Nanoscale Architecture Research Articles

Illuminating cellular architecture and dynamics with fluorescence polarization microscopy.

Ever since Robert Hooke's 17th century discovery of the cell using a humble compound microscope, light-matter interactions have continuously redefined our understanding of cell biology. Fluorescence microscopy has been particularly transformative and remains an indispensable tool for many cell biologists. The subcellular localization of biomolecules is now routinely visualized simply by manipulating the wavelength of light. Fluorescence polarization microscopy (FPM) extends these capabilities by exploiting another optical property - polarization - allowing researchers to measure not only the location of molecules, but also their organization or alignment within larger cellular structures. With only minor modifications to an existing fluorescence microscope, FPM can reveal the nanoscale architecture, orientational dynamics, conformational changes and interactions of fluorescently labeled molecules in their native cellular environments. Importantly, FPM excels at imaging systems that are challenging to study through traditional structural approaches, such as membranes, membrane proteins, cytoskeletal networks and large macromolecular complexes. In this Review, we discuss key discoveries enabled by FPM, compare and contrast the most common optical setups for FPM, and provide a theoretical and practical framework for researchers to apply this technique to their own research questions.

Strongly Enhanced Electronic Bandstructure Renormalization by Light in Nanoscale Strained Regions of Monolayer MoS2/Au(111) Heterostructures.

Understanding and controlling the photoexcited quasiparticle (QP) dynamics in monolayer (ML) transition metal dichalcogenides (TMDs) lays the foundation for exploring the strongly interacting, nonequilibrium two-dimensional (2D) QP and polaritonic states in these quantum materials and for harnessing the properties emerging from these states for optoelectronic applications. In this study, scanning tunneling microscopy/spectroscopy (STM/scanning tunneling spectroscopy) with light illumination at the tunneling junction is performed to investigate the QP dynamics in ML MoS2 on an Au(111) substrate with nanoscale corrugations. The corrugations on the surface of the substrate induce nanoscale local strain in the overlaying ML MoS2 single crystal, which result in energetically favorable spatial regions where photoexcited QPs, including excitons, trions, and electron-hole plasmas, accumulate. These strained regions exhibit pronounced electronic bandstructure renormalization as a function of the photoexcitation wavelength and intensity as well as the strain gradient, implying strong interplay among nanoscale structures, strain, and photoexcited QPs. In conjunction with the experimental work, we construct a theoretical framework that integrates nonuniform nanoscale strain into the electronic bandstructure of a ML MoS2 lattice using a tight-binding approach combined with first-principle calculations. This methodology enables better understanding of the experimental observation of photoexcited QP localization in the nanoscale strain-modulated electronic bandstructure landscape. Our findings illustrate the feasibility of utilizing nanoscale architectures and optical excitations to manipulate the local electronic bandstructure of ML TMDs and to enhance the many-body interactions of excitons, which is promising for the development of nanoscale energy-adjustable optoelectronic and photonic technologies, including quantum emitters and solid-state quantum simulators for interacting exciton polaritons based on engineered periodic nanoscale trapping potentials.

Extracellular filaments revealed by affinity capture cryo-electron tomography.

Cryogenic-electron tomography (cryo-ET) has provided an unprecedented glimpse into the nanoscale architecture of cells by combining cryogenic preservation of biological structures with electron tomography. Micropatterning of extracellular matrix proteins is increasingly used as a method to prepare adherent cell types for cryo-ET as it promotes optimal positioning of cells and subcellular regions of interest for vitrification, cryo-focused ion beam (cryo-FIB) milling, and data acquisition. Here we demonstrate a micropatterning workflow for capturing minimally adherent cell types, human T-cells and Jurkat cells, for cryo-FIB and cryo-ET. Our affinity capture system facilitated the nanoscale imaging of Jurkat cells, revealing extracellular filamentous structures. It improved workflow efficiency by consistently producing grids with a sufficient number of well positioned cells for an entire cryo-FIB session. Affinity capture can be extended to facilitate high resolution imaging of other adherent and non-adherent cell types with cryo-ET.

Thermally drawn multi-material fibers: from fundamental research to industrial applications

Thermally drawn fiber devices, with their complex micro- to nanoscale architectures, hold great promises not only for scientific research but also for scalable industrial applications in soft smart systems.

Commands of Synthetic Biology to Modernize and Re-design the Biological Systems

The scope of synthetic biology continues to expand and has encompassed a huge number of biological features. Its scope starts from scratch, enabling the de novo synthesis of biological systems. It has re-designed the biological systems and empowered the production of synthetic genes, RNA, DNA and proteins by undertaking the control of pathways involved in genetic regulation. It has increased the production of nano-scale RNA architectures and synthetic biological circuits which either have therapeutic or other productive uses. Furthermore, advancements in synthetic biology have enabled the generation of diversity through methods such as epPCR and site-directed mutagenesis, allowing for the creation of complex genetic variations. Additionally, synthetic biology intersects with computer engineering to design functional biological devices and circuits, utilizing computational analysis to guide the design process. Moreover, ethical and regulatory considerations are paramount in synthetic biology, with careful examination required to address dual-use concerns, environmental impacts, and issues of social justice and equitable access to benefits. As synthetic biology continues to advance, it presents opportunities to address pressing challenges in fields ranging from medicine and agriculture to environmental conservation and beyond. Thus, the fusion of synthetic biology with other scientific disciplines holds promise for transformative innovation and societal benefit. The present discussion enlightened the core of generating complex biological systems and has given a brief overview on the fusion of synthetic biology with other fields of science.Keywords: Biological Systems; Genetic Regulation; Synthetic biology circuits

Uncovering the Complex Nanoscale Architecture of Human Enamel and Insights in Its Nanoscale Mechanical Properties

Uncovering the Complex Nanoscale Architecture of Human Enamel and Insights in Its Nanoscale Mechanical Properties

Nanoscale architecture of synaptic vesicles and scaffolding complexes revealed by cryo-electron tomography

The spatial distribution of proteins and their arrangement within the cellular ultrastructure regulates the opening of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors in response to glutamate release at the synapse. Fluorescence microscopy imaging revealed that the postsynaptic density (PSD) and scaffolding proteins in the presynaptic active zone (AZ) align across the synapse to form a trans-synaptic "nanocolumn," but the relation to synaptic vesicle release sites is uncertain. Here, we employ focused-ion beam (FIB) milling and cryoelectron tomography to image synapses under near-native conditions. Improved image contrast, enabled by FIB milling, allows simultaneous visualization of supramolecular nanoclusters within the AZ and PSD and synaptic vesicles. Surprisingly, membrane-proximal synaptic vesicles, which fuse to release glutamate, are not preferentially aligned with AZ or PSD nanoclusters. These synaptic vesicles are linked to the membrane by peripheral protein densities, often consistent in size and shape with Munc13, as well as globular densities bridging the synaptic vesicle and plasma membrane, consistent with prefusion complexes of SNAREs, synaptotagmins, and complexin. Monte Carlo simulations of synaptic transmission events using biorealistic models guided by our tomograms predict that clustering AMPARs within PSD nanoclusters increases the variability of the postsynaptic response but not its average amplitude. Together, our data support a model in which synaptic strength is tuned at the level of single vesicles by the spatial relationship between scaffolding nanoclusters and single synaptic vesicle fusion sites.

Molybdenum Disulfide-Assisted Spontaneous Formation of Multistacked Gold Nanoparticles for Deep Learning-Integrated Surface-Enhanced Raman Scattering.

Several fabrication methods have been developed for label-free detection in various fields. However, fabricating high-density and highly ordered nanoscale architectures by using soluble processes remains a challenge. Herein, we report a biosensing platform that integrates deep learning with surface-enhanced Raman scattering (SERS), featuring large-area, close-packed three-dimensional (3D) architectures of molybdenum disulfide (MoS2)-assisted gold nanoparticles (AuNPs) for the on-site screening of coronavirus disease (COVID-19) using human tears. Some AuNPs are spontaneously synthesized without a reducing agent because the electrons induced on the semiconductor surface reduce gold ions when the Fermi level of MoS2 and the gold electrolyte reach equilibrium. With the addition of polyvinylpyrrolidone, a two-dimensional large-area MoS2 layer assisted in the formation of close-packed 3D multistacked AuNP structures, resembling electroless plating. This platform, with a convolutional neural network-based deep learning model, achieved outstanding SERS performance at subterascale levels despite the microlevel irradiation power and millisecond-level acquisition time and accurately assessed susceptibility to COVID-19. These results suggest that our platform has the potential for rapid, low-damage, and high-throughput label-free detection of exceedingly low analyte concentrations.

Design and Optimization of Mechano transduction Sensors for effective analysis of proteins with Robotic interference

Méchano transduction sensors convert mechanical inputs into electrical signals, allowing robots to detect and interact with their environments in various bio-imaging applications. Current bio-sensor systems have some drawbacks that prevent them from being widely used in robotic applications. These include low sensitivity, short durability, and expensive manufacturing costs regarding picture prediction and categorization. To overcome these obstacles and improve robotic mechanotransduction sensors for efficient protein analysis, this work suggests Unique Sensor Fabrication Techniques (USFT). These methods enhance sensor performance in protein analysis while keeping costs low and scalability high via integrating complex micro- and nano-scale materials and architectures. In comparison to traditional sensor designs, comprehensive evaluations based on predefined parametric criteria show significant improvements in areas such as sensitivity, response time, and predictability in protein biomolecules. In addition, assessments of scalability and manufacturability point to the possibility of widespread use in robotic systems for protein categorization and prediction. In bioimaging applications, this study helps advance sensor technology for reliable and efficient robot-environment interaction.

AI analysis of super-resolution microscopy: Biological discovery in the absence of ground truth.

Super-resolution microscopy, or nanoscopy, enables the use of fluorescent-based molecular localization tools to study molecular structure at the nanoscale level in the intact cell, bridging the mesoscale gap to classical structural biology methodologies. Analysis of super-resolution data by artificial intelligence (AI), such as machine learning, offers tremendous potential for the discovery of new biology, that, by definition, is not known and lacks ground truth. Herein, we describe the application of weakly supervised paradigms to super-resolution microscopy and its potential to enable the accelerated exploration of the nanoscale architecture of subcellular macromolecules and organelles.

Application and Development of Electrospun Nanofiber Scaffolds for Bone Tissue Engineering.

Nanofiber scaffolds have gained significant attention in the field of bone tissue engineering. Electrospinning, a straightforward and efficient technique for producing nanofibers, has been extensively researched. When used in bone tissue engineering scaffolds, electrospun nanofibers with suitable surface properties promote new bone tissue growth and enhance cell adhesion. Recent advancements in electrospinning technology have provided innovative approaches for scaffold fabrication in bone tissue engineering. This review comprehensively examines the utilization of electrospun nanofibers in bone tissue engineering scaffolds and evaluates the relevant literature. The review begins by presenting the fundamental principles and methodologies of electrospinning. It then discusses various materials used in the production of electrospun nanofiber scaffolds for bone tissue engineering, including natural and synthetic polymers, as well as certain inorganic materials. The challenges associated with these materials are also described. The review focuses on novel electrospinning techniques for scaffold construction in bone tissue engineering, such as multilayer nanofibers, multifluid electrospinning, and the integration of electrospinning with other methods. Recent advancements in electrospinning technology have enabled the fabrication of precisely aligned nanofiber scaffolds with nanoscale architectures. These innovative methods also facilitate the fabrication of biomimetic structures, wherein bioactive substances can be incorporated and released in a controlled manner for drug delivery purposes. Moreover, they address issues encountered with traditional electrospun nanofibers, such as mechanical characteristics and biocompatibility. Consequently, the development and implementation of novel electrospinning technologies have revolutionized scaffold fabrication for bone tissue engineering.

Single-Molecule Orientation Imaging Reveals the Nano-Architecture of Amyloid Fibrils Undergoing Growth and Decay.

Amyloid-beta (Aβ42) aggregates are characteristic Alzheimer's disease signatures, but probing how their nanoscale architectures influence their growth and decay remains challenging using current technologies. Here, we apply time-lapse single-molecule orientation-localization microscopy (SMOLM) to measure the orientations and rotational "wobble" of Nile blue (NB) molecules transiently binding to Aβ42 fibrils. We correlate fibril architectures measured by SMOLM with their growth and decay over the course of 5 to 20 min visualized by single-molecule localization microscopy (SMLM). We discover that stable Aβ42 fibrils tend to be well-ordered and signified by well-aligned NB orientations and small wobble. SMOLM also shows that increasing order and disorder are signatures of growing and decaying fibrils, respectively. We also observe SMLM-invisible fibril remodeling, including steady growth and decay patterns that conserve β-sheet organization. SMOLM reveals that increased fibril architectural heterogeneity is correlated with dynamic remodeling and that large-scale fibril remodeling tends to originate from strongly heterogeneous local regions.

Presynaptic nanoscale components of retrograde synaptic signaling.

While our understanding of the nanoscale architecture of anterograde synaptic transmission is rapidly expanding, the qualitative and quantitative molecular principles underlying distinct mechanisms of retrograde synaptic communication remain elusive. We show that a particular form of tonic cannabinoid signaling is essential for setting target cell-dependent synaptic variability. It does not require the activity of the two major endocannabinoid-producing enzymes. Instead, by developing a workflow for physiological, anatomical, and molecular measurements at the same unitary synapse, we demonstrate that the nanoscale stoichiometric ratio of type 1 cannabinoid receptors (CB1Rs) to the release machinery is sufficient to predict synapse-specific release probability. Accordingly, selective decrease of extrasynaptic CB1Rs does not affect synaptic transmission, whereas in vivo exposure to the phytocannabinoid Δ9-tetrahydrocannabinol disrupts the intrasynaptic nanoscale stoichiometry and reduces synaptic variability. These findings imply that synapses leverage the nanoscale stoichiometry of presynaptic receptor coupling to the release machinery to establish synaptic strength in a target cell-dependent manner.

Unveiling the nanoscale architectures and dynamics of protein assembly with in situ atomic force microscopy

AbstractProteins play a vital role in different biological processes by forming complexes through precise folding with exclusive inter‐ and intra‐molecular interactions. Understanding the structural and regulatory mechanisms underlying protein complex formation provides insights into biophysical processes. Furthermore, the principle of protein assembly gives guidelines for new biomimetic materials with potential applications in medicine, energy, and nanotechnology. Atomic force microscopy (AFM) is a powerful tool for investigating protein assembly and interactions across spatial scales (single molecules to cells) and temporal scales (milliseconds to days). It has significantly contributed to understanding nanoscale architectures, inter‐ and intra‐molecular interactions, and regulatory elements that determine protein structures, assemblies, and functions. This review describes recent advancements in elucidating protein assemblies with in situ AFM. We discuss the structures, diffusions, interactions, and assembly dynamics of proteins captured by conventional and high‐speed AFM in near‐native environments and recent AFM developments in the multimodal high‐resolution imaging, bimodal imaging, live cell imaging, and machine‐learning‐enhanced data analysis. These approaches show the significance of broadening the horizons of AFM and enable unprecedented explorations of protein assembly for biomaterial design and biomedical research.

Design and Function of α-Helix-Rich, Heme-Binding Peptide Materials.

Peptide materials often employ short peptides that self-assemble into unique nanoscale architectures and have been employed across many fields relevant to medicine and energy. A majority of peptide materials are high in β-sheet, secondary structure content, including heme-binding peptide materials. To broaden the structural diversity of heme-binding peptide materials, a small series of peptides were synthesized to explore the design criteria required for (1) folding into an α-helix structure, (2) assembling into a nanoscale material, (3) binding heme, and (4) demonstrating functions similar to that of heme proteins. One peptide was identified to meet all four criteria, including the heme protein function of CO binding and its microsecond-to-millisecond recombination rates, as measured by transient absorption spectroscopy. Implications of new design criteria and peptide material function through heme incorporation are discussed.

Additive-Driven Nanoscale Architecture of Solid Electrolyte Interphase Revealed by Cryogenic Transmission Electron Microscopy.

In Li metal batteries (LMBs), which boast the highest theoretical capacity, the chemical structure of the solid electrolyte interphase (SEI) serves as the key component that governs the growth of reactive Li. Various types of additives have been developed for electrolyte optimization, representing one of the most effective strategies to enhance the SEI properties for stable Li plating. However, as advanced electrolyte systems become more chemically complicated, the use of additives is empirically optimized. Indeed, their role in SEI formation and the resulting cycle life of LMBs are not well-understood. In this study, we employed cryogenic transmission electron microscopy combined with Raman spectroscopy, theoretical studies including molecular dynamics (MD) simulations and density functional theory (DFT) calculations, and electrochemical measurements to explore the nanoscale architecture of SEI modified by the most representative additives, lithium nitrate (LiNO3) and vinylene carbonate (VC), applied in a localized high-concentration electrolyte. We found that LiNO3 and VC play distinct roles in forming the SEI, governing the solvation structure, and influencing the kinetics of electrochemical reduction. Their collaboration leads to the desired SEI, ensuring prolonged cycle performance for LMBs. Moreover, we propose mechanisms for different Li growth and cycling behaviors that are determined by the physicochemical properties of SEI, such as uniformity, elasticity, and ionic conductivity. Our findings provide critical insights into the appropriate use of additives, particularly regarding their chemical compatibility.

Synthesis and Electrochemical Performance of Flexible and Freestanding Graphene-Encapsulated PANi@MnO2/ECNFs Nanoscale Architectures for Electrochemical Supercapacitors

Synthesis and Electrochemical Performance of Flexible and Freestanding Graphene-Encapsulated PANi@MnO2/ECNFs Nanoscale Architectures for Electrochemical Supercapacitors

Hydration and wetting mechanism of borosilicate – Polyvinyl alcohol (PVA) hybrid aerogels of potential bioactivity

Mesoporous borosilicate – polyvinyl alcohol (PVA) hybrid aerogels show positive bioactivity when interacting with dental pulp stem cells. The surface characteristics and the nanostructures of the hydrated aerogel particles are important in determining the biological response. This study reports the comparative structural characterization of pristine and stepwise hydrated hybrid aerogels, and proposes a qualitative mechanism for the wetting and pore-filling processes of these mesoporous materials. Nuclear magnetic resonance (NMR) relaxometry and cryoporometry revealed the extensive hydration of PVA macromolecules in the hybrid skeleton when contrasted to the wetting of pure silica aerogels. In spite of this extensive hydration, the open and permeable pore-structure of the hybrid borosilicate-PVA aerogels are preserved even when completely filled with liquid water. The conservation of the nanoscale architecture of the hybrid aerogels upon wetting was further confirmed by SANS. Finally, it was shown that the incorporation of microcrystalline hydroxyapatite into the hybrid skeleton does not alter the advantageous morphological features and wetting mechanism of the hybrid aerogels. The rough nanostructured skeleton is advantageous for cell binding and ensures facile mass transport through the particles in aqueous suspensions.

Nanoscale myelinogenesis image in developing brain via super-resolution nanoscopy by near-infrared emissive curcumin-BODIPY derivatives

Understanding the intricate nanoscale architecture of neuronal myelin during central nervous system development is of utmost importance. However, current visualization methods heavily rely on electron microscopy or indirect fluorescent method, lacking direct and real-time imaging capabilities. Here, we introduce a breakthrough near-infrared emissive curcumin-BODIPY derivative (MyL-1) that enables direct visualization of myelin structure in brain tissues. The remarkable compatibility of MyL-1 with stimulated emission depletion nanoscopy allows for unprecedented super-resolution imaging of myelin ultrastructure. Through this innovative approach, we comprehensively characterize the nanoscale myelinogenesis in three dimensions over the course of brain development, spanning from infancy to adulthood in mouse models. Moreover, we investigate the correlation between myelin substances and Myelin Basic Protein (MBP), shedding light on the essential role of MBP in facilitating myelinogenesis during vertebral development. This novel material, MyL-1, opens up new avenues for studying and understanding the intricate process of myelinogenesis in a direct and non-invasive manner, paving the way for further advancements in the field of nanoscale neuroimaging.Graphical

Ribbontail Stingray Skin Employs a Core–Shell Photonic Glass Ultrastructure to Make Blue Structural Color

AbstractStructural blue colors are common in animals, with the tissue nanostructures and material systems that produce them—especially bright blues—typically based on highly ordered nano‐architectures. In this study, we describe an unusually bright and angle‐independent structural blue from the skin of ribbontail stingray, arising from a more disordered array of scattering elements with a previously undescribed core–shell ultrastructure, involving nano‐vesicles enclosing guanine nano‐platelets. We show that this skin architecture functions as an intracellular photonic glass, coherently scattering blue, while broadband absorption from closely associated melanophores obviates the low color saturation typical for photonic glasses. Our characterization of skin ultrastructure and color in a stingray demonstrates how disordered systems can be harnessed to produce brilliant hues while illustrating that the capacity for guanine‐based colors likely arose extremely early in vertebrate evolution. Moreover, the material‐structure‐function associations underlying ribbontail stingray coloration, employing two distinct photonic phenomena, illustrate how the evolution of nanoscale architectures can have profound effects at much larger size scales (e.g., in visual ecology and communication), and provide fundamental guidelines for color‐saturated manmade photonic glasses.