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Chemical Engineering Journal

○ Elsevier BV

Preprints posted in the last 30 days, ranked by how well they match Chemical Engineering Journal's content profile, based on 11 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.

1
Structural Insights into the Expanded Substrate Scope of a Cysteine-Dependent Hydrolase from Rhodococcus opacus for Polyethylene, Polypropylene, and Polystyrene Biodegradation

Aggarwal, S.; Singh, S.; Kayastha, A.; Aggarwal, D.; Jangid, K.; Shakib, M.; Singh, D.; Sharma, A. K.; Kumar, P.

2026-10-09 biophysics 10.64898/2026.10.07.757487 medRxiv
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Microplastic pollution from homopolymers such as polypropylene (PP), polystyrene (PS), and polyethylene (PE) poses growing health and environmental concerns, highlighting the need for robust polymer-degrading biocatalysts. We previously identified a naturally occurring cysteine-dependent hydrolase (CsdH) from Rhodococcus opacus, featuring a unique Cys160-Lys127-Asp39 catalytic triad and providing a novel mechanism for polyethylene terephthalate (PET) degradation. In this study, we have determined crystal structures of CsdH in complex with PP, PS, PE, and styrene and demonstrated the potential of the enzyme to directly degrade these homopolymers into their respective low molecular weight degradation products using LC-MS. Structural analysis reveals that the enzyme retains a conserved principal access tunnel while undergoing subtle substrate-dependent changes to accommodate different substrates. The enzyme exhibited broad plastic degradation activity with the highest weight loss observed for PE, followed by PP and PS. SEM analysis reveals surface roughness, cracks and grooves, confirming polymer degradation. Further, these results corroborate through FTIR and TGA analysis. These findings establish a strong foundation for enzyme engineering and aim at developing efficient microplastic degradation.

2
Enhancing Carbon Conversion Efficiency and Product Yield Through Systematic Biocatalyst Design for Microbial Electrosynthesis

Abbas, A.; Islam, M. A.

2026-09-23 microbiology 10.64898/2026.09.22.753537 medRxiv
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The unprecedented rise in greenhouse gases such as carbon dioxide (CO2), and their detrimental effects on the atmosphere have intensified the current climate emergency. This challenge has inspired the development of novel carbon capture and utilisation (CCU) technologies, specifically microbial electrosynthesis (MES), for the bioelectrochemical fixation of CO2 into commodity chemical compounds (CCCs) using microbial biocatalysts. In this study, we systematically enriched and maintained robust mixed microbial communities of electroactive bacteria (EAB) from wastewater treatment sludge to serve as biocatalysts for MES. The MES performance of these biocatalysts under different operational conditions in bioelectrochemical systems (BES) reactors were investigated. BES reactors with enriched biocatalysts incubated and maintained under controlled conditions produced higher CCCs yields than those developed at ambient temperatures, while strict anaerobic operations further improved the MES efficiency compared to aerobic conditions. At an applied potential of -1000 mV vs Ag/AgCl, CO2 conversion reached up to 88.11%, significantly outperforming the lower potential (-600 mV) operation. These findings underscore the importance of systematic development of robust and stable biocatalysts, as well as maintaining strict anaerobic conditions, for achieving efficient MES performance, thereby demonstrating the potential of our approach for scalable industrial CCU applications.

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Passive Cell-Flux Partitioning Enables Single-Cell-Constrained Impedance Sensing From High-Density Microbial Cultures

Alsadoun, W.; Pungan, L.; Patel, Y. H.; Robayo Yepes, J. J.; Yang, Y.; Yazicigil, R. T.; Jimenez, M.

2026-10-02 bioengineering 10.64898/2026.09.30.755765 medRxiv
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Fermentation is a process through which microorganisms are used to transform basic molecules into high value substances in various applications such as biopharma, food production, and biofuel generation. In such processes, monitoring the health of microbial cells is essential, as it is a key factor in the final product yield. Traditional methods of assessing the health of fermenter populations have involved manually extracting samples from the fermenter for benchtop testing, which lacked the accuracy and efficacy of real-time continuous measurements. This has opened the door for inline sensors to be integrated into fermenters for continuous measurement; including microfluidic based Electrochemical Impedance Spectroscopy (EIS). EIS utilizes a range of frequencies to gain insight into the characteristics of microbial populations, such as cell size and membrane capacitance. EIS cytometry, in particular, has emerged as a relevant tool, as it enables single-cell level detection in real-time. However, current EIS cytometry devices cannot be deployed directly within fermenters due to the high cell density conditions. This has limited EIS analysis in fermenters to bulk measurements averaged across a population. Here, we present a microfluidic chip that uses passive cell-flux-partitioning geometry to direct cells from high-density culture through a single-cell-constrained flow path containing integrated impedance-sensing electrodes. The proposed chip combines geometric channel design and embedded electrodes to enable continuous impedance measurements from cell-containing flow while operating at input cell densities on the scale of 10^9 CFU/mL. This work demonstrates a first step toward integrating single-cell-constrained microfluidic handling with impedance sensing for inline monitoring in industrial biomanufacturing.

4
Surfactant-Assisted Colorimetric Signal Enhancement in Paper-Based Glucose Sensing

Kang, D.; Lee, J.; Bae, M.; Roh, S.; Cheong, D. Y.; Lee, H.; Lee, T.; Lee, G.

2026-09-27 bioengineering 10.64898/2026.09.21.753053 medRxiv
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Paper-based colorimetric sensors offer a low-cost and accessible platform for point-of-care (POC) analysis, but enzyme activity loss during coating and drying can weaken analytical signals and require high enzyme loadings or complex immobilization procedures. Although surfactants are widely used to improve wettability in paper-based assays, their potential contribution to colorimetric performance beyond these effects remains unclear. Here, we investigated surfactant-assisted colorimetric signal enhancement in a glucose assay implemented on a 96-puddle paper plate (96-PPP) and identified Tween 20 as the most effective surfactant. Its effect on detection performance became more pronounced as glucose oxidase (GOx) loading decreased; at 0.1 mg/mL GOx, Tween 20 lowered the limit of detection (LoD) from 0.113 to 0.034 mg/mL (approximately 3.3-fold) over a working range of 0-5 mg/mL, despite no statistically significant change in the measured contact angle at this loading. Tween 20 had no appreciable effect on the reaction in solution but preserved 95% of the apparent reaction rate constant after drying, compared with 11% without it, and atomic force microscopy (AFM) revealed a more dispersed dried enzyme morphology on mica. Tween 20-containing sensors also showed slower signal decay during repeated wetting-drying cycles and thermal stress, retained 77% (vs 26%) of the response at 400 mM NaCl, and exhibited within-PPP and between-batch coefficients of variation (CVs) below 10% (vs 12.3-19.5%), while maintaining glucose selectivity over potentially interfering molecules. These results indicate that Tween 20 enhances paper-based glucose sensing beyond wettability, in part by retaining enzyme cascade activity during drying, although the contributions of the individual enzymes and the underlying mechanism remain to be established.

5
Fed-batch production of antiviral OP7 chimera defective interfering influenza A particles

Holste, W.; Kupke, S. Y.; Seitz, C.; Reichl, U.; Ziehr, H.

2026-10-01 bioengineering 10.64898/2026.09.30.755589 medRxiv
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Influenza A virus (IAV) defective interfering particles (DIPs) are regarded as promising broad-spectrum antivirals due to their high efficacy demonstrated in animal trials. Previously, an OP7 chimera DIP was generated that showed markedly enhanced antiviral efficacy compared to conventional IAV DIPs. In addition, a high-yield cell culture-based production process for OP7 chimera DIPs was established in perfusion mode. However, due to the technical complexity of this technology, we aimed to combine the advantages of perfusion in terms of yield with that of a simple and less complex batch process. In the present work, we established a fed-batch production process for OP7 chimera DIPs that allows a more straightforward implementation into existing production facilities. Using a feeding regime that was able to overcome the cell density effect, we achieved productive virus infection in stirred tank reactors until a cell density of 10E+6 cells/mL. Furthermore, we obtained a high virus titer of 3.8 log10(HAU/100 uL), corresponding to a 3.4-fold increase compared to a reference batch production. Moreover, the produced material demonstrated a significantly increased interfering bioactivity shown by an in vitro potency assay. Interestingly, this efficacy was similarly high as compared to OP7 chimera DIP material previously produced in perfusion mode, despite twofold lower virus titers. Finally, we demonstrate robustness of OP7 chimera DIP seed virus trains, which is significant step towards later pharmaceutical production. Further, corresponding GMP MDCK-PB2(sus) cell and OP7 chimera virus banks are now available for later biomanufacturing further use. In conclusion, the established fed-batch process offers a valid n additional option for pharmaceutical grade OP7 chimera DIP GMP manufacturing production under GMP conditions required for subsequent clinical testing and for later large-scale manufacturing.

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Chronic nanoplastic exposure causes size-dependent cytotoxicity and ANGPTL4 induction in human kidney cells

Gillings, H. L.; Rojas-Canales, D. M.; Wong, S. W.; Burton, T.; Gleadle, J. M.; MacGregor, M.

2026-10-09 cell biology 10.64898/2026.10.08.757574 medRxiv
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Nanoplastics (NPs) are widespread environmental contaminants, yet most toxicity studies rely on short-term, single-dose exposures that poorly reflect daily human exposure. The kidney, particularly the proximal tubule, is a likely site of repeated NP exposure given its role in filtration and reabsorption, but chronic exposure effects are largely unexplored. Here, a long-term in vitro model was developed in which human proximal tubule (HK-2) cells were continuously exposed to 20 nm or 100 nm carboxylated polystyrene NPs (100 {micro}g/mL) over 12 days. Continuous 20 nm NP exposure caused progressive loss of viability whereas 100 nm NPs left viable cell numbers largely unaffected. RNA-sequencing showed 20 nm NPs drove extensive, time-dependent transcriptional dysregulation (1,548 differentially expressed genes at day 6, rising to 4,431 at day 9), far exceeding the minimal alterations in gene expression (35 genes) caused by 100 nm NPs. Cell-cycle analysis and pathway enrichment revealed KRAS pathway activation and S-phase arrest in 20 nm-treated cells, with ANGPTL4 the most upregulated gene. Validation with qRT-PCR confirmed increased ANGPTL4, HMOX1 and FN1 expression, genes implicated in renal fibrosis and chronic kidney disease. These findings show that continuous, size-dependent NP exposure elicits progressive cytotoxic and transcriptional responses in kidney proximal tubule cells and indicate ANGPTL4 as a candidate early biomarker of NP-induced renal stress.

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Embedded Printing-Derived Pyrolytic Carbon Electrodes with Graphene-like Features for Neural Stem Cell Differentiation and Dopamine Sensing

Gurbuz, H.; Dogan, A. A.; Rezaei, B.; Scordo, G.; Hansen, T. W.; Kajtez, J.; P. Pereira, M.; Keller, S. S.; Dufva, M.; Heiskanen, A.; Emneus, J.

2026-10-06 bioengineering 10.64898/2026.10.04.756553 medRxiv
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Carbon is a versatile electrode material that is used in applications ranging from electrical energy storage and electrosynthesis to CO2 conversion, H2 production, and biosensing. The development of pyrolytic carbon electrodes derived from lithographically patterned photoresist structures has expanded the possibilities for creating diverse 2D and 3D electrode designs. In this paper, we present disc-shaped SU-8-derived pyrolytic carbon scaffold electrodes with an open hexagonal honeycomb lattice. The scaffolds were fabricated, using embedded 3D printing within a shear-thinning support bath composed of fused silica nanoparticles (7% w/v) in mineral oil. The rheological properties of the support bath were optimized to enable the printing of low-viscosity materials like SU-8, which would otherwise lack structural integrity in standard extrusion-based 3D printing. The SU-8 scaffolds were then pyrolyzed and characterized using SEM, Raman spectroscopy, Energy Dispersive X-ray, X-ray Photoelectron Spectrometry, and Transmission Electron Microscopy, which revealed graphene-like 'microflowers' on its surface. Electrochemical analysis demonstrated excellent electrochemical properties. The functionality of the scaffold electrodes was validated by differentiation of human neural stem cells into dopaminergic neurons on the scaffold surface, followed by real-time detection of dopamine exocytosis upon cell depolarization.

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Toward Digital-Twin-Enabled Bioprocess Monitoring: Fault-Inclusive Soft Sensing of Penicillin Concentration Under Process Deviations

Behlim, A. B.; Tilewale, A.; Patel, D.

2026-09-23 bioengineering 10.64898/2026.09.21.753176 medRxiv
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Data-driven soft sensors can estimate fermentation product concentrations from routinely recorded process variables, but strong performance during normal operation does not establish reliability during process deviations. This study evaluated current-time penicillin-concentration estimation using 100 simulated IndPenSim batches comprising 90 normal-operation batches and ten documented deviation batches, with 113,935 observations in total. Initial normal-trained models and five follow-up experiments examined complete-batch validation, dependence on batch-progress features, phase-specific error, model-family comparisons, early out-of-distribution warnings and empirical prediction ranges. These analyses motivated a matched comparison between normal-only and fault-inclusive HistGradientBoosting regressors using 36 current and causal history-based inputs. Normal performance was evaluated in five regime-balanced complete-batch folds, and deviation performance by leave-one-fault-batch-out evaluation; every tested deviation batch was excluded from its own model fit. Batch-balanced sample weights were used, with a factor of three assigned to permitted deviation batches in fault-inclusive fitting. On held-out deviation batches, pooled RMSE decreased from 3.195 to 2.564 g/L, a reduction of 19.73%, while MAE decreased from 2.076 to 1.441 g/L and R2 increased from 0.8580 to 0.9085. Normal-operation RMSE was nearly unchanged at 1.981 and 1.983 g/L. Eight of ten deviation batches improved. The mean paired fault-batch RMSE difference was -0.7063 g/L, with a descriptive 95% batch-bootstrap interval of -1.2844 to -0.2194 g/L. Improvement was largest within the first-to-last recorded fault-reference window, but late-stage errors persisted. Batch 100 remained poorly predicted, with fault-inclusive RMSE of 6.631 g/L and R2 of -2.4837. A fault-risk classifier, Isolation Forest OOD detector and empirical error ranges offered incomplete reliability information. Fault-inclusive training therefore improved this benchmark on average, but did not establish generalization to unseen fault mechanisms, calibrated safety warnings or deployment in physical fermentation.

9
A climate-resilient microalga, Desmodesmus ecotolerans sp. nov., for biophotovoltaic applications

Yoon, H.; Yoon, J.-T.; Cheng, M.; Muhammad, S.; Li, T.; Han, Z.; Lee, J.; Kim, J.; Lee, H.-S.; Kim, J.; Kim, E. Y.

2026-09-25 microbiology 10.64898/2026.09.24.754046 medRxiv
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Microalgae are promising biological platforms for sustainable energy production because they can convert photosynthetic activity into electricity in biophotovoltaic (BPV) systems. Identifying strains that grow well at elevated temperatures and under reduced irradiance is an important step toward BPV applications in seasonally variable environments. Microalgae were isolated from Seondong Lake (Seoul, Republic of Korea) during three sampling periods and screened for growth at different temperatures. Among 45 isolates, KHUC-11 showed the highest weighted growth index based on growth rates at 25, 30, and 35 under dark conditions and was selected for further characterization. Phylogenetic reconstruction of the 45S rRNA gene cluster, internal transcribed spacer 2 (ITS2) secondary-structure comparison, and morphological characterization supported the description of KHUC-11 as Desmodesmus ecotolerans sp. nov. D. ecotolerans produced more biomass than Chlamydomonas reinhardtii CC-125 under both moderate- and low-light conditions. Under low light, its final dry biomass concentrations were 1.81 and 1.58 times those of CC-125 under mixotrophic and photoautotrophic conditions, respectively. Despite its smaller cell size, D. ecotolerans showed higher photosynthetic performance than CC-125, and screen-printed electrode (SPE)-based electrochemical assays demonstrated enhanced anodic current generation and CV-derived estimated power output. Taken together, these findings identify D. ecotolerans as a novel climate-resilient Desmodesmus species with bioelectrochemical properties that support further evaluation for BPV applications.

10
bioRheoFlow A Rheometric Platform for In Situ Biofilm Mechanics Under Controlled Flow Conditions

Ianniello, V.; Geisel, S.; Secchi, E.; Tervoort, T.; Vermant, J.

2026-10-05 biophysics 10.64898/2026.09.29.755442 medRxiv
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Biofilm mechanics depend strongly on growth history, hydration, nutrient availability, and interfacial attachment, yet conventional rheology requires harvesting and transfer that can perturb the as-grown structure. Here, we introduce bioRheoFlow, a 3D-printed rheometer-mounted platform for cultivation and mechanical characterization without sample transfer. The platform combines evaporation compensation with static or axial nutrient flow, and benchmark measurements validate its rheometric performance. Applied to Pseudomonas putida and Pantoea sp., bioRheoFlow reveals that biofilms cultivated in situ under axial flow exhibit substantially higher elastic moduli than conventionally grown and scraped samples. Despite similar linear-viscoelastic stress ranges, the species show distinct nonlinear responses: P. putida exhibits a lower crossover stress and more abrupt failure, whereas Pantoea sp. sustains larger stresses and deformations. Creep suggests contributions from bulk deformation and biofilm-substrate interactions. bioRheoFlow provides a controlled framework for probing growth-conditioned mechanics in living biofilms.

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Assessment of Microbial Consortia for Biogenic Mineralization Potential of Lead (Pb) using Microbiologically Induced Calcite Precipitation and Nitrate Reduction

Bhattacharya, A.; Hiremath, S.; Nagarajan, D.; Ghosh, T.

2026-09-23 microbiology 10.64898/2026.09.22.753425 medRxiv
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Groundwater contamination by lead and nitrate exceeding the permissible limits of the World Health Organization (WHO) and the Bureau of Indian Standards (BIS) of 10 ppb lead and 45 to 50 ppm nitrate poses a severe health risk of systemic toxicity in humans and animals. Microbial nitrate reduction coupled with microbiologically induced calcite precipitation (MICP) proved to be a novel bioremediation strategy to transform soluble lead nitrate into insoluble lead biominerals. This study presents statistical optimization of operational parameters for nitrate reduction and co-precipitation of biogenic lead carbonate-calcium carbonate by nitrate-reducing bacterial consortia. The SEM, TEM with SEAD, and XRD analysis of the biomineral confirmed lead carbonate co-precipitation with CaCO3. A two-level factorial design was applied to screen significant variables and interactive factors that influence nitrate reduction and biomineral precipitation. The highest nitrate reduction, maximum ammonia production, and biogenic Pb-mineralization efficiency of > 90% were obtained at the optimum conditions (initial nitrate requirement of 600 ppm, temperature 37 oC, pH 8, and carbon content of 5.5 g/L) compared to those obtained under the common process parameters. ANOVA with a high correlation coefficient (R2 > 0.99) corroborated the linear model for the biogenic mineralization process. This study on the biogenic removal of Pb by nitrate-reducing bacterial consortia revealed possible opportunities for large-scale treatment of Pb-contaminated surface and subsurface water bodies.

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Strategies to improve neurite outgrowth from primary neurons ingelatin methacrylate hydrogels polymerized with visible lightexposure inside a microscale 3D model

Liubchak, I.; Sadden, J.; Solomon, T.; Xie, Y.; Ng, S. C.; Bennet, T.; Zohreh, N.; Van den Doel, P.; Pieters, A.; Juralowicz, P. R.; Hilts, A.; Fung, A.; Mung, S.; Liu, K.; Caffrey, T. M.; Cheung, K. C.

2026-09-29 bioengineering 10.64898/2026.09.28.755099 medRxiv
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Gelatin methacrylate (GelMA) hydrogels offer many advantageous properties such as excellent biocompatibility, tunable stiffness, and rapid fabrication, making them attractive materials for neural systems-on-a-chip devices used to study axonal outgrowth in three-dimensional (3D) environments. In this study, we evaluate properties of GelMA hydrogels crosslinked with visible blue light and application of these hydrogels for encapsulation of primary dorsal root ganglion (DRG) explants inside a custom microscale device. We selected low GelMA polymer concentrations of 3 % and 6 % w/v for hydrogel preparation to create soft materials and demonstrate the effect of degree of functionalization (DoF) on stiffness of GelMA in a blue light-induced crosslinking system. Additionally, a decrease in crosslinking efficiency and stiffness of GelMA was observed upon reconstitution of the polymer in DMEM cell culture media compared to PBS. To evaluate the axonal outgrowth, DRG explants were encapsulated in various GelMA formulations and cultured for 7 days. Following incubation, the explants were fixed and immunochemically labelled with anti-beta-III-tubulin antibody. We further describe an application of custom-developed semi-automated image analysis tool together with linear mixed effects modeling to evaluate axonal outgrowth across different GelMA formulations. Among the formulations tested in our study, 3 % GelMA 95 % DoF hydrogels supported the longest neurite outgrowth suggesting that matrix properties influenced neurite extension.

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Thermodynamically controlled biokinetics modelling of a lindane-degrading anaerobic enrichment culture

Liang, J.; Lomheim, L.; Puentes Jacome, L.; Edwards, E. A.; Sleep, B. E.

2026-10-02 microbiology 10.64898/2026.10.01.755988 medRxiv
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The anaerobic biotransformation of lindane ({gamma}-hexachlorocyclohexane), a persistent legacy pesticide and challenging subsurface contaminant was modelled using an integrated Monod biokinetics framework. Calibrated against batch experimental data, this model accounted for the dissolution of solid phase lindane and the thermodynamics of reactions involved. The study focused on a methanogenic, lindane-degrading enrichment culture (GT2) that used ethanol as the electron donor, where ethanol fermentation supplied hydrogen to support reductive dechlorination of lindane. A Dehalobacter strain was identified as the lindane-degrading organism, while a member of bacterial order Geobacterales carried out ethanol fermentation. First-order decay constants for lindane-degrading Dehalobacter were estimated from experimental data and showed variation across different growth conditions. The biokinetics model captured interactions among key microbial processes, namely lindane dechlorination, ethanol fermentation, hydrogenotrophic methanogenesis, and acetoclastic methanogenesis. Thirteen biokinetics parameters including maximum substrate utilization rates (k), half-velocity constants (Ks), and decay constants for these microbial processes were estimated through a Bayesian optimization approach. Global sensitivity analysis showed that eight parameters, primarily k and Ks, had significant linear impact on the model output, whereas responses to decay constants were more variable and potentially non-linear. This study proposed an effective modelling approach for characterizing syntrophic microbial growth within enrichment cultures and provides valuable biokinetics parameters estimates for real-world applications of anaerobic lindane bioremediation.

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Coumarin-based blue excitable probe for functional screening of dehalogenase activity

Mion, S.; Mallet, M.; Louis, Y.; Fontanay, S.; Ruaudel, F.; Bastian, F.; Jacolot, M.; Popowycz, F.; Oger, P. M.

2026-10-05 biochemistry 10.64898/2026.10.02.756220 medRxiv
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In the enzymatic toolbox of depollution, hydrolytic dehalogenases are of particular interest for the bioremediation of organohalogenated compounds. To better identify and characterize these enzymes, it is important to develop appropriate sensing methods. Fluorescent probes for dehalogenase detection have been developed in the past years, however, to this date none were available for application using the common FITC parameters (i.e. excitation laser at 488 nm). To address this limitation, we herein report a new fluorescent probe, COU4-Cl, excitable in the violet (405 nm) and blue (488 nm) wavelengths adapted for the detection and characterization of haloalkane dehalogenases. Its applicability is discussed and evaluated in comparison to the previously described COU2-Cl probe only excitable in the violet (405 nm). This study shows the advantages and complementarity of the two probes, and further demonstrate their application for the discrimination of dehalogenase activity in whole cell assays.

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High-throughput microfluidic encapsulation of cells in extracellular matrix microbeads for microtissue engineering.

Mukherjee, D.; Radecka-Rudzinska, M.; Gizynski, K.; Klak, M.; Wszoła, M.; Guzowski, J.

2026-10-02 bioengineering 10.64898/2026.09.30.755758 medRxiv
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Microfluidics-assisted encapsulation of cells in hydrogel microbeads has found diverse applications in tissue engineering, disease modelling, and drug testing. However, upscaled production of submillimeter-sized microbeads, each encapsulating optimally tens to hundreds of living cells, remains a challenge. Excessive viscous stresses or non-homogeneous crosslinking reactions hamper droplet monodispersity, hydrogel integrity, and/or cell viability. Herein, we present a device consisting of (i) tens of parallel step-emulsifiers arranged radially around the hydrogel inlet and (ii) an in-flow UV crosslinking system capable of continuous generation and crosslinking of up to around 45000 microbeads/min, each encapsulating N~50 cells, at cell viability exceeding 80%. We use gelatin methacryloyl (GelMA) as the biomaterial of choice and establish a unique sweet spot in terms of UV wavelength, irradiance, and exposure time- the latter controlled via the net applied flow rate and the length of the UV-exposed microchannel- at which we achieve an optimal balance between long-term microbead stability and cell viability. In particular, we observe a strong correlation between reduced cell viability and poor crosslinking efficiency, the latter attributed to the presence of a spontaneous core-shell structure. We further study the impact of added methacrylated hyaluronic acid (HAMA) and extracellular matrix (ECM) on cell proliferation and microtissue formation in the case of triple-negative breast cancer (TNBC) cells for future application in drug testing. The upscaled production of the encapsulated microtissues demonstrated here provides new perspectives for both drug testing and cell therapies where the precision in microenvironment formulation as well as production throughput remain of primary importance.

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Metabolic tagging of adipose-derived stem cells for targeted modulation of regenerative potency within mineralized collagen scaffolds

Kim, J.; Baskaran, D.; Nunes, A.; Rios Adorno, G.; Wang, H.; Harley, B.

2026-09-28 bioengineering 10.64898/2026.09.25.754411 medRxiv
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Recent efforts to reconstruct critical-sized craniomaxillofacial defects using biomaterials have increasingly sought strategies to accelerate proangiogenic processes immediately after surgical implantation to improve host-graft integration. A class of mineralized collagen scaffolds has recently been identified to promote osteogenesis of bone marrow and adipose-derived mesenchymal stem cells both in vivo and in vitro, motivating efforts to identify strategies to promote osteogenic-angiogenic coupling in order to support regenerative healing. Here, we report the first-time use of a glycoengineering approach to generate a population of engineered ASCs (eASCs) from human adipose-derived stem cells (hASCs). This effort inserts an azido sugar onto the cell membrane that can be selectively targeted using DBCO-tagged biomolecules to selectively boost eASCs activity. We report the effects of azido sugar labeling conditions (concentration and incubation time) on eASCs labeling efficiency. We show proliferation and pro-regenerative gene expression activity of eASCs in mineralized collagen scaffolds are largely similar to conventional hASCs. And we demonstrate that molecular cargo functionalized with dibenzocyclooctyne (DBCO) can be conjugated to azido groups on eASCs via click chemistry. Together, this work shows metabolically labeled eASCs have the potential to be used for selective delivery of activity-inducing bioactive cues to enhance regenerative potential.

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hMSCs for Osteocyte-like Cell Networks within Strain-Stiffening Bottlebrush Polymer Hydrogels

Ohnsorg, M. L.; Friend, N. E.; Givens, S. E.; Saeb, D.; Mash, K. M.; Anseth, K. S.

2026-09-23 bioengineering 10.64898/2026.09.22.753603 medRxiv
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Bone formation and remodeling depend on dynamic biochemical and biomechanical signaling from the collagen-rich osteoid that precedes mineralization, yet the role of osteoid nonlinear mechanics in regulating osteocyte-like network formation remains poorly understood. Here, we engineered a synthetic bottlebrush polymer hydrogel (BB) that mimics key mechanical features of osteoid and compared it to collagen type-I (Col1) matrices with matched shear modulus (~70 Pa) and strain-stiffening behavior. Human bone marrow-derived mesenchymal stem/stromal cells (hMSCs) were cultured for 28 days in growth (GM) or osteogenic media (OM) to examine network formation, and functional connectivity using live cell fluorescence recovery after photobleaching. hMSCs cultured in BB networks and OM showed upregulation of early osteocyte markers compared to Col1. We find that strain-stiffening materials with minimal stress relaxation promote osteocyte-like cell differentiation with functional connectivity, establishing osteoid-mimetic BB hydrogels as a promising matrix to study human osteocytogenesis and osteocyte mechanotransduction in vitro.

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Linking Polysaccharide Structure, Gelation Kinetics, and Function in Dynamic Acylhydrazone Hydrogels

Kazemi-Aghdam, F.; Varchulova, Z.; Zvicer, J.; Stojkovska, J.; Krizov, A.; Dinparvar, S.; Vojtova, L.; Danisovic, L.; Lacik, I.; Heydari, A.

2026-09-28 bioengineering 10.64898/2026.09.25.752777 medRxiv
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Dynamic covalent hydrogels formed through reversible acylhydrazone crosslinking have emerged as promising injectable biomaterials. However, a fundamental gap remains in understanding how the macromolecular structure of oxidized polysaccharides (OxPs) governs gelation kinetics and how these kinetics pathways translate into material properties and cellular responses. We address this question by developing an acylhydrazone hydrogel library composed of alginate adipohydrazide crosslinked with oxidized alginate (OxA) or oxidized dextran (OxD), two reactive aldehyde-bearing polymers with comparable chemical functionality but fundamentally distinct backbone structure. By varying polysaccharide type, oxidation degree, and reaction pH, we decoupled the effects of chemical functionality from macromolecular structure and established quantitative structure-kinetics-property-function relationships. OxD-based hydrogels undergo rapid, largely pH-independent gelation, whereas OxA-based systems display pronounced pH-dependent kinetics with significantly delayed network formation under physiological pH. These differences in gelation kinetics and OxPs macromolecular structures lead to marked variations in hydrogel mechanics, including stiffness, stress relaxation, stability, injectability, and post-injection recovery. Importantly, differences in gelation kinetics modulate cell-matrix interactions in three-dimensional culture. Slowly forming OxA hydrogels maintained rounded chondrocyte shape, while rapidly gelling OxD networks induced transient cell elongation. Mesenchymal stem cells displayed similar shapes regardless of gelation kinetics, indicating cell-type-specific responses to matrix formation dynamics.

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Xolographic printing of cell-dense engineered living matter via iodixanol-driven enhancement of type II photoinitiation

Anspach, A.; Wolfel, A.; Cano-Jorge, M.; Dalenoord, F.; König, N. F.; Custodio, C. A.; Rolfes, S.; Mano, J. F.; Passier, R.; Leijten, J.

2026-09-30 bioengineering 10.64898/2026.09.29.755253 medRxiv
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Type II photoinitiators are essential for numerous applications, including advanced 3D printing techniques such as Xolography. Despite offering tunable wavelengths and reaction mechanisms, their limited photoreactivity hinders widespread adoption. Solutions to increase reactivity, particularly in aqueous solutions and in a biocompatible manner, are urgently needed. Here, we report the surprising finding that iodixanol enhances reactivity of type II photoinitiation systems. Supplementing Xolographic print resins with iodixanol increases photoreactivity, which reduces print times and light dosage tenfold, and enables printing of previously unprintable material formulations. Surprisingly, iodixanol supplementation also improves cell viability in a dose-dependent manner, while reducing cell-mediated light scattering. Together, this enables accurate Xolographic printing of highly cell-dense bioresins, which facilitated the biofabrication of engineered living matter with up to 100 M cells mL-1 (>40% cells by volume) with a resolution of ~65 microns. These advances enabled the first demonstration of tissue function in Xolographically-printed materials. Human induced pluripotent stem cell-derived cardiomyocytes were printed into contractile cardiac-like engineered living matter, which exhibited enhanced cell-cell contact and synchronous contractions, confirming tissue level function. As a highly water soluble, cytocompatible, and clinically approved compound, iodixanol therefore represents a valuable and translatable solution to improve the reactivity of type II photoinitiation systems, which enables volumetric biofabrication of highly cell dense living matter. This unlocks a new role for iodixanol in a wide variety of fields including dentistry, chemistry, organic photovoltaics, tissue engineering, and 3D printing.

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Interconnected Macroporous GelMA Scaffolds for Cell Culture through Temperature Controlled Spinodal Decomposition

Dumas, S.; Gonzalez Martinez, D.; Peixoto De Oliveira, A.; Ferri-Angulo, D.; Bacchin, L.; Arcas, A.; Blatche, C.; Goudouneche, D.; Paounov, R.; Hut, M.; Puaud, M.; Foncy, J.; Moran-Mirabal, J.; Malaquin, L.

2026-10-05 bioengineering 10.64898/2026.10.02.755893 medRxiv
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Developing biomaterials that faithfully recapitulate the complex architecture of native tissues is central to tissue engineering. Conventional hydrogels typically exhibit nanoscale porosity, which limits mass transport and cell migration and thereby constrains tissue development. Here, we exploit liquid-liquid phase separation (LLPS) to generate interconnected macroporous gelatin methacryloyl (GelMA) scaffolds with tunable pore sizes ranging from 2 to 50 m under physiological pH conditions. By mapping the GelMA/dextran phase diagram, we identify a composition range in which LLPS occurs through spinodal decomposition, resulting in a spontaneous bicontinuous, trabecular-like architecture. Pore size can be further tuned by varying polymer concentrations and temperature. We advantageously combined thermal gradients and photopatterning to enable spatial control over pore morphology to fabricate hierarchically structured materials. The biological relevance of these architectures is assessed using fibroblasts cultured within controlled porosity gradients. We show that pore size strongly influences cell infiltration, growth, and spatial organization, with larger pores providing sufficient space for cell migration while reducing the dependence on matrix degradation. Pore size of 7-15 m is identified for maximizing fibroblast growth. Overall, our approach provides a versatile platform for porosity screening, enabling the engineering of biomimetic hydrogels with optimized microarchitectures tailored to specific biological contexts for three-dimensional cell culture.