{"title":"3D-printed magnesium/strontium-co-doped calcium silicate scaffolds promote angiogenesis and bone regeneration through synergistic bioactive ion stimulation.","authors":"Chia-Che Ho, Tuan-Ti Hsu, Yung-Cheng Chiu, Yen-Hong Lin, Pei-Cheng Xie, Chen-Ying Wang","doi":"10.1186/s13036-025-00528-6","DOIUrl":"10.1186/s13036-025-00528-6","url":null,"abstract":"<p><p>Bone defects resulting from trauma, infection, or surgical resection require biomaterials that support osteogenesis and vascularization for effective regeneration. In this study, we developed a 3D-printed magnesium- and strontium-co-doped calcium silicate (MSCS) scaffold using direct ink writing to optimize its bioactivity and structural integrity. X-ray diffraction confirmed the successful incorporation of Sr and Mg, leading to phase modifications that influenced ion release and degradation. Wettability and mechanical testing showed that Sr improved the stability, while Mg accelerated degradation, with M5S5 co-doping exhibiting a balanced degradation profile. In vitro, Wharton's jelly mesenchymal stromal cells cultured on M5S5 scaffolds displayed enhanced proliferation, cytoskeletal organization, and osteogenic differentiation, as evidenced by increased alkaline phosphatase activity and bone matrix protein expression. Angiogenesis assays using human umbilical vein endothelial cells revealed that Sr and Mg co-doping synergistically enhanced vascular endothelial growth factor and angiopoietin-1 secretion, thereby promoting endothelial tube formation. In vivo micro-computed tomography and histological analysis of a rabbit femoral defect model confirmed that M5S5 facilitated extensive new bone formation, exhibiting superior trabecular architecture and mineralization. These findings highlight MSCS scaffolds as promising biomaterials for bone tissue engineering applications.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"58"},"PeriodicalIF":5.7,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12182697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Biology-inspired engineering for circular bioeconomy systems.","authors":"Brahm P Verma, James W Jones","doi":"10.1186/s13036-025-00527-7","DOIUrl":"10.1186/s13036-025-00527-7","url":null,"abstract":"<p><p>This article presents perspectives on the need to transition from the current unsustainable consumptive fossil-based linear (take-make-use-dispose) systems that produces huge quantities of wastes, pollutes land, water and air, and contributes to climate change to sustainable bio-based circular (take-make-use-decay-reuse) systems. In the article, the word 'fossil' refers to all forms of mined carbon and minerals from the Earth, including water from aquafers, which cannot be replenished at the rate that will maintain their capacity to provide for the future. The natural world through its many circular systems uses energy and renewable resources to perform functions that produce zero waste. One organism's waste becomes another organism's food, material, and energy, forming a circular loop (take-make-use-decay-reuse). Over the past 4 years, deliberate engagements with leaders of multiple disciplines and stakeholders resulted in conclusions that the problems of the complex biologically active systems (biosystems) that are intertwined with natural systems and socio-economic systems can only be addressed by having a robust culture of convergent science and engineering and systems-thinking for transitioning from linear fossil-based to circular bioeconomy systems. We present the need and propose forming a multidisciplinary professional society alliance to promote and support networks of multidisciplinary teams to address problems of complex, intertwined bio-natural-socio-economic systems of systems. This article proposes that the Institute of Biological Engineering (IBE), a society whose primary objective is to \"to apply biology-inspired engineering principles to design systems to improve the quality of the human condition\", and inculcates a culture of convergent science and engineering that has members representing expertise of multiple science and engineering discipline, is potentially an excellent candidate to play a pivotal role in designing innovative solutions for advancing sustainable circular bioeconomy systems.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"57"},"PeriodicalIF":5.7,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12180189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144333199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Seong Keun Kim, Seung-Gyun Woo, Jun-Hong Park, Seung-Goo Lee, Dae-Hee Lee
{"title":"Modular and signal-responsive transcriptional regulation using CRISPRi-aided genetic switches in Escherichia coli.","authors":"Seong Keun Kim, Seung-Gyun Woo, Jun-Hong Park, Seung-Goo Lee, Dae-Hee Lee","doi":"10.1186/s13036-025-00526-8","DOIUrl":"10.1186/s13036-025-00526-8","url":null,"abstract":"<p><strong>Background: </strong>Precise and dynamic transcriptional regulation is a cornerstone of synthetic biology, enabling the construction of robust genetic circuits and programmable cellular systems. However, existing regulatory tools are often limited by issues such as leaky transcription and insufficient tunability, particularly in high-expression or complex genetic contexts. This study aimed to develop a CRISPRi-aided genetic switch platform that overcomes these limitations and expands the functionality of transcriptional regulation tools in synthetic biology.</p><p><strong>Results: </strong>We established a versatile CRISPRi-aided genetic switch platform by integrating transcription factor-based biosensors with the Type V-A FnCas12a CRISPR system. Exploiting the RNase activity of FndCas12a, this system processes CRISPR RNAs (crRNAs) directly from biosensor-responsive mRNA transcripts, enabling precise, signal-dependent transcriptional regulation. To mitigate basal transcription and enhance regulatory precision, transcriptional terminator filters were incorporated, reducing leaky expression and increasing the dynamic range of target gene regulation. The platform demonstrated exceptional adaptability across diverse applications, including ligand-inducible genetic switches for transcriptional control, signal amplification circuits for enhanced output, and metabolic genetic switches for pathway reprogramming. Notably, the metabolic genetic switch dynamically repressed the endogenous gapA gene while compensating with orthologous gapC expression, effectively redirecting metabolic flux to balance cell growth.</p><p><strong>Conclusions: </strong>The CRISPRi-aided genetic switch provides a powerful and flexible toolkit for synthetic biology, addressing the limitations of existing systems. By enabling precise and tunable transcriptional regulation, it offers robust solutions for a wide array of biotechnological applications, including pathway engineering and synthetic gene networks.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"56"},"PeriodicalIF":5.7,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12142916/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144248043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wonhee Kim, Jinjoo Han, Shraddha Chauhan, Jeong Wook Lee
{"title":"Cell-free protein synthesis and vesicle systems for programmable therapeutic manufacturing and delivery.","authors":"Wonhee Kim, Jinjoo Han, Shraddha Chauhan, Jeong Wook Lee","doi":"10.1186/s13036-025-00523-x","DOIUrl":"10.1186/s13036-025-00523-x","url":null,"abstract":"<p><p>The convergence of cell-free protein synthesis (CFPS) and vesicle-based delivery platforms presents a promising avenue for therapeutic development. The open environment of CFPS offers precise control over protein synthesis by enabling the modulation of synthetic conditions. Additionally, vesicle-based platforms provide enhanced stability, bioavailability, and targeted delivery. This synergy facilitates the efficient production of complex proteins-including membrane proteins, antibody fragments, and proteins requiring post-translational modifications (PTMs)-and supports novel drug delivery strategies. While existing reviews have covered synthetic cells and biomanufacturing broadly, a dedicated analysis of CFPS system-containing vesicles (CFVs) for therapeutic applications remains absent from the literature. This review addresses this knowledge gap by providing a comprehensive examination of CFVs, highlighting their potential as programmable drug delivery platforms through the integration of genetic circuits. It emphasizes the advantages of CFPS over traditional cell-based approaches and explores the synergistic benefits of combining CFPS with various vesicle systems. These systems offer dynamic control over therapeutic protein production and targeted delivery, enabling precise responses to specific signals in complex environments. Although challenges such as low protein yield and imperfect targeting remain, potential optimization strategies are discussed. This analysis highlights the significant potential of integrating CFPS and vesicle-based delivery to advance biomanufacturing, therapeutic development, and synthetic cell systems, thereby opening new avenues in medicine and healthcare.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"55"},"PeriodicalIF":5.7,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139124/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mélanie Dhayer, Vivien Barral, Damien Cleret, Amélia Jordao, Anne-Sophie Drucbert, Nicolas Germain, Sophie Dropsit, Patrice Maboudou, Salim Dekiouk, Stéphanie Brun, Christine Campagne, Éric Devaux, Pierre Guerreschi, Aurélie Cayla, Philippe Marchetti
{"title":"Material and biological characterization of 3D knitted bioresorbable poly (D,L-lactide) (PLA) and polycaprolactone (PCL) scaffolds for soft tissue regeneration: from fabrication to in vivo performance.","authors":"Mélanie Dhayer, Vivien Barral, Damien Cleret, Amélia Jordao, Anne-Sophie Drucbert, Nicolas Germain, Sophie Dropsit, Patrice Maboudou, Salim Dekiouk, Stéphanie Brun, Christine Campagne, Éric Devaux, Pierre Guerreschi, Aurélie Cayla, Philippe Marchetti","doi":"10.1186/s13036-025-00504-0","DOIUrl":"10.1186/s13036-025-00504-0","url":null,"abstract":"<p><strong>Background: </strong>Soft-tissue reconstruction is crucial in fields such as plastic surgery and oncology to address the repair of damaged tissues. Knitted scaffolds from bioresorbable copolymers, specifically poly(D,L-lactide) (PLA) and polycaprolactone (PCL), offer mechanical and biological properties that are essential for tissue engineering. This study assessed three-dimensional knitted scaffolds fabricated from melt-spun PLA and PCL multifilaments for soft tissue engineering applications. It examined the impact of the PLA/PCL ratio on the knitted scaffold structure, mechanical properties, and biological responses to determine the optimal composition for adipose tissue reconstruction.</p><p><strong>Results: </strong>Knitted scaffolds fabricated with the PLA/PCL blends (PLA<sub>70</sub>/PCL<sub>30</sub> and PLA<sub>90</sub>/PCL<sub>10</sub>) exhibited distinct mechanical and biological profiles. PLA<sub>70</sub>/PCL<sub>30</sub> scaffolds with a higher PCL content showed enhanced elasticity and porosity, whereas PLA<sub>90</sub>/PCL<sub>10</sub> scaffolds maintained better structural integrity and stiffness. Biological assays confirmed the biocompatibility of all scaffolds in vitro, with no cytotoxic effects. The scaffolds supported adipogenic differentiation in vitro, although PLA<sub>70</sub>/PCL<sub>30</sub> exhibited slightly reduced efficacy. Vascularization was evident using chorioallantoic membrane assays, in which blood vessel formation and penetration were observed, regardless of the scaffold composition. In vivo implantation in rat models revealed effective adipocyte integration, structural stability, and minimal inflammatory response, with PLA<sub>90</sub>/PCL<sub>10</sub> scaffolds outperforming PLA<sub>70</sub>/PCL<sub>30</sub> in terms of vascularization and less macrophage infiltration of connective tissue.</p><p><strong>Conclusion: </strong>PLA/PCL knitted scaffolds offer a promising solution for enhancing graft volume maintenance and improving long-term outcomes, with tunable mechanical properties and biodegradability. The PLA<sub>90</sub>/PCL<sub>10</sub> scaffold is a superior candidate for adipose tissue reconstruction, balancing the structural stability with biological compatibility. These findings underscore the potential of PLA/PCL scaffolds for reconstructive surgery. Future studies should focus on scalability and long-term biocompatibility to facilitate clinical translation.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"53"},"PeriodicalIF":5.7,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144225500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Felipe Carvajal, Valentina Vargas-Torres, Daniela Becerra, Nicolás González-Quezada, José Tomás Egaña
{"title":"Effect of recombinant protein production and release on microalgal fitness and the impact of environmental conditions for localized therapeutic delivery.","authors":"Felipe Carvajal, Valentina Vargas-Torres, Daniela Becerra, Nicolás González-Quezada, José Tomás Egaña","doi":"10.1186/s13036-025-00525-9","DOIUrl":"10.1186/s13036-025-00525-9","url":null,"abstract":"","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"54"},"PeriodicalIF":5.7,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144225499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Serum-free endothelial cell culture medium for vascular smooth muscle cells sheet formation.","authors":"Jing Yang, Xuheng Sun, Hongjing Jiang, Jiandong Li, Jierong Liang, Zhanyi Lin","doi":"10.1186/s13036-025-00522-y","DOIUrl":"10.1186/s13036-025-00522-y","url":null,"abstract":"<p><strong>Background: </strong>Cell sheet technology has been identified as a promising approach for the construction of tissue-engineered vascular grafts (TEVGs). However, concerns regarding immunogenicity and ethical issues, which are raised by the use of fetal bovine serum (FBS) in traditional culture systems, limit its potential for clinical translation. Serum-free medium (SFM) has emerged as a safer and more controllable alternative, but further validation is required to determine its effectiveness and superiority in generating high-quality cell sheets.</p><p><strong>Methods: </strong>This study systematically compared cell sheets generated under SFM and 10% FBS culture conditions in terms of structure, cellular phenotype, and functional properties. The expression levels of α-SMA and SM22, markers of vascular smooth muscle cells(VSMCs), were evaluated using immunofluorescence staining, qRT-PCR, and Western blot analysis to assess cellular phenotype. Histological staining and mechanical testing were employed to compare the morphology and mechanical properties of the cell sheets, while extracellular matrix (ECM) deposition and biochemical characteristics were also analyzed.</p><p><strong>Results: </strong>Under SFM conditions, cells exhibited significantly higher α-SMA and SM22 expression levels (qRT-PCR showed a 1.8-fold and 2-fold increase, respectively; ****p < 0.0001) with clearer cytoskeletal arrangement. Cell sheets formed in SFM displayed comparable area(ns, p > 0.05), thickness(**p < 0.01), and mechanical properties to those cultured in 10% FBS, while ECM deposition was significantly enhanced (collagen content increased by approximately 40%, **p < 0.01). Furthermore, histological analysis revealed that cell sheets generated under SFM conditions were more compact and uniform, exhibiting superior structural organization.</p><p><strong>Conclusion: </strong>SFM facilitates the generation of cell sheets that exhibit structural and functional properties analogous to those cultured in FBS. Additionally, SFM promotes cellular phenotype transition and ECM deposition. Consequently, SFM provides a safer, more controllable, and clinically translatable solution for cell sheet construction.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"51"},"PeriodicalIF":5.7,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12121044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cameron T Roots, Alexis M Hill, Claus O Wilke, Jeffrey E Barrick
{"title":"Codon usage modulates the relationship between the burden and yield of protein overexpression.","authors":"Cameron T Roots, Alexis M Hill, Claus O Wilke, Jeffrey E Barrick","doi":"10.1186/s13036-025-00521-z","DOIUrl":"10.1186/s13036-025-00521-z","url":null,"abstract":"<p><strong>Background: </strong>Excess utilization of translational resources is a critical source of burden on cells engineered to overexpress exogenous proteins. To improve translational efficiency, researchers often modify codon usage in an exogenous gene to more closely match the composition of a host organism's highly expressed genes. Despite empirical data showing the benefits of codon optimization, little is known about the quantitative relationships between codon usage, protein yield, and the burden imposed on a host cell by protein overexpression.</p><p><strong>Results: </strong>We develop and experimentally evaluate a stochastic gene expression model that considers the impact of codon usage bias on the availability of ribosomes and different tRNAs in a cell. In agreement with other studies, our model shows that increasing exogenous protein expression decreases production of native cellular proteins in a linear fashion. We also find that the slope of this relationship is modulated by how well the codon usage bias of the exogenous gene and the host's genes match. Lastly, our model predicts that an overoptimization domain exists where further increasing usage of optimal codons worsens yield and burden. We test our model by expressing sfGFP and mCherry2 from constructs that have a wide range of codon optimization levels in Escherichia coli. The results agree with our model, including for an mCherry2 gene sequence that appears to less efficiently express this gene due to codon overoptimization.</p><p><strong>Conclusions: </strong>Our model reproduces experimentally observed relationships between codon usage bias, gene expression, and burden for overexpressed proteins. Furthermore, it suggests that more nuanced recoding strategies that seek to match a host's overall codon usage bias are less burdensome and will lead to greater protein yields compared to strategies that simply maximize usage of optimal codons. Increasing the level of mechanistic detail in gene expression models can lead to insights that allow researchers to engineer more optimal cellular systems.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"50"},"PeriodicalIF":5.7,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12100883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144127723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Bio-engineered thermo-sensitive alginate/PNIA-g-CS co-polymeric injectable hydrogel laden with GDF-5 to stimulate nucleus pulposus for IVD regeneration.","authors":"Guangnan Chen, Chong Bian, Xiangyang Cheng, Jun Xu, Kaifeng Zhou, Yiming Zhang","doi":"10.1186/s13036-025-00520-0","DOIUrl":"10.1186/s13036-025-00520-0","url":null,"abstract":"<p><p>Chronic back pain and disability are primarily caused by intervertebral disc degeneration (IDD) that requires novel therapies to regenerate the nucleus pulposus (NP) and restore disc function. In this study, a bioengineered thermo-sensitive injectable hydrogel composed of co-polymeric poly-N-isopropyl acrylamide-grafted-chondroitin sulfate cross-linked with sodium alginate microspheres (PNIA-g-CS-NaA Ms: denote HMs) loaded with growth differentiation factor 5 (GDF-5), to stimulate Nucleus Pulposus cells (NPCs) activity and promote intervertebral disc (IVD) regeneration. The Low critical solution temperature (LCST) of PNIA-g-CS was 31.8 and 32.3 °C at 5% (w/v) and 15% (w/v), respectively. In the in vitro study, GDF-5-loaded hydrogel (1 mg/mL) marginally enhanced NPC proliferation and reduced inflammatory cytokines (TNF-α, IL-6, IL-1β) after 24 h. HMs-GDF-5 combined with Adipose-Derived Mesenchymal Stem Cells (ADMSCs) was delivered to NP tissue using a minimally invasive technique, promoting NP regeneration in rats. At 8 weeks, significant upregulation of COL-II and ACAN proteins and mRNA expressions was observed. X-ray imaging showed disc height recovery and increased water content, while histology revealed partial restoration of NPCs and matrix. The outcomes show that the biodegradable hydrogel could be used as a potential therapeutic agent for IVD repair.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"49"},"PeriodicalIF":5.7,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12100944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144127722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}