Assembly Of Structures Research Articles

Live-Cell Imaging of miRNAs with the Combination of CHA and HCR Techniques.

The abnormal expression of miRNA-21 is closely related to many cancers, and its sensitive detection plays an important role in the diagnosis and treatment of cancers. In the report, we designed a non-enzymatic amplification sensing system based on the catalytic hairpin assembly (CHA) and palindrome-based hybridization chain reaction (PHCR) technique for the detection and imaging of miRNA in living cells. Based on PHCR technology, two ingeniously designed palindrome-contained fluorescently labeled hairpin probes are sequentially opened upon the stimulation of short oligonucleotide triggers, promoting the autonomous assembly of cross-linked network-like structures (CNSs) and generating fluorescence resonance energy transfer (FRET) signal. Moreover, the PHCR technique can be combined with CHA technology to sufficiently improve amplification efficiency and signal output. By utilizing the CHA-PHCR sensing system, one miRNA-21 activates many triggers through CHA process and in turn initiates the assembly of CNSs by PHCR reaction, efficiently amplifying the FRET signal output. As such, the sensing system can detect target miRNAs down to 10pm with high detection specificity. Moreover, the CNS exhibits the enhanced intracellular stability, enabling the living cell imaging of miRNA-21. The CHA-PHCR sensing system can also screen the expression level of miRNA-21 in different living cells and differentiate cancer cells from healthy cells, which is consistent with the gold-standard PCR method.

Structures of complete extracellular assemblies of type I and type II Oncostatin M receptor complexes.

Oncostatin M (OSM) is a unique Interleukin 6 (IL-6) family cytokine that plays pivotal roles in numerous biological events by signaling via two types of receptor complexes. While type I OSM receptor complex is formed by glycoprotein 130 (gp130) heterodimerization with Leukemia Inhibitory Factor receptor (LIFR), type II OSM receptor complex is composed of gp130 and OSM receptor (OSMR). OSM is an important contributor to multiple inflammatory diseases and cancers while OSM inhibition has been shown to be effective at reducing symptoms, making OSM an attractive therapeutic target. Using cryogenic electron microscopy (cryo-EM), we characterize full extracellular assemblies of human type I OSM receptor complex and mouse type II OSM receptor complex. The juxtamembrane domains of both complexes are situated in close proximity due to acute bends of the receptors. The rigid N-terminal extension of OSM contributes to gp130 binding and OSM signaling. Neither glycosylation nor pro-domain cleavage of OSM affects its activity. Mutagenesis identifies multiple OSM and OSMR residues crucial for complex formation and signaling. Our data reveal the structural basis for the assemblies of both type I and type II OSM receptor complexes and provide insights for modulation of OSM signaling in therapeutics.

Flexural and vibration behaviours of novel covered CFRP composite joints with an MWCNT-modified adhesive

Abstract Co-curing bonding is more efficient than co-bonding and secondary bonding for structural component assembly. This work used novel covered laminas with co-cured joining techniques (CL-CCT) to create carbon fibre-reinforced polymer (CFRP) composite adhesive-bonded joints. Additionally, the researchers evaluated how multi-walled carbon nanotubes (MWCNTs) affect the bending and dynamic properties of CFRP composite joints. The researchers added various weights of MWCNTs to the covered laminas along with co-cured CFRP adhesive-bonded joints. The study revealed that epoxy and 0.25 wt% MWCNT adhesive produced the strongest and most flexible joints. These joints were 118 and 15% stronger than joints made from pure epoxy CL-CC CFRP, respectively. Compared to pure epoxy CC-CFRP composite joints, the strength of CL-CC CFRP composite joints with 0.25 wt% MWCNTs increased by 374 and 109%, respectively. Interestingly, MWCNTs with a wt% of 1.25 had the greatest natural frequency in all three vibration modes, which are 19, 19, and 13% higher than that of the pure epoxy CL-CC CFRP composite joint. There are 28, 30, and 24% more natural frequencies in 1.25 wt% MWCNT-based CL-CC CFRP composite joints than those in pure epoxy-based joints in all three modes. Analysis of variance was employed for statistical investigation. Optimization and prediction were done using an artificial neural network and the Levenberg–Marquardt technique.

MotY modulates proton-driven flagellar motor output in Pseudomonas aeruginosa

MotY homologs are present in a variety of monotrichous bacterial strains and are thought to form an additional structural T ring in flagellar motors. While MotY potentially plays an important role in motor torque generation, its impact on motor output dynamics remains poorly understood. In this study, we investigate the role of MotY in P. aeruginosa, elucidating its interactions with the two sets of stator units (MotAB and MotCD) using Förster resonance energy transfer (FRET) assays. Employing a newly developed bead assay, we characterize the dynamic behavior of flagellar motors in motY mutants, identifying MotY as the key functional protein to affect the clockwise bias of naturally unbiased motors in P. aeruginosa. Our findings reveal that MotY enhances stator assembly efficiency without affecting the overall assembly of the flagellar structure. Additionally, we demonstrate that MotY is essential for maintaining motor torque and regulating switching rates. Our study highlights the physiological significance of MotY in fine-tuning flagellar motor function in complex environments.

Merged-nets enumeration for the systematic design of multicomponent reticular structures.

Rational design of intricate multicomponent reticular structures is often hindered by the lack of suitable blueprint nets. We established the merged-net approach, proffering optimal balance between designability and complexity, as a systematic solution for the rational assembly of multicomponent structures. In this work, by methodically mapping node-net relationships among 53 basic edge-transitive nets, we conceived a signature net map to identify merging net pairs, resulting in the enumeration of 53 merged nets. We developed a practical design algorithm and proposed more than 100 multicomponent metal-organic framework platforms. The effectiveness of this approach is commended by the successful synthesis of four classes of materials, which is based on merging three-periodic nets with the four possible net periodicities. The construction of multicomponent materials based on derived nets of merged nets highlights the potential of the merged-net approach in accelerating the discovery of intricate reticular materials.

Electrostatic Assembly of Gold Nanoclusters in Reverse Emulsion Enabling Nanoassemblies with Tunable Structure and Size for Enhanced NIR-II Fluorescence Imaging.

The precise control of the assembly structure and size of gold nanoclusters (AuNCs) can potentially amplify their near-infrared II (NIR-II) fluorescence imaging and targeting properties. However, the conventional electrostatic assembly of AuNCs and charged molecules faces challenges in balancing the inherent electrostatic repulsions among charged units and regulating the diffusion of assembly units. These difficulties limit precise control over assembly size and structure, along with limited options for coassembled molecules, thereby restricting imaging properties and targeting capability. To circumvent this challenge, we developed a reverse emulsion-confined electrostatic assembly method. This technique efficiently constructs AuNC nanoassemblies with diverse coassembled molecules, allowing for the fine-tuning of assembly size and structure, including both core-satellite and homogeneous AuNC nanoassemblies. The development of two distinct nanoassemblies can be partially attributed to the varying diffusive rates of AuNCs or the AuNCs/polymer complex within the fused emulsion droplets. This variance arises from steric hindrances encountered during the emulsion fusion process. Interestingly, core-satellite nanoassemblies exhibit the strongest NIR-II fluorescence enhancement. Finally, the introduction of a hyaluronic acid coating on the surfaces of nanoassemblies with varying sizes enables the nanoprobes to achieve enhanced lymph node imaging through size modulation and macrophage targeting, which are used for surgical navigation to remove lymph node metastases. We envision that this self-assembly strategy can be extended to a wide range of electrostatic assembly systems for the development of multicomponent functional materials.

Control of spin liquid-like dynamics by geometry of 2D nanocluster networks

Network structures of magnetic molecular assemblies on a two-dimensional (2D) material are attractive platforms for molecular spintronics and for the study of 2D magnetic materials. However, it is still a challenging task to connect such assemblies with appropriate magnetic interactions. Recently, uniform nanoclusters consisting of about 100 magnetic amino-ferrocene molecules were self-organized on a graphene oxide nanosheet by on-surface synthesis. Here, the dynamics of weakly interacting molecular spins in the nanocluster networks is investigated by exploiting the tunability of the intercluster distance through the chemical reaction. The stochastic simulation shows that the entanglement of the spin orientations at the sites in the nanocluster by magnetic dipole interactions leads to a liquid-like behavior of the spins (S = 5/2) at T ≲ 15 K, generating spin correlations and slow dynamics observed in Mössbauer spectroscopy and magnetic susceptibility. The energy barrier for generating magnetic relaxation and the deviation temperature from thermally activated relaxation depend on the intercluster distance, i.e., the interactions between the nanoclusters, indicating that the relaxation can be tuned by the geometry of the nanocluster networks. The present results pave the way for the chemical design of 2D nanocluster networks and chemically functionalized 2D materials.

Tailoring ternary complexes of lactoferrin, EGCG, and α-lactalbumin by assembly sequence strategies: Structural characterization, assembly mechanism, and emulsification elucidation

Tailoring ternary complexes of lactoferrin, EGCG, and α-lactalbumin by assembly sequence strategies: Structural characterization, assembly mechanism, and emulsification elucidation

SERS-lateral flow immunoassay based on AuNR@Ag@SiO2-AuNP assembly for ultra-sensitive detection of deoxynivalenol in grain

In view of the serious harm and widespread pollution caused by deoxynivalenol (DON), it is crucial to quantify its presence in the food safety assessment process. Here, we designed a core-shell-satellite nano assembly structure as a probe, composed of an anisotropic AuNR@Ag core, an ultra-thin SiO2 layer and a high surface coverage AuNPs satellites, which showed outstanding SERS activity and high stability. Anti-DON antibodies were modified on the surface of the prepared core-shell-satellite nano-assembly structure as SERS immunoprobe for DON specific detection using SERS-based lateral flow immunoassay (LFIA) with the advantages of simplicity, rapidity, and high sensitivity. Under optimal conditions, the detection limit for detecting DON using the SERS-LFIA method was 0.053 fg/mL, and the linear detection ranged from 0.1 fg/mL to 1 μg/mL. The SERS-LFIA strips based on AuNR@Ag@SiO2-AuNP nanostructures demonstrated the great potential for quick quantitative DON detection, providing a reference for trace detection of highly toxin mycotoxins.

Structure-function relationship for functional films with constructed graded channels in dye/salt separation and fouling resistance

The structural assembly of polypyrrole particle stacking, combined with polydopamine space-filling, forms composite film with a network of interconnected fluid channels. The composite films achieve high water flus, separation efficiency and ratio of organic dyes/inorganic salts (flux: >600 L m−2 h−1 bar−1; dye rejection: ~100 %; salt rejection: <5 %). Simulation using different dye fouling models show that the dye only interacts at the surface, and hardly affects internal pores of the film throughout the filtration process. Owing to the patterned surface structure as constructed by microsphere arrangement and inter-structure adaptation assembly, the functional film has excellent contamination tolerance and rinsing regeneration for macromolecular pollutants. The results of computational fluid dynamics simulations further indicate that the high shear stress above the microspheres with vortex flow in the interstitial space has a positive effect on reducing contaminant deposition. In addition to the separation property, the composite film shows good structural stability and mechanical strength in various complex water environments, benefiting their future practical applications. This work unveils the structure-function relationship for composite function films with constructed graded channels in dye/salt separation, which is important for the design and future application of these functional films.

Quality control for single-cell analysis of high-plex tissue profiles using CyLinter.

Tumors are complex assemblies of cellular and acellular structures patterned on spatial scales from microns to centimeters. Study of these assemblies has advanced dramatically with the introduction of high-plex spatial profiling. Image-based profiling methods reveal the intensities and spatial distributions of 20-100 proteins at subcellular resolution in 103-107 cells per specimen. Despite extensive work on methods for extracting single-cell data from these images, all tissue images contain artifacts such as folds, debris, antibody aggregates, optical aberrations and image processing errors that arise from imperfections in specimen preparation, data acquisition, image assembly and feature extraction. Here we show that these artifacts dramatically impact single-cell data analysis, obscuring meaningful biological interpretation. We describe an interactive quality control software tool, CyLinter, that identifies and removes data associated with imaging artifacts. CyLinter greatly improves single-cell analysis, especially for archival specimens sectioned many years before data collection, such as those from clinical trials.

Super-Resolution Microscopy as a Versatile Tool in Probing Molecular Assembly.

Molecular assembly is promising in the construction of advanced materials, obtaining structures with specific functions. In-depth investigation of the relationships between the formation, dynamics, structure, and functionality of the specific molecular assemblies is one of the greatest challenges in nanotechnology and chemistry, which is essential in the rational design and development of functional materials for a variety of applications. Super-resolution microscopy (SRM) has been used as a versatile tool for investigating and elucidating the structures of individual molecular assemblies with its nanometric resolution, multicolor ability, and minimal invasiveness, which are also complementary to conventional optical or electronic techniques that provide the direct observation. In this review, we will provide an overview of the representative studies that utilize SRM to probe molecular assemblies, mainly focusing on the imaging of biomolecular assemblies (lipid-based, peptide-based, protein-based, and DNA-based), organic-inorganic hybrid assemblies, and polymer assemblies. This review will provide guidelines for the evaluation of the dynamics of molecular assemblies, assembly and disassembly processes with distinct dynamic behaviors, and multicomponent assembly through the application of these advanced imaging techniques. We believe that this review will inspire new ideas and propel the development of structural analyses of molecular assemblies to promote the exploitation of new-generation functional materials.

Solvent-adaptive hydrogels with lamellar confinement cellular structure for programmable multimodal locomotion

Biological organisms can perform flexible and controllable multimodal motion under external stimuli owing to the hierarchical assembly of anisotropic structures across multiple length scales. However, artificial soft actuators exhibit the limited response speed, deformation programmability and movement capability especially in harsh environments because of insufficient anisotropic hierarchy and precision in structural design. Here, we report a programmed assembly directed confinement polymerization method for the fabrication of environmentally tolerant and fast responsive hydrogels with lamellar assembly-confined cellular structure interpenetrated with highly aligned nanopillars by the directional freezing-assisted polymerization in the predesigned anisotropic laminar scaffold. The obtained hydrogel exhibits ultrafast responsiveness and anisotropic deformation exposed to temperature/light/solvent stimulation, maintaining highly consistent responsive deformation capability in all-polarity solvents over 100 days of soaking. Moreover, the hydrogels implement photoactive programmable multi-gait locomotion whose amplitude and directionality are precisely regulated by the intrinsic structure, including controlled crawling and rotation in water and non-polar solvents, and 3D self-propulsion floating and swimming in polar solvents. Thus, this hydrogel with hierarchically ordered structure and dexterous locomotion may be suitable for flexible intelligent actuators serving in harsh solvent environments.

Cooperative augmented assembly (CAA): augmented reality for on-site cooperative robotic fabrication

Recent years have witnessed significant advances in computational design and robotic fabrication for large-scale manufacturing. Although these advances have enhanced the speed, precision, and reproducibility of digital fabrication processes, they often lack adaptability and fail to integrate manual actions in a digital model. Addressing this challenge, the present study introduces cooperative augmented assembly (CAA), a phone-based mobile Augmented Reality (AR) application that facilitates cooperative assembly of complex timber structures between humans and robots. CAA enables augmented manual assembly, intuitive robot control and supervision, and task sharing between humans and robots, creating an adaptive digital fabrication process. To allocate tasks to manual or robotic actions, the mobile AR application allows multiple users to access a shared digital workspace. This is achieved through a flexible communication system that allows numerous users and robots to cooperate seamlessly. By harnessing a cloud-based augmented reality system in combination with an adaptive digital model, CAA aims to better incorporate human actions in robotic fabrication setups, facilitating human–machine cooperation workflows and establishing a highly intuitive, adaptable digital fabrication process within the Architecture, Engineering, and Construction sector.

A Discrete Four-Stranded β-Sheet through Catenation of M2L2 Metal-Peptide Rings.

Methods for precisely constructing a β-sheet assembly with number-defined strands in solution remains quite limited due to its intense aggregation property. Here, we report the precise construction of a four-stranded anti-parallel β-sheet by utilizing a non-covalent approach. This was achieved by folding and assembly of Ag+ and a pentapeptide (1) with the Ala-D3pa-Gly-3pa-Val (3pa: β-(3-pyridyl)-alanine) sequence, which was designed to form an interlocking Ag2(1)2 ring through metal cross-linking of the side chains. NMR analyses and X-ray crystallographic studies characterized the structure of the discrete β-sheet assembly as well as the remarkable structural selectivity in terms of strands' number, orientation and the sheet type.

Essential tremor with tau pathology features seeds indistinguishable in conformation from Alzheimer's disease and primary age-related tauopathy.

Neurodegenerative tauopathies are characterized by the deposition of distinct fibrillar tau assemblies whose rigid core structures correlate with defined neuropathological phenotypes. Essential tremor (ET) is a progressive neurological disease that, in some cases, is associated with cognitive impairment and tau accumulation. Consequently, we explored the tau assembly conformation in ET patients with tau pathology using cytometry-based tau biosensor assays. These assays quantify tau prion seeding activity present in brain homogenates based on conversion of intracellular tau-fluorescent protein fusions from a soluble to an aggregated state. Prions exhibit seeding barriers, whereby a specific assembly structure cannot serve as a template for a native monomer if the amino acids are not compatible. We recently exploited the tau prion species barrier to define tauopathies by systematically substituting alanine (Ala) in the tau monomer and measuring its incorporation into seeded aggregates within biosensor cells. The Ala scan precisely classified the conformation of tau seeds from diverse tauopathies. We next studied 18 ET patient brains with tau pathology. Only one case had concurrent high amyloid-β plaque pathology consistent with Alzheimer's disease (AD). We detected robust tau seeding activity in 9 (50%) of the patients. This predominantly localized to the temporal pole and temporal cortex. We examined 8 ET cases with the Ala scan and determined that the amino acid requirements for tau monomer incorporation into aggregates seeded from these ET brain homogenates were identical to those of AD and primary age-related tauopathy (PART), and completely distinct from other tauopathies such as corticobasal degeneration, chronic traumatic encephalopathy, and progressive supranuclear palsy. Based on these studies, tau assembly cores in a pathologically confined subset of ET cases with high tau pathology are identical to AD and PART. This could facilitate more precise diagnosis and therapy for ET patients with cognitive impairment.

Sequence Flow: interactive web application for visualizing partial order alignments

BackgroundMultiple sequence alignment (MSA) has proven extremely useful in computational biology, especially in inferring evolutionary relationships via phylogenetic analysis and providing insight into protein structure and function. An alternative to the standard MSA model is partial order alignment (POA), in which aligned sequences are represented as paths in a graph rather than rows in a matrix. While the POA model has proven useful in several applications (e.g. sequencing reads assembly and pangenome structure exploration), we lack efficient visualization tools that could highlight its advantages.ResultsWe propose Sequence Flow – a web application designed to address the above problem. Sequence Flow presents the POA as a Sankey diagram, a kind of graph visualisation typically used for graphs representing flowcharts. Sequence Flow enables interactive alignment exploration, including fragment selection, highlighting a selected group of sequences, modification of the position of graph nodes, structure simplification etc. After adjustment, the visualization can be saved as a high-quality graphic file. Thanks to the use of SanKEY.js – a JavaScript library for creating Sankey diagrams, designed specifically to visualize POAs, Sequence Flow provides satisfactory performance even with large alignments.ConclusionsWe provide Sankey diagram-based POA visualization tools for both end users (Sequence Flow) and bioinformatic software developers (SanKEY.js). Sequence Flow webservice is available at https://sequenceflow.mimuw.edu.pl/. The source code for SanKEY.js is available at https://github.com/Krzysiekzd/SanKEY.js and for Sequence Flow at https://github.com/Krzysiekzd/SequenceFlow.

Updating assembly parameters for spacecraft assembly process state changes: based on data fusion method

Thermal protection systems (TPSs) are important components of reusable spacecraft, and their assembly quality has a crucial impact on flight safety. Owing to the complex assembly process and variable states of spacecraft thermal protection systems, assembly parameters may vary under different assembly states. Therefore, to obtain assembly parameters accurately and efficiently under different assembly states, in this study, 3D point cloud data and fiber optic sensor data were fused to develop an assembly parameter update method for assembly process state changes. Firstly, based on the measured data of thermal protection components and load-bearing structure, the gap, flush and matching parameters solution model are proposed. Secondly, to address the deformation problem of the load-bearing structure caused by changes in assembly status, a fusion method based on laser scanning and sensor detection was devised to achieve deformation prediction of the assembly structure during the assembly process. Thirdly, based on the assembly parameter solution model and point cloud prediction model, a constraint-based assembly parameter optimisation model was established, and an improved quantum particle swarm optimisation (LQPSO) algorithm was employed to achieve assembly parameter updates oriented toward changes in assembly status. Finally, an experimental system for array-based thermal protection structure simulation was established to validate the proposed method. The results show that the proposed parameter update method can achieve ideal results for different assembly state simulation components.

Fabrication of a Partial Encapsulation Architecture on S-Scheme Heterojunctions toward Durable Selective Photocatalytic CO2 Reduction.

It remains a challenging issue to achieve durably stable photocatalytic CO2 reduction over heterojunctions owing to their inherent structural assembly features. Herein, a unique partial encapsulation architecture is fabricated on the 3D/2D CoWO4/C3N5 heterojunction by embedding CoWO4 microspheres on C3N5 nanosheets, which achieves efficient, durable, stable, and selective photocatalytic CO2 reduction. For the optimal 5%-CoWO4/C3N5 heterojunction, the yield of selective CO2 reduction to CO is 7.70 and 3.82 times higher than those of CoWO4 and C3N5 in 4 h, respectively, and it maintains a stable CO generation rate within 20 cycles over 80 h. A series of characterization experiments and density functional theory calculations reveal that the structural stability is reinforced significantly via strong interfacial interaction owing to the unique partial encapsulation architecture fabricated on the 3D/2D CoWO4/C3N5 heterojunction, the separation efficiency of photogenerated carriers is improved by inducing a built-in electric field and triggering the S-scheme charge-transport path, and the high CO product selectivity is attributed to the much lower free energy required for the generation path of CO compared to that for CH4.

A highly capacitive Graphene/Multiholed N‐CNTs hybrid evolved from black humate‐Co‐melamine precursor

Black humic acid (BA) is a black mixture of organic macromolecules isolated from humic acid, which has a greater potential for graphene transformation than fulvic acid and ulmic acid because of more and larger aromatic units and higher molecular weights exceeding 5000 Dalton. Here, chemically bonded BA‐Co‐Melamine precursors are initially constructed using different BA fractions as substrate, Co2+ as bridge bond and melamine as ligand. A series of Graphene/N‐CNTs hybrids (GNCs) is eventually synthesized after the precursor pyrolysis. Resultantly, Fraction Ⅰ, separated at a pH value of 4.16, plays a significant role on constructing the BA‐Co‐Melamine precursor and further producing multiholed GNCs. Due to abundant CNTs, rich mesopores, moderate nitrogen incorporation and a certain graphitized assembly structure, the prepared GNC‐Ⅰ‐b has high capacitance performances. The assembled AC//GNC‐Ⅰ‐b supercapacitor has high specific capacitance (147 F g‐1 at 0.5 A g‐1), rate capability, cycling stability and energy density (16.8 Wh kg‐1 at 14.4 KW kg‐1). The 2032 coin‐type Li//GNC‐Ⅰ‐b half‐cell has high initial discharge capacity (759 mAh g‐1 at 0.03 A g‐1), initial Coulombic efficiency (81.8%), rate performance and cycling stability. Hence, the GNC is a favorable high‐performance carbon material hopefully applied as electrode materials of supercapacitors and LIBs.