3D Structure Research Articles

Architectural Decoration of Bioleached NiFeP Surfaces by Co3O4 Flowers for Efficient Electrocatalytic Hydrogen Generation.

In the quest for sustainable hydrogen production via water electrolysis, the development of high-performance, noble-metal-free catalytic systems is highly desired. Herein, we proposed an innovative strategy for the development of an electrocatalyst by refining the surface characteristics of a NiFeP alloy through microbiological techniques and subsequent enrichment of active sites by tailoring 3D hierarchical flower-like structures with intact and interconnected two-dimensional (2D) Co3O4. The resultant 3D Co3O4@NiFeP-5/24h has a porous structure comprised of intercrossed nanoparticles covering the entirety of the catalytic surface. This design ensures comprehensive electrolyte ion penetration and facilitates the release of gas bubbles while reducing bubble adhesion rates. Remarkably, the Co3O4@NiFeP-5/24h electrode demonstrates superior hydrogen evolution (HER) performance in an alkaline medium, characterized by its high stability, low overpotential (106 mV at a current density of 10 mA cm-2), and reduced Tafel slope (98 mV dec-1). Besides, the minimized interfacial contact resistance among the phases of electrode and electrolyte emphasizes the high HER performance of the 3D Co3O4@NiFeP-5/24h electrode. The innovative design and fabrication strategy employed herein holds significant potential for advancing the field of water-splitting electrocatalysis, offering a promising path toward the rational design and development of noble-metal-free electrocatalysts.

Bee morphology: A skeletomuscular anatomy of Thyreus (Hymenoptera: Apidae).

Although the knowledge of the skeletal morphology of bees has progressed enormously, a corresponding advance has not happened for the muscular system. Most of the knowledge about bee musculature was generated over 50 years ago, well before the digital revolution for anatomical imaging, including the application of microcomputed tomography. This technique, in particular, has made it possible to dissect small insects digitally, document anatomy efficiently and in detail, and visualize these data three dimensionally. In this study, we document the skeletomuscular system of a cuckoo bee, Thyreus albomaculatus and, with that, we provide a 3D atlas of bee skeletomuscular anatomy. The results obtained for Thyreus are compared with representatives of two other bee families (Andrenidae and Halictidae), to evaluate the generality of our morphological conclusions. Besides documenting 199 specific muscles in terms of origin, insertion, and structure, we update the interpretation of complex homologies in the maxillolabial complex of bee mouthparts. We also clarify the complicated 3D structure of the cephalic endoskeleton, identifying the tentorial, hypostomal, and postgenal structures and their connecting regions. We describe the anatomy of the medial elevator muscles of the head, precisely identifying their origins and insertions as well as their homologs in other groups of Hymenoptera. We reject the hypothesis that the synapomorphic propodeal triangle of Apoidea is homologous with the metapostnotum, and instead recognize that this is a modification of the third phragma. We recognize two previously undocumented metasomal muscle groups in bees, clarifying the serial skeletomusculature of the metasoma and revealing shortcomings of Snodgrass' "internal-external" terminological system for the abdomen. Finally, we elucidate the muscular structure of the sting apparatus, resolving previously unclear interpretations. The work conducted herein not only provides new insights into bee morphology but also represents a source for future phenomic research on Hymenoptera.

Molecular Docking of Phytomolecules of Grain Amaranth (Amaranthus hypochondriacus) with AKR1C3Protein Involved in Prostate Cancer in Human Beings

Abstract: This study focuses on exploring how the bioactive compounds found in amaranth— phytol, squalene, and α-tocopherol—could potentially offer medicinal benefits in the context of prostate cancer. The investigation involves a docking study with AKRC13, an important target linked to the control of prostate cancer, aiming to uncover their potential effects against this disease. Costeffective and efficient cancer treatment options are crucial because of the high expenses associated with current cancer therapies as well as their side effects. Amaranth (Amaranthus hypochondriacus) is a pseudocereal crop abundant in squalene, α-tocopherol, and phytol, which shows promising foodbased therapy for various diseases, including cancer. Prostate cancer has been a significant contributor to mortality globally, but the introduction of relugolix has emerged as a crucial therapeutic intervention in its treatment. Hence, this study was conducted to investigate the interactions between grain amaranth bioactive compounds squalene, phytol, and α-tocopherol with AKRC13 protein utilizing a molecular docking approach facilitated by Autodock Vina software. Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB-PDB) (http://www.rcsb.org/) was used for retrieving the 3D crystal structure of the target protein, AKRC13 (PDB ID: 7c7f). The 3D structure of bioactive compounds squalene, phytol, and α-tocopherol were retrieved from the PubChem database, following which Open-Babel was used to change the format from .sdf to .pdb. Furthermore, pharmacokinetics characteristics were also considered along with Lipinski’s rule of five using SwissADME (http://www. Swiss adme.ch/index.php) and pkCSM (http://structure.bioc.cam.ac.uk/pkcsm), indicating their potential as a drug candidate in the initial stage. The potential anticancer properties of the ligands were predicted using PASS software. Following the completion of the docking study, it became evident that α-tocopherol demonstrated the most significant binding energy, followed by squalene and phytol, in comparison to the established drug, relugolix. This implies that the chosen bioactive compounds might possess enzyme-inhibiting properties, indicating their potential for further in vivo anticancer screening using model organisms. The findings serve as stepping stones for advancing the potential use of the discussed bioactive compounds as a potential drug candidate for prostate cancer.

Diversity and selection analyses identify transmission-blocking antigens as the optimal vaccine candidates in Plasmodium falciparum

A highly effective vaccine for malaria remains an elusive target, at least in part due to the under-appreciated natural parasite variation. This study aimed to investigate genetic and structural variation, and immune selection of leading malaria vaccine candidates across the Plasmodium falciparum's life cycle. We analysed 325P.falciparum whole genome sequences from Zambia, in addition to 791 genomes from five other African countries available in the MalariaGEN Pf3k Database. Ten vaccine antigens spanning three life-history stages were examined for genetic and structural variations, using population genetics measures, haplotype network analysis, and 3D structure selection analysis. Among the ten antigens analysed, only three in the transmission-blocking vaccine category display P. falciparum 3D7 as the dominant haplotype. The antigens AMA1, CSP, MSP119 and CelTOS, are much more diverse than the other antigens, and their epitope regions are under moderate to strong balancing selection. In contrast, Rh5, a blood stage antigen, displays low diversity yet slightly stronger immune selection in the merozoite-blocking epitope region. Except for CelTOS, the transmission-blocking antigens Pfs25, Pfs48/45, Pfs230, Pfs47, and Pfs28 exhibit minimal diversity and no immune selection in epitopes that induce strain-transcending antibodies, suggesting potential effectiveness of 3D7-based vaccines in blocking transmission. These findings offer valuable insights into the selection of optimal vaccine candidates against P.falciparum. Based on our results, we recommend prioritising conserved merozoite antigens and transmission-blocking antigens. Combining these antigens in multi-stage approaches may be particularly promising for malaria vaccine development initiatives. Purdue Department of Biological Sciences; Puskas Memorial Fellowship; National Institute of Allergy and Infectious Diseases (U19AI089680).

ScHiCyclePred: a deep learning framework for predicting cell cycle phases from single-cell Hi-C data using multi-scale interaction information

The emergence of single-cell Hi-C (scHi-C) technology has provided unprecedented opportunities for investigating the intricate relationship between cell cycle phases and the three-dimensional (3D) structure of chromatin. However, accurately predicting cell cycle phases based on scHi-C data remains a formidable challenge. Here, we present scHiCyclePred, a prediction model that integrates multiple feature sets to leverage scHi-C data for predicting cell cycle phases. scHiCyclePred extracts 3D chromatin structure features by incorporating multi-scale interaction information. The comparative analysis illustrates that scHiCyclePred surpasses existing methods such as Nagano_method and CIRCLET across various metrics including accuracy (ACC), F1 score, Precision, Recall, and balanced accuracy (BACC). In addition, we evaluate scHiCyclePred against the previously published CIRCLET using the dataset of complex tissues (Liu_dataset). Experimental results reveal significant improvements with scHiCyclePred exhibiting improvements of 0.39, 0.52, 0.52, and 0.39 over the CIRCLET in terms of ACC, F1 score, Precision, and Recall metrics, respectively. Furthermore, we conduct analyses on three-dimensional chromatin dynamics and gene features during the cell cycle, providing a more comprehensive understanding of cell cycle dynamics through chromatin structure. scHiCyclePred not only offers insights into cell biology but also holds promise for catalyzing breakthroughs in disease research. Access scHiCyclePred on GitHub at https:// github.com/HaoWuLab-Bioinformatics/ scHiCyclePred.

Efficient fabrication of 3D bioprinted functional sensory neurons using an inducible Neurogenin-2 human pluripotent stem cell line.

Three-dimensional (3D) tissue models have gained recognition for their improved ability to mimic the native cell microenvironment compared to traditional two-dimensional (2D) models. This progress has been driven by advances in tissue-engineering technologies such as 3D bioprinting, a promising method for fabricating biomimetic living tissues. While bioprinting has succeeded in generating various tissues to date, creating neural tissue models remains challenging. In this context, we present an accelerated approach to fabricate 3D sensory neuron (SN) structures using a transgenic human pluripotent stem cell (hPSC)-line that contains an inducible neurogenin-2 (NGN2) expression cassette. The NGN2 hPSC line was first differentiated to neural crest cell (NCC) progenitors, then incorporated into a cytocompatible GelMA-based bioink for 3D bioprinting. Upregulated NGN2 expression in the bioprinted NCCs resulted in induced SN (iSN) populations that exhibited specific cell markers, with 3D analysis revealing widespread neurite outgrowth through the scaffold volume. Calcium imaging demonstrated functional activity of iSNs, including membrane excitability properties and voltage-gated sodium channel (NaV) activity. This efficient approach to generate 3D bioprinted iSN structures streamlines the development of neural tissue models, useful for the study of neurodevelopment and disease states and offering translational potential.

Analysis of spontaneous ignition of hydrogen-enriched methane in a rectangular tube

This study investigates the spontaneous ignition of high-pressure hydrogen-enriched methane in air within a rectangular tube. A computationally efficient approach has been adopted, utilizing a reduced reaction mechanism and ignition delay model within a 3D Large Eddy Simulation (LES) framework. This approach overcomes the limitations of traditional 1D and 2D simulations with detailed chemistry models, which are unable to accurately reproduce the complex 3D shock wave structures within the tube. The simulated shock wave behavior during 9 MPa hydrogen leakage (case 1) and 11 MPa 90 vol% hydrogen/10 vol% methane mixture leakage (case 2) are found to agree well with experimental observations. In case 2, the hot spots generated by reflected shock waves and Mach reflections ignite the hydrogen/methane-air mixture, resulting in three sequential spontaneous ignitions. The flame is observed to primarily propagate along the tube corners and wall centers, with the central ignition spreading across the entire cross-section. For the 25 MPa 24 vol% hydrogen/76 vol% methane mixture leakage (case 6), the shock intensity is significantly reduced due to the increased methane proportion, leading to spontaneous ignition only at the tube corners when the hemispherical shock wave reflects from the wall. The flame predominantly forms downstream along the tube corner, gradually spreading along the tube wall. It is indicated that while the probability of spontaneous ignition decreases with increasing methane content, the risk remains significant under sufficiently high pressures. To the best our knowledge, this study represents the first 3D large eddy simulation of spontaneous ignition for high-pressure hydrogen-enriched methane leakage into air, providing valuable insights into the underlying physical phenomena.

First demonstration of Sn diffusion into gallium oxide from poly-tetraallyl tin deposited by initiated chemical vapor deposition by thermal treatment.

Gallium oxide (Ga2O3) is attracting attention as a next-generation semiconductor material for power device because it has a
wide energy band gap and high breakdown electric field. We deposited a Sn polymer, poly-tetraallyl tin (pTASn), on Ga2O3
samples using a disclosed chemical vapor deposition (iCVD) process. The Sn dopant of the Sn polymer layer is injected into
the Ga2O3 through a heat treatment process. Diffusion model of Sn into the Ga2O3 is proposed through secondary ion mass
spectroscopy (SIMS) analysis and bond dissociation energy. The fabricated device exhibited typical n-type FET behavior.
Ga2O3 Sn-doping technology using iCVD will be applied to 3D structures and trench structures in the future, opening up many
possibilities in the Ga2O3-based power semiconductor device manufacturing process.

Inverse Modeling of Heterogeneous Structures in Electron Probe Microanalysis.

Electron probe microanalysis (EPMA) is a powerful tool for chemical characterization of materials on a microscopic scale. However, EPMA has the drawback that its information volume has a spatial extent of some 100 nm to a few µm. With the introduction of new electron sources, i.e., Schottky Thermal Field and Cold Field Emitter, where the electron beam is focused down to a few nm, measurements can be nowadays performed on the sub-micrometer scale. The goal of the work is to reveal the chemical composition of structures smaller than the excitation volume. New strategies are presented where the acquisition is performed at different positions on the sample and as a scan across a fine structure by using one or more single beam energies. Besides the well-known Monte-Carlo simulation, a deterministic model is also used. The deterministic model is based on moment equations of the Boltzmann equation. Inverse modeling is presented for several case studies. Due to the highly complex nonlinearity of the inverse model, an ill-posed and well-posed problem is shown as well. Finally, the method is extended to reconstruct 2D structures, i.e., rectangular shaped particles, with heterogeneous composition on lateral and depth scale.

Quantitative 3D structural analysis of small colloidal assemblies under native conditions by liquid-cell fast electron tomography

Electron tomography has become a commonly used tool to investigate the three-dimensional (3D) structure of nanomaterials, including colloidal nanoparticle assemblies. However, electron microscopy is typically done under high-vacuum conditions, requiring sample preparation for assemblies obtained by wet colloid chemistry methods. This involves solvent evaporation and deposition on a solid support, which consistently alters the nanoparticle organization. Here, we suggest using electron tomography to study nanoparticle assemblies in their original colloidal liquid environment. To address the challenges related to electron tomography in liquid, we devise a method that combines fast data acquisition in a commercial liquid-cell with a dedicated alignment and reconstruction workflow. We present the advantages of this methodology in accurately characterizing two different systems. 3D reconstructions of assemblies comprising polystyrene-capped Au nanoparticles encapsulated in polymeric shells reveal less compact and more distorted configurations for experiments performed in a liquid medium compared to their dried counterparts. A similar expansion can be observed in quantitative analysis of the surface-to-surface distances of self-assembled Au nanorods in water rather than in a vacuum, in agreement with bulk measurements. This study, therefore, emphasizes the importance of developing high-resolution characterization tools that preserve the native environment of colloidal nanostructures.

Macro-Calcium Carbonate-Hydrogel Hybrid Spheroids: Design and Biomedical Applications.

In advancing tissue engineering, we introduce a particle system combining the strength of calcium carbonate with the flexibility of hydrogels enhanced with alkaline phosphatase (ALP) for improved bone regeneration. Our innovation lies in creating large hybrid macrospheroids by bonding mineral nanostructured microparticles loaded with ALP through hydrogel polymerization. These composite macrospheroids address critical challenges in cell seeding, growth, and handling within three-dimensional (3D) environments. We conducted extensive characterization of these particles using scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), mechanical property assessment, and fluorescence microscopy. The results demonstrate that the hybrid macrospheroids significantly enhance cell manipulation and growth in three-dimensional structures. Specifically, ALP-loaded macrospheroids showed a marked improvement in osteogenic activity, promoting effective bone tissue regeneration. This study not only showcases a unique approach to overcoming the limitations of traditional hydrogels in tissue engineering but also opens pathways for bone tissue regeneration. Our findings offer a promising tool for cell seeding and growth in 3D structures, potentially revolutionizing practices in tissue engineering and regenerative medicine.

Thermal Rectification in Graphene-Boron Nitride Nanotube Hybrid Structures: An Independent Control Mechanism for Forward and Backward Heat Flux.

The weak van der Waals interactions in the out-of-plane direction result in markedly low thermal conductivity in one-dimensional (1D) and two-dimensional (2D) materials, which substantially restricts their applications. Developing three-dimensional (3D) columnar hybrid structures, featuring high thermal conductivity both within and beyond the plane, effectively addresses this challenge. This study investigated a 3D hybrid structure composed of graphene and boron nitride nanotubes (GR-BNNTs) using non-equilibrium molecular dynamics simulations. This approach allowed the examination of the formation mechanisms and key factors influencing thermal rectification (TR) in these materials. Our findings reveal a novel mechanism for independently regulating forward and backward heat fluxes in GR-BNNTs. By manipulating the thermal properties of the BNNTs and the graphene layer, the TR ratio can be controlled flexibly. Additionally, we identify specific strategies for independently adjusting the heat flux, such as altering the intercolumn distance of BNNTs, which impacts the backward flux merely, while applying strain to affect the forward flux merely. This research introduces a novel concept of independent regulation of forward and backward heat fluxes, providing significant insights into phonon thermal transport in 3D hybrid structures.

FURNA: A database for functional annotations of RNA structures.

Despite the increasing number of 3D RNA structures in the Protein Data Bank, the majority of experimental RNA structures lack thorough functional annotations. As the significance of the functional roles played by noncoding RNAs becomes increasingly apparent, comprehensive annotation of RNA function is becoming a pressing concern. In response to this need, we have developed FURNA (Functions of RNAs), the first database for experimental RNA structures that aims to provide a comprehensive repository of high-quality functional annotations. These include Gene Ontology terms, Enzyme Commission numbers, ligand-binding sites, RNA families, protein-binding motifs, and cross-references to related databases. FURNA is available at https://seq2fun.dcmb.med.umich.edu/furna/ to enable quick discovery of RNA functions from their structures and sequences.

3D Structure of Low‐Angle Normal Faults and Tectono‐Sedimentary Processes of Nascent Continental Core‐Complexes in the SE South China Sea

AbstractThis contribution explores the formation and evolution of hyper‐extended basins, associated with the early stage of core complex formation, controlled by low‐angle normal faults active at <30°. Based on a high‐resolution industrial 3D seismic reflection survey along the southern margin of the South China Sea (SCS) (Dangerous Grounds), we mapped and analyzed the 3D geometry of low‐angle normal fault systems and the related stratigraphy. Two main hyper‐extended basins were documented, filled by up to 6 km of sediments including pre‐ to post‐rift sequences. The observed normal faults on depth migrated seismic sections show an average dip angle of <30° and appear planar, characterized by continuous reflections with no clear steepening at depth and sole‐out on distinct decollement levels. Detailed fault surface mapping reveals the occurrence of km‐scale corrugations together with large wavelength undulation. The formation of these hyper‐extended basins is associated with polyphased syn‐rift infill during the development of the low‐angle normal faults. The first syn‐rift sequence appears as chaotic and discontinuous packages that has been dismembered and fragmented during the activity of low‐angle normal faults. The second syn‐rift package shows unexpected sedimentary wedges developing successively toward the footwall and the hangingwall. This geometry results from the interplay between the main low‐angle normal fault and antithetic faults defining a so‐called extensional fishtail. The deep structure of these basins shows nascent domes with limited evidence of magmatism. Eventually, these basins likely capture the earliest stage of core complex development in the proximal margin of the southern SCS.

Plasmon-Enhanced Light Absorption Below the Bandgap of Semiconducting SnS2 Microcubes for Highly Efficient Solar Water Evaporation.

Semiconducting materials show high potential for solar energy harvesting due to their suitable bandgaps, which allow the efficient utilization of light energy larger than their bandgaps. However, the photon energy smaller than their bandgap is almost unused, which significantly limits their efficient applications. Herein, plasmonic Pd/SnS2 microcubes with abundant Pd nanoparticles attached to the SnS2 nanosheets are fabricated by an in situ photoreduction method. The as-prepared Pd/SnS2 microcubes extend the light-harvesting ability of SnS2 beyond its cutoff wavelength, which is attributed to the localized surface plasmon resonance (LSPR) effect of the Pd nanoparticles and the 3D structure of the SnS2 microcubes. Pd nanoparticles can also enhance the light absorption of TiO2 nanoparticles and NiPS3 nanosheets beyond their cutoff wavelengths, revealing the universality for promoting absorption above the cutoff wavelength of the semiconductors. When the plasmonic Pd/SnS2 microcubes are integrated into a hydrophilic sponge acting as the solar evaporator, a solar-to-vapor efficiency of up to 89.2% can be achieved under one sun. The high solar-to-vapor conversion efficiency and the broad applicability of extending the light absorption far beyond the cutoff wavelength of the semiconductor comprise the potential of innovative plasmonic nanoparticle/semiconductor composites for solar desalination.

Enhancing the Supercapacitive Behaviour of Cobalt Layered Hydroxides by 3D Structuring and Halide Substitution

Enhancing the Supercapacitive Behaviour of Cobalt Layered Hydroxides by 3D Structuring and Halide Substitution

Modeling of solar radiation and sub-canopy light regime on forest inventory plots of mixed conifer and deciduous temperate forests using point clouds from personal laser scanning

Solar radiation is a major driver of forest ecosystems and affects the hydrological cycle and energy balance. The vitality of trees strongly depends on the amount of light input to individual trees, and successful forest regeneration demands a certain level of solar radiation. Therefore, characterization of the light regime inside a plant canopy (i.e., quantification and timing of light penetration) is of particular importance. Because these parameters greatly depend on the 3D structure of the forest canopy, Light Detection and Ranging (LiDAR) systems provide suitable technology for solving this task. In this study, an algorithm was developed to estimate the amount of potential solar radiation reaching the forest floor from a point cloud collected in a temperate mixed forest located in Lanzenkirchen (Lower Austria) using terrestrial LiDAR. The path length through the canopy was calculated for 40 forest inventory plots as the distance between the first and last canopy hit along a sun ray, that is, for each day during the vegetation period at an hourly resolution. This distance was easily derived from the z-coordinates of the point cloud after transforming the latter into a coordinate system in which the z-axis ran parallel to the sun rays. Applying Beer’s law, the amount of solar radiation on the forest floor was expressed as a function of the solar radiation above the canopy and the path length through the canopy. To validate the results, we used two sets of reference data: (1) hemispherical photographs taken at the same plots, using a camera on a self-levelling mount, which were processed with the HemiView software, and (2) data from a Solariscope survey. Both the Solariscope and HemiView software calculate below-canopy radiation as a percentage of above-canopy radiation, joining direct and diffuse radiation (Total Site Factor, TSF). The TSF values obtained from our modeling procedure were consistent with the Solariscope (R²=0.61) and HemiView (R²=0.71) results for the entire growing season. Because modern LiDAR-based forest inventories provide all the necessary data for our light modeling approach (the point cloud, the geographical position, and a record of the occurring tree species) without additional requirements, together with the easy applicability of the algorithm, this tool is a promising asset for ecological and silvicultural activities.

Visualization of 2D and 3D Tissue Models via Size-Selected Aqueous AgInS/ZnS Quantum Dots.

Three-dimensional (3D) spheroid cell cultures of fibroblast (L929) and tumor mammary mouse (4T1) were chosen as in vitro tissue models for tissue imaging of ternary AgInS/ZnS fraction quantum dots (QDs). We showed that the tissue-mimetic morphology of cell spheroids through well-developed cell-cell and cell-matrix interactions and distinct diffusion/transport characteristics makes it possible to predict the effect of ternary AgInS/ZnS fraction QDs on the vital activity of cells while simultaneously comparing with classical two-dimensional (2D) cell cultures. The AgInS/ZnS fractions, emitting in a wide spectral range from 635 to 535 nm with a mean size from ∼3.1 ± 0.8 to ∼1.8 ± 0.4 nm and a long photoluminescence lifetime, were separated from the initial QD ensemble by using antisolvent-induced precipitation. For ternary AgInS/ZnS fraction QDs, the absence of toxicity at different QD concentrations was demonstrated on 2D and 3D cell structures. QDs show a robust correlation between numerous factors: their sizes in biological fluids over time, penetration capabilities into 2D and 3D cell structures, and selectivity with respect to penetration into cancerous and healthy cell spheroids. A reproducible protocol for the preparation of QDs along with their unique biological properties allows us to consider ternary AgInS/ZnS fraction QDs as attractive fluorescent contrast agents for tissue imaging.

Cryo-EM Structure of the Mnx Protein Complex Reveals a Tunnel Framework for the Mechanism of Manganese Biomineralization.

The global manganese cycle relies on microbes to oxidize soluble Mn(II) to insoluble Mn(IV) oxides. Some microbes require peroxide or superoxide as oxidants, but others can use O2 directly, via multicopper oxidase (MCO) enzymes. One of these, MnxG from Bacillus sp. strain PL-12, was isolated in tight association with small accessory proteins, MnxE and MnxF. The protein complex, called Mnx, has eluded crystallization efforts, but we now report the 3D structure of a point mutant using cryo-EM single particle analysis, cross-linking mass spectrometry, and AlphaFold Multimer prediction. The β-sheet-rich complex features MnxG enzyme, capped by a heterohexameric ring of alternating MnxE and MnxF subunits, and a tunnel that runs through MnxG and its MnxE3F3 cap. The tunnel dimensions and charges can accommodate the mechanistically inferred binuclear manganese intermediates. Comparison with the Fe(II)-oxidizing MCO, ceruloplasmin, identifies likely coordinating groups for the Mn(II) substrate, at the entrance to the tunnel. Thus, the 3D structure provides a rationale for the established manganese oxidase mechanism, and a platform for further experiments to elucidate mechanistic details of manganese biomineralization.

Transitions in chromatin conformation shaped by fatty acids and the circadian clock underlie hepatic transcriptional reorganization in obese mice

The circadian clock system coordinates metabolic, physiological, and behavioral functions across a 24-h cycle, crucial for adapting to environmental changes. Disruptions in circadian rhythms contribute to major metabolic pathologies like obesity and Type 2 diabetes. Understanding the regulatory mechanisms governing circadian control is vital for identifying therapeutic targets. It is well characterized that chromatin remodeling and 3D structure at genome regulatory elements contributes to circadian transcriptional cycles; yet the impact of rhythmic chromatin topology in metabolic disease is largely unexplored. In this study, we explore how the spatial configuration of the genome adapts to diet, rewiring circadian transcription and contributing to dysfunctional metabolism. We describe daily fluctuations in chromatin contacts between distal regulatory elements of metabolic control genes in livers from lean and obese mice and identify specific lipid-responsive regions recruiting the clock molecular machinery. Interestingly, under high-fat feeding, a distinct interactome for the clock-controlled gene Dbp strategically promotes the expression of distal metabolic genes including Fgf21. Alongside, new chromatin loops between regulatory elements from genes involved in lipid metabolism control contribute to their transcriptional activation. These enhancers are responsive to lipids through CEBPβ, counteracting the circadian repressor REVERBa. Our findings highlight the intricate coupling of circadian gene expression to a dynamic nuclear environment under high-fat feeding, supporting a temporally regulated program of gene expression and transcriptional adaptation to diet.