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At least 109 records · Page 6

Enhancers in Plant Development, Adaptation and Evolution

Understanding plant responses to developmental and environmental cues is crucial for studying morphological divergence and local adaptation. Gene expression changes, governed by cis-regulatory modules (CRMs) including enhancers, are a major source of plant phenotypic variation. However, while genome-wide approaches have revealed thousands of putative enhancers in mammals, far fewer have been identified and functionally characterized in plants. This review provides an overview of how enhancers function to control gene regulation, methods to predict DNA sequences that may have enhancer activity, methods utilized to functionally validate enhancers and the current knowledge of enhancers in plants, including how they impact plant development, response to environment and evolutionary adaptation.

59 BASIC BIOLOGICAL SCIENCES↗

Operando XAS and DFT Uncover Structure-Performance Relationships in Re/TiO 2 for Selective CO 2 Hydrogenation to Methanol

The conversion of CO 2 into value-added chemicals, such as methanol, offers a promising pathway toward a renewable energy future. However, a precise kinetic control and a highly selective catalyst are necessary to overcome the thermodynamic preference for CO 2 hydrogenation to methane. Rhenium-based catalysts, particularly Re/TiO 2 , demonstrate high activity and selectivity for methanol under high-pressure conditions. For example, at 100 bar and 200 °C, a methanol selectivity of 97−99% was obtained. Catalysts with 1 wt % Re and 5 wt % Re/ TiO 2 were used to study the effect of cluster sizes. At 250 °C, the 1 wt % catalyst achieves 97% selectivity at 23% conversion, whereas 5 wt % Re/TiO 2 achieves 74% selectivity at 40% conversion, corresponding to a drop in space-time yield from 65 to 16 g CH 3 OH ·g Re −1 ·h −1 , respectively. X-ray absorption spectroscopy provided insights into the structure of the active sites, while density functional theory calculations revealed the effects of cluster size on the energy barriers for H 2 activation, CH 3 OH dissociation, and CH 3 OH desorption, all of which directly influence conversion and selectivity. These results underscore the importance of balancing cluster size for optimal catalyst performance and provide insights into the design of efficient and selective catalysts for renewable methanol production.

XAS↗

Curiosity driven exploration to optimize structure–property learning in microscopy

Rapidly determining structure–property correlations in materials is an important challenge in better understanding fundamental mechanisms and greatly assists in materials design. In microscopy, imaging data provides a direct measurement of the local structure, while spectroscopic measurements provide relevant functional property information. Deep kernel active learning approaches have been utilized to rapidly map local structure to functional properties in microscopy experiments, but are computationally expensive for multi-dimensional and correlated output spaces. Here, we present an alternative lightweight curiosity algorithm which actively samples regions with unexplored structure–property relations, utilizing a deep-learning based surrogate model for error prediction. We show that the algorithm outperforms random sampling for predicting properties from structures, and provides a convenient tool for efficient mapping of structure–property relationships in materials science.

36 MATERIALS SCIENCE↗

Investigation of the cesium activation of Ga⁢N photocathodes by low-energy electron microscopy

Low-energy electron microscopy (LEEM) was performed on p-Ga⁢N samples during in situ cesium deposition. LEEM images of electron reflectivity recorded as a function of the incident electron energy at different Cs coverages allowed to spatially resolve the evolution of the local work function (WF) during the activation process. While the average WF drops by more than 3 eV, the local WF remains quite uniform across the surface throughout the activation process. Maximum fluctuations of less than 0.2 eV were observed in the WF maps for Cs coverage of a fraction of a monolayer. These fluctuations are mainly related to the surface topography, in particular, to the atomic steps’ structure, which replicates the substrate miscut. Apart from these weak spatial fluctuations, no Cs clusters that would induce strong local WF contrast were observed at the scale of the 20-nm resolution of the measurements. These observations agree with the simple model of semiconductor activation to negative electron affinity that describes the formation of a dipole layer as responsible for the lowering of the WF. Additionally, at complete Cs coverage, the WF becomes fully homogeneous over the surface, smoothing out features originating from defects and topography.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A Unified Wireless Charger, On-Board Charger, and Auxiliary Power Module for Electric Vehicle Charging Systems

This paper proposes a unified electric vehicle (EV) charging architecture that integrates wireless power transfer (WPT), an on-board charger (OBC), and an auxiliary power module (APM) within a single architecture. By sharing a multi-functional magnetic structure and active switch bridges, the proposed topology eliminates additional transformers and converter stages, reducing hardware complexity and improving power density. A multipurpose magnetic design achieves magnetic decoupling among the WPT, OBC, and APM functions while maintaining the required coupling for each mode. Through electrical reconfiguration, the WPT operates as an LCC-S converter, whereas the OBC and APM operate as dual-active-bridge (DAB) converters. The system supports multiple operating modes, including simultaneous high-voltage and lowvoltage battery charging. Finite-element and circuit simulations verify the magnetic characteristics and system operation, demonstrating the feasibility of the proposed unified architecture for EV charging applications.

Jo, Cheolhui [ORNL] (ORCID:0000000322692434)↗

Optimizing CO 2 -Loaded Aqueous Amine Solutions for Higher Electrocatalytic CO 2 Reduction Activity

The activity of aqueous-based carbon dioxide reduction (CO 2 R) reactions is often limited by the solubility of CO 2 . The addition of amines can increase the total dissolved carbon in water through the formation of bicarbonate and carbamate species, which has been used to a great effect to capture CO 2 from dilute streams. Here, in this study, we explore the effect of 12 primary and secondary amines of varying Brønsted basicity, steric profile, and hydrogen-bonding capabilities on the aqueous CO 2 R to CO activity of a molecular Ni(cyclam)Cl 2 catalyst with a Hg electrode. Addition of some of the amines results in greater activity and selectivity for CO production compared to equivalent aqueous solutions without added amines. Under optimal conditions (0.4 M 3-amino-propionitrile), there is an over sevenfold increase in partial current density and greater selectivity for CO compared to equivalent conditions with no amine. Interestingly, the increase in activity did not correlate to any single property across the 12 amines. To elucidate the effect of the amine additives on catalysis, we used vapor–liquid equilibrium modeling (VLE), 13 C NMR spectroscopy, and computational analysis to determine the carbon speciation of the solutions. These results indicate that for amines without ethylalcohol functionalities, CO 2 R activity correlates with carbamate concentration, which is in turn governed by amine basicity and steric effects. However, this correlation does not persist for amines with ethylalcohol functionalities, which can form more stable carbamates through intramolecular-hydrogen bonding. These studies demonstrate that amine additives can enhance aqueous CO 2 R activity and selectivity and describe amine properties that lead to these higher performance metrics.

Amines↗

Editorial: Structure and mechanism of microbial membrane active transporters

Membrane active transporters play essential roles in microbial physiology. They couple energy transduction to conformational changes that drive translocation of nutrients, substrates and ions, as well as molecular communication. The structure and function of microbial membrane active transporters are highly diverse. Typical examples include the primary active transporters in the ATP-binding cassette (ABC) superfamily (Thomas and Tampé, 2020; Davidson et al., 2008; Locher et al., 2002), the secondary active transporters in the Major Facilitator Superfamily (MFS) (Drew et al., 2021; Kaback and Guan, 2019), and the ligand-gated porins in the TonB-dependent transporter (TBDT) family (Klebba et al., 2021). As structural, proteogenomic, and computational methods advance, active transporters are increasingly recognized as dynamic molecular machines whose mechanisms can now be visualized and modeled with remarkable precision, building on decades of biochemical and biophysical discovery that established the foundations of this field. The transporter studies recruited in this Research Topic provide us with new insights into the field including structure-function of sugar transporters in yeast, structural prediction and classification of ABC complexes in Bacillus subtilis, Type VI Secretion System (T6SS) in Bacteroides fragilis, amino acids uptake in Escherichia coli and bacterial spore germination.

mechanism↗

Impacts of A‐Site Composition on the Cation Dissolution‐Mediated Surface Restructuring of Layered Nickelate Oxide Electrocatalysts During Alkaline Oxygen Evolution Reaction

The oxygen evolution reaction (OER) is a key anodic counter‐reaction for electrochemical production of fuels and chemicals. It is hindered by sluggish four‐electron transfer kinetics requiring highly oxidative operating potentials to achieve commercially relevant rates. NiFeO x H y electrocatalysts are among the most promising for OER in alkaline electrolytes. The Ni(OH) 2 /NiOOH redox couple has been reported as the active phase in Ni‐based electrocatalysts; however, its activity is often hindered by deactivation arising from the formation of OER‐inactive insulating species. Limited strategies exist for mitigating this deactivation. This study aims to address this by interrogating the evolution of OER active sites as a function of precatalyst composition and structural properties using a series of layered, crystalline Ni‐based Ruddlesden–Popper (RP) oxides (A 2 NiO 4+δ ). In situ evolution of the active NiO x H y surface is probed through Ni‐site OER turnover frequency analysis, and electrochemical impedance spectroscopy coupled with scanning transmission electron microscopy. We show that the stability of layered nickelate oxide electrocatalysts is governed by the dynamic competition between cation dissolution and Ni‐site reversibility, which can be tuned through the A‐site composition of RP oxides. These findings yield insights toward engineering OER oxide precatalysts that optimize the stability of in situ‐generated OER active phases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Polymer connectivity governs electrophotocatalytic activity in the solid state

The reductive functionalization of inert substrates such as chloroarenes is a critical yet challenging transformation relevant to both environmental remediation and organic synthesis. Combining electricity and light is an emerging strategy to access the deeply reducing potentials required for single electron transfer to chloroarenes, yet this approach is limited by poor stability and mechanistic ambiguity. Here, in this work, we demonstrate heterogeneous electrophotocatalysis using redox-active rylene diimide polymers for the reduction of chloroarenes. We find that the electrophotocatalytic activity varies dramatically as a function of the rylene diimide and the redox-inactive polymer backbone. In particular, a flexible, non-conjugated perylenediimide polymer outperforms all other tested electrophotocatalysts. Transient absorption spectroscopy reveals that precomplexation between the doubly reduced perylenediimide and the haloarene substrate is key to productive catalysis. Overall, this work highlights heterogeneous electrophotocatalysis using insoluble redox-active organic materials and provides critical structure–property insights into solid-state electrophotocatalytic activity, informing the development of next-generation materials for sustainable synthesis.

electrocatalysis↗

A global database of soil microbial phospholipid fatty acids and enzyme activities

Abstract Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.

Science & Technology - Other Topics↗

Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers

ABSTRACT Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non‐canonical regions where, for example, the nucleic‐acid backbone bends, deviating from an A‐form helix geometry, or a base forms a non‐standard hydrogen bond (not a Watson‐Crick base pair). These bends and non‐canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.

Biochemistry & Molecular Biology↗

A Perspective into Operando Methods for Probing Catalytic Interfaces

Rational design of electrocatalysts for (photo)electrochemical (PEC) processes like hydrogen and oxygen evolution and CO2 reduction reactions is aided by the recent improvements in capabilities of operando measurements, where morphology, composition, and/or function are probed during active catalysis. Through operando microscopy and spectroscopy, structure, catalytic microenvironment, oxidation state, adsorbates, and products can be measured to gain a better understanding of catalyst behavior and suggest possible improvements. Visualizing evolving catalyst morphologies, surface compositions, and electrochemical behavior also helps address many fundamental research questions for a better understanding of catalytic mechanisms. Correlating morphology with chemical identity or functional behavior using a variety of innovative microscopy methods is particularly promising for guiding development of next generation catalysts, and there are also many recent examples of using AI and robotics tools to innovate and speed development. In this Perspective, advances made over the past few years in operando imaging of catalysts relevant to solar fuels will be explored, followed by an outlook on technological developments in instrumentation, sample design, and computational power that may be applied to this field.

Catalysts↗

Lost and Found: Rediscovering Microbiome-Associated Phenotypes that Reshape Agricultural Sustainability

Modern agriculture faces an urgent need to improve nutrient use efficiency while reducing environmental impacts. Here, we show that ancestral traits controlling rhizosphere microbiome functions can be reintroduced into elite maize through targeted teosinte introgressions. Using near-isogenic lines, we mapped microbiome-associated phenotypes (MAPs) derived from teosinte that suppress nitrification and denitrification—key microbial processes contributing to nitrogen loss. These introgressions altered root exudate chemistry, resulting in distinct microbial assemblies and enhanced nitrogen retention. We identified candidate loci and metabolites responsible for suppressive activity and demonstrated their functional effects in vitro. Our findings reveal a genetic and biochemical basis for rewilding microbiome-mediated ecosystem services in crops, offering a scalable path toward sustainable nutrient management in global agriculture. ---- These maize root exduate metabolomics data are a subset of this larger project and make up a phenotyping for candidate lines.

Favela, Alonso [School of Plant Sciences, Universi↗

Lost and found: Rediscovering microbiome-associated phenotypes that reshape agricultural sustainability

Modern agriculture faces an urgent need to improve nutrient use efficiency while reducing environmental impacts. Here, we show that ancestral traits controlling rhizosphere microbiome functions can be reintroduced into elite maize through targeted teosinte introgressions. Using near-isogenic lines, we mapped microbiome-associated phenotypes (MAPs) derived from teosinte that suppress nitrification and denitrification—key microbial processes contributing to nitrogen loss. These introgressions altered root exudate chemistry, resulting in distinct microbial assemblies and enhanced nitrogen retention. We identified candidate loci and exudate metabolites responsible for suppressive activity and demonstrated their functional effects in vitro. These findings reveal a genetic and biochemical basis for rewilding microbiome-mediated ecosystem services in crops, offering a scalable path toward sustainable nutrient management in global agriculture.

60 APPLIED LIFE SCIENCES↗

Exsolution of NiCo alloys over Ruddlesden-Popper perovskite for mild electrochemical synthesis of ammonia on protonic ceramic electrochemical cells

Ammonia synthesis from renewable energies on protonic ceramic electrochemical cells (PCECs) shows great potential. The primary challenges in ammonia synthesis on PCECs include sluggish catalytic activity, competition from the hydrogen evolution reaction, and unsatisfactory durability of the cathode, which is the active site of ammonia generation. Here, in this study, we report an elaborate design of the cathode with an intended formula of Pr 4 Ni 1.79 Co 1.2R u 0.01 O 10-δ , where NiCo alloy nanoparticles are exsolved from Ruddlesden-Popper perovskite substrates after the reduction in 5 % H 2 /Ar at 400 °C for 1 h, for electrocatalysis of the nitrogen reduction reaction to ammonia. The host material Pr 4 Ni 1.8 Co 1.2 O 10-δ with embeddable layered structure and stability was deliberately chosen to fix the Ru cation and maximize the catalytic activity of NiCo. Also, density functional theory calculations suggest that Ru doping provides an optimal balance between structural stability and redox activity, facilitating the controlled exsolution of NiCo nanoparticles and enhancing catalytic performance. As a result, the composite electrode with exsolved NiCo alloy and abundant oxygen vacancies on fuel-electrode-supported PCECs achieves a superior electrochemical activity towards ammonia synthesis: a peak ammonia formation rate of 27.84 μg h −1 cm −2 and excellent Faradaic efficiencies of 62.6 % at 350 °C.

30 DIRECT ENERGY CONVERSION↗

Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils

Ecosystems are shaped by communities of microorganisms whose niches and impacts depend on functional profiles influenced by gene gains and losses. Culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, but quantitative understanding of these dynamics in natural systems remains limited. Here we develop and apply a systematic, meta-omic framework to investigate MGEs in a complex natural system using an 8-year soil time series collected at Stordalen Mire, in Sweden’s thawing permafrost margin. In this climate-critical peatland, we identify ~2.1 million MGE recombinases across 89 microbial phyla and assess ecological distributions, affected functions, past mobility and current activity. This revealed an active mobilome that shapes natural genetic diversity via differential impacts on major phyla and affects a wide range of functions, including metabolic genes involved in carbon flux and nutrient cycling. These findings and this analytic framework suggest avenues towards a better understanding of MGE diversity, activity, mobility and impacts across ecosystems.

Biological and medical sciences↗

Distinguishing Desirable and Undesirable Reactions in Multicomponent Systems for Redox Activation of the Uranyl Ion

Although it has been established that covalent functionalization of the U–O bonds in the uranyl dication (UO 2 2+ ) generally requires use of strong reductants and electrophiles, little work has examined how interactions between the individual reaction components could affect final outcomes in solution. Here, the patterns of such reactivity have been studied in a UO 2 2+ -containing model system supported by a workhorse pentadentate ligand, 2,2′-[(methylimino)bis(2,1-ethanediylnitrilomethylidyne)]bis-phenol. Oxo activation and functionalization have been tested with (i) electrochemical and chemical reduction, and (ii) coordinating and noncoordinating solvents. In acetonitrile, uranyl reduction was achieved cleanly, but treatment of the reduced species with tris(pentafluorophenyl)borane (BCF) resulted in a mixture of products arising from direct electron transfer to BCF. In dichloromethane (CH 2 Cl 2 ), electrochemical reduction of uranyl was achieved cleanly, but clean chemical reactivity was inaccessible. Despite these challenges, one trinuclear and oxo-deficient uranium-containing product was crystallized from CH 2 Cl 2 solution and characterized; thus, desirable electrophilic reactivity can proceed to some degree in CH 2 Cl 2 with BCF. Computational studies were used to investigate the properties of the trinuclear uranium product and the changes that could be inducible by further reduction. Here, taken together, the reactivity patterns identified here could inform design of improved systems for actinyl oxo functionalization.

cations↗

Advanced multi-modal mass spectrometry imaging reveals functional differences of placental villous compartments at microscale resolution

The placenta is a complex and heterogeneous organ that links the mother and fetus, playing a crucial role in nourishing and protecting the fetus throughout pregnancy. Integrative spatial multi-omics approaches can provide a systems-level understanding of molecular changes underlying the mechanisms leading to the histological variations of the placenta during healthy pregnancy and pregnancy complications. Herein, we advance our metabolome-informed proteome imaging (MIPI) workflow to include lipidomic imaging, while also expanding the molecular coverage of metabolomic imaging by incorporating on-tissue chemical derivatization (OTCD). The improved MIPI workflow advances biomedical investigations by leveraging state-of-the-art molecular imaging technologies. Lipidome imaging identifies molecular differences between two morphologically distinct compartments of a placental villous functional unit, syncytiotrophoblast (STB) and villous core. Next, our advanced metabolome imaging maps villous functional units with enriched metabolomic activities related to steroid and lipid metabolism, outlining distinct molecular distributions across morphologically different villous compartments. Complementary proteome imaging on these villous functional units reveals a plethora of fatty acid- and steroid-related enzymes uniquely distributed in STB and villous core compartments. Integration across our advanced MIPI imaging modalities enables the reconstruction of active biological pathways of molecular synthesis and maternal-fetal signaling across morphologically distinct placental villous compartments with micrometer-scale resolution.

60 APPLIED LIFE SCIENCES↗