Three-dimensional Structure Research Articles

Molecular recognition between volatile molecules and odorant binding proteins 7 by homology modeling, molecular docking and molecular dynamics simulation.

Odorant-binding proteins (OBPs) in insects are key to detection and recognition of external chemical signals associated with survival. OBP7 in Spodoptera frugiperda's larval stage (SfruOBP7) may search for host plants by sensing plant volatiles, which are important sources of pest attractants and repellents. However, the atomic-level basis of binding modes remains elusive. SfruOBP7 structure was constructed through homology modeling, and complex models of six plant volatiles ((E)-2-hexenol, α-pinene, (Z)-3-hexenyl acetate, lauric acid, O-cymene and 1-octanol) and SfruOBP7 were obtained through molecular docking. To study the detailed interactions between the six plant volatile molecules and SfruOBP7, we conducted three 300 ns molecular dynamics simulations for each study object. The correlation coefficients between binding free energy obtained by molecular mechanics/generalized Born surface area together with solvated interaction energy methods and experimental values are 0.90 and 0.88, respectively, showing a good correlation. By comparing binding free energy along with interaction patterns between SfruOBP7 and the six volatile molecules, hotspot residues of SfruOBP7 when binding with different volatile molecules were determined. Hydrophobic interactions stemming from van der Waals interactions play a significant role in SfruOBP7 and these plant volatile systems. The optimized three-dimensional structure of SfruOBP7 and its binding modes with six plant volatiles revealed their interactions, thus providing a means for estimating the binding energies of other plant volatiles. Our study will help to guide the rational design of effective and selective insect attractants. © 2024 Society of Chemical Industry.

Essential Guidelines for Manufacturing and Application of Organoids.

An organoid is a self-organized three-dimensional structure derived from stem cells that mimics the structure, cell composition, and functional characteristics of specific organs and tissues and is used for evaluating the safety and effectiveness of drugs and the toxicity of industrial chemicals. Organoid technology is a new methodology that could replace testing on animals testing and accelerate development of precision and regenerative medicine. However, large variations in production can occur between laboratories with low reproducibility of the production process and no internationally agreed standards for quality evaluation factors at endpoints. To overcome these barriers that hinder the regulatory acceptance and commercialization of organoids, Korea established the Organoid Standards Initiative in September 2023 with various stakeholders, including industry, academia, regulatory agencies, and standard development experts, through public and private partnerships. This developed general guidelines for organoid manufacturing and quality evaluation and for quality evaluation guidelines for organoid-specific manufacturing for the liver, intestines, and heart through extensive evidence analysis and consensus among experts. This report is based on the common standard guideline v1.0, which is a general organoid manufacturing and quality evaluation to promote the practical use of organoids. This guideline does not focus on specific organoids or specific contexts of use but provides guidance to organoid makers and users on materials, procedures, and essential quality assessment methods at end points that are essential for organoid production applicable at the current technology level.

Modification of Living Diatom, Thalassiosira weissflogii, with a Calcium Precursor through a Calcium Uptake Mechanism: A Next Generation Biomaterial for Advanced Delivery Systems.

The diatom's frustule, characterized by its rugged and porous exterior, exhibits a remarkable biomimetic morphology attributable to its highly ordered pores, extensive surface area, and unique architecture. Despite these advantages, the toxicity and nonbiodegradable nature of silica-based organisms pose a significant challenge when attempting to utilize these organisms as nanotopographically functionalized microparticles in the realm of biomedicine. In this study, we addressed this limitation by modulating the chemical composition of diatom microparticles by modulating the active silica metabolic uptake mechanism while maintaining their intricate three-dimensional architecture through calcium incorporation into living diatoms. Here, the diatom Thalassiosira weissflogii was chemically modified to replace its silica composition with a biodegradable calcium template, while simultaneously preserving the unique three-dimensional (3D) frustule structure with hierarchical patterns of pores and nanoscale architectural features, which was evident by the deposition of calcium as calcium carbonate. Calcium hydroxide is incorporated into the exoskeleton through the active mechanism of calcium uptake via a carbon-concentrating mechanism, without altering the microstructure. Our findings suggest that calcium-modified diatoms hold potential as a nature-inspired delivery system for immunotherapy through antibody-specific binding.

Combining Computational Fluid Dynamics and Experimental Data to Understand Fish Schooling Behavior.

Understanding the flow physics behind fish schooling poses significant challenges due to the difficulties in directly measuring hydrodynamic performance and the three-dimensional, chaotic, and complex flow structures generated by collective moving organisms. Numerous previous simulations and experiments have utilized computational, mechanical, or robotic models to represent live fish. And existing studies of live fish schools have contributed significantly to dissecting the complexities of fish schooling. But the scarcity of combined approaches that include both computational and experimental studies, ideally of the same fish schools, has limited our ability to understand the physical factors that are involved in fish collective behavior. This underscores the necessity of developing new approaches to working directly with live fish schools. An integrated method that combines experiments on live fish schools with computational fluid dynamic (CFD) simulations represents an innovative method of studying the hydrodynamics of fish schooling. CFD techniques can deliver accurate performance measurements and high-fidelity flow characteristics for comprehensive analysis. Concurrently, experimental approaches can capture the precise locomotor kinematics of fish and offer additional flow information through particle image velocimetry (PIV) measurements, potentially enhancing the accuracy and efficiency of CFD studies via advanced data assimilation techniques. The flow patterns observed in PIV experiments with fish schools and the complex hydrodynamic interactions revealed by integrated analyses highlight the complexity of fish schooling, prompting a reevaluation of the classic Weihs model of school dynamics. The synergy between CFD models and experimental data grants us comprehensive insights into the flow dynamics of fish schools, facilitating the evaluation of their functional significance and enabling comparative studies of schooling behavior. In addition, we consider the challenges in developing integrated analytical methods and suggest promising directions for future research.

Fast computational approach with prior dimension reduction for three-dimensional chemical component analysis using CT data of spectral imaging.

Spectral image (SI) measurement techniques, such as X-ray absorption fine structure (XAFS) imaging and scanning transmission electron microscopy (STEM) with energy-dispersive X-ray spectroscopy (EDS) or electron energy loss spectroscopy (EELS), are useful for identifying chemical structures in composite materials. Machine-learning techniques have been developed for automatic analysis of SI data, and their usefulness has been proven. Recently, an extended measurement technique combining SI with a computed tomography (CT) technique (CT-SI), such as CT-XAFS and STEM-EDS/EELS tomography, was developed to identify the three-dimensional (3D) structures of chemical components. CT-SI analysis can be conducted by combining CT reconstruction algorithms and chemical component analysis based on machine learning techniques. However, this analysis incurs high computational costs owing to the size of the CT-SI datasets. To address this problem, this study proposed a fast computational approach for 3D chemical component analysis in an unsupervised learning setting. The primary idea for reducing the computational cost involved compressing the CT-SI data prior to CT computation and performing 3D reconstruction and chemical component analysis on the compressed data. The proposed approach significantly reduced the computational cost without losing information about the 3D structure and chemical components. We experimentally evaluated the proposed approach using synthetic and real CT-XAFS data, which demonstrated that our approach achieved a significantly faster computational speed than the conventional approach while maintaining analysis performance. As the proposed procedure can be implemented with any CT algorithm, it is expected to accelerate 3D analyses with sparse regularized CT algorithms in noisy and sparse CT-SI datasets.

C5 Pentacle Structures: A Localization-Delocalization Matrices Approach.

This article explores the possible presence of a pentacle valence bond structure in C cyclic molecules. At this end, we have used quantum chemistry tools to elucidate the possible arrangement and the nature of chemical bonds within linear, cyclic, and three-dimensional structures only formed by five carbon atoms. While the linear structure is clearly the most stable one, local minima were obtained for both bi- and three-dimensional structures. Using the localization-delocalization matrices approach, we characterize both the minimum linear structure and the cyclic ones. Interestingly, the linear structure is a combination of ionic and covalent bonds, albeit the four distances are almost identical, when using Density Functional Theory. For cyclic C , the pentacle bonding arrangement emerges as a significant Lewis structure, indicative of an unusual formal configuration characterized by five intersecting C-C bonds. Our calculations show that this pentacle arrangement in cyclic C scheme is also present in the more known cyclo-pentadienyl molecule.

E3 ubiquitin ligase UBR5 promotes gemcitabine resistance in pancreatic cancer by inducing O-GlcNAcylation-mediated EMT via destabilization of OGA.

Pancreatic cancer (PC) is among the deadliest malignancies, with an extremely poor diagnosis and prognosis. Gemcitabine (GEM) remains the first-line drug for treating PC; however, only a small percentage of patients benefit from current immunotherapies or targeted therapies. Resistance to GEM is prevalent and affects long-term survival. We found that ubiquitin-protein ligase E3 module N-recognition 5 (UBR5) is a therapeutic target against GEM resistance. UBR5 was markedly upregulated in clinical GEM-resistant PC samples and GEM-resistant PC cells. UBR5 knockdown markedly increased GEM sensitivity in GEM-resistant PC cell lines. UBR5-mediated GEM resistance was accompanied by activation of epithelial-mesenchymal transition (EMT) and could be mitigated by inhibiting EMT. Further analysis revealed that UBR5 promoted GEM resistance in PC cells by enhancing O-GlcNAcylation-mediated EMT. In addition, UBR5 knockdown resulted in increased O-GlcNAase (OGA) levels, an essential negatively regulated enzyme in the O-GlcNAcylation process. We identified a negative association between OGA and UBR5 levels, which further supported the hypothesis that O-GlcNAcylation-mediated GEM resistance induced by UBR5 is OGA-dependent in PC cells. Mechanistic studies revealed that UBR5 acts as an E3 ubiquitin ligase of OGA and regulates O-GlcNAcylation by binding and modulating OGA, facilitating its degradation and ubiquitination. Additionally, high-throughput compound library screening using three-dimensional protein structure analysis and drug screening identified a Food and Drug Administration drug, Y-39983 dihydrochloride, as a potent GEM sensitiser and UBR5 inhibitor. The combination of Y-39983 dihydrochloride and GEM attenuated tumour growth in a mouse xenograft tumour model. Collectively, these data demonstrated that UBR5 plays a pivotal role in the sensitisation of PC to GEM and provides a potential therapeutic strategy to overcome GEM resistance.

Engineering High-Performance Li Metal Batteries through Dual-Gradient Porous Cu-CuZn Host.

Porous copper (Cu) current collectors show promise in stabilizing Li metal anodes (LMAs). However, insufficient lithiophilicity of pure Cu and limited porosity in three-dimensional (3D) porous Cu structures led to an inefficient Li-Cu composite preparation and poor electrochemical performance of Li-Cu composite anodes. Herein, we propose a porous Cu-CuZn (DG-CCZ) host for Li composite anodes to tackle these issues. This architecture features a pore size distribution and lithiophilic-lithiophobic characteristics designed in a gradient distribution from the inside to the outside of the anode structure. This dual-gradient porous Cu-CuZn exhibits exceptional capillary wettability to molten Li and provides a high porosity of up to 66.05%. This design promotes preferential Li deposition in the interior of the porous structure during battery operation, effectively inhibiting Li dendrite formation. Consequently, all cell systems achieve significantly improved cycling stability, including Li half-cells, Li-Li symmetric cells, and Li-LFP full cells. When paired synergistically with the double-coated LiFePO4 cathode, the pouch cell configured with multiple electrodes demonstrates an impressive discharge capacity of 159.3 mAh g-1 at 1C. We believe this study can inspire the design of future 3D Li anodes with enhanced Li utilization efficiency and facilitate the development of future high-energy Li metal batteries.

How three-dimensional forest structure regulates the amount and timing of snowmelt across a climatic gradient of snow persistence

How three-dimensional forest structure regulates the amount and timing of snowmelt across a climatic gradient of snow persistence

Research on high sensitivity piezoresistive sensor based on structural design.

With the popularity of smart terminals, wearable electronic devices have shown great market prospects, especially high-sensitivity pressure sensors, which can monitor micro-stimuli and high-precision dynamic external stimuli, and will have an important impact on future functional development. Compressible flexible sensors have attracted wide attention due to their simple sensing mechanism and the advantages of light weight and convenience. Sensors with high sensitivity are very sensitive to pressure and can detect resistance/current changes under pressure, which has been widely studied. On this basis, this review focuses on analyzing the performance impact of device structure design strategies on high sensitivity pressure sensors. The design of structures can be divided into interface microstructures and three-dimensional framework structures. The preparation methods of various structures are introduced in detail, and the current research status and future development challenges are summarized.

A Label-Free Approach for Relative Spatial Quantitation of c-di-GMP in Microbial Biofilms.

Microbial biofilms represent an important lifestyle for bacteria and are dynamic three-dimensional structures. Cyclic dimeric guanosine monophosphate (c-di-GMP) is a ubiquitous signaling molecule that is known to be tightly regulated with biofilm processes. While measurements of global levels of c-di-GMP have proven valuable toward understanding the genetic control of c-di-GMP production, there is a need for tools to observe the local changes of c-di-GMP production in biofilm processes. We have developed a label-free method for the direct detection of c-di-GMP in microbial colony biofilms using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). We applied this method to the enteric pathogen Vibrio cholerae, the marine symbiont V. fischeri, and the opportunistic pathogen Pseudomonas aeruginosa PA14 and detected spatial and temporal changes in c-di-GMP signal that accompanied genetic alterations in factors that synthesize and degrade the compound. We further demonstrated how this method can be simultaneously applied to detect additional metabolites of interest from a single sample.

Design Principle and Development Trends of Silicon-Based Anode Binders for Lithium-ion Batteries: A Mini Review

Abstract: Silicon (Si), recognized as a promising alternative material for the anodes of lithium-ion batteries, boasts a high theoretical specific capacity and abundant natural availability. During the preparation of silicon-based anodes, binders play a pivotal role in ensuring the cohesion of silicon particles, conductive agents, and current collectors. The structure and performance of these binders are critical for the mechanical stability, electrical conductivity, and stress dissipation capacity of the anodes. This review initially outlines the structural characteristics of various binders, including linear, branched, and three-dimensional cross-linked types. It then delves into the relationship between the structure and properties of these binders in the context of their application in high-performance lithium-ion batteries, focusing on their mechanical properties, electrical conductivity, and self-healing capabilities. Particular attention is given to the design strategies for binders that facilitate stress dissipation, with an emphasis on integrating multifunctional polymer binders renowned for their superior conductive and self-healing features. Such binders contribute to the formation of a robust three-dimensional network structure via multiple bonding mechanisms, including chemical, non-covalent, and coordination interactions. This configuration significantly enhances the adhesion between silicon particles, thereby facilitating the efficient dissipation of stress, which is a key aspect for ensuring the long-term cycling stability of lithium-ion batteries. Lastly, the paper explores future development directions for silicon anode binders, advocating for a thorough investigation into the synergy of diverse structural and functional combinations, with the aim of advancing the performance and practical application of silicon-based lithium-ion batteries.

Effects of Curing Defects in Adhesive Layers on Carbon Fiber–Quartz Fiber Bonded Joint Performance

Due to their mechanical load-bearing and functional wave transmission, adhesively bonded joints of carbon fiber–quartz fiber composites have been widely used in the new generation of stealth aviation equipment. However, the curing defects, caused by deviations between the process environment and the setting parameters, directly affect the service performance of the joint during the curing cycle. Therefore, the thermophysical parameter evolution of adhesive films was analyzed via dynamic DSC (differential scanning calorimeter), isothermal DSC and TGA (thermal gravimetric analyzer) tests. The various prefabricating defects within the adhesive layer were used to systematically simulate the impacts of void defects on the tensile properties, and orthogonal tests were designed to clarify the effects of the curing process parameters on the joints’ bonding performance. The results demonstrate that the J-116 B adhesive film starts to cure at a temperature of 160 °C and gradually forms a three-dimensional mesh-bearing structure. Furthermore, a bonding interface between the J-116 B adhesive film and the components to be connected is generated. When the curing temperature exceeds 200 °C, both the adhesive film and the resin matrix thermally degrade the molecular structure. The adhesive strength weakens with an increasing defect area ratio and number, remaining more sensitive to triangle, edge and penetration defects. By affecting the molecular structure of the adhesive film, the curing temperature has a significant impact on the bonding properties; when the curing degree is ensured, the curing pressure directly impacts the adhesive’s performance by influencing the morphology, number and distribution of voids. Conversely, the heating rate and heat preservation time have minimal effects on the bonding performance.

Crystalline CdS/amorphous Cd(OH)2 Composite for Electrochemical CO2 Reduction to CO in a Wide Potential Window.

Electrochemical CO2 reduction is a promising method for converting atmospheric CO2 into valuable low-carbon chemicals. In this study, a crystalline cadmium sulfide/amorphous cadmium hydroxide composite was successfully deposited on the carbon paper substrate surface by in-situ chemical bath deposition (named as c-CdS/a-Cd(OH)2/CP electrodes) for the efficient electrochemical CO2 reduction to produce CO. The c-CdS/a-Cd(OH)2/CP electrode exhibited high CO Faradaic efficiencies (>90%) under a wide potential window of 1.0 V, with the highest value reaching ~100% at the applied potential ranging from -2.16 V to -2.46 V vs. ferrocene/ferrocenium (Fc/Fc+), superior to the crystalline counterpart c-CdS/CP and c-CdS/c-Cd(OH)2@CP electrodes. Meanwhile, the CO partial current density reached up to 154.7 mA cm-2 at -2.76 V vs. Fc/Fc+ on the c-CdS/a-Cd(OH)2/CP electrode. The excellent performance of this electrode was mainly ascribed to its special three-dimensional structure and the introduction of a-Cd(OH)2. These structures could provide more active sites, accelerate the charge transfer, and enhance adsorption of *COOH intermediates, thereby improving the CO selectivity. Moreover, the electrolytes consisting of 1-butyl-3-methylimidazolium tetrafluoroborate and acetonitrile also enhanced the reaction kinetics of electrochemical CO2 reduction to CO.

Advances in the study of gastric organoids as disease models.

Gastric organoids are models created in the laboratory using stem cells and sophisticated three-dimensional cell culture techniques. These models have shown great promise in providing valuable insights into gastric physiology and advanced disease research. This review comprehensively summarizes and analyzes the research advances in culture methods and techniques for adult stem cells and induced pluripotent stem cell-derived organoids, and patient-derived organoids. The potential value of gastric organoids in studying the pathogenesis of stomach-related diseases and facilitating drug screening is initially discussed. The construction of gastric organoids involves several key steps, including cell extraction and culture, three-dimensional structure formation, and functional expression. Simulating the structure and function of the human stomach by disease modeling with gastric organoids provides a platform to study the mechanism of gastric cancer induction by Helicobacter pylori. In addition, in drug screening and development, gastric organoids can be used as a key tool to evaluate drug efficacy and toxicity in preclinical trials. They can also be used for precision medicine according to the specific conditions of patients with gastric cancer, to assess drug resistance, and to predict the possibility of adverse reactions. However, despite the impressive progress in the field of gastric organoids, there are still many unknowns that need to be addressed, especially in the field of regenerative medicine. Meanwhile, the reproducibility and consistency of organoid cultures are major challenges that must be overcome. These challenges have had a significant impact on the development of gastric organoids. Nonetheless, as technology continues to advance, we can foresee more comprehensive research in the construction of gastric organoids. Such research will provide better solutions for the treatment of stomach-related diseases and personalized medicine.

Phylum-level studies of bacterial cutinases for unravelling enzymatic specificity toward PET degradation: an in silico approach.

The overwhelming use of PET plastic in various day-to-day activities led to the voluminous increase in PET waste and growing environmental hazards. A plethora of methods have been used that are associated with secondary pollutants. Therefore, microbial degradation of PET provides a sustainable approach due to its versatile metabolic diversity and capacity. The present work highlights the cutinase enzyme's role in PET degradation. This study focuses on the bacterial cutinases homologs screened from 43 reported phylum of bacteria. The reported bacterial cutinases for plastic degradation have been chosen as reference sequences, and 917 sequences have shown homology across the bacterial phyla. The dienelactone hydrolase (DLH) domain was identified for attaining specificity towards PET binding in 196 of 917 sequences. Various computational tools have been used for the physicochemical characterization of 196 sequences. The analysis revealed that most selected sequences are hydrophilic, extracellular, and thermally stable. Based on this analysis, 17 sequences have been further pursued for three-dimensional structure prediction and validation. The molecular docking studies of 17 selected sequences revealed efficient PET binding with the three sequences derived from the phylum Bacteroidota, the lowest binding energy of -5.9kcal/mol, Armatimonadota, and Nitrososphaerota with -5.8kcal/mol. The two enzyme sequences retrieved from the phylum Bacteroidota and Armatimonadota are metagenomically derived. Therefore, the present studies concluded that there is a high probability of finding cutinase homologs in various environmental resources that can be further explored for PET degradation.

On the evidence of helico-spiralling recirculation within coherent cores of eddies using Lagrangian approach

Oceanic eddies exhibit remarkable coherence and longevity compared to other transient features in the surrounding flow. They possess the ability to transport properties over extensive distances while maintaining their material identity intact. The Lagrangian Coherent Structure (LCS) framework has proven effective in capturing these coherent eddies, where they display a solid-body-like rotation. Although various LCS approaches have been employed to investigate different facets of coherent eddies, a comprehensive understanding of their three-dimensional structures and internal dynamics remains elusive. This study aims to advance our comprehension of coherent eddies’ structural characteristics and delve into the precise nature of their internal dynamics by utilizing the Lagrangian Averaged Vorticity Deviation approach. Two eddies, one cyclonic and the other anti-cyclonic, were chosen from a high-resolution simulation carried out in the Bay of Bengal using the Regional Ocean Modeling System (ROMS). The findings unveil that these eddies have three-dimensional coherent cores resembling gently tapered cones that are broader at the surface and gradually narrow towards the bottom. Intriguingly, the dynamically coherent core of these eddies exhibits simultaneous upwelling and downwelling while maintaining their volumes during advection due to persistent material coherence. The three-dimensional trajectories followed by the fluid parcels inside the coherent core are helical. Their two-dimensional horizontal projections show alternating spiral bands of upwelling and downwelling which are the manifestations of Vortex Rossby Waves. These observations lead to a conceptual framework of a three-dimensional helico-spiralling recirculation pattern within the coherent cores of eddies.

Exploring heart dissection techniques for enhancing anatomical education: a pilot study to replicate transthoracic echocardiography.

For novice learners, converting two-dimensional (2D) images of echocardiography to three-dimensional (3D) cardiac structures is deemed challenging. This study aimed to develop an accurate dissection method of the heart to reproduce the transthoracic echocardiographic views on cadavers and elucidate new educational methods in human anatomy dissection courses. A total of 18 hearts were used in this study. After reflecting the anterior thoracic wall inferiorly, the hearts were excised from embalmed cadavers. Thereafter, three landmarks were set on the heart for each plane of the incision, and the hearts were incised to observe the three different echocardiographic views, which include the apical four-chamber view (A4C), parasternal long axis (PLAX) view, and parasternal short axis (PSAX) view at the papillary muscle level. If all structures for observation during routine echocardiography are clearly observed in each view, a successful incision is considered. All procedures and incisions were performed by the medical students. After a successful incision, hearts were returned to the original position in the pericardial sac for further observation. The success rates of incision for each view were 83.3% (5/6 success cases), 83.3% (5/6 success cases), and 66.7% (4/6 success cases) in the A4C view, PLAX view, and PSAX view at the papillary muscle level, respectively. This dissection method could probably be employed to reproduce transthoracic echocardiographic views on cadaveric hearts, which is beneficial for novice learners for a deeper understanding of the anatomy.

Decoding Active Sites for Highly Efficient Semihydrogenation of Acetylene in Palladium-Copper Nanoalloys.

Accurately decoding the three-dimensional atomic structure of surface active sites is essential yet challenging for a rational catalyst design. Here, we used comprehensive techniques combining the pair distribution function and reverse Monte Carlo simulation to reveal the surficial distribution of Pd active sites and adjacent coordination environment in palladium-copper nanoalloys. After the fine-tuning of the atomic arrangement, excellent catalytic performance with 98% ethylene selectivity at complete acetylene conversion was obtained in the Pd34Cu66 nanocatalysts, outperforming most of the reported advanced catalysts. The quantitative deciphering shows a large number of active sites with a Pd-Pd coordination number of 3 distributed on the surface of Pd34Cu66 nanoalloys, which play a decisive role in highly efficient semihydrogenation. This finding not only opens the way for guiding the precise design of bimetal nanocatalysts from atomic-level insight but also provides a method to resolve the spatial structure of active sites.

Crashworthiness capability comparison of a 3D Greek cross fractal structure additively manufactured with polyamide and thermoplastic polyurethane

Crashworthiness capability comparison of a 3D Greek cross fractal structure additively manufactured with polyamide and thermoplastic polyurethane