Plasticity-induced actin polymerization in the dendritic shaft regulates intracellular AMPA receptor trafficking.

AMPA-type receptors (AMPARs) are rapidly inserted into synapses undergoing plasticity to increase synaptic transmission, but it is not fully understood if and how AMPAR-containing vesicles are selectively trafficked to these synapses. Here, we developed a strategy to label AMPAR GluA1 subunits expressed from their endogenous loci in cultured rat hippocampal neurons and characterized the motion of GluA1-containing vesicles using single-particle tracking and mathematical modeling. We find that GluA1-containing vesicles are confined and concentrated near sites of stimulation-induced structural plasticity. We show that confinement is mediated by actin polymerization, which hinders the active transport of GluA1-containing vesicles along the length of the dendritic shaft by modulating the rheological properties of the cytoplasm. Actin polymerization also facilitates myosin-mediated transport of GluA1-containing vesicles to exocytic sites. We conclude that neurons utilize F-actin to increase vesicular GluA1 reservoirs and promote exocytosis proximal to the sites of synaptic activity.

Multiple Particle Tracking: A Method for Probing Biologically Relevant Mobility of Bacterial Extracellular Vesicles.

Bacterial extracellular vesicles (bEVs) are produced by both Gram-negative and Gram-positive bacteria. These biological nanoparticles transport small molecules, nucleic acids, and proteins, enabling communication with both bacterial and mammalian cells. bEVs can evade and disrupt biological barriers, and their lipid membranes protect their cargo from degradation, facilitating long-distance communication in vivo. Furthermore, bacteria are easily manipulated and easily cultured. These combined factors make bEVs an ideal candidate for drug delivery applications. Thus, the study of how bEVs interact with biological barriers is interesting from both a signaling and drug delivery perspective. Here we describe methods for tracking bEV motion in biological matrices ex vivo. We outline methods for growth, isolation, quantification, and labeling, as well as techniques for tracking bEV motion ex vivo and quantifying these data. The methods described here are relevant to bEV communication with host cells as well as drug delivery applications using bEVs.

Reduction scenarios of plastic waste emission guided by the probability distribution model to avoid additional ocean plastic pollution by 2050s.

Marine plastic pollution is progressing worldwide and will become increasingly serious if plastic waste emissions continue at the current rate or increase with economic growth. Here, we report a particle tracking-based probability distribution model for predicting the abundances of marine macroplastics and microplastics, which undergo generation, transport, and removal processes in the world's upper ocean, under various scenarios of future land-to-sea plastic waste emissions. To achieve the Osaka Blue Ocean Vision, which aims to reduce additional pollution by marine plastic litter to zero by 2050, plastic waste emission in ∼2035 should be reduced by at least 32 % relative to 2019. It is necessary to take stringent measures such as 'system change scenario' or 'improve waste management scenario' proposed in previous studies to reduce the marine plastic pollution by 2050.

Simultaneous Mapping of the Nanoscale Organization and Redox State of Extracellular Space in Living Brain Tissue.

The spatial organization characteristics and redox status of the extracellular space (ECS) are crucial in the development of brain diseases. However, it remains a challenge to simultaneously capture dynamic changes in microstructural features and redox states at the submicron level within the ECS. Here, we developed a reversible glutathione (GSH)-responsive nanoprobe (RGN) for mapping the spatial organization features and redox status of the ECS in brain tissues with nanoscale resolution. The RGN is composed of polymer nanoparticles modified with GSH-responsive molecules and amino-functionalized methoxypoly(ethylene glycol), which exhibit exceptional single-particle brightness and excellent free diffusion capability in the ECS of brain tissues. Tracking single RGNs in acute brain slices allowed us to dynamically map spatial organizational features and redox levels within the ECS of brain tissues in disease models. This provides a powerful super-resolution imaging method that offers a potential opportunity to study the dynamic changes in the ECS microenvironment and to understand the physiological and pathological roles of the ECS in vivo.

Making Rift Valley Fever Viral Particles Fluorescent.

Rift Valley fever virus (RVFV) is a mosquito-borne pathogen that represents a significant threat to both human and veterinary public health. Since its discovery in the Great Rift Valley of Kenya in the 1930s, the virus has spread across Africa and beyond, now posing a risk of introduction into Southern Europe and Asia. Despite recent progresses, early RVFV-host cell interactions remain largely uncharacterized. In this method chapter, we delineate the procedure for labeling RVFV particles with fluorescent organic dyes. This approach makes it feasible to visualize single viral particles in both fixed and living cells and study RVFV entry into host cells. We provide additional examples with two viruses closely related to RVFV, namely, Toscana virus and Uukuniemi virus. Furthermore, we illustrate how to utilize fluorescent viral particles to examine and quantify each step of the cell entry program of RVFV, which includes state-of-the-art fluorescence-based detection techniques such as fluorescence microscopy, flow cytometry, and fluorimetry.

Investigating local trawl fishing as a source of plastic beach litter.

This paper uses a particle tracking model to simulate the distribution of fishing-related marine-sourced plastic litter from demersal trawling activities along the Atlantic coast of Scotland. The modelled fishing litter dispersed widely across the region, with ∼50% of the particles beaching along the northwestern Scottish coast after a year-long simulation. The model was tuned using observations of beached litter loadings along the same coastline to estimate the annual input, by mass, of small (<1 kg) plastic litter. Model results suggest that between 107 g and 280 g of small fishing-related litter enters the ocean per hour of fishing, resulting in an estimated 234 t to 614 t of small fishing-related litter entering the ocean annually on the Scottish west coast. These results suggest that fishing on the Atlantic coast of Scotland may be a significant source of marine plastic. However, more modelled and observational data are required to reduce uncertainty.

Understanding stratification and turnover dynamics of a tropical lake using extensive field observations and 3D hydrodynamic simulations.

The stratification and turnover dynamics of a tropical lake were evaluated using field observations and 3D hydrodynamic simulations. Located in the Philippines, Sampaloc Lake is a 104-ha and 27-m deep volcanic crater lake with enclosed watershed, which is at risk of the impacts of intensive aquaculture, rapid urbanization and climate change. Temperature, dissolved oxygen (DO) and chlorophyll-a (Chl-a) were measured at seven sampling stations using a multiprobe. Kruskal-Wallis test revealed that the three parameters are not significantly different among stations, indicating that one sampling station can represent the water quality of the whole lake. Schmidt's Stability Index (SSI) and thermocline strength, together with DO and Chl-a gradients decreased from October 2022 (stratified) to January 2023 (turnover). After successfully verifying the 3D numerical model, sensitivity analyses of water temperature to varying weather, together with particle tracking simulations, were implemented to determine the timing of isothermal state, upwelling, partial mixing, and full turnover. Compared to air temperature, variations in wind speed have more pronounced effects on the delay or progression of isothermal conditions in the lake based on SSI, Lake Number and Wedderburn Number. Isothermal conditions do not necessarily coincide with the timing of full turnover, with the latter being delayed by two days than the former, on average. Results revealed that full turnover can occur several weeks earlier with the decrease in AT and increase in WS. This study can advance the understanding of thermal and turnover dynamics of stratified tropical lakes, leading to better management of the water quality of these water bodies.

A live cell imaging-based assay for tracking particle uptake by clathrin-mediated endocytosis.

A popular strategy for therapeutic delivery to cells and tissues is to encapsulate therapeutics inside particles that cells internalize via endocytosis. The efficacy of particle uptake by endocytosis is often studied in bulk using flow cytometry and Western blot analysis and confirmed using confocal microscopy. However, these techniques do not reveal the detailed dynamics of particle internalization and how the inherent heterogeneity of many types of particles may impact their endocytic uptake. Toward addressing these gaps, here we present a live-cell imaging-based method that utilizes total internal reflection fluorescence microscopy to track the uptake of a large ensemble of individual particles in parallel, as they interact with the cellular endocytic machinery. To analyze the resulting data, we employ an open-source tracking algorithm in combination with custom data filters. This analysis reveals the dynamic interactions between particles and endocytic structures, which determine the probability of particle uptake. In particular, our approach can be used to examine how variations in the physical properties of particles (size, targeting, rigidity), as well as heterogeneity within the particle population, impact endocytic uptake. These data impact the design of particles toward more selective and efficient delivery of therapeutics to cells.

Multi-laser nanoparticle tracking analysis (NTA): A unique method to visualize dynamic (shear) and dynamic (Brownian motion) light scattering and quantify nonliving natural organic matter (NNOM) in environmental water.

Application of simultaneous multi-laser nanoparticle tracking analysis (NTA) to environmental water samples to investigate nonliving natural organic matter (NNOM) is introduced as an innovative method for observing particles directly in their native media. Multi-laser NTA results of particle visualization, particle number concentration, and particle size distribution elucidated particle dynamics in low and high total dissolved solids (TDS) aqueous environmental samples. A pond water sample and concentrate from a reverse osmosis (RO) treatment process (Stage 1) had 1.3 × 108 and 5.62 × 1019 particles/mL, respectively, (at time = 0) after filtration at 0.45 µm. Beyond the traditional applications for this instrument, this research presents novel evidence-based investigations that probe the existence of supramolecular structures in environmental waters during turbulence or quiescence. The pond water sample exhibited time-dependent aggregation as the volume distribution shifted to greater diameter during quiescence, compared to turbulence. Disaggregation (increased numbers of particles over time) was noted in the >250 nm to <600 nm region, and aggregation of >450 nm particles was also noted in the quiescent RO concentrate sample, indicative of depletion of small particles to form larger ones. Multi-laser NTA and dynamic light scattering (DLS) capabilities were compared and contrasted. DLS and NTA are different (complementary) particle sizing techniques. DLS yielded more information about the physical hydrogel in the NNOM hierarchy whereas multi-laser NTA better characterized meta-chemical and chemical hydrogel characteristics. Operationalization of innovation-moving from fundamental investigations to application-is supported by implementing novel analytical instrumentation as we address issues involving climate change, drought, and the scarcity of potable water. Multi-laser NTA can be used as a tool to study and optimize complex water and wastewater treatment processes. Questions about water treatment efficiencies, membrane fouling, assistance of pollutant transport, and carbon capture cycles affected by NNOM will benefit from insights from multi-laser NTA.

Reciprocal effect on lateral diffusion of receptor for advanced glycation endproducts and toll-like receptor 4 in the HEK293 cell membrane.

Receptor for advanced glycation endproducts (RAGE) and toll-like receptor 4 (TLR4) are pattern-recognition receptors that bind to molecular patterns associated with pathogens, stress, and cellular damage. Diffusion plays an important role in receptor functionality in the cell membrane. However, there has been no prior investigation of the reciprocal effect of RAGE and TLR4 diffusion properties in the presence and absence of each receptor. This study reports how RAGE and TLR4 affect the mobility of each other in the human embryonic kidney (HEK) 293 cell membrane. Diffusion properties were measured using single-particle tracking (SPT) with quantum dots (QDs) that are selectively attached to RAGE or TLR4. The Brownian diffusion coefficients of RAGE and TLR4 are affected by the presence of the other receptor, leading to similar diffusion coefficients when both receptors coexist in the cell. When TLR4 is present, the average Brownian diffusion coefficient of RAGE increases by 40%, while the presence of RAGE decreases the average Brownian diffusion coefficient of TLR4 by 32%. Diffusion in confined membrane domains is not altered by the presence of the other receptor. The mobility of the cell membrane lipid remains constant whether one or both receptors are present. Overall, this work shows that the presence of each receptor can affect a subset of diffusion properties of the other receptor without affecting the mobility of the membrane.

Visualization, Quantification, and Statistical Evaluation of Dynamics for DNA-Binding Proteins in Bacteria by Single-Molecule Tracking.

All DNA-binding proteins in vivo exist as a population of freely diffusing molecules and of DNA-bound molecules. The molecules bound to DNA can be split into specifically/tightly and nonspecifically bound proteins. Single-molecule tracking (SMT) is a method allowing to visualize protein dynamics in living cells, revealing their behavior in terms of mode of motion, diffusion coefficient/speed, change of dwell times, and unveiling preferred subcellular sites of dwelling. Bleaching-type SMT or fluorescent protein-tagged SMT involves rapid laser-induced bleaching of most fluorophore-labeled molecules. The remaining single fluorescent proteins are then continuously tracked. The trajectories of several fluorescent molecules per cell for a population of cells are analyzed and combined to permit a robust analysis of average behavior of single molecules in live cells, including analyses of protein dynamics in mutant cells or cells exposed to changes in environmental conditions.In this chapter, we describe the preparation of Bacillus subtilis cells, the recording of movies of those cells expressing a monomeric variant of a yellow fluorescent protein (mNeonGreen) fused to a protein of choice, and the subsequent curation of the movie data including the statistical analysis of the protein dynamics. We present a short overview of the analysis program SMTracker 2.0, highlighting its ability to analyze SMT data by non-expert scientists.

Applications of mathematical modelling for assessing microplastic transport and fate in water environments: a comparative review.

Microplastics in the environment are considered complex pollutants as they are chemical and corrosive-resistant, non-biodegradable and ubiquitous. These microplastics may act as vectors for the dissemination of other pollutants and the transmission of microorganisms into the water environment. The currently available literature reviews focus on analysing the occurrence, environmental effects and methods of microplastic detection, however lacking a wide-scale systematic review and classification of the mathematical microplastic modelling applications. Thus, the current review provides a global overview of the modelling methodologies used for microplastic transport and fate in water environments. This review consolidates, classifies and analyses the methods, model inputs and results of 61 microplastic modelling studies in the last decade (2012-2022). It thoroughly discusses their strengths, weaknesses and common gaps in their modelling framework. Five main modelling types were classified as follows: hydrodynamic, process-based, statistical, mass-balance and machine learning models. Further, categorisations based on the water environments, location and published year of these applications were also adopted. It is concluded that addressed modelling types resulted in relatively reliable outcomes, yet each modelling framework has its strengths and weaknesses. However, common issues were found such as inputs being unrealistically assumed, especially biological processes, and the lack of sufficient field data for model calibration and validation. For future research, it is recommended to incorporate macroplastics' degradation rates, particles of different shapes and sizes and vertical mixing due to biofouling and turbulent conditions and also more experimental data to obtain precise model inputs and standardised sampling methods for surface and column waters.

United under stress: High-speed transport network emerging at bacterial living edge.

Individuals tend to move freely when there is enough room but would act collectively for their survival under external stress. In the case of living cells, for instance, when a drop of low-density flagellated bacterial solution is transferred onto the agar surface, the initially disordered movement of individual bacteria would be replaced with coordinated cell swarming after a lag phase of a few hours. Here, we study how such cooperation is established while overcoming the disorder at the onset of the lag phase with single nanoparticle tracking. Upon the spreading of the droplet, the bacteria in the solution cluster and align near the almost immobilized contact line confining the drop, forming a narrow ring of cells. As individual cells move in and out of the ring continuously, certain flow patterns emerge in the inter-bacterial fluid. We reveal high-speed long-distance unidirectional flows with definite chirality along the outside of the ring, along the inside of the ring and across the ring. We speculate that these flows enable the fast and efficient transport, facilitating the communication and unification of the bacterial community.

Effect of cross-linking density on the rheological behavior of ultra-soft chitosan microgels at the oil-water interface.

In this paper, microgels with uniform particle size were prepared by physically cross-linking the hydrophobically modified chitosan (h-CS) with sodium phytate (SP). The effects of cross-linking density on the interfacial adsorption kinetics, viscoelasticity, stress relaxation, and micorheological properties of the hydrophobically modified chitosan microgels (h-CSMs) at the oil-water interface were extensively investigated by the dilatational rheology, compressional rheology, and particle tracing microrheology. The results were correlated with the particle size, morphology, and elasticity of the microgels characterized by dynamic light scattering and atomic force microscopy. It was found that with the increase of cross-linking density, the h-CSMs changed from a polymer-like state to ultra-soft fussy spheres with higher elastic modulus. The compression isotherms demonstrated multi-stage increase caused by the interaction between the shells and that between the cores of the microgels successively. As the increase of cross-linking density, the h-CSMs diffused slower to the oil-water interface, but demonstrating faster permeation adsorption and rearrangement at the oil-water interface, finally forming interfacial layers of higher viscoelastic modulus due to the core-core interaction. Both the initial tension relaxation and the microgel rearrangement after interface expansion became faster as the microgel elasticity increased. The interfacial microrheology demonstrated dynamic caging effect caused by neighboring microgels. This article provides a more comprehensive understanding of the behaviors of polysaccharide microgels at the oil-water interface.

Defect-Engineered Metal-Organic Frameworks as Nanocarriers for Pharmacotherapy: Insights into Intracellular Dynamics at The Single Particle Level.

Nanoscale Metal-Organic Frameworks (nanoMOFs) are widely implemented in a host of assays involving drug delivery, biosensing catalysis, and bioimaging. However, the cell pathways and cell fate remain poorly understood. Here, a new fluorescent nanoMOF integrating ATTO 655 into surface defects of colloidal UiO-66 is synthesized, allowing to track the spatiotemporal localization of Single nanoMOF in live cells. density functional theory reveals the stronger binding of ATTO 655 to the Zr6 cluster nodes compared with phosphate and Alendronate Sodium. Parallelized tracking of the spatiotemporal localization of thousands of nanoMOFs and analysis using machine learning platforms reveals whether nanoMOFs remain outside as well as their cellular internalization pathways. To quantitatively assess their colocalization with endo/lysosomal compartments, a colocalization proxy approach relying on the nanoMOF detection of particles in one channel to the signal in the corresponding endo/lysosomal compartments channel, considering signal versus local background intensity ratio and signal-to-noise ratio is developed. This strategy mitigates colocalization value inflation from high or low signal expression in endo/lysosomal compartments. The results accurately measure the nanoMOFs' colocalization from early to late endosomes and lysosomes and emphasize the importance of understanding their intracellular dynamics based on single-particle tracking for optimal and safe drug delivery.

Pre-ribosomal particles from nucleoli to cytoplasm.

The analysis of nucleocytoplasmic transport of proteins and messenger RNA has been the focus of advanced microscopic approaches. Recently, it has been possible to identify and visualize individual pre-ribosomal particles on their way through the nuclear pore complex using both electron and light microscopy. In this review, we focused on the transport of pre-ribosomal particles in the nucleus on their way to and through the pores.

Understanding the role of the structure of single-stimuli hybrid systems on their behaviour as platforms for colonic delivery.

The success of colon-targeted oral hybrid systems relies in the proper control over the release of the entrapped nanostructures at the colon. This work describes the design of hybrid systems for their colonic enzyme-triggered release. The hybrid systems were constituted by nanoemulsions, with adequate characteristics for the treatment of ulcerative colitis, included in a pectin hydrogel-like matrix. For that purpose, pectins with similar degrees of methylation (< 50%) and increasing degree of amidation, i.e. 0, 13 and 20%, were selected. Hybrid systems were formulated by a novel aggregation induced gelation method, using Ca2+, Ba2+ or Zn2+ as aggregating agents, as well as by a polyelectrolyte condensation approach, obtaining structures in the micrometric range (< 10 µm). Despite the resistance of pectins to the upper gastrointestinal tract stimuli, the analysis of the behaviour of the different prototypes showed that the non-covalent crosslinks that allow the formation of the hybrid structure may play a relevant role on the performance of the formulation.Our results indicated that the partial disassembling of the hybrid system's microstructure due to the intestinal conditions may facilitate the stimuli-triggered release of the nanoemulsions at the colon. More interestingly, the particle tracking experiments showed that the condensation process that occurs during the formation of the system may affect to the enzymatic degradation of pectin. In this sense, the effect of the high degree of amidation of pectin may be more prevalent as structural feature rather than as a promoter of the enzyme-triggered release.

Investigation of cardiopulmonary bypass parameters on embolus transport in a patient-specific aorta.

Neurological complexities resulting from surgery requiring cardiopulmonary bypass (CPB) remain a major concern, encompassing a spectrum of complications including thromboembolic stroke and various cognitive impairments. Surgical manipulation during CPB is considered the primary cause of these neurological complications. This study addresses the overall lack of knowledge concerning CPB hemodynamics within the aorta, employing a combined experimental-computational modeling approach, featuring computational fluid dynamics simulations validated with an in vitro CPB flow loop under steady conditions. Parametric studies were systematically performed, varying parameters associated with CPB techniques (pump flow rate and hemodiluted blood viscosity) and properties related to formed emboli (size and density). This represents the first comprehensive investigation into the individual and combined effects of these factors. Our findings reveal critical insights into the operating conditions of CPB, indicating a positive correlation between pump flow rate and emboli transport into the aortic branches, potentially increasing the risk of stroke. It was also found that larger emboli were more often transported into the aortic branches at higher pump flow rates, while smaller emboli preferred lower flow rates. Further, as blood is commonly diluted during CPB to decrease its viscosity, more emboli were found to enter the aortic branches with greater hemodilution. The combined effects of these parameters are captured using the non-dimensional Stokes number, which was found to positively correlate with emboli transport into the aortic branches. These findings contribute to our understanding of embolic stroke risk factors during CPB and shed light on the complex interplay between CPB parameters.

Mucus-Inspired Self-Healing Hydrogels: A Protective Barrier for Cells against Viral Infection.

Mucus is a dynamic biological hydrogel, composed primarily of the glycoprotein mucin, exhibits unique biophysical properties and forms a barrier protecting cells against a broad-spectrum of viruses. Here, this work develops a polyglycerol sulfate-based dendronized mucin-inspired copolymer (MICP-1) with ≈10% repeating units of activated disulfide as cross-linking sites. Cryo-electron microscopy (Cryo-EM) analysis of MICP-1 reveals an elongated single-chain fiber morphology. MICP-1 shows potential inhibitory activity against many viruses such as herpes simplex virus 1 (HSV-1) and SARS-CoV-2 (including variants such as Delta and Omicron). MICP-1 produces hydrogels with viscoelastic properties similar to healthy human sputum and with tuneable microstructures using linear and branched polyethylene glycol-thiol (PEG-thiol) as cross-linkers. Single particle tracking microrheology, electron paramagnetic resonance (EPR) and cryo-scanning electron microscopy (Cryo-SEM) are used to characterize the network structures. The synthesized hydrogels exhibit self-healing properties, along with viscoelastic properties that are tuneable through reduction. A transwell assay is used to investigate the hydrogel's protective properties against viral infection against HSV-1. Live-cell microscopy confirms that these hydrogels can protect underlying cells from infection by trapping the virus, due to both network morphology and anionic multivalent effects. Overall, this novel mucin-inspired copolymer generates mucus-mimetic hydrogels on a multi-gram scale. These hydrogels can be used as models for disulfide-rich airway mucus research, and as biomaterials.

DNA choreography: correlating mobility and organization of DNA across different resolutions from loops to chromosomes.

The dynamics of DNA in the cell nucleus plays a role in cellular processes and fates but the interplay of DNA mobility with the hierarchical levels of DNA organization is still underexplored. Here, we made use of DNA replication to directly label genomic DNA in an unbiased genome-wide manner. This was followed by live-cell time-lapse microscopy of the labeled DNA combining imaging at different resolutions levels simultaneously and allowing one to trace DNA motion across organization levels within the same cells. Quantification of the labeled DNA segments at different microscopic resolution levels revealed sizes comparable to the ones reported for DNA loops using 3D super-resolution microscopy, topologically associated domains (TAD) using 3D widefield microscopy, and also entire chromosomes. By employing advanced chromatin tracking and image registration, we discovered that DNA exhibited higher mobility at the individual loop level compared to the TAD level and even less at the chromosome level. Additionally, our findings indicate that chromatin movement, regardless of the resolution, slowed down during the S phase of the cell cycle compared to the G1/G2 phases. Furthermore, we found that a fraction of DNA loops and TADs exhibited directed movement with the majority depicting constrained movement. Our data also indicated spatial mobility differences with DNA loops and TADs at the nuclear periphery and the nuclear interior exhibiting lower velocity and radius of gyration than the intermediate locations. On the basis of these insights, we propose that there is a link between DNA mobility and its organizational structure including spatial distribution, which impacts cellular processes.