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Molecular Pharmaceutics Sep 2022Formulations containing nanosized drug particles such as nanocrystals and nanosized amorphous drug aggregates recently came into light as promising strategies to improve...
Formulations containing nanosized drug particles such as nanocrystals and nanosized amorphous drug aggregates recently came into light as promising strategies to improve the bioavailability of poorly soluble drugs. However, the increased solubility due to the reduction in particle size cannot adequately explain the enhanced bioavailability. In this study, the mechanisms and extent of enhanced passive permeation by drug particles were investigated using atazanavir, lopinavir, and clotrimazole as model drugs. Franz diffusion cells with lipid-infused membranes were utilized to evaluate transmembrane flux. The impact of stirring rate, receiver buffer condition, and particle size was investigated, and mass transport analyses were conducted to calculate transmembrane flux. Flux enhancement by particles was found to be dependent on particle size as well as the partitioning behavior of the drug between the receiver solution and the membrane, which is determined by both the drug and buffer used. A flux plateau was observed at high particle concentrations above amorphous solubility, confirming that mass transfer of amorphous drug particles from the aqueous solution to the membrane occurs only through the molecularly dissolved drug. Mass transport models were used to calculate flux enhancement by particles for various drugs at different conditions. Good agreements were obtained between experimental and predicted values. These results should contribute to improved bioavailability prediction of nanosized drug particles and better design of formulations containing colloidal drug particles.
Topics: Diffusion; Drug Compounding; Lopinavir; Membranes; Solubility
PubMed: 35998304
DOI: 10.1021/acs.molpharmaceut.2c00124 -
The Journal of Chemical Physics Aug 2023Most biological processes in living cells rely on interactions between proteins. Live-cell compatible approaches that can quantify to what extent a given protein... (Review)
Review
Most biological processes in living cells rely on interactions between proteins. Live-cell compatible approaches that can quantify to what extent a given protein participates in homo- and hetero-oligomeric complexes of different size and subunit composition are therefore critical to advance our understanding of how cellular physiology is governed by these molecular interactions. Biomolecular complex formation changes the diffusion coefficient of constituent proteins, and these changes can be measured using fluorescence microscopy-based approaches, such as single-molecule tracking, fluorescence correlation spectroscopy, and fluorescence recovery after photobleaching. In this review, we focus on the use of single-molecule tracking to identify, resolve, and quantify the presence of freely-diffusing proteins and protein complexes in living cells. We compare and contrast different data analysis methods that are currently employed in the field and discuss experimental designs that can aid the interpretation of the obtained results. Comparisons of diffusion rates for different proteins and protein complexes in intracellular aqueous environments reported in the recent literature reveal a clear and systematic deviation from the Stokes-Einstein diffusion theory. While a complete and quantitative theoretical explanation of why such deviations manifest is missing, the available data suggest the possibility of weighing freely-diffusing proteins and protein complexes in living cells by measuring their diffusion coefficients. Mapping individual diffusive states to protein complexes of defined molecular weight, subunit stoichiometry, and structure promises to provide key new insights into how protein-protein interactions regulate protein conformational, translational, and rotational dynamics, and ultimately protein function.
Topics: Single Molecule Imaging; Diffusion; Microscopy, Fluorescence; Photobleaching; Protein Conformation
PubMed: 37589409
DOI: 10.1063/5.0155638 -
Bioinformatics (Oxford, England) Feb 2023Gene-disease associations are fundamental for understanding disease etiology and developing effective interventions and treatments. Identifying genes not yet associated...
MOTIVATION
Gene-disease associations are fundamental for understanding disease etiology and developing effective interventions and treatments. Identifying genes not yet associated with a disease due to a lack of studies is a challenging task in which prioritization based on prior knowledge is an important element. The computational search for new candidate disease genes may be eased by positive-unlabeled learning, the machine learning (ML) setting in which only a subset of instances are labeled as positive while the rest of the dataset is unlabeled. In this work, we propose a set of effective network-based features to be used in a novel Markov diffusion-based multi-class labeling strategy for putative disease gene discovery.
RESULTS
The performances of the new labeling algorithm and the effectiveness of the proposed features have been tested on 10 different disease datasets using three ML algorithms. The new features have been compared against classical topological and functional/ontological features and a set of network- and biological-derived features already used in gene discovery tasks. The predictive power of the integrated methodology in searching for new disease genes has been found to be competitive against state-of-the-art algorithms.
AVAILABILITY AND IMPLEMENTATION
The source code of NIAPU can be accessed at https://github.com/AndMastro/NIAPU. The source data used in this study are available online on the respective websites.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Software; Algorithms; Machine Learning; Diffusion
PubMed: 36727493
DOI: 10.1093/bioinformatics/btac848 -
Optics Express Mar 2021Anomalous diffusion dynamics in confined nanoenvironments govern the macroscale properties and interactions of many biophysical and material systems. Currently, it is...
Anomalous diffusion dynamics in confined nanoenvironments govern the macroscale properties and interactions of many biophysical and material systems. Currently, it is difficult to quantitatively link the nanoscale structure of porous media to anomalous diffusion within them. Fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) has been shown to extract nanoscale structure and Brownian diffusion dynamics within gels, liquid crystals, and polymers, but has limitations which hinder its wider application to more diverse, biophysically-relevant datasets. Here, we parallelize the least-squares curve fitting step on a GPU improving computation times by up to a factor of 40, implement anomalous diffusion and two-component Brownian diffusion models, and make fcsSOFI more accessible by packaging it in a user-friendly GUI. We apply fcsSOFI to simulations of the protein fibrinogen diffusing in polyacrylamide of varying matrix densities and super-resolve locations where slower, anomalous diffusion occurs within smaller, confined pores. The improvements to fcsSOFI in speed, scope, and usability will allow for the wider adoption of super-resolution correlation analysis to diverse research topics.
Topics: Computational Biology; Diffusion; Fibrinogen; Fluorescent Dyes; Microscopy, Fluorescence; Quinolinium Compounds; Spatio-Temporal Analysis
PubMed: 33726259
DOI: 10.1364/OE.416465 -
Journal of Colloid and Interface Science Dec 2022The application of dynamic light scattering to soft matter systems has strongly profited from advanced approaches such as the so-called modulated 3D cross correlation...
The application of dynamic light scattering to soft matter systems has strongly profited from advanced approaches such as the so-called modulated 3D cross correlation technique (Mod3D-DLS) that suppress contributions from multiple scattering, and can therefore be used for the characterization of turbid samples. Here we now extend the possibilities of this technique to allow for depolarized light scattering (Mod3D-DDLS) and thus obtain information on both translational and rotational diffusion, which is important for the characterization of anisotropic particles. We describe the required optical design and test the performance of the approach for increasingly turbid samples using well defined anisotropic colloidal models systems. Our measurements demonstrate that 3D-DDLS experiments can be performed successfully for samples with a reduced transmission due to multiple scattering as low as 1%. We compare the results from this approach with those obtained by standard DDLS experiments, and point out the importance of using an appropriate optical design when performing depolarized dynamic light scattering experiments with turbid systems.
Topics: Diffusion; Dynamic Light Scattering; Light; Scattering, Radiation
PubMed: 35839555
DOI: 10.1016/j.jcis.2022.06.113 -
Redox Biology Apr 2022Hydrogen peroxide is a major redox signaling molecule underlying a novel paradigm of cell function and communication. A role for HO as an intercellular signaling...
Hydrogen peroxide is a major redox signaling molecule underlying a novel paradigm of cell function and communication. A role for HO as an intercellular signaling molecule and neuromodulator in the brain has become increasingly apparent, with evidence showing this biological oxidant to regulate neuronal polarity, connectivity, synaptic transmission and tuning of neuronal networks. This notion is supported by its ability to diffuse in the extracellular space, from source of production to target. It is, thus, crucial to understand extracellular HO concentration dynamics in the living brain and the factors which shape its diffusion pattern and half-life. To address this issue, we have used a novel microsensor to measure HO concentration dynamics in the brain extracellular matrix both in an ex vivo model using rodent brain slices and in vivo. We found that exogenously applied HO is removed from the extracellular space with an average half-life of t = 2.2 s in vivo. We determined the in vivo effective diffusion coefficient of HO to be D* = 2.5 × 10 cm s. This allows it to diffuse over 100 μm in the extracellular space within its half-life. Considering this, we can tentatively place HO within the class of volume neurotransmitters, connecting all cell types within the complex network of brain tissue, regardless of whether they are physically connected. These quantitative details of HO diffusion and half-life in the brain allow us to interpret the physiology of the redox signal and lay the pavement to then address dysregulation in redox homeostasis associated with disease processes.
Topics: Brain; Diffusion; Hydrogen Peroxide; Oxidation-Reduction; Signal Transduction
PubMed: 35101799
DOI: 10.1016/j.redox.2022.102250 -
Nature Communications Nov 2022Control over vesicle size during nanoscale liposome synthesis is critical for defining the pharmaceutical properties of liposomal nanomedicines. Microfluidic...
Control over vesicle size during nanoscale liposome synthesis is critical for defining the pharmaceutical properties of liposomal nanomedicines. Microfluidic technologies capable of size-tunable liposome generation have been widely explored, but scaling these microfluidic platforms for high production throughput without sacrificing size control has proven challenging. Here we describe a microfluidic-enabled process in which highly vortical flow is established around an axisymmetric stream of solvated lipids, simultaneously focusing the lipids while inducing rapid convective and diffusive mixing through application of the vortical flow field. By adjusting the individual buffer and lipid flow rates within the system, the microfluidic vortex focusing technique is capable of generating liposomes with precisely controlled size and low size variance, and may be operated up to the laminar flow limit for high throughput vesicle production. The reliable formation of liposomes as small as 27 nm and mass production rates over 20 g/h is demonstrated, offering a path toward production-scale liposome synthesis using a single continuous-flow vortex focusing device.
Topics: Liposomes; Microfluidics; Diffusion; Lipids
PubMed: 36384946
DOI: 10.1038/s41467-022-34750-3 -
Scientific Reports May 2023Transport processes of many structures inside living cells display anomalous diffusion, such as endosomes in eukaryotic cells. They are also heterogeneous in space and...
Transport processes of many structures inside living cells display anomalous diffusion, such as endosomes in eukaryotic cells. They are also heterogeneous in space and time. Large ensembles of single particle trajectories allow the heterogeneities to be quantified in detail and provide insights for mathematical modelling. The development of accurate mathematical models for heterogeneous dynamics has the potential to enable the design and optimization of various technological applications, for example, the design of effective drug delivery systems. Central questions in the analysis of anomalous dynamics are ergodicity and statistical ageing which allow for selecting the proper model for the description. It is believed that non-ergodicity and ageing occur concurrently. However, we found that the anomalous dynamics of endosomes is paradoxical since it is ergodic but shows ageing. We show that this behaviour is caused by ensemble heterogeneity that, in addition to space-time heterogeneity within a single trajectory, is an inherent property of endosomal motion. Our work introduces novel approaches for the analysis and modelling of heterogeneous dynamics.
Topics: Eukaryotic Cells; Models, Theoretical; Motion; Diffusion; Endosomes
PubMed: 37258614
DOI: 10.1038/s41598-023-35903-0 -
Magnetic Resonance in Medicine Sep 2020To investigate diffusion-time dependency of diffusional kurtosis in the mouse brain using pulsed-gradient spin-echo (PGSE) and oscillating-gradient spin-echo (OGSE)...
PURPOSE
To investigate diffusion-time dependency of diffusional kurtosis in the mouse brain using pulsed-gradient spin-echo (PGSE) and oscillating-gradient spin-echo (OGSE) sequences.
METHODS
3D PGSE and OGSE kurtosis tensor data were acquired from ex vivo brains of adult, cuprizone-treated, and age-matched control mice with diffusion-time (t ) ~ 20 ms and frequency (f) = 70 Hz, respectively. Further, 2D acquisitions were performed at multiple times/frequencies ranging from f = 140 Hz to t = 30 ms with b-values up to 4000 s/mm . Monte Carlo simulations were used to investigate the coupled effects of varying restriction size and permeability on time/frequency-dependence of kurtosis with both diffusion-encoding schemes. Simulations and experiments were further performed to investigate the effect of varying number of cycles in OGSE waveforms.
RESULTS
Kurtosis and diffusivity maps exhibited significant region-specific changes with diffusion time/frequency across both gray and white matter areas. PGSE- and OGSE-based kurtosis maps showed reversed contrast between gray matter regions in the cerebellar and cerebral cortex. Localized time/frequency-dependent changes in kurtosis tensor metrics were found in the splenium of the corpus callosum in cuprizone-treated mouse brains, corresponding to regional demyelination seen with histological assessment. Monte Carlo simulations showed that kurtosis estimates with pulsed- and oscillating-gradient waveforms differ in their sensitivity to exchange. Both simulations and experiments showed dependence of kurtosis on number of cycles in OGSE waveforms for non-zero permeability.
CONCLUSION
The results show significant time/frequency-dependency of diffusional kurtosis in the mouse brain, which can provide sensitivity to probe intrinsic cellular heterogeneity and pathological alterations in gray and white matter.
Topics: Animals; Brain; Corpus Callosum; Diffusion; Diffusion Magnetic Resonance Imaging; Mice; White Matter
PubMed: 32022313
DOI: 10.1002/mrm.28189 -
Lab on a Chip Sep 2019Hydrogels allow for controlling the diffusion rate and amount of solute according to the hydrogel network and thus have found many applications in drug delivery,...
Hydrogels allow for controlling the diffusion rate and amount of solute according to the hydrogel network and thus have found many applications in drug delivery, biomaterials, toxicology, and tissue engineering. This paper describes a 3D-printed microfluidic chip for the straightforward partitioning of hydrogel barriers between microchannels. We use a previously-reported 3-channel architecture whereby the middle channel is filled with a hydrogel - acting like a porous barrier for diffusive transport - and the two side channels act as sink and source; the middle channel communicates with the side channels via orthogonal, small capillary channels that are also responsible for partitioning the hydrogel during filling. Our 3D-printed microfluidic chip is simple to fabricate by stereolithography (SL), inexpensive, reproducible, and convenient, so it is more adequate for transport studies than a microchip fabricated by photolithographic procedures. The chip was fabricated in a resin made of poly(ethylene glycol) diacrylate (PEG-DA) (MW = 258) (PEG-DA-258). The SL process allowed us to print high aspect ratio (37 : 1) capillary channels (27 μm-width and 1 mm-height) and enable the trapping of liquid-phase hydrogels in the hydrogel barrier middle channel. We studied the permeability of hydrogel barriers made of PEG-DA (MW = 700) (PEG-DA-700, 10% polymer content by wt. in water) - as a model of photopolymerizable barriers - and agarose (MW = 120 000, 2% polymer content by wt. in water) - as a model of thermally-gelled barriers. We measured the diffusion of fluorescein, 10k-dextran-Alexa 680 and BSA-Texas Red through these barriers. Fluorescein diffusion was observed through both 10% PEG-DA-700 and 2% agarose barriers while 10k-dextran-Alexa 680 and BSA-Texas Red diffused appreciably only through the 2% agarose hydrogel barrier. Our microfluidic chip facilitates the tuning of such barriers simply by altering the hydrogel materials. The straightforward trapping of selective barriers in 3D-printed microchannels should find wide applicability in drug delivery, tissue engineering, cell separation, and organ-on-a-chip platforms.
Topics: Diffusion; Hydrogels; Microfluidic Analytical Techniques; Polyethylene Glycols; Printing, Three-Dimensional
PubMed: 31502633
DOI: 10.1039/c9lc00535h