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At least 955 records · Page 53

Cryo-electron tomography provides topological insights into mutant huntingtin exon 1 and polyQ aggregates

Huntington disease (HD) is a neurodegenerative trinucleotide repeat disorder caused by an expanded poly-glutamine (polyQ) tract in the mutant huntingtin (mHTT) protein. The formation and topology of filamentous mHTT inclusions in the brain (hallmarks of HD implicated in neurotoxicity) remain elusive. Using cryo-electron tomography and subtomogram averaging, here we show that mHTT exon 1 and polyQ-only aggregates in vitro are structurally heterogenous and filamentous, similar to prior observations with other methods. Yet, we find filaments in both types of aggregates under ~2 nm in width, thinner than previously reported, and regions forming large sheets. In addition, our data show a prevalent subpopulation of filaments exhibiting a lumpy slab morphology in both aggregates, supportive of the polyQ core model. This provides a basis for future cryoET studies of various aggregated mHTT and polyQ constructs to improve their structure-based modeling as well as their identification in cells without fusion tags.

59 BASIC BIOLOGICAL SCIENCES↗

Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi

Abstract Diverse members of early-diverging Mucoromycota, including mycorrhizal taxa and soil-associated Mortierellaceae, are known to harbor Mollicutes-related endobacteria (MRE). It has been hypothesized that MRE were acquired by a common ancestor and transmitted vertically. Alternatively, MRE endosymbionts could have invaded after the divergence of Mucoromycota lineages and subsequently spread to new hosts horizontally. To better understand the evolutionary history of MRE symbionts, we generated and analyzed four complete MRE genomes from two Mortierellaceae genera: Linnemannia (MRE-L) and Benniella (MRE-B). These genomes include the smallest known of fungal endosymbionts and showed signals of a tight relationship with hosts including a reduced functional capacity and genes transferred from fungal hosts to MRE. Phylogenetic reconstruction including nine MRE from mycorrhizal fungi revealed that MRE-B genomes are more closely related to MRE from Glomeromycotina than MRE-L from the same host family. We posit that reductions in genome size, GC content, pseudogene content, and repeat content in MRE-L may reflect a longer-term relationship with their fungal hosts. These data indicate Linnemannia and Benniella MRE were likely acquired independently after their fungal hosts diverged from a common ancestor. This work expands upon foundational knowledge on minimal genomes and provides insights into the evolution of bacterial endosymbionts.

59 BASIC BIOLOGICAL SCIENCES↗

High-throughput feedback-enabled optogenetic stimulation and spectroscopy in microwell plates

Abstract The ability to perform sophisticated, high-throughput optogenetic experiments has been greatly enhanced by recent open-source illumination devices that allow independent programming of light patterns in single wells of microwell plates. However, there is currently a lack of instrumentation to monitor such experiments in real time, necessitating repeated transfers of the samples to stand-alone analytical instruments, thus limiting the types of experiments that could be performed. Here we address this gap with the development of the optoPlateReader (oPR), an open-source, solid-state, compact device that allows automated optogenetic stimulation and spectroscopy in each well of a 96-well plate. The oPR integrates an optoPlate illumination module with a module called the optoReader, an array of 96 photodiodes and LEDs that allows 96 parallel light measurements. The oPR was optimized for stimulation with blue light and for measurements of optical density and fluorescence. After calibration of all device components, we used the oPR to measure growth and to induce and measure fluorescent protein expression in E. coli . We further demonstrated how the optical read/write capabilities of the oPR permit computer-in-the-loop feedback control, where the current state of the sample can be used to adjust the optical stimulation parameters of the sample according to pre-defined feedback algorithms. The oPR will thus help realize an untapped potential for optogenetic experiments by enabling automated reading, writing, and feedback in microwell plates through open-source hardware that is accessible, customizable, and inexpensive.

59 BASIC BIOLOGICAL SCIENCES↗

A multi-ancestry GWAS of Fuchs corneal dystrophy highlights the contributions of laminins, collagen, and endothelial cell regulation

Fuchs endothelial corneal dystrophy (FECD) is a leading indication for corneal transplantation, but its molecular etiology remains poorly understood. We performed genome-wide association studies (GWAS) of FECD in the Million Veteran Program followed by multi-ancestry meta-analysis with the previous largest FECD GWAS, for a total of 3970 cases and 333,794 controls. We confirm the previous four loci, and identify eight novel loci: SSBP3, THSD7A, LAMB1, PIDD1, RORA, HS3ST3B1, LAMA5, and COL18A1. We further confirm the TCF4 locus in GWAS for admixed African and Hispanic/Latino ancestries and show an enrichment of European-ancestry haplotypes at TCF4 in FECD cases. Among the novel associations are low frequency missense variants in laminin genes LAMA5 and LAMB1 which, together with previously reported LAMC1, form laminin-511 (LM511). AlphaFold 2 protein modeling, validated through homology, suggests that mutations at LAMA5 and LAMB1 may destabilize LM511 by altering inter-domain interactions or extracellular matrix binding. Finally, phenome-wide association scans and colocalization analyses suggest that the TCF4 CTG18.1 trinucleotide repeat expansion leads to dysregulation of ion transport in the corneal endothelium and has pleiotropic effects on renal function.

59 BASIC BIOLOGICAL SCIENCES↗

Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida

Although synthetic biology can produce valuable chemicals in a renewable manner, its progress is still hindered by a lack of predictive capabilities. Media optimization is a critical, and often overlooked, process which is essential to obtain the titers, rates and yields needed for commercial viability. Here, we present a molecule- and host-agnostic active learning process for media optimization that is enabled by a fast and highly repeatable semi-automated pipeline. Its application yielded 60% and 70% increases in titer, and 350% increase in process yield in three different campaigns for flaviolin production in Pseudomonas putida KT2440. Explainable Artificial Intelligence techniques pinpointed that, surprisingly, common salt (NaCl) is the most important component influencing production. The optimal salt concentration is very high, comparable to seawater and close to the limits that P. putida can tolerate. The availability of fast Design-Build-Test-Learn (DBTL) cycles allowed us to show that performance improvements for active learning are rarely monotonous. This work illustrates how machine learning and automation can change the paradigm of current synthetic biology research to make it more effective and informative, and suggests a cost-effective and underexploited strategy to facilitate the high titers, rates and yields essential for commercial viability.

59 BASIC BIOLOGICAL SCIENCES↗

Structure of an anti-PEG antibody reveals an open ring that captures highly flexible PEG polymers

Polyethylene glycol (PEG) is a polymer routinely used to modify biologics and nanoparticles to prolong blood circulation and reduce immunogenicity of the underlying therapeutic. However, several PEGylated therapeutics induce the development of anti-PEG antibodies (APA), leading to reduced efficacy and increased adverse events. Given the highly flexible structure of PEG, how APA specifically bind PEG remains poorly understood. Here, we report a crystal structure illustrating the structural properties and conformation of the APA 6-3 Fab bound to the backbone of PEG. The structure reveals an open ring-like sub-structure in the Fab paratope, whereby PEG backbone is captured and then stabilized via Van der Waals interactions along the interior and exterior of the ring paratope surface. Our finding illustrates a strategy by which antibodies can bind highly flexible repeated structures that lack fixed conformations, such as polymers. This also substantially advances our understanding of the humoral immune response generated against PEG.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The importance of localized modes spectral contribution to thermal conductivity in amorphous polymers

Abstract Polymers are a unique class of materials from the perspective of normal mode analysis. Polymers consist of individual chains with repeating units and strong intra-chain covalent bonds, and amorphous arrangements among chains with weak inter-chain van der Waals and for some polymers also electrostatic interactions. Intuitively, this strong heterogeneity in bond strength can give rise to special features in the constituent phonons, but such effects have not been studied deeply before. Here, we use lattice dynamics and molecular dynamics to perform modal analysis of the thermal conductivity in amorphous polymers. We find an abnormally large population of localized modes in amorphous polymers, which is fundamentally different from amorphous inorganic materials. Contrary to the common picture of thermal transport, localized modes in amorphous polymers are found to be the dominant contributors to thermal conductivity. We find that a significant portion of the localization happens within individual chains, but heat is dominantly conducted when localized modes involve two chains. These results suggest localized modes generally play a key role in thermal transport for different polymers. The results provide an alternative perspective on why polymer thermal conductivity is generally quite low and gives insight into how to potentially change it.

36 MATERIALS SCIENCE↗

X-ray free electron laser heating of water and gold at high static pressure

Probing of reactive materials such as H 2 O ices and fluids at the high pressures and temperatures of planetary interiors is limited by unwanted chemical reactions and confinement failure. Faster experiments can mitigate such issues, but the common approach of adiabatic compression limits the conditions achieved. This study demonstrates a fast experimental strategy for the creation and probing of selected extreme states using static compression coupled with ultrafast X-ray laser heating. Indirect X-ray heating of H 2 O through the use of a gold absorber is evidenced by sample melting inferred from textural changes in the H 2 O diffraction lines and inter-dispersion of gold and H 2 O melts. Coupled with numerical analysis of femtosecond energy absorption, thermal equilibration, and heat transfer, all evidence indicates that temperatures in excess of an electron volt have been reached in the H 2 O at high pressure. Even after repeated heating, samples stayed chemically unchanged from the starting material.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Programmable low-coherence wavefronts for enhanced localization

Engineering the properties of electromagnetic wavefronts has become essential to imaging, wireless security, sensing, and wireless communication. In particular, wavefronts that exhibit low spatial coherence can enable sensing functionalities with high accuracy and low latency. The typical use of such wavefronts cannot take advantage of these possibilities, as they require the ability to dynamically reconfigure the wavefront in a controllable and repeatable fashion, over a broad spectral bandwidth. Here, we propose a new approach for generating broadband reconfigurable wavefronts which not only exhibit low spatial coherence at a particular frequency, but are also decorrelated with the wavefronts simultaneously generated at other frequencies. We demonstrate that this frequency-domain decorrelation is a key feature that, in combination with dynamic reconfigurability, enables localization measurements with an order-of-magnitude improvement in accuracy compared to the state of the art.

36 MATERIALS SCIENCE↗

ALS mutations disrupt self-association between the ubiquilin STI1 hydrophobic groove and internal placeholder sequences

Ubiquilins are molecular chaperones that play multifaceted roles in proteostasis, with point mutations in UBQLN2 leading to altered phase-separation properties and amyotrophic lateral sclerosis (ALS). Our mechanistic understanding of this essential process has been hindered by a lack of structural information on the STI1 domain, which is essential for ubiquilin chaperone activity and phase separation. Here, we present the first crystal structure of a ubiquilin-family STI1 domain bound to a transmembrane domain (TMD), and show that ALS mutations disrupt the STI1-TMD interaction. We further demonstrate that ubiquilins contain multiple conserved internal sequences that bind to the STI1 domain, including the PXX-repeat region that is a hotspot for ALS mutations. We propose that these placeholder sequences prevent solvent exposure of the STI1 hydrophobic groove and contribute to the multivalency that drives ubiquilin phase-separation. Together, this work provides a new paradigm for understanding how STI1 domains modulate ubiquilin chaperone activity and phase separation, and offers insights into the molecular basis of ALS pathogenesis.

Onwunma, Joan [Univ. of Toledo, OH (United States)↗

Real-time process monitoring and automated control for direct ink write 3D printing of frontally polymerizing thermosets

Additive manufacturing (AM) enables the fabrication of complex geometries, yet its application to thermosets remains limited by post-processing requirements. Frontal ring-opening metathesis polymerization (FROMP) offers a promising alternative, enabling energy-efficient, in situ curing of freestanding thermoset structures. This study presents a real-time process monitoring and automated control system for direct ink writing (DIW) of FROMP thermosets. By integrating thermochromic leuco dyes and computer vision, we enable real-time polymerization front tracking, allowing autonomous printing parameter adjustments for consistent geometries across resin formulations. The system’s accuracy was validated against manual tracking, demonstrating precise front velocity detection. Its adaptability was confirmed by printing freestanding mechanical springs with different resins, achieving consistent geometries and mechanical properties despite front velocity variations. These findings highlight the potential of automated DIW control for scalable, repeatable, and material-agnostic 3D printing of thermosets.

Mejia, Edgar Brian [Sandia National Laboratories (↗

Quinonoid vs. aromatic structures of heteroconjugated polymers from oligomer calculations

Conjugated polymers with quinonoid ground states can display low optical band gaps. The design of novel conjugated polymers with quinonoid ground states offers insights into the relative stabilities of aromatic vs. quinonoid structures. In this work, we present parameters such as the quinonoid (Q)/aromatic (A) energy difference, the band gap, and the C–C distances between the repeat units. This study reveals eight new polymers which exist in quinonoid ground state among twenty-nine polymers of varying structural composition that were subject to analysis. We expect that copolymerizing such quinonoid ground state monomers with aromatic ground state monomers will modulate the bandgap of the resulting polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spatial dynamics of lithiation and lithium plating during high-rate operation of graphite electrodes

The principal inhibitor of fast charging lithium ion cells is the graphite negative electrode, where favorable conditions for lithium plating occur at high charge rates, causing accelerated degradation and safety concerns. The local response of graphite, both at the electrode and particle level, when exposed to fast charging conditions of around 6C is not well understood. Consequently, the conditions that lead to the onset of lithium plating, as well as the local dynamics of lithium plating and stripping, have also remained elusive. Here, we use high-speed (100 Hz) pencil-beam X-ray diffraction to repeatedly raster along the depth of a 101 μm thick graphite electrode in 3 μm steps during fast (up to 6C) charge and discharge conditions. Consecutive depth profiles from separator to current collector were each captured in 0.5 seconds, giving an unprecedented spatial and temporal description of the state of the electrode and graphite's staging dynamics during high rate conditions. The electrode is preferentially activated near the separator, and the non-uniformity increases with rate and is influenced by free-energy barriers between graphite's lithiation stages. The onset of lithium plating and stripping was quantified, occurring only within the first 15 μm from the separator. The presence of lithium plating changed the behavior of the underlying graphite, such as causing co-existence of LiC 6 and graphite in the fully discharged state. Finally, the staging behavior of graphite at different rates was quantified, revealing a high dependency on rate and drastic hysteresis between lithiation and delithiation.

25 ENERGY STORAGE↗

Identifying geologic characteristics and operational decisions to meet global carbon sequestration goals

Geologic carbon sequestration is the process of injecting and storing CO 2 in subsurface reservoirs and is an essential technology for global environmental security (e.g., climate change mitigation) and economic security (e.g., CO 2 tax credits). To meet energy, economic, and environmental goals, society will have to identify vast volumes of high-capacity, low-cost, and viable storage reservoirs for sequestering CO 2 . In turn, this requires understanding how major geologic characteristics (such as reservoir depth, thickness, permeability, porosity, and temperature) and design and operational decisions (such as injection well spacing) impact CO 2 injection rates, storage capacity, and economics. Although many numerical simulation tools exist, they cannot repeat the required thousands or millions of simulations to identify ideal reservoir properties and the sensitivity and interaction between geologic parameters and operational decisions. Here, we use SCO 2 T—a fast-running, reduced-order modeling framework—to explore the sensitivity of major geologic parameters and operational decisions to engineering (CO 2 injection rates, plume dimensions, and storage capacities and effectiveness) and costs. Our results show, for the first time, benefits and impacts such as allowing CO 2 plumes to overlap, how different well spacing patterns affect CO 2 sequestration, the effects on costs of including brine treatment and disposal, and the effect of restricting injection rates to 1 MtCO 2 per y based on well limitations. We reveal multiple novel and unintuitive findings including: (i) deeper reservoirs have reduced carbon sequestration costs until injection rates reach 1 MtCO 2 per y, at which point deeper reservoirs become more expensive, (ii) thicker formations allow for increased injection rates and storage capacity, but thickness barely impacts plume areas, (iii) higher geothermal gradients result in reduced sequestration costs, unless brine treatment/disposal costs are included, at which point reservoirs having lower geothermal gradients are more economical because they produce less brine for each unit of injected CO 2 , and (iv) allowing plumes to overlap has a significantly positive impact of increasing storage capacities but has only a small influence on reducing sequestration costs. Altogether, our results illustrate new scientific conclusions to help identify suitable sites to inject and store CO 2 , to help understand the complex interaction between geology and resulting costs, and to help support the pursuit of meeting global sequestration targets.

58 GEOSCIENCES↗

Programmable chiral states in flocks of active magnetic rollers

Inspired by nature, active matter exemplified by self-organization of motile units into macroscopic structures holds great promise for advanced tunable materials capable of flocking, shape-shifting, and self-healing. Active particles driven by external fields have repeatedly demonstrated potential for complex self-organization and collective behavior, yet how to guide the direction of their collective motion largely remains unexplored. Here, we report a system of microscopic ferromagnetic rollers driven by an alternating magnetic field that demonstrates programmable control of the direction of a self-organized coherent vortical motion (i.e., chirality). Facilitated by a droplet confinement, the rollers get synchronized and display either right- or left-handed spontaneous vortical motion, such that their moving direction determines the vortex chirality. Here, we reveal that one can remotely command a flock of magnetic rollers to switch or maintain its chiral state by modulating a phase shift of the sinusoidal magnetic field powering the active rollers. Building on our findings, we realize a self-assembled remotely controlled micro-pump architecture capable of switching the fluid transport direction on demand. Our studies may stimulate new design strategies for directed transport and flocking robotics at the microscale based on active colloids.

36 MATERIALS SCIENCE↗

Influence of NaCl on shape deformation of polymersomes

Polymersomes frequently appear in the literature as promising candidates for a wide range of applications from targeted drug delivery to nanoreactors. From a cell mimetic point of view, it is important to understand the size and shape changes of the vesicles in the physiological environment since that can influence the drug delivery mechanism. In this work we studied the structural features of polymersomes consisting of poly(ethylene glycol)–poly(dimethylsiloxane)–poly(ethylene glycol) at the nanoscopic length scale in the presence of NaCl, which is a very common molecule in the biotic aqueous environment. Here, we used dynamic light scattering (DLS), cryo-TEM, small angle neutron scattering (SANS) and small angle X-ray scattering (SAXS). We observed transformation of polymersomes from spherical to elongated vesicles at low salt concentration and into multivesicular structures at high salt concentration. Model fitting analysis of SANS data indicated a reduction of vesicle radius up to 47% and from the SAXS data we observed an increase in membrane thickness up to 8% and an increase of the PDMS hydrophobic segment up to 11% indicating stretching of the membrane due to osmotic imbalance. Also, from the increase in the interlamellar repeat distance up to 98% under high salt concentrations, we concluded that the shape and structural changes observed in the polymersomes are a combined result of osmotic pressure change and ion–membrane interactions.

36 MATERIALS SCIENCE↗

Investigation of Rh–titanate (ATiO 3 ) interactions on high-surface-area perovskite thin films prepared by atomic layer deposition

Thin, ~1 nm films of CaTiO 3 , SrTiO 3 , and BaTiO 3 were deposited onto MgAl 2 O 4 by Atomic Layer Deposition (ALD) and studied as catalyst supports for Rh. Scanning Transmission Electron Microcopy (STEM) and X-Ray Diffraction (XRD) demonstrated that the films had the perovskite structure and formed uniform coatings stable up to 1073 K. Rh, added by ALD, interacted strongly with CaTiO 3 and somewhat less strongly with SrTiO 3 , while Rh on BaTiO 3 was similar to Rh on unmodified MgAl 2 O 4 . STEM measurements of Rh on CaTiO 3 films showed Rh remained well dispersed after repeated oxidations and reductions at 1073 K; however, the Rh was inactive for CO-oxidation. Rh formed small particles on SrTiO 3 films and was active for CO oxidation after reduction at 1073 K. The reducibility and catalytic activity of Rh/BaTiO 3 /MgAl 2 O 4 were similar to that of Rh/MgAl 2 O 4 . Evidence from CO-TPR, FTIR, and XPS all indicated that the degree of interaction between Rh and the three perovskite films can be ranked in the following order: Rh/CaTiO 3 /MgAl 2 O 4 > Rh/SrTiO 3 /MgAl 2 O 4 > Rh/BaTiO 3 /MgAl 2 O 4 . Here, bulk ex-solution catalysts, synthesized by reduction of ATi 0.98 Rh 0.02 O 3 (A = Ca, Sr, and Ba), were also examined for comparison.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗