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The Journal of Physical Chemistry. B Aug 2023Immunoglobulin G (IgG) is the most common type of antibody found in blood and extracellular fluids and plays an essential role in our immune response. However, studies...
Immunoglobulin G (IgG) is the most common type of antibody found in blood and extracellular fluids and plays an essential role in our immune response. However, studies of the dynamics and reaction kinetics of IgG-antigen binding under physiological crowding conditions are scarce. Herein, we develop a coarse-grained model of IgG consisting of only six beads that we find minimal for a coarse representation of IgG's shape and a decent reproduction of its flexibility and diffusion properties measured experimentally. Using this model in Brownian dynamics simulations, we find that macromolecular crowding affects only slightly the IgG's flexibility, as described by the distribution of angles between the IgG's arms and stem. Our simulations indicate that, contrary to expectations, crowders slow down the translational diffusion of an IgG less strongly than they do for a smaller Ficoll 70, which we relate to the IgG's conformational size changes induced by crowding. We also find that crowders affect the binding kinetics by decreasing the rate of the first binding step and enhancing the second binding step.
Topics: Immunoglobulin G; Diffusion; Ficoll; Kinetics
PubMed: 37591305
DOI: 10.1021/acs.jpcb.3c02383 -
Scientific Reports Sep 2023To control African swine fever (ASF) efficiently, easily interpretable metrics of the outbreak dynamics are needed to plan and adapt the required measures. We found that...
To control African swine fever (ASF) efficiently, easily interpretable metrics of the outbreak dynamics are needed to plan and adapt the required measures. We found that the spread pattern of African Swine Fever cases in wild boar follows the mechanics of a diffusion process, at least in the early phase, for the cases that occurred in Germany. Following incursion into a previously unaffected area, infection disseminates locally within a naive and abundant wild boar population. Using real case data for Germany, we derive statistics about the time differences and distances between consecutive case reports. With the use of these statistics, we generate an ensemble of random walkers (continuous time random walks, CTRW) that resemble the properties of the observed outbreak pattern as one possible realization of all possible disease dissemination patterns. The trained random walker ensemble yields the diffusion constant, the affected area, and the outbreak velocity of early ASF spread in wild boar. These methods are easy to interpret, robust, and may be adapted for different regions. Therefore, diffusion metrics can be useful descriptors of early disease dynamics and help facilitate efficient control of African Swine Fever.
Topics: Animals; Swine; African Swine Fever; Benchmarking; Diffusion; Disease Outbreaks; Sus scrofa
PubMed: 37704714
DOI: 10.1038/s41598-023-42300-0 -
Environmental Monitoring and Assessment Aug 2023The unplanned urban expansion is a major environmental challenge in Iran resulting in vast degradation of agricultural lands. Focusing on an agricultural-urbanized...
The unplanned urban expansion is a major environmental challenge in Iran resulting in vast degradation of agricultural lands. Focusing on an agricultural-urbanized landscape in Central Iran, the spatial pattern of built-up expansion was assessed from Landsat data processed in 1992 (TM), 2002 (ETM+), 2012 (TM), and 2022 (OLI). Multi-year crop NDVI was also used as a proxy for cropland suitability to assess the intensity of the urban growth impact. Results showed that (1) the area of built-up surfaces increased almost up to double than that of 1992 and passed 36% (413.42 km) by 2022, (2) the region experienced a coalescence-diffusion transition phase with decreasing spatial connectivity of newly developed patches with old ones, (3) the most suitable croplands were lost in the middle period (2002-2012) when urban patches started to diffuse, and (4) a significantly positive spatial (Spearman's) relationship (r (22100) = 0.181, p = 0.000) was found between the area and quality of croplands which further highlights the high importance of cropland protection in the region.
Topics: Iran; Environmental Monitoring; Agriculture; Diffusion
PubMed: 37648944
DOI: 10.1007/s10661-023-11730-8 -
ACS Nano Sep 2023An important goal for bottom-up synthetic biology is to construct tissue-like structures from artificial cells. The key is the ability to control the assembly of the...
An important goal for bottom-up synthetic biology is to construct tissue-like structures from artificial cells. The key is the ability to control the assembly of the individual artificial cells. Unlike most methods resorting to external fields or sophisticated devices, inspired by the hanging drop method used for culturing spheroids of biological cells, we employ a capillary-driven approach to assemble giant unilamellar vesicles (GUVs)-based protocells into colonized prototissue arrays by means of a coverslip with patterned wettability. By spatially confining and controllably merging a mixed population of lipid-coated double-emulsion droplets that hang on a water/oil interface, an array of synthetic tissue-like constructs can be obtained. Each prototissue module in the array comprises multiple tightly packed droplet compartments where interfacial lipid bilayers are self-assembled at the interfaces both between two neighboring droplets and between the droplet and the external aqueous environment. The number, shape, and composition of the interconnected droplet compartments can be precisely controlled. Each prototissue module functions as a processer, in which fast signal transports of molecules via cell-cell and cell-environment communications have been demonstrated by molecular diffusions and cascade enzyme reactions, exhibiting the ability to be used as biochemical sensing and microreactor arrays. Our work provides a simple yet scalable and programmable method to form arrays of prototissues for synthetic biology, tissue engineering, and high-throughput assays.
Topics: Artificial Cells; Biological Transport; Cell Communication; Diffusion; High-Throughput Screening Assays; Water
PubMed: 37639562
DOI: 10.1021/acsnano.3c03516 -
Soft Matter Oct 2023The lateral diffusion of cell membrane inclusions, such as integral membrane proteins and bound receptors, drives critical biological processes, including the formation...
The lateral diffusion of cell membrane inclusions, such as integral membrane proteins and bound receptors, drives critical biological processes, including the formation of complexes, cell-cell signaling, and membrane trafficking. These diffusive processes are complicated by how concentrated, or "crowded", the inclusions are, which can occupy between 30-50% of the area fraction of the membrane. In this work, we elucidate the effects of increasing concentration of model membrane inclusions in a free-standing artificial cell membrane on inclusion diffusivity and the apparent viscosity of the membrane. By multiple particle tracking of fluorescent microparticles covalently tethered to the bilayer, we show the transition from expected Brownian dynamics, which accurately measure the membrane viscosity, to subdiffusive behavior with decreased diffusion coefficient as the particle area fraction increases from 1% to around 30%, approaching physiological levels of crowding. At high crowding, the onset of non-Gaussian behavior is observed. Using hydrodynamic models relating the 2D diffusion coefficient to the viscosity of a membrane, we determine the apparent viscosity of the bilayer from the particle diffusivity and show an increase in the apparent membrane viscosity with increasing particle area fraction. However, the scaling of this increase is in contrast with the behavior of monolayer inclusion diffusion and bulk suspension rheology. These results demonstrate that physiological levels of model membrane crowding nontrivially alter the dynamics and apparent viscosity of the system, which has implications for understanding membrane protein interactions and particle-membrane transport processes.
Topics: Membranes; Membrane Proteins; Molecular Dynamics Simulation; Biophysical Phenomena; Diffusion; Membranes, Artificial; Viscosity
PubMed: 37791427
DOI: 10.1039/d3sm01269g -
Bulletin of Mathematical Biology Dec 2023We propose a two stages mosquito egg-larvae model with seasonality as a simplification of a four stages one. For the simplified model we characterize the dynamics in...
We propose a two stages mosquito egg-larvae model with seasonality as a simplification of a four stages one. For the simplified model we characterize the dynamics in terms of the vectorial reproduction number, [Formula: see text], obtaining extinction if [Formula: see text] and convergence to a unique positive periodic orbit if [Formula: see text]. We illustrate each case with an example, by providing general conditions on the periodic coefficients for its occurrence. These examples are further developed using numerical simulations where the periodic parameters satisfy the conditions obtained. In the [Formula: see text] case, real climatic data is used for inferring the parameter behaviour. For the four stage system, using alternative oviposition rate functions, we present a result which generalizes others given for models with delays and even with diffusion to the case in which competition between the larvae is introduced. The analytical study of our initial four stages system when [Formula: see text] remains open, since we were not able to prove that in this case the system is dissipative.
Topics: Animals; Female; Mathematical Concepts; Models, Biological; Culicidae; Diffusion; Larva
PubMed: 38108949
DOI: 10.1007/s11538-023-01238-0 -
Journal of Contaminant Hydrology Nov 2023Nuclide transport in fractured media involves the advection, dispersion, adsorption, etc. The dispersion and adsorption properties of the rock matrix have spatial...
Nuclide transport in fractured media involves the advection, dispersion, adsorption, etc. The dispersion and adsorption properties of the rock matrix have spatial variability, which results in an anomalous transport of nuclides. In this study, a time-fractional advection-diffusion equation (t-FADE) model is utilized to capture the sub-diffusion transport behavior with heavy-tail property, including the breakthrough curves (BTCs) of uranium and thorium transport in granite plates. Moreover, hydrodynamic dispersion of tritiated water, strontium and cesium in granite fractures are also studied. The results indicate that BTCs of nuclides transport in the granite fractures are unimodal and asymmetric. The decrease of the fractional order α reflects the stronger sub-diffusion. Furthermore, small initial velocity enhances sub-diffusion effect of nuclides and lengthens the breakout time of BTCs, which results in obvious heavy-tail phenomena. The analysis results demonstrate that the t-FADE model can accurately describe sub-diffusion behavior of nuclides transport. At last, the advantages of the t-FADE model in prediction and remediation of nuclides contamination are put forward.
Topics: Models, Theoretical; Water Movements; Silicon Dioxide; Diffusion
PubMed: 37980823
DOI: 10.1016/j.jconhyd.2023.104265 -
Nano Letters Dec 2023Nanopore analysis relies on ensemble averaging of translocation signals obtained from numerous molecules, requiring a relatively high sample concentration and a long...
Nanopore analysis relies on ensemble averaging of translocation signals obtained from numerous molecules, requiring a relatively high sample concentration and a long turnaround time from the sample to results. The recapture and subsequent re-reading of the same molecule is a promising alternative that enriches the signal information from a single molecule. Here, we describe how an asymmetric nanopore improves molecular ping-pong by promoting the recapture of the molecule in the trans reservoir. We also demonstrate that the molecular recapture could be improved by linking the target molecule to a long DNA carrier to reduce the diffusion, thereby achieving over 100 recapture events. Using this ping-pong methodology, we demonstrate its use in accurately resolving nanostructure motifs along a DNA scaffold through repeated detection. Our method offers novel insights into the control of DNA polymer dynamics within nanopore confinement and opens avenues for the development of a high-fidelity DNA detection platform.
Topics: Nanopores; DNA; Nanotechnology; Diffusion; Polymers
PubMed: 38033205
DOI: 10.1021/acs.nanolett.3c03605 -
International Journal of Molecular... Aug 2023Septins are considered the fourth component of the cytoskeleton with the septin7 isoform playing a critical role in the formation of diffusion barriers in phospholipid...
Septins are considered the fourth component of the cytoskeleton with the septin7 isoform playing a critical role in the formation of diffusion barriers in phospholipid bilayers and intra- and extracellular scaffolds. While its importance has already been confirmed in different intracellular processes, very little is known about its role in skeletal muscle. Muscle regeneration was studied in a conditional knock-down mouse model to prove the possible role of septin7 in this process. Sterile inflammation in skeletal muscle was induced which was followed by regeneration resulting in the upregulation of septin7 expression. Partial knock-down of resulted in an increased number of inflammatory cells and myofibers containing central nuclei. Taken together, our data suggest that partial knock-down of hinders the kinetics of muscle regeneration, indicating its crucial role in skeletal muscle functions.
Topics: Animals; Mice; Cytoskeleton; Diffusion; Disease Models, Animal; Infertility; Muscle, Skeletal; Septins
PubMed: 37686339
DOI: 10.3390/ijms241713536 -
Neural Networks : the Official Journal... Sep 2023Zero-shot learning (ZSL) aims to predict unseen classes without using samples of these classes in model training. The ZSL has been widely used in many knowledge-based...
Zero-shot learning (ZSL) aims to predict unseen classes without using samples of these classes in model training. The ZSL has been widely used in many knowledge-based models and applications to predict various parameters, including categories, subjects, and anomalies, in different domains. Nonetheless, most existing ZSL methods require the pre-defined semantics or attributes of particular data environments. Therefore, these methods are difficult to be applied to general data environments, such as ImageNet and other real-world datasets and applications. Recent research has tried to use open knowledge to enhance the ZSL methods to adapt it to an open data environment. However, the performance of these methods is relatively low, namely the accuracy is normally below 10%, which is due to the inadequate semantics that can be used from open knowledge. Moreover, the latest methods suffer from a significant "semantic gap" problem between the generated features of unseen classes and the real features of seen classes. To this end, this paper proposes a multi-view graph representation with a similarity diffusion model, applying the ZSL tasks to general data environments. This model applies a multi-view graph to enhance the semantics fully and proposes an innovative diffusion method to augment the graph representation. In addition, a feature diffusion method is proposed to augment the multi-view graph representation and bridge the semantic gap to realize zero-shot predicting. The results of numerous experiments in general data environments and on benchmark datasets show that the proposed method can achieve new state-of-the-art results in the field of general zero-shot learning. Furthermore, seven ablation studies analyze the effects of the settings and different modules of the proposed method on its performance in detail and prove the effectiveness of each module.
Topics: Humans; Learning; Benchmarking; Diffusion; Knowledge; Knowledge Bases
PubMed: 37480768
DOI: 10.1016/j.neunet.2023.06.045