces are more straightforward to characterize. Furthermore, the well-defined nature of thin-film metal oxides allows precise tuning of structural and chemical variables for structure-activity-relationship mapping. The proposed research has two technical objectives. The first is to experimentally assess whether the binding energies of surface oxygen can serve as an activity descriptor for oxygen electrocatalysis on metal oxides and then how to control them by tuning the structure and chemical variables. The second is to find the rate-limiting process in oxygen electrocatalysis and other small-molecule reactions. Similar mechanistic insights have been developed on well-defined platinum surfaces but not yet on oxides. This research addresses this gap and uses electrochemistry and X-ray photoemission spectroscopy to study oxide surface chemistry. The obtained insights are collectively analyzed to reveal how the oxides’ structural and chemical variables affect kinetics and can be used to design more active electrocatalysts for energy-critical reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Range and Performance Optimized Version of the Computer-Aided Speckle Interferometry Algorithm for Real-Time Displacement-Strain Field Monitoring

Abstract This work presents an optimized implementation of the Computer-Aided Speckle Interferometry algorithm which enables full-field determination of displacements and strains on commodity Graphics Processing Units at high resolution and frame rates. By combining careful control of the average speckle size in a laser speckle pattern with a simple sampling rate conversion scheme, a compact representation of the optical speckle is achieved. This allows for optimal use of Graphics Processing Unit architecture with robust range extension. The optimal mapping of the Computer-Aided Speckle Interferometry algorithm to Graphics Processing Unit architecture is shown in detail, and a straightforward method for disambiguating large displacements is illustrated. Lastly, this paper demonstrates a two-step subimage-tapering modification to the original algorithm that enables robust range enhancement while maintaining resolution. Results from numerical simulations on synthetic speckle patterns are shown, and runtime performance metrics are provided, with performance ranging up to 60 frames per second in some cases. The method is suitable for interactive experimental mechanics research, process and testing or any application where real-time high-resolution displacement-strain monitoring is needed. A .NET Framework class library enabling the incorporation of the algorithm into 3rd -party applications is available for download.

42 ENGINEERING↗

Multimodal Nanoscale Mapping of Local Structure and CO 2 Adsorption in Metal–Organic Frameworks

Diamine functionalization of the metal−organic framework Mg 2 (dobpdc) (dobpdc 4− = 4,4′-dioxidobiphenyl-3,3′-dicarboxylate) significantly enhances its selectivity for CO 2 capture from flue gases and air. The structure and CO 2 capacity of such materials are typically assessed using bulk techniques that rely on averaging signal over large ensembles of unit cells, obscuring local heterogeneities, such as variations in CO 2 occupancy across individual nanocrystals. To resolve this limitation, we demonstrate a multimodal, nanoscale characterization of Mg 2 (dobpdc) appended with 1,3-diaminopropane. By employing recently developed characterization techniques at progressively smaller length scales, we uncover insights from correspondingly smaller populations of unit cells. First, we use parallel-beam 3D electron diffraction (3D ED) to identify a prominent expansion in lattice parameters upon desorption of CO 2 , as observed at the level of single nanocrystals. Second, we use convergent-probe 4D scanning transmission electron microscopy (4D-STEM) to quantify associated differences in lattice strain as a function of gas loading and diamine appending. These measurements sample small subvolumes within individual nanocrystals. Finally, we apply infrared scattering scanning near-field optical microscopy (IR s- SNOM) to confirm variable CO 2 chemisorption across adsorption sites at the surface of single nanocrystals. This multimodal, multiscale approach allows us to map heterogeneity within individual nanocrystals. Collectively, these findings emphasize the importance of local, nanoscale characterization of metal−organic frameworks in revealing previously unresolvable features that impact their performance.

Karstens, Sarah L. [University of California, Berk↗

Frustrated Ising charge correlations in the kagome metal ScV 6 Sn 6

Here we resolve the real-space nature of the high-temperature, short-range charge correlations in the kagome metal ScV 6 Sn 6 . Diffuse scattering appears along a frustrated wave vector q H = ($\frac{1}{3}, \frac{1}{3}, \frac{1}{2}$) at temperatures far exceeding the charge order T CO = 92 K, preempting long-range charge order with wave vectors along q$_{\bar{K}}$ = ($\frac{1}{3}, \frac{1}{3}, \frac{1}{3}$). Using a combination of real space and reciprocal space analysis, we resolve the nature of the interactions between the primary out-of-plane Sc-Sn chain instability and the secondary strain-mediated distortion of the in-plane V kagome network. Finally, a minimal model of the diffuse scattering data reveals a high-temperature, short-ranged "zig-zag" phase of in-plane correlations that maps to a frustrated triangular lattice Ising model with antiferromagnetic interactions and provides a real-space understanding of the origin frustrated charge order in this material.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Transmission of Human Influenza A Virus in Pigs Selects for Adaptive Mutations on the HA Gene

Influenza A viruses (FLUAV) cause respiratory diseases in many host species, including humans and pigs. The spillover of FLUAV between swine and humans has been a concern for both public health and the swine industry. With the emergence of the triple reassortant internal gene (TRIG) constellation, establishment of human-origin FLUAVs in pigs has become more common, leading to increased viral diversity. However, little is known about the adaptation processes that are needed for a human-origin FLUAV to transmit and become established in pigs. Here, we generated a reassortant FLUAV (VIC11pTRIG) containing surface gene segments from a human FLUAV strain and internal gene segments from the 2009 pandemic and TRIG FLUAV lineages and demonstrated that it can replicate and transmit in pigs. Sequencing and variant analysis identified three mutants that emerged during replication in pigs, which were mapped near the receptor binding site of the hemagglutinin (HA). The variants replicated more efficiently in differentiated swine tracheal cells compared to the virus containing the wildtype human-origin HA, and one of them was present in all contact pigs. These results show that variants are selected quickly after replication of human-origin HA in pigs, leading to improved fitness in the swine host, likely contributing to transmission.

60 APPLIED LIFE SCIENCES↗

A Germline-Targeting Chimpanzee SIV Envelope Glycoprotein Elicits a New Class of V2-Apex Directed Cross-Neutralizing Antibodies

HIV-1 and its SIV precursors share a broadly neutralizing antibody (bNAb) epitope in variable loop 2 (V2) at the envelope glycoprotein (Env) trimer apex. Here, we tested the immunogenicity of germ line-targeting versions of a chimpanzee SIV (SIVcpz) Env in human V2-apex bNAb heavy-chain precursor-expressing knock-in mice and as chimeric simian-chimpanzee immunodeficiency viruses (SCIVs) in rhesus macaques (RMs). Trimer immunization of knock-in mice induced V2-directed NAbs, indicating activation of V2-apex bNAb precursor-expressing mouse B cells. SCIV infection of RMs elicited high-titer viremia, potent autologous tier 2 neutralizing antibodies, and rapid sequence escape in the canonical V2-apex epitope. Six of seven animals also developed low-titer heterologous plasma breadth that mapped to the V2-apex. Antibody cloning from two of these animals identified multiple expanded lineages with long heavy chain third complementarity determining regions that cross-neutralized as many as 7 of 19 primary HIV-1 strains, but with low potency. Negative stain electron microscopy (NSEM) of members of the two most cross-reactive lineages confirmed V2 targeting but identified an angle of approach distinct from prototypical V2-apex bNAbs, with antibody binding either requiring or inducing an occluded-open trimer. Probing with conformation-sensitive, nonneutralizing antibodies revealed that SCIV-expressed, but not wild-type SIVcpz Envs, as well as a subset of primary HIV-1 Envs, preferentially adopted a more open trimeric state. These results reveal the existence of a cryptic V2 epitope that is exposed in occluded-open SIVcpz and HIV-1 Env trimers and elicits cross-neutralizing responses of limited breadth and potency.

59 BASIC BIOLOGICAL SCIENCES↗

Cross-family and phage-specific gene requirements for Klebsiella infection revealed by scalable RB-TnSeq genetic screens.

Bacteriophages are being cataloged at an accelerating pace and are recognized as key players in nutrient and energy cycling across ecosystems. Yet the bacterial genetic determinants that govern phage-host specificity and infection success remain poorly understood, particularly in clinically and ecologically important genera such as Klebsiella where prior receptor characterization has been almost entirely limited to capsulated strains. Here we used a randomly barcoded, genome-wide, loss-of-function transposon mutant library (RB-TnSeq) of Klebsiella sp. M5al, a naturally acapsular, nitrogen-fixing rhizobacterium, to generate the first systematic, cross-family map of phage receptor gene dependencies in Klebsiella. Challenging the library against 25 double-stranded DNA phages spanning five families in 213 parallel assays, we identified 42 bacterial genes associated with phage infection, of which 15 had no prior association with phage infection in any bacterial system. Disruption of surface receptor biosynthesis genes conferred cross-resistance across multiple phage families, while intracellular gene disruptions had predominantly phage-specific effects. Clonal validation of eight genes confirmed LPS outer core biosynthesis genes as primary receptor determinants alongside additional host factors spanning outer membrane transport, cofactor biosynthesis, and two-component signaling. Comparative analysis across all 25 phages revealed that phage genus rather than family is the stronger predictor of host gene dependency profiles, a finding with direct implications for the functional annotation of uncharacterized phage isolates and rational phage cocktail design. Together, these findings provide a community resource for linking phage genomic diversity to functional host interaction space in this ecologically and clinically important genus.

Gittrich, Marissa R↗