Biotechnology and Bioengineering最新文献

{"title":"Porphyrin-Based Carbon Dots: Navigating the Nanoscale Frontier of Precision Biomedicine.","authors":"Qian He","doi":"10.1002/bit.70032","DOIUrl":"https://doi.org/10.1002/bit.70032","url":null,"abstract":"As natural aromatic macrocyclic compounds with an 18-π electron system, porphyrins exhibit key values in multiple fields such as biosensing, imaging, and photothermal/photodynamic therapy due to their unique photophysical properties and chemical tunability. Their integration with low-toxicity carbon dots (CDs) with tunable optical and physicochemical properties has opened diverse innovative pathways for interdisciplinary nanotechnology research. This review presents a critical analysis of porphyrin-based CDs (p-CDs), highlighting their structural versatility and transformative applications in nanomedicine. By integrating porphyrin's photophysical prowess with CDs' biocompatibility, these hybrid materials enable breakthroughs in near-infrared bioimaging, enzymatic-optical dual sensing, and synergistic phototherapies. Synthetic strategies, including covalent π-conjugation, natural precursor carbonization, and metal-nanozyme engineering, are discussed to underscore their structure-activity relationships. In the landscape of biomedicine, p-CDs have emerged as a revolutionary tool, facilitating early disease detection, precise molecular diagnosis, and targeted therapeutic interventions, thereby reshaping the paradigms of clinical practice and patient care. However, challenges remain in large-scale production and biocompatibility assessment. Future research should prioritize biomimetic design and multimodal integration to realize the full potential of p-CDs in precision medicine.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"119 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144701338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generation of Clonal Cultures of Adherent or Suspension Cells Using Flat Sessile Drops for Assurance of Monoclonality.","authors":"Joseph A E Morgan,Peter R Cook,Alfonso A Castrejón-Pita,Edmond J Walsh","doi":"10.1002/bit.70030","DOIUrl":"https://doi.org/10.1002/bit.70030","url":null,"abstract":"Single-cell isolation is an essential step in many biomedical workflows, including genetic analyses and drug-based assays. It is commonly attempted through limiting dilution into microtiter wells. However, dark optical edge effects at the well periphery make it difficult to confirm which wells contain just one cell. Consequently, statistical methods are used to obtain the probability that a well contains a single cell. Sessile microdrops can be deposited in the center of wells away from obscuring walls. If these drops have low contact angles, optical edge effects are minimal. A dilute cell suspension can be infused into such drops, which are then imaged to confirm the presence of a single cell with certainty. Subsequently, wells are flooded with media and incubated to allow clonal growth. The fraction of single cells yielding colonies then provides an accurate and non-probabilistic measure of cloning efficiency. We demonstrate average cloning efficiencies between 62% and 78% with human embryonic kidney, cancer, and induced pluripotent stem cells, as well as Chinese-hamster suspension cells. We verify that stem cells continue to express pluripotency markers after cloning and incorporate the method into a gene-editing workflow for cell-line development. This demonstrates the seamless integration of sessile microdrops into established protocols, providing assurance of monoclonality with high cloning efficiency.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"111 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144664181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interpretable-AI-Based Model Structural Transfer Learning to Accelerate Bioprocess Model Construction.","authors":"Alexander W Rogers,Fernando Vega-Ramon,Amanda Lane,Philip Martin,Dongda Zhang","doi":"10.1002/bit.70026","DOIUrl":"https://doi.org/10.1002/bit.70026","url":null,"abstract":"Determining accurate kinetic models for new biochemical systems is time-intensive, requiring experimental data collection, model construction, validation, and discrimination. Traditional black-box machine learning-based transfer learning methods leverage prior knowledge but lack interpretability and physical insights. To address this, we propose a novel model structural transfer learning approach that combines symbolic regression with artificial neural network feature attribution. The method enables automatic structural modification of an inaccurate or low-fidelity mechanistic model developed for one system when being applied to another system. Through a comprehensive in silico case study, our framework successfully adapted a kinetic model from one biochemical system to a different but related one, improving predictive accuracy. Moreover, the framework can significantly accelerate model identification when being integrated with model-based design of experiments. By comparing the old and new model structures, physical insight can be obtained, altogether highlighting the framework's potential for advancing automated knowledge discovery and facilitating high-fidelity predictive digital twin design for novel biochemical processes.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"28 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144652903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitigating Night Biomass Loss in Outdoor Pilot-Scale Mixotrophic Algal Cultivation of Monoraphidium minutum Using Flue Gas Condensate and Cheese Whey.","authors":"Quyen Nham,Tristan Gordon,Hanna Farnelid,Catherine Legrand,Elin Lindehoff","doi":"10.1002/bit.70027","DOIUrl":"https://doi.org/10.1002/bit.70027","url":null,"abstract":"In algal cultivation, nighttime biomass loss due to respiration and cell mortality can considerably reduce the amount of biomass produced during daylight. The adverse effect can be counteracted by mixotrophic cultivation, where an organic carbon (OC) source is used to supply the energy required for cell maintenance and division during darkness. The potential for mixotrophic cultivation to mitigate night biomass loss has yet to be tested under outdoor, large-scale conditions that use raw industrial waste streams, particularly during low-light seasons. We investigated night biomass loss in cultivation of the strain Monoraphidium minutum KAC90 in outdoor 1 m3 raceway ponds during the Nordic autumn. Flue gas condensate (nitrogen source) and cheese whey (phosphorus and OC source) were used for the mixotrophic treatment, while potassium monophosphate (phosphorus source) was used for the photoautotrophic control. Results indicate that under high OC availability, the mixotrophic treatment had a night biomass gain of 33% ± 16%, whereas it experienced a night biomass loss of 10% ± 9% under low OC. In contrast, the photoautotrophic control showed a night biomass loss of 5% ± 15%. In the mixotrophic treatment, algal biomass had a higher carbohydrate content, but lower levels of lipids and proteins than the photoautotrophic cultures. The cultivation of algae using cheese whey may increase biomass accumulation in darkness, enhancing the overall production of algal biomass rich in carbohydrates.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"20 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144652901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mathematical Model for Measles Virus Production in Batch Bioreactors.","authors":"Shiny Samuel,Todd Przybycien","doi":"10.1002/bit.70017","DOIUrl":"https://doi.org/10.1002/bit.70017","url":null,"abstract":"Measles virus (MeV) is a promising vector for vaccines, gene therapy, and oncolytic virus therapy due to its safety, efficacy, and natural ability to target tumor cells. However, MeV production in bioreactors, typically with microcarrier cultures of Vero cells, is challenging because of the sensitivity of the virus to temperature, shear stress, and low pH. At 37°C, the optimal growth temperature of Vero cells, MeV has a short half-life of 1 h, requiring precise control of the harvest time (TOH) to maximize yield. We developed a mathematical model to predict the TOH for recombinant MeV production in Vero cells. Model predictions for TOH were in good agreement with observations across five separate bioreactor runs, despite significant run-to-run performance variations. Parameter analysis revealed that virus attachment parameters and thermal degradation rate significantly influence infection dynamics. Furthermore, the model highlights the critical importance of accurately characterizing seed virus quality, particularly concerning defective interfering particle (DIP) content, to minimize production variability and optimize yield.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"84 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144645986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Scalable, High-Density Expansion of Human Mesenchymal Stem Cells on Microcarriers Using the Bach Impeller in Stirred-Tank Reactors.","authors":"Tom A Wyrobnik,Laia Miranda,Alan Lam,Steve Oh,Andrea Ducci,Martina Micheletti","doi":"10.1002/bit.70025","DOIUrl":"https://doi.org/10.1002/bit.70025","url":null,"abstract":"This paper describes the results of process developmental experiments to achieve higher cell densities in the manufacturing of hMSCs using the novel Bach impeller in a stirred-tank bioreactor. Engineering experiments have previously shown that the Bach impeller represents an efficient mixing device that suspends particles in fluids at low power inputs. To assess the impeller during biological experiments, the growth performance of Wharton Jelly (WJ)-hMSCs in a 1 L STR equipped with the Bach impeller was evaluated at a variety of culture conditions. The cells attached to Cytodex 1 microcarriers at a concentration of 5.6 g/L and were cultured for 5-7 days. The growth phase was carried out at varying impeller speeds N $N$  = 75, 115, and 150 rpm. Cell growth was additionally evaluated at a microcarrier concentration of 11.2 g/L Cytodex 1. Here, a maximum cell density of up to 1.7 × 106 cells/mL and cell viability > 90% was achieved within 5 culture days, which is amongst the highest cell densities ever attained for a hMSC batch culture. Critical cell quality attributes of the WJ-hMSCs were assessed upon completion of the growth phase, that is, FACS to identify stem cell surface markers, tri-lineage differentiation, and capacity of the cells to form colonies. In addition, informed by the previously described engineering characterization, the 1 L process at N $N$  = 75 rpm was scaled up to the 5 L scale, where WJ-hMSCs were again confirmed to have retained the relevant cell quality attributes. The reported findings are important to determine the design space to which scale-ups to even larger tank sizes can adhere.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"679 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144652904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Manufacturing Process Intensification of Adeno-Associated Viral Vectors Type-8 Using Weak Partitioning Chromatography With UV-Based Process Analytical Technology (PAT).","authors":"Garima Thakur,Sheldon Mink,Hanne Bak,Andrew D Tustian","doi":"10.1002/bit.70021","DOIUrl":"https://doi.org/10.1002/bit.70021","url":null,"abstract":"Separation of full and empty capsids is a critical step in manufacturing of recombinant adeno-associated viral vector (AAV) based gene therapies. Anion exchange chromatography (AEX) is well-established as a scalable method for full/empty separations. Due to the small differences in surface charge between full and empty capsids, shallow linear gradients of increasing conductivity are commonly used to resolve the two species. However, the resolution is adversely impacted by higher column loading, and most linear gradient processes load at 2e13-2e14 capsids/mL of monolith volume (cp/mL monolith) to achieve full capsid purity targets. With the rapid increase reported in upstream AAV titers up to > 1e12 vg/mL in the bioreactor over the last few years, current downstream purification processes utilizing linear gradient AEX are rapidly approaching scalability limits. This is particularly true for processes utilizing monoliths and membranes which are preferred over resins in AAV purifications due to elimination of pore size diffusion limitations. There is a pressing need for next-generation processes that can load more material in the range of > 1e15 cp/mL, while maintaining operating time and process robustness suitable for GMP manufacturing. This study presents a scalable method for empty/full separations for AAV8 using weak partitioning AEX combined with isocratic elution, demonstrated on CIM QA monoliths which are currently extensively used in the industry for AAV manufacturing. By optimizing load conditions and automating the process with UV-based signals, the strategy achieves > 80% full capsid purity and > 80% genomic yields. Compared to standard linear gradient AEX, the weak partitioning method achieves higher % full capsids as well as higher genomic yield due to combined effects of (i) removal of empty capsids in the flowthrough, (ii) reduction of nonspecific binding interactions as a result of column overloading, and (iii) elimination of peak-cutting by using isocratic elution. The approach enables > 10-fold higher loading per cycle while reducing processing time by 10-fold and is well-suited to rapid cycling or continuous processing operations to support next-generation, high-titer processes.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"3 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144652963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Scaling-up the Bioconversion of Lignin to 2,4-Pyridinedicarboxylic Acid With Engineered Pseudomonas putida for Bio-Based Plastics Production.","authors":"Jan Seeger,Susanne Müller,Helena Gómez-Álvarez,Goran M M Rashid,Timothy D H Bugg,Eduardo Díaz,Ralf Takors","doi":"10.1002/bit.70020","DOIUrl":"https://doi.org/10.1002/bit.70020","url":null,"abstract":"2,4-pyridinedicarboxylic acid (PDCA) is a promising bio-based compound to substitute petroleum-derived terephthalic acid in plastics. It is produced through the microbial conversion of lignin substrates with engineered microorganisms like Pseudomonas putida. To this point, an efficient bioproduction process for PDCA has not yet been established. In this study, we optimized PDCA production with engineered P. putida ligAB and demonstrated bioproduction at up to 30 L scale. PDCA was produced with a volumetric productivity of 390 mg/L/h from the precursor protocatechuate and the product titer was doubled compared to previously reported work. Lignin feedstock and pretreatment combinations were screened to access lignin as substrate for PDCA production. Sodium hydroxide lignin with alkali + heat pretreatment yielded 33 mg/L PDCA at a production rate of 0.1 mg/g/h. Low PDCA production rates could be overcome by developing a bacterial mixed culture by adding the engineered strain Rhodococcus jostii ΔpcaHG that supplies PCA from lignin degradation. The mixed culture increased PDCA productivity of P. putida ligAB by factor 19 (1.9 mg/gP. putida/h).","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"72 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144622023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Bioprocess Engineering Approach to Boost Selection of Fully Segregated Transformants in Cyanobacteria.","authors":"Cecilia Salvagnini,Eliana Gasparotto,Veronica Lucato,Elisabetta Bergantino,Matteo Ballottari,Elena Barbera,Nico Betterle,Eleonora Sforza","doi":"10.1002/bit.70024","DOIUrl":"https://doi.org/10.1002/bit.70024","url":null,"abstract":"Cyanobacteria are photoautotrophic microorganisms with significant applications in biotechnology. Although many cyanobacteria, including Picosynechococcus sp. (formerly called Synechococcus sp.) PCC 11901 (Picosynechococcus) and Synechocystis sp. PCC 6803 (Synechocystis), are readily and naturally transformable, their polyploidy poses a major challenge. To obtain a stable phenotype, transgenic strains must be fully segregated, i.e. mutations must appear in all chromosome copies. Traditional protocols rely on re-streaking of colonies on increasingly selective plates, a time-intensive laboratory procedure that requires continuous intervention from the operator. This study proposes an alternative protocol that combines transformation in a batch system in liquid culture with transformant selection in a continuous-flow stirred-tank reactor system. This protocol led to the successful selection of homoplasmic transformants of Picosynechococcus containing, alternatively, an antibiotic resistance alone (construct \"SmR\") or a more complex construct (\"bKT\") that leads to the accumulation of a ketocarotenoid. The stability of SmR transformants under semi-continuous cultivation in the absence of antibioticsf was tested for 42 days, proving their potential fitness to industrial cultivation conditions. The selection process was also validated on the model species Synechocystis, demonstrating its applicability to other cyanobacterial strains.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"52 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144622025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulating Transport Preferences of Fucosylated Sugars: Revealing Transport Mechanisms via Sugar Efflux Transporter A Transformation Into a “Tight‐in, Tight‐out” Mode","authors":"Liu Wenxian, Sun Shengjie, Peng Jing, Zou Sini, Cheng Haina, Chen Zhu, Wang Yuguang, Zhou Hongbo","doi":"10.1002/bit.70019","DOIUrl":"https://doi.org/10.1002/bit.70019","url":null,"abstract":"Sugar transporters play a crucial role in cellular metabolism across diverse organisms, regulating essential biological processes through efficient substrate transport. Despite extensive research efforts, the structures and mechanisms of transporters responsible for sugars have remained elusive. In this study, we investigated the transport efficiency of the <jats:italic>Escherichia coli</jats:italic> sugar efflux transporter A (SetA) for lactose and fucosylated lactose. By employing site and combinatorial mutations, we obtained a mutant exhibiting approximately sixfold enhanced transporter efficiency for fucosylated lactose while retaining its potency for lactose transport. In this mutant, the fundamental amino acids responsible for recognizing the galactosyl moiety remained unchanged, yet the introduction of two face‐to‐face aromatic ring residues facilitated the enhanced recognition of the fucosyl moiety. This indicated the transformation of SetA from a universal transporter into a specific “tight‐in, tight‐out” transporter. Utilizing SetA‐based structural modeling, we mapped and investigated mutations associated with diseases. The structural and biochemical insights from SET in this study offer a valuable investigating framework for understanding substrate specificity mechanisms of fucosylated sugar transporters and, by extension, other transporters in broader contexts.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"22 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144603105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}