Transport of Glucose and Poly(ethylene glycol)s in Agarose Gels Studied by the Refractive Index Method

Agarose-Based Hydrogel Film with Embedded Oriented Photonic Nanochains for Sensing pH

Responsive photonic crystal hydrogel sensors are renowned for their colorimetric sensing ability and can be utilized in many fields such as medical diagnosis, environmental detection, food safety, and industrial production. Previously, our group invented responsive photonic nanochains (RPNCs), which improve the response speed of photonic crystal hydrogel sensors by at least 2 to 3 orders of magnitude. However, RPNCs are dispersed in a liquid medium, which needs a magnetic field to orient them for the generation of structural colors. In addition, during repeated use, the process of cleaning and redispersing can cause entanglement, breakage, and a loss of RPNCs, resulting in poor stability. Moreover, when mixing with the samples in liquid, the RPNCs may lead to the contamination of the samples being tested. In this paper, we incorporate one-dimensional oriented RPNCs with agarose gel film to prepare heterogeneous hydrogel films. Thanks to the non-responsive and porous nature of the agarose gel, the protons diffuse freely in the gel, which facilitates the fast response of the RPNCs. Furthermore, the "frozen" RPNCs in agarose gel not only enable the display of structural colors without the need for a magnet but also improve the cycling stability and long-term durability of the sensor, and will not contaminate the samples. This work paves the way for the application of photonic crystal sensors.

High-Throughput Gel Microbeads as Incubators for Bacterial Competition Study

Bacteria primarily live in structured environments, such as colonies and biofilms, attached to surfaces or growing within soft tissues. They are engaged in local competitive and cooperative interactions impacting our health and well-being, for example, by affecting population-level drug resistance. Our knowledge of bacterial competition and cooperation within soft matrices is incomplete, partly because we lack high-throughput tools to quantitatively study their interactions. Here, we introduce a method to generate a large amount of agarose microbeads that mimic the natural culture conditions experienced by bacteria to co-encapsulate two strains of fluorescence-labeled Escherichia coli. Focusing specifically on low bacterial inoculum (1-100 cells/capsule), we demonstrate a study on the formation of colonies of both strains within these 3D scaffolds and follow their growth kinetics and interaction using fluorescence microscopy in highly replicated experiments. We confirmed that the average final colony size is inversely proportional to the inoculum size in this semi-solid environment as a result of limited available resources. Furthermore, the colony shape and fluorescence intensity per colony are distinctly different in monoculture and co-culture. The experimental observations in mono- and co-culture are compared with predictions from a simple growth model. We suggest that our high throughput and small footprint microbead system is an excellent platform for future investigation of competitive and cooperative interactions in bacterial communities under diverse conditions, including antibiotics stress.

Two‐ and three‐dimensional in vitro nucleus pulposus cultures: An in silico analysis of local nutrient microenvironments

Background

It is well established that the unique biochemical microenvironment of the intervertebral disc plays a predominant role in cell viability and biosynthesis. However, unless the effect of microenvironmental conditions is primary to a study objective, in vitro culture parameters that are critical for reproducibility are both varied and not routinely reported.

Aims

This work aims to investigate the local microenvironments of commonly used culture configurations, highlighting physiological relevance, potential discrepancies, and elucidating possible heterogeneity across the research field.

Materials and Methods

This work uses nutrient‐transport in silico models to reflect on the effect of often underappreciated parameters, such as culture geometry and diffusional distance (vessel, media volume, construct size), seeding density, and external boundary conditions on the local microenvironment of two‐dimensional (2D) and three‐dimensional (3D) in vitro culture systems.

Results

We elucidate important discrepancies between the external boundary conditions such as the incubator level or media concentrations and the actual local cellular concentrations. Oxygen concentration and cell seeding density were found to be highly influential parameters and require utmost consideration when utilizing 3D culture systems.

Discussion

This work highlights that large variations in the local nutrient microenvironment can easily be established without consideration of several key parameters. Without careful deliberation of the microenvironment within each specific and unique system, there is the potential to confound in vitro results leading to heterogeneous results across the research field in terms of biosynthesis and matrix composition.

Conclusion

Overall, this calls for a greater appreciation of key parameters when designing in vitro experiments. Better harmony and standardization of physiologically relevant local microenvironments are needed to push toward reproducibility and successful translation of findings across the research field.

Large variations in the local nutrient microenvironment can easily be established without careful consideration of several key parameters. While one external concentration may be suitable for one culture configuration, they may not be appropriate for another. External conditions need to be tailored to the specific cells and culture system to establish homogeneous and physiologically relevant microenvironments. Taken together, more deliberate consideration of the external boundary concentrations and in vitro culture design, harmony and standardization of a physiologically relevant microenvironment will push toward greater reproducibility and more successful translation of findings across the field.

Design of a versatile microfluidic device for imaging precision-cut-tissue slices

Precision-cut-tissues (PCTs), which preserve many aspects of a tissue's microenvironment, are typically imaged using conventional sample dishes and chambers. These can require large amounts of reagent and, when used for flow-through experiments, the shear forces applied on the tissues are often ill-defined. Their physical design also makes it difficult to image large volumes and repetitively image smaller regions of interest in the living slice. We report here on the design of a versatile microfluidic device capable of holding mouse or human pancreas PCTs for 3D fluorescence imaging using confocal and selective plane illumination microscopy (SPIM). Our design positions PCTs within a 5 × 5 mm × 140µm deep chamber fitted with 150µm tall channels to facilitate media exchange. Shear stress in the device is localized to small regions on the surface of the tissue and can be easily controlled. This design allows for media exchange at flowrates ∼10-fold lower than those required for conventional chambers. Finally, this design allows for imaging the same immunofluorescently labeled PCT with high resolution on a confocal and with large field of view on a SPIM, without adversely affecting image quality.

Microbial competition reduces metabolic interaction distances to the low µm-range

Metabolic interactions between cells affect microbial community compositions and hence their function in ecosystems. It is well-known that under competition for the exchanged metabolite, concentration gradients constrain the distances over which interactions can occur. However, interaction distances are typically quantified in two-dimensional systems or without accounting for competition or other metabolite-removal, conditions which may not very often match natural ecosystems. We here analyze the impact of cell-to-cell distance on unidirectional cross-feeding in a three-dimensional aqueous system with competition for the exchanged metabolite. Effective interaction distances were computed with a reaction-diffusion model and experimentally verified by growing a synthetic consortium of 1 µm-sized metabolite producer, receiver, and competitor cells in different spatial structures. We show that receivers cannot interact with producers located on average 15 µm away from them, as product concentration gradients flatten close to producer cells. We developed an aggregation protocol and varied the receiver cells’ product affinity, to show that within producer–receiver aggregates even low-affinity receiver cells could interact with producers. These results show that competition or other metabolite-removal of a public good in a three-dimensional system reduces metabolic interaction distances to the low µm-range, highlighting the importance of concentration gradients as physical constraint for cellular interactions.

Membrane-protein crystals for neutron diffraction

Neutron macromolecular crystallography (NMX) has the potential to provide the experimental input to address unresolved aspects of transport mechanisms and protonation in membrane proteins. However, despite this clear scientific motivation, the practical challenges of obtaining crystals that are large enough to make NMX feasible have so far been prohibitive. Here, the potential impact on feasibility of a more powerful neutron source is reviewed and a strategy for obtaining larger crystals is formulated, exemplified by the calcium-transporting ATPase SERCA1. The challenges encountered at the various steps in the process from crystal nucleation and growth to crystal mounting are explored, and it is demonstrated that NMX-compatible membrane-protein crystals can indeed be obtained.

Spinning-disc confocal microscopy in the second near-infrared window (NIR-II)

Fluorescence microscopy in the second near-infrared optical window (NIR-II, 1000–1350 nm) has become a technique of choice for non-invasive in vivo imaging. The deep penetration of NIR light in living tissue, as well as negligible tissue autofluorescence within this optical range, offers increased resolution and contrast with even greater penetration depths. Here, we present a custom-built spinning-disc confocal laser microscope (SDCLM) that is specific to imaging in the NIR-II. The SDCLM achieves a lateral resolution of 0.5 ± 0.1 µm and an axial resolution of 0.6 ± 0.1 µm, showing a ~17% and ~45% enhancement in lateral and axial resolution, respectively, compared to the corresponding wide-field configuration. We furthermore showcase several applications that demonstrate the use of the SDCLM for in situ, spatiotemporal tracking of NIR particles and bioanalytes within both synthetic and biological systems.

An Efficient, Recyclable, and Stable Immobilized Biocatalyst Based on Bioinspired Microcapsules-in-Hydrogel Scaffolds

Design and preparation of high-performance immobilized biocatalysts with exquisite structures and elucidation of their profound structure-performance relationship are highly desired for green and sustainable biotransformation processes. Learning from nature has been recognized as a shortcut to achieve such an impressive goal. Loose connective tissue, which is composed of hierarchically organized cells by extracellular matrix (ECM) and is recognized as an efficient catalytic system to ensure the ordered proceeding of metabolism, may offer an ideal prototype for preparing immobilized biocatalysts with high catalytic activity, recyclability, and stability. Inspired by the hierarchical structure of loose connective tissue, we prepared an immobilized biocatalyst enabled by microcapsules-in-hydrogel (MCH) scaffolds via biomimetic mineralization in agarose hydrogel. In brief, the in situ synthesized hybrid microcapsules encapsulated with glucose oxidase (GOD) are hierarchically organized by the fibrous framework of agarose hydrogel, where the fibers are intercalated into the capsule wall. The as-prepared immobilized biocatalyst shows structure-dependent catalytic performance. The porous hydrogel permits free diffusion of glucose molecules (diffusion coefficient: ∼6 × 10(-6) cm(2) s(-1), close to that in water) and retains the enzyme activity as much as possible after immobilization (initial reaction rate: 1.5 × 10(-2) mM min(-1)). The monolithic macroscale of agarose hydrogel facilitates the easy recycling of the immobilized biocatalyst (only by using tweezers), which contributes to the nonactivity decline during the recycling test. The fiber-intercalating structure elevates the mechanical stability of the in situ synthesized hybrid microcapsules, which inhibits the leaching and enhances the stability of the encapsulated GOD, achieving immobilization efficiency of ∼95%. This study will, therefore, provide a generic method for the hierarchical organization of (bio)active materials and the rational design of novel (bio)catalysts.

A polysulfobetaine hydrogel for immobilization of a glucose-binding protein

A hydrogel based on sulfobetaine methacrylate monomer and crosslinker was investigated as a potential material for fluorescent glucose biosensor applications.

Growing yeast into cylindrical colonies

Microorganisms often form complex multicellular assemblies such as biofilms and colonies. Understanding the interplay between assembly expansion, metabolic yield, and nutrient diffusion within a freely growing colony remains a challenge. Most available data on microorganisms are from planktonic cultures, due to the lack of experimental tools to control the growth of multicellular assemblies. Here, we propose a method to constrain the growth of yeast colonies into simple geometric shapes such as cylinders. To this end, we designed a simple, versatile culture system to control the location of nutrient delivery below a growing colony. Under such culture conditions, yeast colonies grow vertically and only at the locations where nutrients are delivered. Colonies increase in height at a steady growth rate that is inversely proportional to the cylinder radius. We show that the vertical growth rate of cylindrical colonies is not defined by the single-cell division rate, but rather by the colony metabolic yield. This contrasts with cells in liquid culture, in which the single-cell division rate is the only parameter that defines the population growth rate. This method also provides a direct, simple method to estimate the metabolic yield of a colony. Our study further demonstrates the importance of the shape of colonies on setting their expansion. We anticipate that our approach will be a starting point for elaborate studies of the population dynamics, evolution, and ecology of microbial colonies in complex landscapes.

Tuning mechanical performance of poly(ethylene glycol) and agarose interpenetrating network hydrogels for cartilage tissue engineering

Hydrogels are attractive for tissue engineering applications due to their incredible versatility, but they can be limited in cartilage tissue engineering applications due to inadequate mechanical performance. In an effort to address this limitation, our team previously reported the drastic improvement in the mechanical performance of interpenetrating networks (IPNs) of poly(ethylene glycol) diacrylate (PEG-DA) and agarose relative to pure PEG-DA and agarose networks. The goal of the current study was specifically to determine the relative importance of PEG-DA concentration, agarose concentration, and PEG-DA molecular weight in controlling mechanical performance, swelling characteristics, and network parameters. IPNs consistently had compressive and shear moduli greater than the additive sum of either single network when compared to pure PEG-DA gels with a similar PEG-DA content. IPNs withstood a maximum stress of up to 4.0 MPa in unconfined compression, with increased PEG-DA molecular weight being the greatest contributing factor to improved failure properties. However, aside from failure properties, PEG-DA concentration was the most influential factor for the large majority of properties. Increasing the agarose and PEG-DA concentrations as well as the PEG-DA molecular weight of agarose/PEG-DA IPNs and pure PEG-DA gels improved moduli and maximum stresses by as much as an order of magnitude or greater compared to pure PEG-DA gels in our previous studies. Although the viability of encapsulated chondrocytes was not significantly affected by IPN formulation, glycosaminoglycan (GAG) content was significantly influenced, with a 12-fold increase over a three-week period in gels with a lower PEG-DA concentration. These results suggest that mechanical performance of IPNs may be tuned with partial but not complete independence from biological performance of encapsulated cells.

Hierarchically designed agarose and poly(ethylene glycol) interpenetrating network hydrogels for cartilage tissue engineering

A new method for encapsulating cells in interpenetrating network (IPN) hydrogels of superior mechanical integrity was developed. In this study, two biocompatible materials-agarose and poly(ethylene glycol) (PEG) diacrylate-were combined to create a new IPN hydrogel with greatly enhanced mechanical performance. Unconfined compression of hydrogel samples revealed that the IPN displayed a fourfold increase in shear modulus relative to a pure PEG-diacrylate network (39.9 vs. 9.9 kPa) and a 4.9-fold increase relative to a pure agarose network (8.2 kPa). PEG and IPN compressive failure strains were found to be 71% ± 17% and 74% ± 17%, respectively, while pure agarose gels failed around 15% strain. Similar mechanical property improvements were seen when IPNs-encapsulated chondrocytes, and LIVE/DEAD cell viability assays demonstrated that cells survived the IPN encapsulation process. The majority of IPN-encapsulated chondrocytes remained viable 1 week postencapsulation, and chondrocytes exhibited glycosaminoglycan synthesis comparable to that of agarose-encapsulated chondrocytes at 3 weeks postencapsulation. The introduction of a new method for encapsulating cells in a hydrogel with enhanced mechanical performance is a promising step toward cartilage defect repair. This method can be applied to fabricate a broad variety of cell-based IPNs by varying monomers and polymers in type and concentration and by adding functional groups such as degradable sequences or cell adhesion groups. Further, this technology may be applicable in other cell-based applications where mechanical integrity of cell-containing hydrogels is of great importance.

Impact of casein gel microstructure on self-diffusion coefficient of molecular probes measured by 1H PFG-NMR

The translational dynamics of poly(ethylene glycol) (PEG) polymers with molecular weights (Mw) varying from 6x10(2) to 5x10(5) were investigated by pulsed field gradient NMR in casein suspensions and in gels induced by acidification, enzyme action, and a combination of both. For molecules with Mw<or=1020, the diffusion was only dependent on the casein concentration whatever the molecular weight of the probe or the sample studied. However, for PEG with Mw>or=8000, there was strong dependence of diffusion on PEG size and on the casein network structure as revealed by scanning electron microscopy images. The diffusion coefficients of the two largest PEGs were increased after coagulation by amounts that depended on the internal structure of the gel. In addition, the 527,000 g/mol PEG was found to deviate from Gaussian diffusion behavior to greater or lesser extents according to the casein concentration and the sample microstructure. The results are discussed in terms of network rearrangements.

Protein diffusion in agarose hydrogel in situ measured by improved refractive index method

The accurate knowledge of the diffusion behavior of protein within biomimetic hydrogel matrix at body temperature has a great implication for the design of efficient controlled release protein-base drug delivery devices. In this paper, we improved our previous in situ refractive index method with great temperature-controlled capability. For the first time, this newly improved method was employed to study the diffusion of protein (bovine serum albumin (BSA) and lysozyme) in agarose hydrogel at body temperature (37 degrees C). The change of the gel refractive index caused by the change of the diffusing protein concentration within the gel during the diffusion process enables the effective diffusion coefficients of protein to be estimated. The diffusion coefficients of proteins decrease with the increase of the concentration of agarose and the solute molecular size. At the considered range of agarose concentration (0.5-3.0 wt.%), the diffusion coefficients range from 4.98 to 8.21 x 10(-7) cm(2)/s for BSA and 1.15 to 1.56 x 10(-6) cm(2)/s for lysozyme, respectively. Temperature dependence of diffusivity of BSA in agarose hydrogel was also investigated. Furthermore, the retardance effect of polymer volume fraction on the diffusivity of both BSA and lysozyme in agarose hydrogels was analyzed with three models, Amsden's, Clauge and Philips', and Ogsten's model.

Needle enzyme electrode based glucose diffusive transport measurement in a collagen gel and validation of a simulation model

Rapid response needle enzyme electrodes were fabricated to measure the glucose concentration at the centre of a cylindrical spiralled collagen gel, which is a relevant constituent for tissue engineering scaffolds. The experimental data were based on a low consumption glucose sensor which minimised the distorting effect of enzymatic degradation. As the measurement was carried out within a collagen gel the stirring independence was compulsory for the biosensor. Glucose concentration changes were derived from a model based on the solution to Fick's Second Law. This had two different expressions for different dimensionless time (T) domains. The expression for large T and a first order approximation for small T were known. The expression for high order approximation for small T was then derived. An analytical expression consisting of fast convergent parts of these two expressions is proposed, which operates for the entire time region. A computational model for glucose concentration evolution where an electrode is located is proposed to operate for extended time periods. The model was confirmed by agreement between the simulated and observed data. An experimental technique is developed here to determine glucose diffusion coefficient by fitting the simulated concentration profile to the observed one. The glucose diffusion coefficient within the collagen gel was estimated to be 1.3 x 10(-6) cm(2) s(-1); higher accuracy is achieved here because errors due to noise, baseline and zero time determination are minimised with best fit.