3D Architecture Research Articles

Epigenetic and 3D genome reprogramming during the aging of human hippocampus.

Age-related cognitive decline is associated with altered physiology of the hippocampus. While changes in gene expression have been observed in aging brain, the regulatory mechanisms underlying these changes remain underexplored. We generated single-nucleus gene expression, chromatin accessibility, DNA methylation, and 3D genome data from 40 human hippocampal tissues spanning adult lifespan. We observed a striking loss of astrocytes, OPC, and endothelial cells during aging, including astrocytes that play a role in regulating synapses. Microglia undergo a dramatic switch from a homeostatic state to a primed inflammatory state through DNA methylome and 3D genome reprogramming. Aged cells experience erosion of their 3D genome architecture. Our study identifies age-associated changes in cell types/states and gene regulatory features that provide insight into cognitive decline during human aging.

Development and Characterization of a Three-Dimensional Organotypic In Vitro Oral Cancer Model with Four Co-Cultured Cell Types, Including Patient-Derived Cancer-Associated Fibroblasts.

Background/Objectives: Cancer organoids have emerged as a valuable tool of three-dimensional (3D) cell cultures to investigate tumor heterogeneity and predict tumor behavior and treatment response. We developed a 3D organotypic culture model of oral squamous cell carcinoma (OSCC) to recapitulate the tumor-stromal interface by co-culturing four cell types, including patient-derived cancer-associated fibroblasts (PD-CAFs). Methods: A stainless-steel ring was used twice to create the horizontal positioning of the cancer stroma (adjoining normal oral mucosa connective tissue) and the OSCC layer (surrounding normal oral mucosa epithelial layer). Combined with a structured bi-layered model of the epithelial component and the underlying stroma, this protocol enabled us to construct four distinct portions mimicking the oral cancer tissue arising in the oral mucosa. Results: In this model, α-smooth muscle actin-positive PD-CAFs were localized in close proximity to the OSCC layer, suggesting a crosstalk between them. Furthermore, a linear laminin-γ2 expression was lacking at the interface between the OSCC layer and the underlying stromal layer, indicating the loss of the basement membrane-like structure. Conclusions: Since the specific 3D architecture and polarity mimicking oral cancer in vivo provides a more accurate milieu of the tumor microenvironment (TME), it could be crucial in elucidating oral cancer TME.

Human macrophage polarisation and regulation of angiogenesis and osteogenesis is dependent on culture extracellular matrix and dimensionality

The immune system plays a crucial role in tissue repair and regeneration. Macrophages have been identified as master regulators of the early immune response and healing outcome, by orchestrating the temporal nature of the initial inflammation phase and coordinating the fate of stem/progenitor cells involved in regeneration. However, traditional in-vitro models for the study of macrophages often fail to fully replicate the complexity of the in-vivo microenvironment, therefore generating models which do not fully capture the extensive spectrum of macrophage behaviour seen in native tissues. To this end, we used a hematoma-mimetic 3D fibrin matrix characteristic of early injured tissues to generate a 3D in-vitro model mirroring the local macrophage microenvironment. Leveraging this framework, we demonstrated significant effects of extracellular matrix and dimensionality on macrophage basal signalling and polarisation, achieving more pronounced regenerative phenotypes upon stimulation with the M2a polarisation factors compared to traditional 2D tissue culture conditions. Moreover, this enhanced physiological macrophage behaviour corresponded to increased coordination of angiogenesis and osteogenesis, better mirroring the healing processes seen in-vivo. Taken together, this study demonstrates the critical importance of integrating tissue composition and 3D architecture when investigating the macrophage behaviour in-vitro, establishing a powerful tool that overcomes known limitations associated with traditional 2D culture on plastic, and can be used to identify and validate novel immunomodulation strategies to enhance tissue regeneration.

Controlled synthesis of 3D pseudocubic Fe2O3/BiFeO3 heterojunction photocatalyst for effective ciprofloxacin-HCl and methyl orange degradation

Nano-particle-based Iron (III) oxide (Fe2O3) and nanosheet-based bismuth ferrite (BiFeO3) photocatalysts were successfully prepared through a solid-state thermal decomposition approach. Especially, loading BiFeO3 over Fe2O3 demonstrated a 3D pseudocubic-based hierarchical architecture of Fe2O3/BiFeO3 (FeBiOx), which exhibits enhanced photodegradation efficiency of about 98.3 % for antibiotic ciprofloxacin-HCl (C-HCl) and 97.8 % for pollutant methyl orange (MO) under ultraviolet (UV) light irradiation within 180 and 150 min, respectively, compared to pure BiFeO3 and Fe2O3. The improved photocatalytic performance of FeBiOx was ascribed to the increased surface area, Type-II charge transfer scheme, effective charge migration efficiency induced by the surface plasmon resonance (SPR) effect of metal-Bi, and reduced bandgap energy.

Controlling Cell Interactions with DNA Directed Assembly.

The creation of complex cellular environments is critical to mimicking tissue environments that will play a critical role in next-generation tissue engineering, stem cell programming, and therapeutic screening. To address this growing need, techniques capable of manipulating cell-cell and cell-material interactions are required that span single-cell to 3D tissue architectures. DNA programmed assembly and placement of cells present a powerful technique for the bottom-up synthesis of living microtissues for probing key questions in cell-cell and cell-material-driven behaviors through its refined control over placement and architecture. This review examines the current state of the art in the programming of cellular interactions with DNA and its applications spanning tissue model building, fundamental cellular biology, and cell manipulation for measurements across a host of applications.

High-Resolution Genome-Wide Mapping of Chromatin Accessibility and Torsional Stress.

Torsional stress in chromatin plays a fundamental role in cellular functions, influencing key processes such as transcription, replication, and chromatin organization. Transcription and other processes may generate and be regulated by torsional stress. In the genome, the interplay of these processes creates complicated patterns of both positive (+) and negative (-) torsion. However, a challenge in generating an accurate torsion map is determining the zero-torsion baseline signal, which is conflated with chromatin accessibility. Here, we introduce a high-resolution method based on the intercalator trimethylpsoralen (TMP) to address this challenge. We describe a method to establish the zero-torsion baseline while preserving the chromatin state of the genome. This approach enables both high-resolution mapping of accessibility and torsional stress in chromatin in the cell. Our analysis reveals transcription-generated torsional domains consistent with the twin-supercoiled-domain model of transcription and suggests a role for torsional stress in recruiting topoisomerases and in regulating 3D genome architecture via cohesin. This new method provides a potential path forward for using TMP to measure torsional stress in the genome without the confounding contribution of accessibility in chromatin.

Geometric mechanics of kiri-origami-based bifurcated mechanical metamaterials.

We explore a new design strategy of leveraging kinematic bifurcation in creating origami/kirigami-based three-dimensional (3D) hierarchical, reconfigurable, mechanical metamaterials with tunable mechanical responses. We start from constructing three basic, thick, panel-based structural units composed of 4, 6 and 8 rigidly rotatable cubes in close-looped connections. They are modelled, respectively, as 4R, 6R and 8R (R stands for revolute joint) spatial looped kinematic mechanisms, and are used to create a library of reconfigurable hierarchical building blocks that exhibit kinematic bifurcations. We analytically investigate their reconfiguration kinematics and predict the occurrence and locations of kinematic bifurcations through a trial-correction modelling method. These building blocks are tessellated in 3D to create various 3D bifurcated hierarchical mechanical metamaterials that preserve the kinematic bifurcations in their building blocks to reconfigure into different 3D architectures. By combining the kinematics and considering the elastic torsional energy stored in the folds, we develop the geometric mechanics to predict their tunable anisotropic Poisson's ratios and stiffnesses. We find that kinematic bifurcation can significantly effect mechanical responses, including changing the sign of Poisson's ratios from negative to positive beyond bifurcation, tuning the anisotropy, and overcoming the polarity of structural stiffness and enhancing the number of deformation paths with more reconfigured shapes.This article is part of the theme issue 'Origami/Kirigami-inspired structures: from fundamentals to applications'.

Organocatalytic Desymmetric Spirocyclization of Enone-Tethered 2,5-Cyclohexadienone with Isoxazolines to Access Enantioenriched Spiro-Fused Scaffolds.

Enantioselective desymmetric spirocyclization is a powerful tool for concisely generating intricate 3D molecular architectures from readily accessible substrates. Herein, we report an organocatalytic desymmetric spirocyclization of enone-tethered 2,5-cyclohexadienone with 3-arylisoxazol-5(4H)-one to access enantioenriched spiro-fused scaffolds featuring four consecutive stereogenic centers in high yields and excellent diastereo- and enantioselectivities. This protocol could proceed smoothly under parts per million-level organocatalyst loading. Furthermore, the reusability of the catalyst and various intriguing derivatizations of the title product highlight its synthetic utility.

Indium oxide decorated graphitic carbon nitride/multiwalled carbon nanotubes ternary composite for supercapacitor applications

A hybrid ternary composite In2O3/g-C3N4/MWCNT (GCI) was synthesized by combining three-dimensional In2O3, two-dimensional g-C3N4, and one-dimensional MWCNTs employing a one-pot solvothermal method. The resulting In2O3/g-C3N4/MWCNTs composite leverages the combined benefits of the integration of different dimensionality materials and the synergy between its components. Integrating 1D, 2D, and 3-D materials can create hybrid structures with 3D architectures. It exhibits hierarchical porosity that provides better conductive pathways for ion transport and improves the rate performance. The distinct spatial structure of the composite with short ion diffusion paths maximizes the exposure of the active sites and enhances the conductivity, leading to superior energy storage performance. The electrochemical assessment of the In2O3/g-C3N4/MWCNTs composite exhibited a remarkable specific capacitance of 1081 F g−1 at 1 A g−1 with a commendable capacitance retention of 97.5 % at 3 A g−1 over 5000 cycles. An asymmetric supercapacitor fabricated using In2O3/g-C3N4/MWCNT//AC showcased a notable energy density of 57.5 Wh Kg−1 with an impressive power density of 2760 W Kg−1 at 1 A g−1. The outstanding electrochemical attributes of the fabricated device underscore the potential of the material for future applications in hybrid energy storage systems.

Electrodeposition of Polymer Networks as Conformal and Uniform Ultrathin Coatings.

Natural systems, synthetic materials, and devices almost always feature interphases that control the flow of mass and energy or stabilize interfaces between incompatible materials. With technologies transitioning to non-planar and 3D mesoscale architectures, novel deposition methods for realizing ultrathin coatings and interphases are required. Polymer networks are of particular interest for their tunable chemical and physical properties combined with their structural integrity. Here, the electrodeposition of polymer networks (EPoN) is introduced as a general approach to uniformly coat non-planar conductive materials. Conceptually, EPoN utilizes electrochemically activated crosslinkers as polymer end groups to confine their network formation exclusively to the material surface upon charge transfer, yielding a passivating and self-limiting growth of conformal and uniform coatings with tunable submicron thickness on conductive materials. EPoN is found to result in thin functional films of various polymer backbones and side group chemistries as demonstrated for poly(ether) and poly(acrylamide) based polymers as solid electrolyte and thermally responsive interphases, respectively.

Self-Adhesive Electronic Skin with Bio-Inspired 3D Architecture for Mechanical Stimuli Monitoring and Human-Machine Interactions.

Recent development of wearable devices is revolutionizing the way of artificial electronic skins (E-skin), physiological health monitoring and human-machine interactions (HMI). However, challenge remains to fit flexible electronic devices to the human skin with conformal deformation and identifiable electrical feedback according to the mechanical stimuli. Herein, an adhesive E-skin is developed that can firmly attach on the human skin for mechanical stimuli perception. The laser-induced adhesive layer serves as the essential component to ensure the conformal attachment of E-skin on curved surface, which ensures the accurate conversion from mechanical deformation to precise electrical readouts. Especially, the 3D architecture facilitates the non-overlapping outputs that bi-directional joint bending and distinguishes strain/pressure. The optimized E-skin with bio-inspired micro-cilia exhibited significantly improved sensing performances with sensitivity of 0.652 kPa-1 in 0-4kPa and gauge factor of 8.13 for strain (0-15%) with robustness. Furthermore, the adhesive E-skin can distinguish inward/outward joint bending in non-overlapping behaviors, allowing the establishment of ternary system to expand communication capacity for logic outputs such as effective Morse code and intelligent control. It expects that the adhesive E-skin can serve as a functional bridge between human and electrical terminals for applications from daily mechanical monitoring to efficient HMI.

3D genome topology distinguishes molecular subgroups of medulloblastoma

Four main medulloblastoma (MB) molecular subtypes have been identified based on transcriptional, DNA methylation, and genetic profiles. However, it is currently not known whether 3D genome architecture differs between MB subtypes. To address this question, we performed in situ Hi-C to reconstruct the 3D genome architecture of MB subtypes. In total, we generated Hi-C and matching transcriptome data for 28 surgical specimens and Hi-C data for one patient-derived xenograft. The average resolution of the Hi-C maps was 6,833bp. Using these data, we found that insulation scores of topologically associating domains (TADs) were effective at distinguishing MB molecular subgroups. TAD insulation score differences between subtypes were globally not associated with differential gene expression, although we identified few exceptions near genes expressed in the lineages of origin of specific MB subtypes. Our studytherefore supports the notion that TAD insulation scores can distinguish MB subtypes independently of their transcriptional differences.

The Chitinous Skeleton of Ianthella basta Marine Demosponge as a Renewable Scaffold-Based Carrier of Antiseptics

The chitinous skeleton of the marine demosponge Ianthella basta exhibits a unique network-like 3D architecture, excellent capillary properties, and chemical inertness, making it highly suitable for interdisciplinary research, especially in biomedical applications. This study investigates the potential of renewable I. basta chitinous scaffolds for drug delivery and wound dressing. The scaffolds, characterized by a microtubular structure, were impregnated with selected commercially available antiseptics, including solutions with hydrophilic and hydrophobic properties. Evaluations against selected clinical strains of bacteria, as well as fungi, demonstrated significant zones of growth inhibition with antiseptics such as brilliant green, gentian violet, decamethoxine, and polyhexanide. Notably, the antibacterial properties of these antiseptic-treated chitin matrices persisted for over 72 h, effectively inhibiting microbial growth in fresh cultures. These findings highlight the considerable potential of I. basta chitin scaffolds as sustainable, innovative biomaterials for controlled drug release and wound dressing applications.

Non-invasive label-free imaging analysis pipeline for in situ characterization of 3D brain organoids

Brain organoids provide a unique opportunity to model organ development in a system similar to human organogenesis in vivo. Brain organoids thus hold great promise for drug screening and disease modeling. Conventional approaches to organoid characterization predominantly rely on molecular analysis methods, which are expensive, time-consuming, labor-intensive, and involve the destruction of the valuable three-dimensional (3D) architecture of the organoids. This reliance on end-point assays makes it challenging to assess cellular and subcellular events occurring during organoid development in their 3D context. As a result, the long developmental processes are not monitored nor assessed. The ability to perform non-invasive assays is critical for longitudinally assessing features of organoid development during culture. In this paper, we demonstrate a label-free high-content imaging approach for observing changes in organoid morphology and structural changes occurring at the cellular and subcellular level. Enabled by microfluidic-based culture of 3D cell systems and a novel 3D quantitative phase imaging method, we demonstrate the ability to perform non-destructive high-resolution quantitative image analysis of the organoid. The highlighted results demonstrated in this paper provide a new approach to performing live, non-destructive monitoring of organoid systems during culture.

Fabrication of a graphene@Ni foam-supported silver nanoplates-PANI 3D architecture electrode for enzyme-free glucose sensing.

Reliable and cost-effective glucose sensors are in rising demand among diabetes patients. The combination of metals and conducting polymers creates a robust electrocatalyst for glucose oxidation, offering enzyme-free, high stability, and sensitivity with outstanding electrochemical results. Herein, graphene is grown on nickel foam by chemical vapor deposition to make a graphene@nickel foam scaffold (G@NF), on which silver nanoplates-polyaniline (Ag-PANI) 3D architecture is developed by sonication-assisted co-electrodeposition. The resulting binder-free 3D Ag-PANI/G@NF electrode was highly porous, as characterized by x-ray photoelectron spectroscopy, Field emission scanning electron microscope, x-ray diffractometer, FTIR, and Raman spectroscopy. The binder-free 3D Ag-PANI/G@NF electrode exhibits remarkable electrochemical efficiency with a superior electrochemical active surface area. The amperometric analysis provides excellent anti-interference performance, a low limit of deduction (0.1 nM), robust sensitivity (1.7 × 1013µA mM-1cm-2), and a good response time. Moreover, the Ag-PANI/G@NF enzyme-free sensor is utilized to observe glucose levels in human blood serums and exhibits excellent potential to become a reliable clinical glucose sensor.

3D genome contributes to MHC-II neoantigen prediction.

Reliable and ultra-fast DNA and RNA sequencing have been achieved with the emergence of high-throughput sequencing technology. When combining the results of DNA and RNA sequencing for tumor cells of cancer patients, neoantigens that potentially stimulate the immune response of either CD4+ or CD8+ T cells can be identified. However, due to the abundance of somatic mutations and the high polymorphic nature of human leukocyte antigen (HLA) it is challenging to accurately predict the neoantigens. Moreover, comparing to HLA-I presented peptides, the HLA-II presented peptides are more variable in length, making the prediction of HLA-II loaded neoantigens even harder. A number of computational approaches have been proposed to address this issue but none of them considers the DNA origin of the neoantigens from the perspective of 3D genome. Here we investigate the DNA origins of the immune-positive and non-negative HLA-II neoantigens in the context of 3D genome and discovered that the chromatin 3D architecture plays an important role in more effective HLA-II neoantigen prediction. We believe that the 3D genome information will help to increase the precision of HLA-II neoantigen discovery and eventually benefit precision and personalized medicine in cancer immunotherapy.

Design of Superlattice Ferroelectric-Metal Field-effect Transistor for triple-level cell 3D NAND flash

Superlattice ferroelectric-metal field-effect transistor (SL-FeMFET) based three-dimensional NAND architecture (3D NAND) is investigated for triple-level cell (TLC) operations. The SL-FeMFET shows a novel approach for designing the gate-stack using a superlattice of ferroelectric/dielectric/ferroelectric for achieving large memory window ∼3.48 V with program/erase voltage ±7 V for 3D NAND architecture. By TCAD modeling, we demonstrate TLC operation of SL-FeMFET with improving memory window and alleviating variability caused by floating metal layer in FeMFET structure. In addition, as the vertical gate stack increases from 256-layer to 512-layer, the read-out current with worst cases in seven read operations for TLC sensing are examined using page buffer circuit for sensing operation. The simulation results suggest that SL-FeMFET based 3D NAND architecture can operate 512-layer with sufficient sense margin for TLC operation.

Reprocessable and Mechanically Tailored Soft Architectures Through 3D Printing of Elastomeric Block Copolymers

AbstractThermoplastic elastomers (TPEs) are nanostructured, melt‐processable, elastomeric block copolymers. When TPEs that form cylindrical or lamellar nanostructures are macroscopically oriented, their material properties can exhibit several orders of magnitude of anisotropy. Here it is demonstrated that the flows applied during the 3D printing of a cylinder‐forming TPE enable hierarchical control over material nanostructure and function. It is demonstrated that 3D printing allows for control over the extent of nanostructural and mechanical anisotropy and that thermal annealing of 3D printed structures leads to highly anisotropic properties (up to 85 × anisotropic tensile modulus). This approach is leveraged to print functional soft 3D architectures with tunable local and macroscopic mechanical responses. Further, these printed TPEs intrinsically achieve melt‐reprocessability over multiple cycles, reprogrammability, and robust self‐healing via a brief period of thermal annealing, enabling facile fabrication of highly tunable, robust, and recyclable soft architectures.

Design of Virtual Reality System for 3D Visualization and Interaction

Nowadays, a virtual environment or metaverse environment is becoming more popular and can be used for various purposes. There are many computer games and more applications for them such as for training, learning and planning. Currently the presentations of 3-Dimensional (3D) models using mixed reality (MR) technology can be used to avoid misinterpretations of oral and 2-Dimensional (2D) model presentations. As an independent concept and MR applications, MR combines the best of virtual reality (VR) and augmented reality (AR). Therefore, this research aimed to present the descriptions of MR systems, which include its devices, applications, literature reviews and create 3D models that were then implemented in Unity 3D using VR applications for 3D architectural visualization. In addition, the assessment results of the VR application showed that the mean score of 2.85 and 3.45 (“neutral”) indicated that the VR application was a new one for the students and they had never used it before, but they certify that learning with VR is not as difficult as with other simulations. The mean scores of 4.55, 4.70, and 4.75 (“strongly agree”) indicated that the use of the VR application’s 3D objects in the scene was beautiful, clear, and realistic. Besides, the student also enjoyed the immersive experience and the learning was very interesting and they felt that they were in the real world.

Optimizing Energy Solutions: Mott-Schottky Engineered 1D/3D CoWO4(OH)2·H2O/MoS2 Heterostructure for Advanced Energy Storage and Conversion Application.

Heterostructure engineering offers a powerful approach to creating innovative electrocatalysts. By combining different materials, it can achieve synergistic effects that enhance both charge storage and electrocatalytic activity. In this work, it is capitalized on this concept by designing a 1D/3D CoWO4(OH)2·H2O/molybdenum disulfide (CTH/MoS2) heterostructure. It is achieved this by in situ depositing 3D MoS2 nanoflowers on 1D CTH nanorods. To explore the impact of precursor choice, various sulfur (S) sources is investigated. Interestingly, the S precursor influenced the dimensionality of the MoS2 component. For example, L-cysteine (L-cys), and glutathione (GSH) resulted in 0D morphologies, thiourea (TU) led to a 2D structure, and thioacetamide (TAA) yielded a desirable 3D architecture. Notably, the 1D/3D CTH/MoS2-TAA heterostructure exhibited exceptional performance in both supercapacitors (SCs) and quantum dot-sensitized solar cells (QDSSCs). This achievement can be attributed to several factors: the synergetic effect between 1D CTH and 3D MoS2, improved accessibility due to the multi-dimensional structure, and a tailored electronic structure facilitated by the Mott-Schottky (M-S) interaction arising from the different material Fermi levels. This interaction further enhances conductivity, ultimately leading to the observed high specific capacity in SCs (154.44mAhg-1 at 3mAcm-2) and remarkable photovoltaic efficiency in QDSSCs (6.48%).