Enantioselective Molecular Transport in Multilayer Graphene Nanopores

Multilayer superstructures based on stacked layered nanomaterials offer the possibility to design three-dimensional (3D) nanopores with highly specific properties analogous to protein channels. In a layer-by-layer design and stacking, analogous to molecular printing, superstructures with lock-and-key molecular nesting and transport characteristics could be prepared. To examine this possibility, we use molecular dynamics simulations to study electric field-driven transport of ions through stacked porous graphene flakes. First, highly selective, tunable, and correlated passage rates of monovalent atomic ions through these superstructures are observed in dependence on the ion type, nanopore type, and relative position and dynamics of neighboring porous flakes. Next, enantioselective molecular transport of ionized l- and d-leucine is observed in graphene stacks with helical nanopores. The outlined approach provides a general scheme for synthesis of functional 3D superstructures.

Osmotically-driven transport in carbon nanotube porins

We report the measurements of transport of ions and uncharged species through carbon nanotube (CNT) porins--short segments of CNTs inserted into a lipid bilayer membrane. Rejection characteristics of the CNT porins are governed by size exclusion for the uncharged species. In contrast, rejection of ionic species is governed by the electrostatic repulsion and Donnan membrane equilibrium. Permeability of monovalent cations follows the general trend in the hydrated ion size, except in the case of Cs(+) ions.

Scale and structure dependent solute diffusivity within microporous tissue engineering scaffolds

Diffusion of nutrients to cells cultured within three-dimensional scaffolds is fundamental for cell survival during development of the tissue construct, when no vasculature is present to aid transport. Significant efforts have been made to characterize the effect of structure on solute diffusivity in nanoporous hydrogels, yet a similar thorough characterization has not been attempted for microporous scaffolds. Here, we make use of freeze-dried collagen scaffolds, possessing pore sizes in the range 150-250 μm and isotropic or aligned morphology, to study the diffusivity of fluorescent dextran molecules. Fluorescence recovery after photobleaching is used to measure the self diffusivity of the solutes within single pores, while Fickian diffusion over scales larger than the pore size is studied by assessing the solute concentration profile within the materials over time. We show that, not only do the morphological parameters of the scaffolds significantly affect the diffusivity of the solutes, but also that the assessment of such diffusivity depends on the length scale of diffusion of the molecules under investigation, with the resulting diffusion coefficients being differently affected by the scaffold structure. The results provided can guide the design of scaffolds with tailored diffusivity and nutrient concentration profiles.

Teleological cooption of Mycobacterium tuberculosis PE/PPE proteins as porins: Role in molecular immigration and emigration

Permeation through bacterial cells for exchange or uptake of biomolecules and ions invariably depend upon the existence of pore-forming proteins (porins) in their outer membrane. Mycobacterium tuberculosis (M. tb) harbours one of the most rigid cell envelopes across bacterial genera and is devoid of the classical porins for solute transport across the cell membrane. Though canonical porins are incompatible with the evolution of permeability barrier, porin like activity has been reported from membrane preparations of pathogenic mycobacteria. This suggests a sophisticated transport mechanism that has been elusive until now, along with the protein family responsible for it. Recent evidence suggests that these slow-growing mycobacteria have co-opted some of PE/PPE family proteins as molecular transport channels, in place of porins, to facilitate uptake of nutrients required to thrive in the restrictive host environment. These reports advocate that PE/PPE proteins, due to their structural ability, have a potential role in importing small molecules to the cell's interior. This mechanism unveils how a successful pathogen overcomes its restrictive membrane's transport limitations for selective uptake of nutrients. If extrapolated to have a role in drug transport, these channels could help understand the emergence of drug resistance. Further, as these proteins are associated with the export of virulence factors, they can be exploited as novel drug targets. There remains, however, an interesting question that as the PE/PPE proteins can allow the 'import' of molecules from outside the cell, is the reverse transport also possible across the M. tb membrane. In this review, we have discussed recent evidence supporting PE/PPE's role as a specific transport channel for selective uptake of small molecule nutrients and, as possible molecular export machinery of M. tb. This newly discovered role as transmembrane channels demands further research on this enigmatic family of proteins to comprehend the pathomechanism of this very smart pathogen.

Comparative genomic analyses of transport proteins encoded within the genomes of Leptospira species

Select species of the bacterial genus Leptospira are causative agents of leptospirosis, an emerging global zoonosis affecting nearly one million people worldwide annually. We examined two Leptospira pathogens, Leptospira interrogans serovar Lai str. 56601 and Leptospira borgpetersenii serovar Hardjo-bovis str. L550, as well as the free-living leptospiral saprophyte, Leptospira biflexa serovar Patoc str. 'Patoc 1 (Ames)'. The transport proteins of these leptospires were identified and compared using bioinformatics to gain an appreciation for which proteins may be related to pathogenesis and saprophytism. L. biflexa possesses a disproportionately high number of secondary carriers for metabolite uptake and environmental adaptability as well as an increased number of inorganic cation transporters providing ionic homeostasis and effective osmoregulation in a rapidly changing environment. L. interrogans and L. borgpetersenii possess far fewer transporters, but those that they have are remarkably similar, with near-equivalent representation in most transporter families. These two Leptospira pathogens also possess intact sphingomyelinases, holins, and virulence-related outer membrane porins. These virulence-related factors, in conjunction with decreased transporter substrate versatility, indicate that pathogenicity was accompanied by progressively narrowing ecological niches and the emergence of a limited set of proteins responsible for host invasion. The variability of host tropism and mortality rates by infectious leptospires suggests that small differences in individual sets of proteins play important physiological and pathological roles.

Bioelectricity inhibits back diffusion from the anolyte into the desalinated stream in microbial desalination cells

Microbial desalination cells (MDCs) taking advantage of energy in wastewater to drive desalination represent a promising approach for energy-efficient desalination, but concerns arise whether contaminants in wastewater could enter the desalinated stream across ion exchange membranes. Such back diffusion of contaminants from the anolyte into the desalinated stream could be controlled by two mechanisms, Donnan effect and molecule transport. This study attempted to understand those mechanisms for inorganic and organic compounds in MDCs through two independently conducted experiments. Donnan effect was found to be the dominant mechanism under the condition without current generation. Under open circuit condition, the MDC fed with 5 g L(-1) salt solution exhibited 1.9 ± 0.7%, 10.3 ± 1.3%, and 1.8 ± 1.2% back diffusion of acetic, phosphate, and sulfate ions, respectively. Current generation effectively suppressed Donnan effect from 68.2% to 7.2%, and then molecule transport became more responsible for back diffusion. A higher initial salt concentration (35 g L(-1)) and a shorter HRT (1.0 d) led to the highest concentration gradient, resulting in the most back diffusion of 7.1 ± 1.2% and 6.8 ± 3.1% of phosphate and sulfate ions, respectively. Three representative organic compounds were selected for test, and it was found that organic back diffusion was intensified with a higher salt concentration gradient and molecular weight played an important role in compound movement. Principal component analysis confirmed the negative correlation between Donnan effect and current, and the positive correlation between molecule transport and concentration gradient related conditions.

A method for assessing ionic and molecular permeation in connexin hemichannels

Connexin hemichannels are permeable to both atomic ions and small molecules. Yet, they have different selectivity for ions and signaling molecules critical for biological functions. Activity of connexin hemichannels in living cells is commonly evaluated by methods that include electrophysiology and fluorescence-based approaches. Although less common, luminescence and radioactivity-based uptake/release assays have been also successfully used to determine selectivity and permeability to different molecules. The current methods, however, have important technical and quantitative limitations that make them unsuitable for simultaneously evaluating ionic and molecular permeability using different stimuli that control channel gating (e.g., voltage or extracellular Ca²⁺). To address this, we have recently designed a novel methodology that combines two-electrode voltage clamp (TEVC) and dye uptake assays in translucent Xenopus oocytes. This method allows for the evaluation of molecular transport kinetics in connexin hemichannels, and its utility can also be extended to other large pore channels, such as those formed by pannexin and CALHM. In this article, we describe step by step the protocol to perform the TEVC/Dye uptake assay.

Single-cell electroporation with high-frequency nanosecond pulse bursts: Simulation considering the irreversible electroporation effect and experimental validation

To study the electroporation characteristics of cells under high-frequency nanosecond pulse bursts (HFnsPBs), the original electroporation mathematical model was improved. By setting a threshold value for irreversible electroporation (IRE) and considering the effect of an electric field on the surface tension of a cell membrane, a mathematical model of electroporation considering the effect of IRE is proposed for the first time. A typical two-dimensional cell system was discretized into nodes using MATLAB, and a mesh transport network method (MTNM) model was established for simulation. The dynamic processes of single-cell electroporation and molecular transport under the application of 50 unipolar HFnsPBs with field intensities of 9 kV cm^-1 and different frequencies (10 kHz, 100 kHz and 500 kHz) to the target system was simulated with a 300 s simulation time. The IRE characteristics and molecular transport were evaluated. In addition, a PI fluorescent dye assay was designed to verify the correctness of the model by providing time-domain and spatial results that were compared with the simulation results. The simulation achieved IRE and demonstrated the cumulative effects of multipulse bursts and intraburst frequency on irreversible pores. The model can also reflect the cumulative effect of multipulse bursts on reversible pores by introducing an assumption of stable reversible pores. The experimental results agreed qualitatively with the simulation results. A relative calibration of the fluorescence data gave time-domain molecular transport results that were quantitatively similar to the simulation results. This article reveals the cell electroporation characteristics under HFnsPBs from a mechanism perspective and has important guidance for fields involving the IRE of cells.

Comparative analyses of transport proteins encoded within the genomes of Leptospira species

Select species of the bacterial genus Leptospira are causative agents of leptospirosis, an emerging global zoonosis affecting nearly one million people worldwide annually. We examined two Leptospira pathogens, Leptospira interrogans serovar Lai str. 56601 and Leptospira borgpetersenii serovar Hardjo-bovis str. L550, as well as the free-living leptospiral saprophyte, Leptospira biflexa serovar Patoc str. 'Patoc 1 (Ames)'. The transport proteins of these leptospires were identified and compared using bioinformatics to gain an appreciation for which proteins may be related to pathogenesis and saprophytism. L. biflexa possesses a disproportionately high number of secondary carriers for metabolite uptake and environmental adaptability as well as an increased number of inorganic cation transporters providing ionic homeostasis and effective osmoregulation in a rapidly changing environment. L. interrogans and L. borgpetersenii possess far fewer transporters, but those that they all have are remarkably similar, with near-equivalent representation in most transporter families. These two Leptospira pathogens also possess intact sphingomyelinases, holins, and virulence-related outer membrane porins. These virulence-related factors, in conjunction with decreased transporter substrate versatility, indicate that pathogenicity arose in Leptospira correlating to progressively narrowing ecological niches and the emergence of a limited set of proteins responsible for host invasion. The variability of host tropism and mortality rates by infectious leptospires suggests that small differences in individual sets of proteins play important physiological and pathological roles.

Molecular transport in collagenous tissues measured by gel electrophoresis

Molecular transport in tissues is important for drug delivery, nutrient supply, waste removal, cell signaling, and detecting tissue degeneration. Therefore, the objective of this study was to investigate gel electrophoresis as a simple method to measure molecular transport in collagenous tissues. The electrophoretic mobility of charged molecules in tissue samples was measured from relative differences in the velocity of a cationic dye passing through an agarose gel in the absence and presence of a tissue section embedded within the gel. Differences in electrophoretic mobility were measured for the transport of a molecule through different tissues and tissue anisotropy, or the transport of different sized molecules through the same tissue. Tissue samples included tendon and fibrocartilage from the proximal (tensile) and distal (compressive) regions of the bovine flexor tendon, respectively, and bovine articular cartilage. The measured electrophoretic mobility was greatest in the compressive region of the tendon (fibrocartilage), followed by the tensile region of tendon, and lowest in articular cartilage, reflecting differences in the composition and organization of the tissues. The anisotropy of tendon was measured by greater electrophoretic mobility parallel compared with perpendicular to the predominate collagen fiber orientation. Electrophoretic mobility also decreased with increased molecular size, as expected. Therefore, the results of this study suggest that gel electrophoresis may be a useful method to measure differences in molecular transport within various tissues, including the effects of tissue type, tissue anisotropy, and molecular size.

Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species

The human microbiome influences human health in both negative and positive ways. Studies on the transportomes of these organisms yield information that may be utilized for various purposes, including the identification of novel drug targets and the manufacture of improved probiotic strains. Moreover, these genomic analyses help to improve our understanding of the physiology and metabolic capabilities of these organisms. The present study is a continuation of our studies on the transport proteins of the major gut microbes. Bifidobacterium species are essential members of the human gut microbiome, and they initiate colonization of the gut at birth, providing health benefits that last a lifetime. In this study we analyze the transportomes of nine bifidobacterial species: B. adolescentis, B. animalis, B. bifidum, B. breve, B. catenulatum, B. dentium, B. longum subsp. infantis, B. longum subsp. longum, and B. pseudocatenulatum. All of these species have proven probiotic characteristics and exert beneficial effects on human health. Surprisingly, we found that all nine of these species have similar pore-forming toxins and drug exporters that may play roles in pathogenesis. These species have transporters for amino acids, carbohydrates, and proteins, essential for their organismal lifestyles and adaption to their respective ecological niches. The strictly probiotic species, B. bifidum, however, contains fewer such transporters, thus indicative of limited interactions with host cells and other gut microbial counterparts. The results of this study were compared with those of our previous studies on the transportomes of multiple species of Bacteroides, Escherichia coli/Salmonella, and Lactobacillus. Overall, bifidobacteria have larger transportomes (based on percentages of total proteins) than the previously examined groups of bacterial species, with a preference for primary active transport systems over secondary carriers. Taken together, these results provide useful information about the physiologies and pathogenic potentials of these probiotic organisms as reflected by their transportomes.

Intronic miRNA mediated gene expression regulation controls protein crowding inside the cell

Gene regulatory effects of microRNAs at a posttranscriptional level have been established over the last decade. In this study, we analyze the interaction networks of mRNA translation regulation through intronic miRNA, under various tissue-specific cellular contexts, taking into account the thermodynamic affinity, chemical kinetics, co-localization, concentration levels, network parameters and the presence of competitive interactors. This database, and analysis has been made available through an open-access web-server, miRiam, to promote further exploration. Here we report that expression of genes involved in Apoptosis Processes, Immune System Processes, Translation Regulator Activities, and Molecular Transport Activities within the cell are predominately regulated by miRNA mediation. Our findings further indicate that this regulatory effect has a profound effect in controlling protein crowding inside the cell. A miRNA mediated gene expression regulation serves as a temporal regulator, allowing the cellular machinery to temporarily 'pause' the translation of mRNA, indicating that the miRNA-mRNA interactions may be important for governing the optimal usage of cell volume.

The effect of the foreign body response on drug elution from subdermal delivery systems

Contrasting findings are presented in the literature regarding the influence of foreign body response (FBR) on drug release from implantable drug delivery systems. To this end, here we sought direct evidence of the effect of the fibrotic tissue on subcutaneous drug release from long-acting drug delivery implants. Specifically, we investigated the pharmacokinetic impact of fibrotic encapsulation on a small molecule drug, islatravir (293 Da), and a large protein, IgG (150 kDa), administered via biocompatible implants. First, solid implants fabricated from biocompatible PMMA resin, nylon, and PLA were used to characterize the degree of FBR in rats. Despite initial material-dependent differences in the early FBR phase, the thickness and composition of the fibrotic capsules normalized in the chronic phase of FBR. Ex vivo assessments indicated an increase in the diffusivity of both molecules over time, aligning with a reduction in collagen density within the fibrotic tissue. Subsequently, reservoir-based drug delivery devices, matching the solid implants in size, shape and material, were implanted to study in vivo pharmacokinetics. The study revealed consistent plasma levels of islatravir across different implant materials and a temporary modulation of IgG release from PMMA resin implants during the acute FBR phase. End-point histological analyses confirmed that the localized delivery neither incited inflammation in the surrounding tissue nor did it alter vascularization. This evidence suggests that, while acute FBR may transiently affect the release of larger molecules, in the absence of acute local inflammation, fibrotic encapsulation does not significantly impact the steady-state release of small molecule drugs from long-acting implantable delivery systems.

Quantitative analysis of molecular transport in the extracellular space using physics-informed neural network

The brain extracellular space (ECS), an irregular, extremely tortuous nanoscale space located between cells or between cells and blood vessels, is crucial for nerve cell survival. It plays a pivotal role in high-level brain functions such as memory, emotion, and sensation. However, the specific form of molecular transport within the ECS remain elusive. To address this challenge, this paper proposes a novel approach to quantitatively analyze the molecular transport within the ECS by solving an inverse problem derived from the advection-diffusion equation (ADE) using a physics-informed neural network (PINN). PINN provides a streamlined solution to the ADE without the need for intricate mathematical formulations or grid settings. Additionally, the optimization of PINN facilitates the automatic computation of the diffusion coefficient governing long-term molecule transport and the velocity of molecules driven by advection. Consequently, the proposed method allows for the quantitative analysis and identification of the specific pattern of molecular transport within the ECS through the calculation of the Péclet number. Experimental validation on two datasets of magnetic resonance images (MRIs) captured at different time points showcases the effectiveness of the proposed method. Notably, our simulations reveal identical molecular transport patterns between datasets representing rats with tracer injected into the same brain region. These findings highlight the potential of PINN as a promising tool for comprehensively exploring molecular transport within the ECS.

Molecular transport through nano-sized multipores of lipid vesicles: a COMSOL simulation study

Biomembranes regulate molecular transport essential to cellular function and numerous biomedical applications, such as drug delivery and gene therapy. This study simulates molecular transport through nano-sized multipores in Giant Unilamellar Vesicles (GUVs) using COMSOL Multiphysics. We analyzed the diffusion dynamics of fluorescent probes-including Calcein, Texas-red dextran 3000 (TRD- 3k), TRD- 10k, and Alexa Fluor-labeled soybean trypsin inhibitor (AF-SBTI)-across different pore sizes, and derived rate constants using curve fitting that closely align with experimental data. Additionally, an analytical model based on Fick's law of diffusion provides further insight into transport efficiency. This approach offers a novel perspective by examining simultaneous transport through multiple nanopores, which better mimics realistic biological environments compared to traditional single-pore studies. We used COMSOL for efficiently simulating large-scale, multi-nanopore systems, particularly in biomedical applications where modeling of complex transport phenomena is essential. This work provides new insights into multipore-mediated transport, critical for optimizing nanopore-based drug delivery and advancing the understanding of cellular transport mechanisms.

Study on ultrasound-enhanced molecular transport in articular cartilage

Local intra-articular administration with minimal side effects and rapid efficacy is a promising strategy for treating osteoarthritis(OA). Most drugs are rapidly cleared from the joint space by capillaries and lymphatic vessels before free diffusion into cartilage. Ultrasound, as a non-invasive therapy, enhances molecular transport within cartilage through the mechanisms of microbubble cavitation and thermal effects. This study investigated the mass transfer behavior of solute molecules with different molecular weights (479 Da, 40 kDa, 150 kDa) within porcine articular cartilage under low-frequency ultrasound conditions of 40 kHz and ultrasound intensities of 0.189 W/cm2 and 0.359 W/cm2. The results revealed that under the conditions of 0.189 W/cm2 ultrasound intensity, the mass transfer concentration of solute molecules were higher compared to passive diffusion, and with an increase in ultrasound intensity to 0.359 W/cm2, the mass transfer effect within the cartilage was further enhanced. Ultrasound promotes molecular transport in different layers of cartilage. Under static conditions, after 2 h of mass transfer, the concentration of small molecules in the superficial layer is lower than that in the middle layer. After applying ultrasound at 0.189 W/cm2, the molecular concentration in the superficial layer significantly increases. Under conditions of 0.359 W/cm2, after 12 h of mass transfer, the concentration of medium and large molecules in the deep layer region increased by more than two times. In addition, this study conducted an assessment of damage to porcine articular cartilage under ultrasound exposure, revealing the significant potential of low-frequency, low-intensity ultrasound in drug delivery and treatment of OA.