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Chemical Engineering Journal

Elsevier BV

Preprints posted in the last 90 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
Dairy wastewater grease stabilizes in situ mesophilic biomethanation for H2-to-CH4 conversion

Ruiz-Lorenzo, M. L.; Angela, L.-Z.; Moreno, A. D.; Ferrari, F.; Diaz, I.; Contreras, J.; Iglesias, R.; Suarez, S.; Acedos, M. G.

2026-06-11 bioengineering 10.64898/2026.06.09.731101 medRxiv
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Power-to-Gas technologies are emerging as a key strategy to integrate surplus renewable electricity into energy systems, through the conversion of green hydrogen into methane. However, the practical implementation of biological in situ biomethanation is still constrained by operational and design requirements that are incompatible with most existing anaerobic digestion infrastructures. This study demonstrates a stable and efficient mesophilic (37{degrees}C) in situ biomethanation process driven by substrate-induced microbial selection rather than relying on continuous hydrogen supply. Anaerobic digesters co-digesting sewage sludge from a wastewater treatment plant with lipid-rich greases recovered from dairy wastewater developed a pre-adapted hydrogenotrophic consortium capable of effective CO2-H2 conversion under mesophilic conditions. Long-term operation confirmed the robustness and persistence of this microbial structure. Upon H2 addition, methane concentrations up to 82 % were achieved under atmospheric pressure, without biogas recirculation, with hydrogen-to-methane conversion efficiencies up to 90% and methane productivities of 1.64 NLCH4.L-1d-1. 16SrRNA-based microbial community analysis revealed that dairy grease co-digestion selectively enriched hydrogenotrophic methanogens, particularly Methanospirillum, together with syntrophic fatty-acid-degrading bacteria such as Syntrophomonas, promoting efficient interspecies hydrogen transfer. Importantly, the lipid co-substrate enabled the establishment and long-term stability of the hydrogenotrophic pathway independently of hydrogen availability, mitigating challenges associated with intermittent renewable energy supply. Overall, these findings challenge the common reliance on thermophilic conditions, continuous hydrogen input, pressurization, and gas recirculation in in situ biomethanation, demonstrating that substrate-driven microbial selection can replace conventional engineering requirements such as thermophilic operation or reactor modifications, providing a simpler and scalable strategy for mesophilic in situ biomethanation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/731101v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@c62086org.highwire.dtl.DTLVardef@1813ed6org.highwire.dtl.DTLVardef@4462bcorg.highwire.dtl.DTLVardef@1ae2cfb_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG Highlights- Lipid-assisted co-digestion promotes stable biogas and biomethane production - Dairy wastewater greases enable mesophilic in situ biomethanation - An enriched hydrogenotrophic methanogenic consortium yields >82% CH4 - 70-90% H2-to-CH4 conversion efficiency under mesophilic, unpressurized conditions - Substrate-driven microbial selection enables in situ biomethanation in WWTP digesters

2
Engineering xylose metabolism for diverse polyhydroxyalkanoates synthesis in Halomonas TD

Shen, C.-L.; Liu, B.-W.; Liu, P.; Deng, Y.-H.; Zhao, L.-L.; Yu, L.-S.; Situ, W.; Lv, J.-Y.; Shen, H.-W.; Yue, H.; Xiao, Y.-C.; Lin, Y.-N.; Ye, J.-W.

2026-06-01 bioengineering 10.64898/2026.05.27.728164 medRxiv
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Engineering the biosynthesis of fully biodegradable polyhydroxyalkanoates (PHAs) from non-food and renewable feedstocks like lignocellulose is becoming an attractive strategy for sustainable biomanufacturing. However, the efficiency and diversity of PHA synthesis from lignocellulosic hydrolysate (LH), mainly containing glucose and xylose, still remains challenge. Here, Halomonas TD, a cost-effective PHA-producing chassis, was developed to utilize glucose and xylose (or LH) for effective production of poly-3-hydroxybutyrate (PHB) and poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] by engineering the phosphoketolase pathway-dependent xylose metabolism in the genome, yielding 50.1 g L-1 PHB and 42.6 g L-1 P(3HB-co- 11.4 mol% 4HB) under fed-batch condition. Subsequently, the introduction of Weimberg pathway was found be able to synthesize terpolymer consisting of 3-hydroxybutyrate (3HB), 4-hydroxybutyrate (4HB) and 3-hydroxyvalerate (3HV), namely [P(3HB-co-4HB-co-3HV)], from glucose and xylose only due to the isoenzyme activity of keto-acid decarboxylase encoded by kivD, which converts xylose-derived intermediate 2,5-dioxopentanoate and -ketoglutarate into butanedial (4HB synthesis) and 2-ketobutyrate (3HV synthesis), respectively. Finally, a tailored-made xylose-induced system was constructed to achieve exquisite xylose transmembrane transportation control for improved synthesis of terpolymer P(3HB-co-4.5 mol% 4HB-co- 3.0 mol% 3HV), reaching to 6.3 g L-1 under shake-flask condition, together with the co-expression of fine-tuned phosphoketolase and Weimberg pathways. This study provides a feasible and sustainable alternative for lignocellulosic resources valorization powered by the engineered Halomonas TD capable of efficient xylose utilization and diverse PHAs synthesis.

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A Passive-Oxygenation Silicone Platform for Biomass Production: Maximizing Labor Productivity and Process Efficiency in Cellular Agriculture Development

Hatano, H.; Takagaki, Y.; Sawada, M.; Kokido, I.; Okabe, H.; Inoue, S.; Miyaoku, K.; Helena, G. A.; Shiotsuka, K.; Tatsumi, S.; Kawashima, I.

2026-06-07 bioengineering 10.64898/2026.06.02.729703 medRxiv
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The commercial production of cell-based food is currently hindered by existing bioreactor technologies, which require substantial capital investment, specialized operating skills, and complex processing setups. To democratize cell-based food production, we developed the "oxy-thru cultivator"--a simple, autoclavable, closed-bag bioreactor fabricated from polydimethylsiloxane (PDMS). By leveraging the high oxygen-permeability of PDMS, this platform enables passive oxygenation across the entire vessel wall, eliminating the need for external aeration or mechanical sparging. During testing, the cultivator maintained a stable culture environment over 23 days, showing no cytotoxic leachables and retaining both structural integrity and sterility across 10 autoclave cycles. This robustness supported the continuous cultivation of DF-1 cells for 74 days. Using a standardized subculture scheme, we successfully harvested an estimated 2.60 g of cell-based biomass per cultivator over five passages. Notably, the platform achieved a 127% monthly labor productivity compared to conventional bioreactors and was easily operated by researchers without specialized training. Additionally, the system successfully supported the expansion of both mammalian and primary avian cell lines. With a minimal equipment footprint that reduces CapEx, and a reusable silicone vessel that lowers OpEx, the oxy-thru cultivator offers a highly practical, accessible pathway toward scaling up cellular agriculture. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/729703v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@bf2abforg.highwire.dtl.DTLVardef@8f9231org.highwire.dtl.DTLVardef@1c6fc63org.highwire.dtl.DTLVardef@e3e537_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Thermal Conductivity of Artificial Materials Engineered from Plant and Bacterial Cells

Odahara, M.; Horii, Y.; Xu, T.; Terada, K.; Daicho, K.; Shiomi, J.; Numata, K.

2026-05-07 bioengineering 10.64898/2026.05.04.722776 medRxiv
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Bio-based materials are known for their excellent biodegradability and, in some cases, their potential to fix carbon dioxide. Owing to these properties, they are increasingly being utilized as environmentally friendly alternatives across various applications. In this study, we focused on using living cells themselves as material components, aiming to evaluate their potential as substitutes for conventional plastic-based thermal insulators. We selected two types of cells, photosynthetic purple non-sulfur bacterium Rhodovulum sulfidophilum and tobacco BY-2 plant suspension cells. After optimizing solidification conditions through the addition of pectin and cellulose nanofibers, we measured the thermal conductivity of the solidified cells under atmospheric pressure. The results showed that R. sulfidophilum exhibited 0.0553 W/m{middle dot}K, while BY-2 exhibited a thermal conductivity of 0.043 W/m{middle dot}K. Both values indicate relatively low thermal conductivity compared to existing bio-based materials, suggesting high insulation performance. Among the solidified cells, the solidified BY-2 cells showed minimal variation in thermal insulation performance under pressure changes, and had a low thermal emissivity as revealed by FT-IR analysis. Based on these findings, we propose that cell-derived materials can serve as potentially biodegradable bio-based thermal insulation materials.

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Unlocking the potential of Gordonia rubripertincta in syngas fermentation for carbon monoxide bioconversion into carotenoids

Vemparala, G.; Kumaraguru, T.; Anupoju, G. R.

2026-05-08 bioengineering 10.64898/2026.05.04.722808 medRxiv
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Fermentation of C1 gases is an emerging technology where waste gases are bio converted into value-added products. This study navigates the gas fermentation potential of Gordonia rubripertincta to produce carotenoids. The crucial carbon monoxide dehydrogenase (CODH) enzyme, necessary for gas uptake by the microbe, was found to be present in G. rubripertincta through blastp on NCBI website. The organism was then used for gas fermentation experiments in a continuous stirred tank reactor (CSTR) in different modes of reactor operation resulting in the production of about 500 mg pigment/g WCW (wet cell weight). Two important reactor parameters, molybdenum content and pH, were optimized for enhanced carotenoid production. Overall, G. rubripertincta was observed to be an efficient candidate organism for C1 gas fermentation. KEY HIGHLIGHTSO_LIGordonia rubripertincta synthesises aerobic carbon monoxide dehydrogenase enzyme. C_LIO_LIIt is a potential gas fermenting microbe that gives carotenoids as product. C_LIO_LIThe gas uptake efficiency of the microbe is more in fed-batch discontinued mode. C_LIO_LIIn FB-D, the resultant carotenoids are 500+9 mg/g wet cell weight (WCW). C_LIO_LIMo/pH of 20 mg/7.0 resulted in highest carotenoids, i.e., 134+41 mg/g WCW. C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/722808v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@8b1185org.highwire.dtl.DTLVardef@2b6f90org.highwire.dtl.DTLVardef@1a9697dorg.highwire.dtl.DTLVardef@14c9dc8_HPS_FORMAT_FIGEXP M_FIG C_FIG

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One-pot lactic acid production from rice straw: A consolidated bioprocess with enzymatic pretreatment-saccharification and Microbial co-fermentation

Althuri, A.; VS, B. S.

2026-06-08 bioengineering 10.64898/2026.06.03.729808 medRxiv
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Global demand for platform chemicals and biomaterials urges us to seek sustainable strategies along with waste valorization to produce lactic acid (LA) sustainably. The study has designed a one-pot fermentation strategy by employing in-house produced ligninolytic and saccharifying enzymes on rice straw along with a consortium of hexose and pentose sugar co-fermenting microorganisms. Biological pretreatment with in-house ligninolytic enzyme was selected for the one-pot strategy from a comparison study of chemical and enzymatic pretreatment of rice straw. In this study, simultaneous pretreatment and saccharification of rice straw followed by LA fermentation by Lactobacillus casei- Lactobacillus rhamnosus system (35.58{+/-}0.29 g/L) was found out to be more efficient than Lactobacillus casei-Lactobacillus pentosus system (29.80{+/-}0.92 g/L). Thus, the L. casei- L. rhamnosus system (CR system) was selected and was further statistically optimized by response surface methodology (RSM) to yield 64.96 g/L of LA. The fermentation broth was decolorized and purified by ion exchange chromatography to yield 85.56% pure LA with 84.95% optical purity. The one-pot fermentation strategy has reduced the number of unit operations involved to synthesize LA from rice straw without compromising the yield and purity through a greener route. The use of in-house enzymes and consortium of lactic acid producing bacteria in one-pot presents a strategic approach to sustainable LA production. The biological enroute and the minimum use of chemicals during upstream, fermentation, and downstream processing adds to the carbon credit of the process. HighlightsO_LILactic acid was produced from rice straw using one-pot co-fermentation strategy C_LIO_LIUpstream processing employed in-house enzymes from fungal solid-state fermentation C_LIO_LIThe process addresses the underutilization of pentose sugars after saccharification C_LIO_LIA consortium LAB produced 64.96 g/L LA with 0.855 g/L.h productivity C_LIO_LIDownstream processing yielded LA with 85.56% purity and 84.95% optical purity C_LI

7
Kombucha-Derived Cellulose Non-wovens: Growth Optimization, Mechanics, and Recycling

He, L. L.; Lopez, J.; Schiffman, J. D.

2026-06-12 bioengineering 10.64898/2026.06.09.730694 medRxiv
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The environmental impact of synthetic textiles has prompted the search for sustainable and biodegradable alternatives. This study correlates the growth conditions used to produce kombucha-derived cellulose non-woven mats with their mechanical performance as a function of post-processing. Systematically, the fermentation and growth parameters of the non-wovens, including inoculum density, carbon-source loading, temperature, and pH value were investigated. Thick, uniform non-wovens were obtained using mildly acidic conditions that balanced nutrient availability and growth rate, moderate inoculum and carbon loading at 30 {degrees}C. Next, we used uniaxial tensile testing and rheology to thoroughly compare the mechanical properties of two post-processing routes, lyophilization and oven-drying against the as-produced wet non-wovens. Overall, the lyophilized non-wovens displayed the highest ultimate tensile strength (14.36 {+/-}0.9 MPa) and elongation at break (24.54 {+/-}1.9%), which were statistically greater than the oven-dried (2.54 {+/-}0.3 MPa, 6.03 {+/-}0.8%) and the wet non-wovens (1.66 {+/-}0.3 MPa, 9.35 {+/-}2.8%). We conclude by performing a proof-of-concept recyclability experiment: we showed that kombucha-derived clothing could be enzymatically degraded and then re-manufactured into new nanofibers by electrospinning. Together, these results demonstrate a circular pathway encompassing the growth and processing of mechanically robust kombucha-derived cellulose non-wovens, as well as their biodegradation and re-manufacturing.

8
CFD-Informed Hybrid Modeling Unlocks Scalable, Tunable Amino Acid Production in Methanothermobacter marburgensis

Haslinger, B.; Reischl, B.; Steger, F.; Krippl, M.; Gsenger, L.; Hilts, E.; Ruddyard, A.; Stadlbauer, M.; Driessler, S.; Palabikyan, H.; Bochmann, G.; Duerkop, M.; Rittmann, S. K.- M. R.

2026-07-10 bioengineering 10.64898/2026.07.09.737395 medRxiv
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Methanogenic archaea, such as Methanothermobacter marburgensis, represent a powerful biological platform for carbon capture and valorization, directly converting carbon dioxide (CO2) and molecular hydrogen (H2) into proteinogenic amino acids (AAs). In this study, we present a controlled and scalable strategy for tailoring AA production (biosynthesis and secretion) in continuous gas fermentation. By applying various Design of Experiments (DOE) techniques, we systematically identified and optimized key process parameters governing AA biosynthesis and shaping a targeted AA secretion profile. A hybrid modeling framework combining experimental data with scale-independent parameters derived from computational fluid dynamics (CFD) enabled robust performance prediction across bioreactor scales. This model-driven approach successfully translated the process from 120 mL glass bottles via 2 L to 150 L reactors, corresponding to a reaction-volume scale-up factor of 2000. These findings set the foundation for a robust and predictive platform for sustainable AA production, positioning archaea as a high-potential alternative in industrial biotechnology.

9
Modelling Anaerobic Co-Digestion with Agricultural Feedstock: Model Validation and Cross-Reactor Verification

Murali, R.; Dekhici, B.; Chen, T.; Zhang, D.; Short, M.

2026-04-30 bioengineering 10.64898/2026.04.27.721061 medRxiv
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As the United Kingdom (UK) targets net-zero emissions by 2050, anaerobic digestion (AD) has become a cornerstone of renewable energy infrastructure. However, mathematical models, such as the Anaerobic Digestion Model No. 1 (ADM1), often struggle with high-solids agricultural feedstocks because they rely on Chemical Oxygen Demand (COD), a metric that introduces significant experimental error. To overcome this, this study applies an established mass-based ADM1 framework tailored for the co-digestion of maize silage and cow manure sourced from a UK AD site. This study uses a parallel reactor framework, using two identical laboratory-scale reactors to physically replicate the dynamic conditions of the full-scale site. A Global Sensitivity Analysis was first conducted, identifying biomass decay and carbohydrate breakdown rates as the most influential factors affecting system stability and model accuracy. The model was calibrated using data from the first reactor and then tested against an independent second reactor subjected to significant organic loading stress. Results show high predictive capabilities, with the model achieving a R2 of 0.81 for biogas production during calibration. The model maintained high predictive accuracy during the validation test of the second physical twin, achieving an R2 of 0.85, proving that the framework is robust and not overfitted to a single dataset. While predicting rapid fluctuations in pH and alkalinity remains challenging, the mass-based approach effectively forecasts gas yields and process stability. This methodology provides a reliable foundation for robust process modelling, offering a scalable tool for the UK biogas sector to optimise AD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/721061v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@92c7e2org.highwire.dtl.DTLVardef@80d723org.highwire.dtl.DTLVardef@ac3d24org.highwire.dtl.DTLVardef@1e21a51_HPS_FORMAT_FIGEXP M_FIG C_FIG

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PETase Kubu enables near-complete enzymatic depolymerization of commercial PLA/PBAT blend mulch film

Kim, H. R.; Kim, H.; Jeong, S.; Hwang, J. H.; Kim, D.; Hong, Y. W.; Suh, D.-E.; Lee, S.; Lee, S.; Cho, J.-H.; Yu, J.; Oh, J.

2026-06-04 bioengineering 10.64898/2026.06.02.729468 medRxiv
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Agricultural mulch films improve crop productivity, but post-use recovery and recycling remain difficult because the films are thin, fragmented, dispersed across fields, and contaminated. Commercial PLA/PBAT blends are increasingly used as biodegradable mulch film materials, yet these films exhibit slow or incomplete degradation under environmental conditions. Here, we show that Kubu, a thermostable PETase from Kutzneria buriramensis, rapidly depolymerizes commercial PLA/PBAT mulch film without pretreatment at 60 {degrees}C, achieving 95% mass loss within 96 h and releasing terephthalate, adipate, and lactate, detected by LC-MS/MS and HPLC, as the major monomeric products of both PBAT and PLA components. GPC and SEM revealed extensive degradation at the polymer-water interface. DiffDock docking against Kubu, IsPETase, and TfCut indicates that the canonical W/F(Y) cleft of the PETase/Cutinase fold accommodates aliphatic and aromatic ester bonds with comparable geometry, suggesting that substrate promiscuity is an inherent property of the cleft architecture. Kubus distinctive contribution combines this permissive cleft with catalytic activity sufficient for near-complete blend depolymerization within 24 h. Integration with a socioeconomic analysis shows that complete enzymatic depolymerization could avoid social costs up to $4,087 per ton of mulch film. These findings establish a single-enzyme approach to end-of-life management of heterogeneous polyester blends.

11
High density culture of bovine embryonic stem cell derived mesenchymal cells on edible scaffolds for structured cultivated meat

Carter, M.; Spitters, T.; Ho, S.; Webb, S.; Hyland, N.; Mee, P. J.; Fehlmann, S.; Rajesh, D.

2026-04-27 cell biology 10.64898/2026.04.23.720345 medRxiv
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Developing structured cultivated meat requires integrated solutions that combine scalable cell sources with edible, foodgrade materials capable of supporting highdensity growth and differentiation. Here, we evaluate bovine mesenchymal stem cells derived from embryonic stem cells (ESCderived iMSCs) as a scalable adipogenic cell source and develop an integrated workflow combining these cells with edible plantbased scaffolds for structured biomass generation. Cell identity and functionality were assessed using transcriptomic, morphological, gene expression, flow cytometric, and adipogenic differentiation analyses, in both adherent and suspension culture systems. In parallel, lentil, pea, and soy-based scaffold formulations were screened for cell attachment, proliferation, and biomass accumulation. Soybased scaffolds supported uniform cell distribution and robust growth and outperformed lentil-based scaffolds. Under dynamic culture conditions, bovine iMSCs cultured on soy-based scaffolds achieved highdensity growth, showing biomass accumulation (cell wet weight/scaffold wet weight) reached an average cell wet weight to scaffold wet weight ratio of 15% within three days. Cultures demonstrated active glucose metabolism and retained adipogenic differentiation capacity, confirmed by lipid accumulation and positive oil red O staining. These findings demonstrate an integrated cell-scaffold platform for rapid threedimensional biomass generation. This approach supports the development of a cell culture strategy for structured cultivated meat by combining defined cell sources with foodgrade scaffold technologies to improve scalability, structure, and nutritional relevance. HighlightsO_LIBovine ESC-derived iMSCs enable scalable adipogenic cell production C_LIO_LIEdible soy-based scaffolds support 3D attachment and biomass accumulation C_LIO_LIDynamic culture achieved [~]15% cell wet weight fraction within 3 days C_LIO_LIiMSCs retained adipogenic differentiation capacity on edible scaffolds C_LIO_LIIntegrated cell-scaffold culture supports structured cultivated meat prototypes C_LI

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Lactate:propionate molar ratio determines valerate production in secondary lactate fermentations

Estevez, A.; Ganigue, R.

2026-05-09 bioengineering 10.64898/2026.05.06.722830 medRxiv
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Odd-chain carboxylates such as valerate and heptanoate are ecologically relevant metabolites and promising platform chemicals, yet the factors leading to their formation during secondary lactate fermentations remain poorly understood. Here, a continuous anaerobic bioreactor was operated for 297 days under mildly acidic conditions to evaluate how lactate:propionate molar ratios shape product spectrum in lactate fermentations. Valerate was the predominant odd-chain product under all conditions, reaching concentrations up to 110 mM, while heptanoate accumulated only at low levels (<10 mM). At low lactate concentrations (10-20 g/L), product selectivity strongly depended on the lactate:propionate ratio. When lactate:propionate ratios were around 1.2 mol/mol, odd-chain products were favored, whereas higher ratios (up to 4.8 mol/mol) shifted metabolism toward caproate and butyrate formation. However, this trend was not maintained at higher lactate concentrations (30-40 g/L; lactate not fully consumed), where odd-chain selectivities remained high even at lactate:propionate ratios of 4.8 mol/mol. Pathway analysis indicated that under high-lactate conditions up to 30% of lactate was redirected toward propionate and acetate formation, likely via the acrylate pathway. Microbial community analysis revealed a stable dominance of Caproiciproducens spp., that could be correlated to valerate production. Overall, this work provides mechanistic insights into the ecology of lactate fermentations and offers a framework for steering product selectivity in engineered anaerobic systems. HighlightsValerate was the dominant product, reaching up to 110 mM. Lactate:propionate ratios drive product selectivities. High lactate concentrations activated in situ propionate formation pathways. Caproiciproducens dominance was associated with sustained valerate production.

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Supercharged binding modules can modulate engineered poly(ethylene terephthalate) hydrolase thermostability and functional persistence

DeChellis, A.; Trivedi, S.; Xie, L.; Khare, S.; Chundawat, S. P. S.

2026-05-27 bioengineering 10.64898/2026.05.24.727315 medRxiv
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Poly(ethylene terephthalate) (PET) is a highly recalcitrant polyester plastic whose resistance to degradation has contributed to widespread environmental accumulation. Enzymatic PET depolymerization has emerged as a promising bioremediation strategy, but PET hydrolysis remains challenging due to the insoluble and semi-crystalline nature of PET and the poor thermostability of many PET hydrolases at elevated temperatures. Here, several electrostatically supercharged PET binding modules (PBM) were fused to a PET-hydrolyzing Cutinase Catalytic Domain (CD) from the thermophilic microbe Thermobifida fusca to investigate how engineered PBM surface charge influences PET hydrolysis behavior. All PBM designs were derived from a native T. fusca family-2a carbohydrate binding module (CBM) as starting template. Since PET exhibited a substantially negative zeta potential, and accordingly, all positively supercharged PBMs displayed the strongest PET binding interactions in pull-down binding assays. However, stronger PET binding did not translate to improved hydrolysis activity for the fusion constructs. Instead, a slightly negatively charged PBM-CD fusion (D2 construct) exhibited activity comparable to the Cutinase CD on finely milled PET powder while showing substantially improved activity on intact PET discs, suggesting potential advantages for depolymerization of minimally processed PET feedstocks. Thermostability analysis identified an approximately 10 {degrees}C increase in melting temperature for the D2 fusion construct, corresponding to enhanced catalytic persistence and a shifted optimal hydrolysis temperature. Consequently, this construct exhibited an approximately 2-fold increase in long-term hydrolysis activity on milled PET and up to a 10-fold increase on intact PET discs, even at high solids loadings, compared to the native Cutinase CD. Collectively, these findings demonstrate that thermostability, rather than adsorption to PET alone, is a dominant factor governing functional persistence of PET hydrolases.

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An Innovative, Low-Cost Medium for the Bioproduction of Prodigiosin by Serratia marcescens.

MASSARD, L.; TOUSTOU, B.; LEROY, T.; KASSA, A.; BAUER, H.; Grimaud, J.; GONCALVES, D.

2026-05-12 bioengineering 10.64898/2026.05.07.723488 medRxiv
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Prodigiosin is a red pigment produced by various bacteria, including Serratia marcescens. Despite its wide and promising range of biological activities, the large-scale production of prodigiosin is currently limited by its high cost and low yields. Here we propose and optimize an innovative, low-cost, peanut-based solid culture medium that enhances the yield of prodigiosin produced by Serratia marcescens. Colorimetric assays revealed that peanut significantly stimulates prodigiosin synthesis. Further HPLC-MS analysis allowed us to unambiguously identify prodigiosin and shows that our medium specifically improves the yield of prodigiosin. Overall, our innovative culture medium could help lower prodigiosin production costs and, ultimately, open new industrial applications.

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Relief of allosteric inhibition, redox imbalance, and transport limitations enables high-yield L-malate production in Escherichia coli

Onyeabor, M.; Nieves, L. M.; Kurgan, G.; Xiao, J.; Kurgan, L.; Retallack, B.; Gu, H.; Wang, X.

2026-05-07 bioengineering 10.64898/2026.05.04.722580 medRxiv
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Malic acid is a C4 dicarboxylic acid traditionally produced from petroleum and widely used in the food industry. As a sustainable alternative, it can also be produced as a value-added platform chemical from biomass. Previously, the Escherichia coli strain XZ658 was engineered to produce L-malate via the carbon-fixation reductive branch of the TCA cycle. In this study, we further improved this system by relieving allosteric regulation of citrate synthase, addressing redox imbalance, and enhancing malate export. These modifications approximately doubled the L-malate titer in the final strain MO128 compared to XZ658 under simple batch fermentation conditions. The process achieved a high mass yield of 1.2 g malate g-{superscript 1} glucose, highlighting the carbon-fixation capacity of the reductive TCA pathway for fermentative malate production.

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Dual-loop involving microbial single-cell protein production from soybean-processing wastewater and effluent-based refinement for circular bioeconomy applications

Vethathirri, R. S.; Santillan, E.; Ng, C. C.; Wuertz, S.

2026-07-08 microbiology 10.64898/2026.07.08.737151 medRxiv
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Nutrient-rich food-processing wastewaters represent valuable yet under-utilised side streams for sustainable protein production in the form of microbial biomass. Here we present an integrated dual-loop bioprocess that converts soybean-processing wastewater into microbial single-cell protein (SCP) while achieving substantial nutrient removal and product refinement. In the first loop, previously enriched microbial consortia were inoculated and cultivated in four parallel sequencing batch reactors (SBRs) for 44days at a hydraulic retention time (HRT) of 3days. This bioprocess configuration demonstrated features that support future scale-up while maintaining process stability, achieving a protein content of 33.3{+/-}3.2%, doubling the protein yield (15.32{+/-}3.49g dry weight per g soluble TKN) and quadrupling the production rate (0.29{+/-}0.06g dry weight L-1 d-1) compared to operating reactors without inoculation (HRT: 7.2days). Effluent treatment was stable, with 84% carbon and 78% nitrogen removal efficiencies, demonstrating efficient nutrient recovery. The SCP biomass was enriched in functional taxa, including Acidipropionibacterium, Lactococcus, Megasphaera, and Azospirillum, suggesting that reactor conditions and inoculum selection promoted a stable, protein-productive microbial community with potential probiotic benefits. In the second loop, bioreactor effluent was reused as aqueous matrix for heat treatment (60{degrees}C) of the SCP biomass, reducing the RNA content from 8.6% to 2.6%, with a 39% biomass loss accompanied by a 30% increase in total amino acid concentration. Hence, our valorisation approach integrates microbial biomass production, effluent reuse, and product refinement within a circular framework. The system provides a resource-efficient pathway for converting food-sector side streams into high-quality microbial community-based SCP, highlighting its potential scalability for sustainable nutrient and water management.

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Optical Fiber-Assisted Bioprinting Enables Freeform Printing of Cell-Laden and Turbid Hydrogel Resins

Pfeiffle, M.; Cianciosi, A.; Beusink, S.; Jungst, T.

2026-05-29 cell biology 10.64898/2026.05.28.728387 medRxiv
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Optical fiber-assisted printing (OFAP) was recently introduced as a straightforward light-based platform for the spatially controlled photopolymerization of hydrogel-based resins. Here, we extend this concept toward optical fiber-assisted bioprinting (OFAB) by processing cell-laden GelMA- and GelMA/PEGDA-based bioresins in a freeform embedded printing configuration. The system relies on a 405 nm LED-coupled optical fiber mounted on an automated 3D motion platform, enabling localized photocrosslinking directly within a resin bath. First, GelMA and GelMA/PEGDA formulations containing LAP and tartrazine were screened to evaluate the influence of light intensity, printing velocity, and material composition at the line width and curing depth. Single-line features with widths down to 70 {+/-} 20 {micro}m were obtained under optimized conditions, while more robust printing conditions yielded reproducible features in the range of 200-300 {micro}m. Photorheological and rotational rheology measurements confirmed that the formulations provide both thermoresponsive support during printing and photocrosslinked stability after processing. The incorporation of L929 cells demonstrated high cytocompatibility for GelMA and GelMA/PEGDA 6000 Da formulations, with viabilities above 90% after 7 days for selected printed constructs. Importantly, increasing the cell concentration up to 1 x 107 cells mL-1 did not prevent printing and reduced the extent of overcuring, suggesting that cell-induced turbidity can improve spatial confinement of polymerization in OFAB. Finally, a customized OFAB printer was developed to enable temperature-controlled processing and the fabrication of centimeter-scale 3D structures, including cell-laden constructs. Overall, this work establishes OFAB as an accessible and modular bioprinting strategy for cell-laden and optically turbid hydrogel resins, complementing existing light-based biofabrication approaches.

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Multi-omics Characterization of Duck Embryonic Stem Cells for Cultivated Meat

Kusters, R.; Mathieu, T.; Kamgang Nzekoue, F.; Manzati, M.; Palma, J.; Chun, B.; Lester, H.

2026-05-01 cell biology 10.64898/2026.04.27.720974 medRxiv
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2.8%
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Industrializing cultivated meat requires cell lines with high proliferative capacity, genetic stability, and suspension adaptability. We present a comprehensive multi-omics framework, integrating genomics, transcriptomics, and proteomics, to characterize a commercial duck Embryonic Stem Cell (dESC) line. Our analysis demonstrates continuous proliferation in protein-free suspension media while maintaining a stable genome and a functional conserved transcriptome. Broad-scale transcriptomics confirms the absence of hazardous pathway activation, and targeted assays verify sustained pluripotency marker expression during scale-up. Compositional analysis reveals a low-fat biomass containing all nine essential amino acids with an amino acid profile comparable to conventional duck meat. Furthermore, proteomic profiling demonstrates inter-batch reproducibility and protein distributions comparable to duck breast and liver. This study provides the first detailed molecular characterization of a commercial cultivated meat cell line, establishing a reference for the stability and safety assessment of future cultivated meat cell lines.

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Biofunctional 2D Graphitic Carbon Nitride-Hydrogel Heterointerfaces for Electrochemical Detection of Interleukin-6 toward Septic Cardiomyopathy Diagnostics in Clinical Biofluids

Agarwal, P.; Yadav, A. K.; Singh, A.; Yadav, S. K.; Praneeth, N. V. S.; Bhatia, D. D.

2026-05-28 bioengineering 10.64898/2026.05.25.727622 medRxiv
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2.6%
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Interleukin-6 (IL-6) is a key pro-inflammatory cytokine closely associated with sepsis progression and septic cardiomyopathy (SCM), a severe clinical condition characterized by acute cardiac dysfunction and high mortality in critically ill patients. Rapid and sensitive monitoring of IL-6 in clinical biofluids is therefore crucial for early diagnosis, disease prognosis, and timely therapeutic intervention in emergency healthcare settings. Herein, we report a biofunctional, label-free electrochemical aptasensor based on a graphitic carbon nitride-incorporated chitosan hydrogel-modified gold screen-printed electrode (MCH/Apt-IL-6/g-C3N4@CS/Au-SPE) for ultrasensitive detection of IL-6 in clinical biofluids. The electroactive g-C3N4@CS hydrogel heterointerface was engineered via electrostatic interactions between the negatively charged surface functionalities of two-dimensional graphitic carbon nitride (g-C3N4) and the protonated amino groups (-NH3+) of chitosan (CS), yielding a porous, conductive, and biocompatible sensing matrix with enhanced aptamer immobilization and accelerated electron-transfer kinetics. Biocompatibility evaluation using MTT assay and confocal fluorescence imaging demonstrated that the hydrogel maintained excellent cellular compatibility at 5 mg/mL, preserving normal cytoskeletal organization, mitochondrial integrity, and nuclear morphology, while higher concentrations induced cellular stress responses. Under optimized experimental conditions, the developed aptasensor exhibited outstanding analytical performance with an ultrawide linear detection range from 1 fg/mL to 10 ng/mL, a high sensitivity of 2.162 A/[log10(ng/mL)] cm-2, a low detection limit of 0.460 pg/mL, and excellent linearity (R2 = 0.979). In addition, the sensor demonstrated remarkable selectivity toward common biological interferents, including ascorbic acid, cysteine, glucose, glycine, and urea, together with excellent reproducibility (RSD = 1.139%). Validation studies performed in spiked human serum samples further confirmed the reliability and practical applicability of the proposed sensing platform for rapid clinical analysis. Owing to its label-free detection strategy, disposable electrode format, high sensitivity, and favorable biocompatibility, the developed g-C3N4-hydrogel heterointerface-based aptasensor represents a promising next-generation platform for early septic cardiomyopathy diagnostics, inflammatory biomarker monitoring, and point-of-care electrochemical biosensing applications.

20
Deep learning-guided design of hydrolases for crystalline PET depolymerization

Wu, B.; Li, M.; Zhang, J.; Li, J.; Wang, X.; Zhong, B.; Liu, J.; Wang, B.; Tan, Y.; Qi, W.; Tan, P.; Zhao, W.; Zheng, L.; Hong, L.

2026-06-05 biochemistry 10.64898/2026.06.04.730138 medRxiv
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2.5%
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Poly(ethylene terephthalate) (PET), a ubiquitous polyester used in packaging and textiles, persists in the environment due to its high crystallinity and stability, contributing substantially to global plastic pollution. Enzymatic depolymerization by PET hydrolase (PETase) offers a chemically precise and environmentally sustainable route to convert PET into its monomeric building blocks, enabling recycling. However, practical implementation remains hindered by the rigid, crystalline architecture of PET, which restricts enzyme access and necessitates energy-intensive pretreatment to enable efficient depolymerization. In addition, most PETases achieve only partial depolymerization with low terephthalic acid (TPA) yields and accumulate inhibitory intermediates, while limited thermostability and slow surface kinetics further restrict efficiency. To overcome these barriers, we report VenusPETase, an engineered variant of KbPETase designed using PET-Flow, a state-of-the-art computational framework for PETase engineering. Compared with KbPETase, VenusPETase exhibits a 3.4-fold increase in hydrolytic activity, up to a 27-fold improvement after heat treatment of protein, and a 12 {degrees}C enhancement in thermostability. VenusPETase exhibits rapid degradation across a wide crystallinity range (8%-50%) at 50 {degrees}C, effectively spanning the entire spectrum of commercial PET products. Moreover, VenusPETase outperformed nine high-performance PETases under their respective optimal conditions and degraded untreated PET substrates across 8%-50% crystallinity, producing TPA as over 95% of the released products with minimal intermediate accumulation. X-ray crystallography and molecular dynamics simulations suggest that dynamic modulation, elevated surface electrostatic potential enhance the interaction of VenusPETase with crystalline PET, thereby lowering the hydrolytic energy barrier and improving catalytic performance. We also demonstrate that untreated, postconsumer-PET from nine different products can all be degraded by VenusPETase. The recovered monomers can be directly repolymerized into virgin-quality PET, demonstrating a closed-loop enzymatic recycling process. In a 100 L bioreactor, VenusPETase completely depolymerizes post-consumer crystalline PET (28% crystallinity) within 24 h under 50 {degrees}C. These results establish VenusPETase as a robust biocatalyst that enables efficient, closed-loop recycling of crystalline PET under mild conditions.