Three-dimensional Structural Model Research Articles

Three-Dimensional Stratigraphic Structure and Property Collaborative Modeling in Urban Engineering Construction

In urban engineering construction, ensuring the stability and safety of subsurface geological structures is as crucial as surface planning and aesthetics. This study proposes a novel multivariate radial basis function (MRBF) interpolant for the three-dimensional (3D) modeling of engineering geological properties, constrained by the stratigraphic structural model. A key innovation is the incorporation of a well-sampled geological stratigraphical potential field (SPF) as an ancillary variable, which enhances the interpolation of geological properties in areas with sparse and uneven sampling points. The proposed MRBF method outperforms traditional interpolation techniques by showing reduced dependency on the distribution of sampling points. Furthermore, the study calculates the bearing capacity of individual pile foundations based on precise stratigraphic thicknesses, yielding more accurate results compared to conventional methods that average these values across the entire site. Additionally, the integration of 3D geological models with urban planning facilitates the development of comprehensive urban digital twins, optimizing resource management, improving decision-making processes, and contributing to the realization of smart cities through more efficient data-driven urban management strategies.

Identification of Key Amino Acids in the A Domains of Polymyxin Synthetase Responsible for 2,4-Diaminobutyric Acid Adenylation in Paenibacillus polymyxa NBRC3020 Strain.

Developing novel nonribosomal peptides (NRPs) requires a comprehensive understanding of the enzymes involved in their biosynthesis, particularly the substrate amino acid recognition mechanisms in the adenylation (A) domain. This study focused on the A domain responsible for adenylating l-2,4-diaminobutyric acid (l-Dab) within the synthetase of polymyxin, an NRP produced by Paenibacillus polymyxa NBRC3020. To date, investigations into recombinant proteins that selectively adenylate l-Dab─exploring substrate specificity and enzymatic activity parameters─have been limited to reports on A domains found in enzymes synthesizing l-Dab homopolymers (pldA from S. celluloflavus USE31 and pddA from S. hindustanus NBRC15115), which remain exceedingly rare. The polymyxin synthetase in NBRC3020 contains five A domains specific to l-Dab, distributed across five distinct modules (modules 1, 3, 4, 5, 8, and 9). In this study, we successfully obtained soluble A domain proteins from modules 1, 5, 8, and 9 by preparing module-specific recombinant proteins. These proteins were expressed in E. coli BAP-1, purified via Ni-affinity chromatography, and demonstrated high specificity for l-Dab. Through sequence homology analysis, three-dimensional structural modeling, docking simulations to estimate substrate-binding sites, and functional validation using alanine mutants, we identified Glu281 and Asp344 as critical residues for recognizing the side chain amino group of l-Dab, and Asp238 as essential for recognizing its main chain amino group in the A domain. Notably, these key residues were conserved not only across the A domains in modules 1, 5, 8, and 9 of P. polymyxa NBRC3020 but also in those of the P. polymyxa PKB1 strain, as confirmed by sequence homology analysis. Interestingly, in pldA and pddA, the key residues involved in recognizing the side-chain amino group of l-Dab, which are conserved among polymyxin synthetases of NBRC3020 and PKB1 strain, were not observed. This suggests a potentially different mechanism for l-Dab recognition.

Analysis of FBN1 gene mutations in six Chinese pedigrees affected with Marfan syndrome

To determine the types of genetic variants in six Chinese pedigrees affected with Marfan syndrome (MFS) and analyze their clinical characteristics and molecular pathogenesis. Six MFS pedigrees presented at the Taizhou Enze Medical Center (Group) between 2017 and 2022 were selected as the study subjects. Clinical data of pedigrees were retrospectively analyzed. Peripheral blood samples were collected from the probands and their family members for the extraction of genomic DNA. Whole exome sequencing (WES) was carried out. Candidate variants of the FBN1 gene were verified by Sanger sequencing. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), pathogenicity of the candidate variants was assessed. AlphaFold3 and PyMOL software were used for homology modeling of the FBN1 protein and analysis of its three-dimensional structure and amino acid sequence conservation. This study was approved by the Medical Ethics Committee of Taizhou Enze Medical Center (Group) (Ethics No. 20231002). Cardiovascular system abnormalities were noted in all pedigrees, ocular abnormalities were present in pedigrees 2 and 5, skeletal system abnormalities were presented in pedigrees 1, and 4 to 6. FBN1 gene mutations were identified in all pedigrees, including c.1957_1958dupGT (p.Asp654fs), c.5014T>A (p.Cys1672Ser), c.8135delC (p.Pro2712fs), c.2302G>T (p.Glu768*), c.3473A>G (p.Glu1158Gly) and c.6169C>T (p.Arg2057*), with each involving a different exon. Four variants were rated as pathogenic, one as likely pathogenic, and one as variant of uncertain significance. Among these, c.5014T>A (p.Cys1672Ser), c.1957_1958dupGT (p.Asp654fs), c.8135delC (p.Pro2712fs), and c.2302G>T (p.Glu768*) were unreported previously. Bioinformatic analysis with SIFT and PolyPhen-2 predicted that the c.5014T>A (p.Cys1672Ser) and c.3473A>G (p.Glu1158Gly) variants were deleterious. Protein homologous sequence alignment analysis revealed that the four novel mutation sites are highly conserved across various species. Homology modeling of the FBN1 protein three-dimensional structure indicated that the six variant sites in the amino acid sequence are all close to hydrogen bonds and may alter the secondary and tertiary structures to varying degrees, thereby confirmed the relationship between the variants and MFS. Four novel variants of the FBN1 gene have been discovered in this study, which has enriched the mutational and phenotypic spectrum of MFS and provided a basis for disease diagnosis and genetic counseling.

A Low-Cost Workflow to Generate Virtual and Physical Three-Dimensional Models of Cardiac Structures.

Three-dimensional modeling and printing (3DMP) of anatomical structures from cross-sectional imaging data can enhance the understanding of spatial relationships in complex congenital heart defects. Partially due to the substantial financial, material and personnel resources required, 3DMP is not yet universally used. Here, we describe a workflow that addresses and eliminates these drawbacks. The workflow utilizes the open-source software "3D Slicer" (The Slicer Community) and "Blender" (Blender Foundation) for segmentation and post-editing of datasets. This approach enables the generation of virtual or physical 3D models. The physical models are printed using a standard fused deposition modeling printer. The financial challenges that likely constrain the wider use of 3DMP are largely addressed by this approach. However, the workflow still requires a considerable amount of time to manually segment the imaging data. Three-dimensional modeling and printing might improve planning and safety of congenital cardiac surgical treatment. Furthermore, it is a useful tool for education of parents and medical professionals. This workflow increases its suitability for routine use also in regions with low economic resources.

A TSC2 recurrent variant c.5126C>T in a Han-Chinese family with tuberous sclerosis complex.

To identify the disease-causing variant in a family with tuberous sclerosis complex (TSC). This study including a Han-Chinese pedigree recruited from the Third Xiangya Hospital, Central South University, Changsha, Hunan, China was conducted between February, 2019 and January, 2023. Detailed clinical examinations were performed on the proband and other family members of a Han-Chinese family with TSC. Whole exome sequencing of the proband and Sanger sequencing of all family members were performed, followed by variant pathogenicity prediction and conservation analysis. SWISS-MODEL and PyMOL software were used for protein modelling and creating the three-dimensional structure model illustration of the critical GTPase-activating protein (GAP) domain. The variant was classified following the American College of Medical Genetics and Genomics (ACMG) standards and guidelines. The female proband exhibited typical features of TSC, including hypomelanotic macules, angiofibromas, shagreen patches, seizures, brain lesions, cognitive impairment, renal abnormalities, and cardiovascular abnormalities. A recurrent c.5126C>T variant in the TSC complex subunit 2 gene (TSC2) was identified as the genetic cause of TSC in this family, classified as "pathogenic" according to ACMG standards and guidelines. The c.5126C>T variant leads to an amino acid change from proline to leucine at position 1709 (p.P1709L) in the functional GAP domain of tuberin protein, which may impair tumor growth inhibition of the hamartin-tuberin complex. This study reported a Han-Chinese TSC patient with a recurrent variant TSC2 c.5126C>T (p.P1709L). These findings broaden the phenotypic spectrum of TSC caused by this variant and may contribute to improving TSC genetic diagnoses as well as understanding of its mechanisms.

Active Sites Determination of Enzyme 1-aminocyclopropane-1-carboxylic acid synthase 2 (ACS2) of Capsicum chinense using Modeling and In Silico Docking

The growth of Chili pepper (Capsicum chinense Jacquin.) is affected by biotic and abiotic stresses. Abiotic stress such as waterlogging increases the expression of ACS (1-aminocyclopropane-1-carboxylic acid synthase) enzyme. This enzyme plays a great role in the process of ethylene biosynthesis and encoded by multiple genes. Waterlogging causes hypoxia condition. One of ACS enzymes that responds to hypoxia condition is ACS2. The different respond to hypoxia stress among plant was assumed to be caused by a different structure of the ACS2 enzyme. This study aimed to identify and confirm the active site of Capsicum chinense Jacquin ACS2 using modeling and in silico docking. The result of the three-dimensional (3D) structure modeling showed 91% similarity of Capsicum chinense Jacquin ACS2 with the structure of the tomato (Solanum lycopersicum L.). The Capsicum chinense ACS2 confirmed five active sites that bind to the substrates asparagin396B, valine397B, thyrosine152B, threonine128B, and thyrosine92A.

Integrated Three-Dimensional Structural and Petrophysical Modeling for Assessment of CO2 Storage Potential in Gas Reservoir

Abstract Carbon dioxide (CO2) storage in oil and gas reservoirs is one of the most effective methods for enhancing hydrocarbon recovery efficiency and mitigating climate change by securely storing CO2. However, building a realistic three-dimensional (3D) geological model for these storage reservoirs poses a significant challenge. To address this, employing a novel methodology combining 3D structural and petrophysical modeling, our study presents a pioneering effort to assess the CO2 storage potential of the faulted reservoir between the G- and E-sands of the Lower Goru Formation in the Kadanwari Gas Field (KGF), Middle Indus Basin (MIB), Pakistan. Analysis of seismic data revealed a complex reservoirs structure affected by normal faults oriented in a northwest–southeast direction. These faults partition the reservoir into several compartments and could serve as potential pathways for CO2 migration. Three-dimensional structural modeling unveiled complex features, for example horsts, grabens, and half-grabens, formed through multiple deformation stages. Petrophysical modeling indicated promising reservoir characteristics, that is high porosity and permeability in the desired zone. Three-dimensional property models were generated using sequential Gaussian simulation to represent the distribution of petrophysical properties, for example porosity, permeability, shale volume, and water saturation. Geological uncertainties were incorporated enabling the calculation of pore volume distribution and corresponding uncertainty. A novel technique was developed to assess the probable CO2 storage potential in the KGF, considering its distinctive features. The study revealed a storage potential ranging from 10.13 million tons (P10) to 101.54 million tons (P90), with an average potential of 53.58 million tons (P50). Our study offers a comprehensive approach to evaluating CO2 storage potential in complex geological zones, filling a knowledge gap in existing literature on carbon neutrality efforts in Pakistan. These findings lay the groundwork for future initiatives in geological CO2 storage in the MIB and support the country’s efforts to reduce carbon emissions.

Enhanced Immune Response Against Echinococcus Granulosus Through a CTLA-4/B7 Affinity-Based Vaccine.

Background: Echinococcosis is a zoonotic infectious disease that poses a significant threat to the health of individuals living in rural regions. While vaccination represents a potential strategy for disease prevention, there is currently no effective vaccine available for humans to prevent cystic echinococcosis (CE). This study aimed to design a novel multi-epitope vaccine (MEV) against Echinococcus granulosus for human use, employing immunoinformatics methods. Methods: We identified core epitopes from two key antigens, EgA31 and EgG1Y162, and integrated them into the immunoglobulin variable region of CTLA-4 (CTLA-4lgV) to create the CVE31-162 vaccine construct. The secondary and tertiary structures of the CVE31-162 were established using bioinformatics methods. The interaction between the CVE31-162 and B7 molecules was assessed through molecular dynamics simulations. Finally, both in vitro and in vivo experiments were conducted to validate the effectiveness of the CVE31-162 against the immunological effects of Echinococcus granulosus. Results: Bioinformatics analysis indicated that CVE31-162 exhibits favorable antigenicity, stability, and non-allergenicity. Furthermore, CVE31-162 demonstrated a stable three-dimensional structural model. Molecular docking (MD) and molecular dynamics simulations (MDS) revealed a strong binding affinity between CVE31-162 and B7 molecules. Immune simulation results suggested that the vaccine elicits robust humoral and cell-mediated immune responses. Both in vitro and in vivo experiments demonstrated that immunized mice exhibited significantly elevated levels of antigen-specific antibodies and enhanced lymphocyte proliferation compared to the control group. Conclusions:CVE31-162, which is based on the interaction between CTLA-4 and B7, represents a promising multi-epitope vaccine for Echinococcus granulosus.

Genome-Wide Identification and Evolutionary Analysis of Functional BBM-like Genes in Plant Species.

Background/Objectives: BABY BOOM (BBM), a transcription factor from the APETALA2 (AP2) protein family, plays a critical role in somatic embryo induction and apomixis. BBM has now been widely applied to induce apomixis or enhance plant transformation and regeneration efficiency through overexpression or ectopic expression. However, the structural and functional evolutionary history of BBM genes in plants is still not well understood. Methods: The protein sequences of 10 selected plant species were used to locate the branch of BBM-Like by key domain identification and phylogenetic tree construction. The identified BBML genes were used for further conserved motif identification, gene structural analysis, miRNA binding site prediction, cis-acting element prediction, collinear analysis, protein-protein interaction network construction, three-dimensional structure modeling, molecular docking, and expression pattern analysis. Results: A total of 24 BBML proteins were identified from 10 representative plant species. Phylogenetic relationship analysis displayed that BBML proteins from eudicots and monocots were divided into two clusters, with monocots exhibiting a higher number of BBMLs. Gene duplication events indicated that whole genome/segmental duplication were the primary drivers of BBML genes' evolution in the tested species, with purifying selection playing a key role during evolution processes. Comparative analysis of motif, domains, and gene structures revealed that most BBMLs were highly evolutionarily conserved. The expression patterns of BBML genes revealed significant tissue specificity, particularly in the root and embryo. We also constructed protein-protein interaction networks and molecular docking models to identify functional pathways and key amino acid residues of BBML proteins. The functions of BBMLs may differ between monocots and eudicots, as suggested by the functional enrichment of interacting proteins. Conclusions: Our research delved into the molecular mechanism, evolutionary relationships, functional differentiation, and expression patterns of BBML genes across plants, laying the groundwork for further investigations into the molecular properties and biological roles of BBMLs.

Utilizing deep learning for alzheimer's disease treatment: Targeting -amyloid for therapeutic intervention

Abstract. Amyloid-beta (A for short) is a protein intricately linked to Alzheimers disease (AD for short). In the brains of AD patients, A forms abnormal deposits known as amyloid plaques, which are considered one of the key factors in the progression of AD. These plaques may disrupt communication between neurons, leading to cell death and a decline in cognitive function. Therefore, this study aims to utilize Computer-aided drug design (CADD) techniques to screen and optimize potential therapeutic agents targeting A. Through literature review and UniProt, we identified the active sites of A and constructed a three-dimensional structural model using AlphaFold. We employed Molecular docking technology to virtually screen a compound library for candidate molecules that may bind to A. The selected candidates were then subjected to Molecular dynamics simulation to verify their stability, and their molecular structures were further optimized using Pharmacophore modeling. Our research results indicate the successful screening of a series of candidate compounds with high affinity and selectivity. These compounds can form stable complexes with the active sites of A, thereby inhibiting its aggregation and deposition. Current structural determination methods for A have certain limitations. Techniques such as cryo-electron microscopy (cryo-EM) and scanning electron microscopy (SEM) can observe the morphology of A fibrils but typically do not provide atomic-level structural information. Additionally, A proteins tend to form non-specific aggregates in vitro, presenting challenges in preparing samples suitable for structural analysis. The innovation of this study lies in the combination of various computer-assisted technologies, offering new perspectives and methods for the drug treatment of AD and laying the groundwork for the development of novel therapeutic agents targeting A.

Noise reduction performance and maintenance time of porous asphalt pavement

The noise reduction performance of porous asphalt (PA) pavement is significantly influenced by the presence of air voids, which act as sound absorbers. However, factors such as traffic-induced compaction and clogging due to the accumulation of dust, sand, and debris can alter the morphology and quantity of these voids, consequently compromising noise reduction effectiveness. In this study, a comprehensive investigation into the noise reduction capabilities and maintenance requirements of porous asphalt pavement was conducted by a novel approach. Initially, a three-dimensional structural model of the PA mixture was constructed using X-ray computed tomography. Subsequently, this model was integrated into finite element analysis software to develop a "tire-pavement-air" coupled model. It is important to note that in our numerical approach, we have made several simplifications. For instance, the "tire-pavement-air" coupled model was simplified within the air model is set to fully absorbing boundary condition (*Nonreflecting), and the pavement material was assumed to be linear elastic to ensure computational efficiency and convergence of the model. The findings revealed that as the air-void content increased, the average sound pressure level (SPL) of tire/pavement noise exhibited a gradual decrease. Furthermore, when air voids became obstructed due to factors like rainwater and clogging materials, the SPL of tire/pavement noise initially increased with rising air-void content before subsequently decreasing. Notably, porous asphalt with an air-void content of 20 % demonstrated relatively effective noise reduction capabilities. Based on simulation results obtained under varying conditions, including rainfall and clogging, critical thresholds for air-void content were identified to determine recommended maintenance time for PA pavements. Specifically, an air-void content of 17 % was proposed as the threshold for cleaning maintenance, while a content of 14 % was suggested as an indicator for failure alert, respectively. These findings contribute valuable insights into optimizing the design and maintenance strategies for porous asphalt pavements to enhance their noise reduction performance and prolong their functional lifespan.

Structural and hydrodynamic modelling of the probability of breakage of branching and plate coral colonies

Climate change is amplifying the intensity of severe weather events, with coastal regions such as coral reefs facing heightened vulnerability to cyclonic wave forces. Structural models to predict bending stress and breakage of corals have been developed for coral colonies to enhance comprehension and prediction of the effects of hydrodynamic disturbances on coral reefs. However, there is scope for improving these predictions by evolving the methodology for quantifying complicated and variable coral morphologies. This study aims to predict breakage thresholds for two of the most prevalent coral morphologies: branching and plate corals (using Acropora muricata and Acropora hyacinthus as study species). Laboratory and field measurements were taken to assess coral morphologies and material characteristics. Morphological features of 47 branching colonies and 100 plate colonies were surveyed at the study site (Heron Reef, southern GBR) and the tensile strength of 80 coral samples was obtained by in situ and laboratory testing. Three-dimensional structural models of branching and plate coral colonies were developed, encompassing multiple coral colonies with varying morphological patterns from relatively shallow (5–7 m) to deep (9–12 m) zones. Model results were calibrated and verified with existing data, revealing that velocity thresholds of 1.7 m/s and 5.0 m/s would destroy 90% of the simulated branching coral structures growing in the deep and shallow parts of the forereef zone, respectively. In contrast, the plate corals have sufficient margins of safety even in extreme flow conditions (7 m/s). Additionally, skeletal strength and structural performance were adjusted based on varying degrees of bioerosion inside the coral skeleton. A higher probability of breakage was observed as the extent of bioerosion increased. The laboratory experiments of hydrodynamic loads on coral colony show that the sheltering effect due to one or two neighbouring colonies in the upwave direction is negligible. These models can be easily adjusted to provide predictions for other coral species, shapes, levels of bioerosion, and locations (e.g., sheltered or exposed areas). Comprehensive predictions about the level of expected damage and rubble generation in different areas can be used in reef management planning and restoration prioritization.

Investigation of Load Characteristics and Stress-Energy Evolution Laws of Gob-Side Roadways Under Thick and Hard Roofs

The stress environments of gob-side roadways (GSRs) are becoming increasingly complex during deep coal mining under thick and hard roofs. This leads to strong strata behaviors, including roadway floor heave, roof subsidence, and even coal bursts. Among them, coal bursts pose the greatest threat to production safety in coal mines. Coal bursts in a GSR strongly correlate with the load characteristics and stress-energy evolution laws of the roadway. This study analyzes the roof structures of double working faces (DWFs) during the initial weighting stage (IWS) and full mining stage (FMS) of gob-side working faces (GSWFs). This study also explores how varying roof structures affect the stability of GSRs. Three-dimensional roof structure models of DWFs and mechanical models of dynamic and static loads superposition on a GSR throughout the IWS and FMS of a GSWF were developed. An analysis identified the primary stress sources affecting the GSR throughout various mining stages of the GSWF. Subsequently, the principle of “three-load” superposition was developed. A novel method was proposed to quantify the stress state in the GSR surrounding rock across different mining stages of the GSWF. The method quantitatively characterizes the load of the GSR surrounding rock. Based on this, the criterion for judging the burst failure of the roadway was established. Numerical simulations are used to analyze the stress-energy evolution laws of the working face, coal pillar, and GSR surrounding rock during the mining process of the GSWF. These findings offer valuable references for studying and preventing coal bursts in GSRs under equivalent geological situations.

Reduction of three-dimensional models of elastic thin-walled structures

Reduction of three-dimensional models of elastic thin-walled structures

A novel PAX9 variant in a Chinese family with non-syndromic oligodontia and genotype-phenotype analysis of PAX9variants.

This study aimed to identifyPAX9variants in non-syndromic tooth agenesis families of China, as well as to analyze the genotype⁃phenotype of non-syndromic tooth agenesis caused by PAX9variants, which can provide a basis for the genetic diagnosis of tooth agenesis. We collected the data of 44 patients with non-syndromic oligodontia who underwent treatment at Stomatological Hospital of Hebei Medical University between 2018 and 2023. Whole-exome sequencing was performed on the peripheral blood of the proband and its core family members, and the variants were verified by Sanger sequencing. Pathogenicity analysis and function prediction of the variants were performed using bioinformatics tools. The correlation between the genotype of PAX9 variant and its corresponding phenotype was examined by reviewing 55 publications retrieved from PubMed. The studies involved 232 tooth agenesis patients with PAX9 variants. A novel PAX9 c.447delG (p.Pro150Argfs*62) and a reported PAX9 c.406C>T (p.Gln136*) were identified in two Chinese families. Through bioinformatics analysis and three-dimensional structural modeling, we postulated that the frameshift variant was pathogenic. The outcome was the premature cessation of PAX9 protein, which caused severe structural and functional deficiencies. Summarizing the PAX9 genotype-phenotype relationship revealed that patients carrying the PAX9 variant commonly led to loss of the second molars. We identified the novel PAX9 c.447delG (p.Pro150Argfs*62) in a Chinese family of non-syndromic oligodontia, expanding the known variant spectrum of PAX9. The most susceptible tooth position for PAX9 variants of tooth agenesis was the second molars and the deciduous molars during the deciduous dentition.

Effects of three-dimensional quality assessment nursing intervention on efficacy and disease management of patients undergoing esophageal cancer surgery.

Esophageal cancer is one of the most common malignant tumors. The three-dimensional quality structure model is a quality assessment theory that includes three dimensions: Structure, process, and results. To investigate the effects of nursing interventions with three-dimensional quality assessment on the efficacy and disease management ability of patients undergoing esophageal cancer surgery. In this prospective study, the control group received routine nursing, and the intervention group additionally received a three-dimensional quality assessment intervention based on the above routine care. Self-efficacy and patient disease management abilities were evaluated using the General Self-Efficacy Scale (GSES) and Exercise of Self-Care Agency scale, respectively. IBM SPSS Statistics for Windows, version 17.0, was used for the data processing. This study recruited 112 patients who were assigned to the control and experimental groups (n = 56 per group). Before the intervention, there was no significant difference in GSES scores between the two groups (P > 0.05). After the intervention, the GSES scores of both groups increased, with the experimental group showing higher values (P < 0.05). At the time of discharge and three months after discharge, the scores for positive attitudes, self-stress reduction, and total score of health promotion in the experimental group were higher than those in the control group (P < 0.05). The implementation of a three-dimensional quality structure model for postoperative patients with esophageal cancer can effectively improve their self-management ability and self-efficacy of postoperative patients.

Unveiling the Catalytic Roles of DsBBS1 and DsBBS2 in the Bibenzyl Biosynthesis of Dendrobium sinense.

Dendrobium sinense, an endemic medicinal herb in Hainan Island, is rich in bibenzyl compounds. However, few studies have explored the molecular mechanisms of bibenzyl biosynthesis. This study presents a comprehensive analysis of DsBBS1 and DsBBS2 function in D. sinense. A molecular docking simulation revealed high-resolution three-dimensional structural models with minor domain orientation differences. Expression analyses of DsBBS1 and DsBBS2 across various tissues indicated a consistent pattern, with the highest expression being found in the roots, implying that they play a pivotal role in bibenzyl biosynthesis. Protein expression studies identified optimal conditions for DsBBS2-HisTag expression and purification, resulting in a soluble protein with a molecular weight of approximately 45 kDa. Enzyme activity assays confirmed DsBBS2's capacity to synthesize resveratrol, exhibiting higher Vmax and lower Km values than DsBBS1. Functional analyses in transgenic Arabidopsis demonstrated that both DsBBS1 and DsBBS2 could complement the Atchs mutant phenotype. The total flavonoid content in the DsBBS1 and DsBBS2 transgenic lines was restored to wild-type levels, while the total bibenzyl content increased. DsBBS1 and DsBBS2 are capable of catalyzing both bibenzyl and flavonoid biosynthesis in Arabidopsis. This study provides valuable insights into the molecular mechanisms underlying the biosynthesis of bibenzyl compounds in D. sinense.

3D physiologically-informed deep learning for drug discovery of a novel vascular endothelial growth factor receptor-2 (VEGFR2)

Angiogenesis is an essential process in tumorigenesis, tumor invasion, and metastasis, and is an intriguing pathway for drug discovery. Targeting vascular endothelial growth factor receptor 2 (VEGFR2) to inhibit tumor angiogenic pathways has been widely explored and adopted in clinical practice. However, most drugs, such as the Food and Drug Administration –approved drug axitinib (ATC code: L01EK01), have considerable side effects and limited tolerability. Therefore, there is an urgent need for the development of novel VEGFR2 inhibitors. In this study, we propose a novel strategy to design potential candidates targeting VEGFR2 using three-dimensional (3D) deep learning and structural modeling methods. A geometric-enhanced molecular representation learning method (GEM) model employing a graph neural network (GNN) as its underlying predictive algorithm was used to predict the activity of the candidates. In the structural modeling method, flexible docking was performed to screen data with high affinity and explore the mechanism of the inhibitors. Small -molecule compounds with consistently improved properties were identified based on the intersection of the scores obtained from both methods. Candidates identified using the GEM-GNN model were selected for in silico modeling using molecular dynamics simulations to further validate their efficacy. The GEM-GNN model enabled the identification of candidate compounds with potentially more favorable properties than the existing drug, axitinib, while achieving higher efficacy.

Simulation and Analysis of Bidirectional Reflection Factors of Southern Evergreen Fruit Trees Based on 3D Radiative Transfer Model

The canopy of perennial evergreen fruit trees in southern China has a unique Bidirectional Reflectance Factor (BRF) due to its complex multi-branch structure and density changes. This study aimed to address the lack of clarity regarding the changes in BRF of evergreen fruit trees in southern China. Litchi, a typical fruit tree in this region, was chosen as the subject for establishing a three-dimensional (3D) real structure model. The canopy BRF of litchi was simulated under different leaf components, illumination geometry, observed geometry, and leaf area index (LAI) using a 3D radiation transfer model. The corresponding changes in characteristics were subsequently analyzed. The findings indicate that the chlorophyll content and equivalent water thickness of leaves exert significant influences on canopy BRF, whereas the protein content exhibit relatively weak effects. Variation in illumination and observation geometry results in the displacement of hotspots, with the solar zenith angle and view zenith angle exerting significant influence on the BRF. As the LAI of the litchi orchard increases, the distribution of hotspots becomes more concentrated, and the differences in angle information are relatively smaller when observed from multiple angles. With the increase in LAI in litchi orchards, the BRF on the principal plane would be saturated, but observation at hotspots could alleviate this phenomenon. The above analysis provides a reference for quantitative inversion of vegetation parameters using remote sensing monitoring information of typical perennial evergreen fruit trees.

Unveiling the 3D Morphology of Epitaxial GaAs/AlGaAs Quantum Dots.

Strain-free GaAs/AlGaAs semiconductor quantum dots (QDs) grown by droplet etching and nanohole infilling (DENI) are highly promising candidates for the on-demand generation of indistinguishable and entangled photon sources. The spectroscopic fingerprint and quantum optical properties of QDs are significantly influenced by their morphology. The effects of nanohole geometry and infilled material on the exciton binding energies and fine structure splitting are well-understood. However, a comprehensive understanding of GaAs/AlGaAs QD morphology remains elusive. To address this, we employ high-resolution scanning transmission electron microscopy (STEM) and reverse engineering through selective chemical etching and atomic force microscopy (AFM). Cross-sectional STEM of uncapped QDs reveals an inverted conical nanohole with Al-rich sidewalls and defect-free interfaces. Subsequent selective chemical etching and AFM measurements further reveal asymmetries in element distribution. This study enhances the understanding of DENI QD morphology and provides a fundamental three-dimensional structural model for simulating and optimizing their optoelectronic properties.