NanoLocz: Image Analysis Platform for AFM, High‐Speed AFM, and Localization AFM DOI Creative Commons
George R. Heath,

Emily Micklethwaite,

Tabitha M. Storer

et al.

Small Methods, Journal Year: 2024, Volume and Issue: unknown

Published: March 1, 2024

Abstract Atomic Force Microscopy (AFM), High‐Speed AFM (HS‐AFM) simulation AFM, and Localization (LAFM) enable the study of molecules surfaces with increasingly higher spatiotemporal resolution. However, effective rapid analysis images movies produced by these techniques can be challenging, often requiring use multiple image processing software applications scripts. Here, NanoLocz, an open‐source solution that offers advanced capabilities for community, is presented. Integration continued development tools essential to improve access data, increase throughput, open new opportunities. NanoLocz efficiently leverages rich data has offer incorporating combining existing newly developed methods HS‐AFM, LAFM seamlessly. It facilitates streamlines workflows from import raw through various workflows. demonstrates it enables including single‐molecule LAFM, time‐resolved LAFM.

Language: Английский

3D‐Printed Functional Hydrogel by DNA‐Induced Biomineralization for Accelerated Diabetic Wound Healing DOI Creative Commons
Nahyun Kim, Hyun Lee, Ginam Han

et al.

Advanced Science, Journal Year: 2023, Volume and Issue: 10(17)

Published: April 19, 2023

Chronic wounds in diabetic patients are challenging because their prolonged inflammation makes healing difficult, thus burdening patients, society, and health care systems. Customized dressing materials needed to effectively treat such that vary shape depth. The continuous development of 3D-printing technology along with artificial intelligence has increased the precision, versatility, compatibility various materials, providing considerable potential meet abovementioned needs. Herein, functional inks comprising DNA from salmon sperm DNA-induced biosilica inspired by marine sponges, developed for machine learning-based wound dressings. biomineralized silica incorporated into hydrogel a fast, facile manner. 3D-printed generates provided appropriate porosity, characterized effective exudate blood absorption at sites, mechanical tunability indicated good fidelity printability during optimized 3D printing. Moreover, act as nanotherapeutics, enhancing biological activity dressings terms reactive oxygen species scavenging, angiogenesis, anti-inflammation activity, thereby accelerating acute healing. These bioinspired hydrogels produce using biomineralization strategy an excellent platform clinical applications chronic repair.

Language: Английский

Citations

80

Recent microfluidic advances in submicron to nanoparticle manipulation and separation DOI Open Access
Samith Hettiarachchi, Haotian Cha, Lingxi Ouyang

et al.

Lab on a Chip, Journal Year: 2022, Volume and Issue: 23(5), P. 982 - 1010

Published: Nov. 1, 2022

Manipulation and separation of submicron nanoparticles are indispensable in many chemical, biological, medical, environmental applications. Conventional technologies such as ultracentrifugation, ultrafiltration, size exclusion chromatography, precipitation immunoaffinity capture limited by high cost, low resolution, purity or the risk damage to biological particles. Microfluidics can accurately control fluid flow channels with dimensions tens micrometres. Rapid microfluidics advancement has enabled precise sorting isolating better resolution efficiency than conventional technologies. This paper comprehensively studies latest progress microfluidic technology for nanoparticle manipulation. We first summarise principles traditional techniques manipulating nanoparticles. Following classification active, passive, hybrid approaches, we elaborate on physics, device design, working mechanism applications each technique. also compare merits demerits different benchmark them Concurrently, seven standard post-separation detection Finally, discuss current challenges future perspectives manipulation separation.

Language: Английский

Citations

62

Cryo-EM of Helical Polymers DOI
Fengbin Wang, O.M. Gnewou, Armin Solemanifar

et al.

Chemical Reviews, Journal Year: 2022, Volume and Issue: 122(17), P. 14055 - 14065

Published: Feb. 8, 2022

While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due huge number macromolecular assemblies viruses, bacteria, archaea, and eukaryotes, use cryo-EM study synthetic soft matter noncovalent been much more limited. This mainly lack familiarity with materials science chemistry communities, contrast fact that was developed as biological technique. Nevertheless, relatively few structures self-assembled peptide nanotubes ribbons solved at near-atomic resolution by have demonstrated should be method choice for structural analysis filaments. In addition, also self-assembly enormous potential polymorphism, something may obscured techniques such scattering spectroscopy. These revealed how far we currently are from being able predict structure these their chaotic behavior.

Language: Английский

Citations

57

Nanomechanical-atomistic insights on interface interactions in asphalt mixtures with various chloride ion erosion statuses DOI
Zhengwu Long, Lingyun You, Fu Xu

et al.

Journal of Colloid and Interface Science, Journal Year: 2022, Volume and Issue: 628, P. 891 - 909

Published: Aug. 5, 2022

Language: Английский

Citations

56

Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images DOI Creative Commons
Romain Amyot, Arin Marchesi, Clemens M. Franz

et al.

PLoS Computational Biology, Journal Year: 2022, Volume and Issue: 18(3), P. e1009970 - e1009970

Published: March 16, 2022

Atomic force microscopy (AFM) can visualize the dynamics of single biomolecules under near-physiological conditions. However, scanning tip probes only molecular surface with limited resolution, missing details required to fully deduce functional mechanisms from imaging alone. To overcome such drawbacks, we developed a computational framework reconstruct 3D atomistic structures AFM scans, employing simulation and automatized fitting experimental images. We provide applications images ranging machines, protein filaments, large-scale assemblies 2D lattices, demonstrate how obtained full information advances understanding beyond original topographic image. show that further allows for quantitative feature assignment within measured topographies. Implementation methods into versatile interactive interface BioAFMviewer software, freely available at www.bioafmviewer.com, presents opportunity broad Bio-AFM community employ enormous amount existing structural modeling data facilitate interpretation resolution-limited

Language: Английский

Citations

46

Visualizing RNA conformational and architectural heterogeneity in solution DOI Creative Commons
Jienyu Ding, Yun-Tzai Lee,

Yuba R. Bhandari

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Feb. 9, 2023

Abstract RNA flexibility is reflected in its heterogeneous conformation. Through direct visualization using atomic force microscopy (AFM) and the adenosylcobalamin riboswitch aptamer domain as an example, we show that a single sequence folds into conformationally architecturally structures under near-physiological solution conditions. Recapitulated 3D topological from AFM molecular surfaces reveal all conformers share same secondary structural elements. Only population-weighted cohort, not any conformer, including crystal structure, can account for ensemble behaviors observed by small-angle X-ray scattering (SAXS). All except one are functionally active terms of ligand binding. Our findings provide visual evidence sequence-structure relationship physiologically relevant conditions more complex than one-to-one well-structured proteins. The conformational architectural ensembles at single-molecule level may suggest new approaches to analyses.

Language: Английский

Citations

42

Current Methods and Prospects for Analysis and Characterization of Nanomaterials in the Environment DOI
Chuanjia Jiang, Songlin Liu, Tong Zhang

et al.

Environmental Science & Technology, Journal Year: 2022, Volume and Issue: 56(12), P. 7426 - 7447

Published: May 18, 2022

Analysis and characterization of naturally occurring engineered nanomaterials in the environment are critical for understanding their environmental behaviors defining real exposure scenarios risk assessment. However, this is challenging primarily due to low concentration, structural heterogeneity, dynamic transformation complex matrices. In review, we first summarize sample pretreatment methods developed separation preconcentration from samples, including natural waters, wastewater, soils, sediments, biological media. Then, review state-of-the-art microscopic, spectroscopic, mass spectrometric, electrochemical, size-fractionation determination number abundance, as well morphological, compositional, properties nanomaterials, with discussion on advantages limitations. Despite recent advances detecting characterizing environment, challenges remain improve analytical sensitivity resolution expand method applications. It important develop simultaneous multifaceted nanomaterial situ analysis under conditions detection nanoscale contaminants emerging concern (e.g., nanoplastics nanoparticles), which will greatly facilitate standardization samples.

Language: Английский

Citations

40

Subcellular visualization: Organelle-specific targeted drug delivery and discovery DOI
Xintian Shao,

Caicai Meng,

Wenjing Song

et al.

Advanced Drug Delivery Reviews, Journal Year: 2023, Volume and Issue: 199, P. 114977 - 114977

Published: June 28, 2023

Language: Английский

Citations

37

A pentameric TRPV3 channel with a dilated pore DOI
Shifra Lansky,

John Michael Betancourt,

Jingying Zhang

et al.

Nature, Journal Year: 2023, Volume and Issue: 621(7977), P. 206 - 214

Published: Aug. 30, 2023

Language: Английский

Citations

37

Humic Substances: From Supramolecular Aggregation to Fractal Conformation—Is There Time for a New Paradigm? DOI Creative Commons
Ruggero Angelico, Claudio Colombo, Erika Di Iorio

et al.

Applied Sciences, Journal Year: 2023, Volume and Issue: 13(4), P. 2236 - 2236

Published: Feb. 9, 2023

Natural organic matter, including humic substances (HS), comprises complex secondary structures with no defined covalent chemical bonds and stabilized by inter- intra-molecular interactions, such as hydrogen bonding, Van der Waal’s forces, pi-pi interactions. The latest view describes HS aggregates a hydrogel-like structure comprised hydrophobic core of aromatic residues surrounded polar amphiphilic molecules akin self-assembled soft material. A different is based on the classification this material either mass or surface fractals. former intended made clustering macromolecules generating dendritic networks, while latter have been modelled in terms solvent-impenetrable layer lyophilic This study reviews evolution increasingly refined models that appeared literature, all capable to describing physicochemical properties HS. All are critically examined revisited their ability provide key information structural organization Understanding how molecular association pathway influences aggregation also provides acknowledgment role environment.

Language: Английский

Citations

26