Journal of Biological Engineering最新文献

{"title":"Gene syntaxes modulate gene expression and circuit behavior on plasmids.","authors":"Yijie Deng, Hannah E Maurais, Kai Etheridge, Rahul Sarpeshkar","doi":"10.1186/s13036-025-00493-0","DOIUrl":"10.1186/s13036-025-00493-0","url":null,"abstract":"<p><p>Achieving consistent and predictable gene expression from plasmids remains challenging. While much attention has focused on intra-genetic elements like promoters and ribosomal binding sites, the spatial arrangement of genes within plasmids-referred to as gene syntax-also plays a crucial role in shaping gene expression dynamics. This study addresses the largely overlooked impact of gene syntaxes on gene expression variability and accuracy. Utilizing a dual-fluorescent protein system, we systematically investigated how different gene orientations and orders affect expression profiles including mean levels, relative expression ratios, and cell-to-cell variations. We found that arbitrary gene placement on a plasmid can cause significantly different expression means and ratios. Genes aligned in the same direction as a plasmid's origin of replication (Ori) typically exhibit higher expression levels; adjacent genes in the divergent orientation tend to suppress each other's expression; altering gene order without changing orientation can yield varied expression. Despite unchanged total cell-to-cell variation across different syntaxes, gene syntaxes can also influence intrinsic and extrinsic noise. Interestingly, cell-to-cell variation appears to depend on the reporter proteins, with RFP consistently showing higher variation than GFP. Moreover, the effects of gene syntax can propagate to downstream circuits, strongly affecting the performance of incoherent feedforward loops and contributing to unpredictable outcomes in genetic networks. Our findings reveal that gene syntaxes on plasmids modulate gene expression and circuit behavior, providing valuable insights for the rational design of plasmids and genetic circuits.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"25"},"PeriodicalIF":5.7,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951768/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143730228","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":"An electrochemical biosensor for the detection of microRNA-31 as a potential oral cancer biomarker.","authors":"Sanket Naresh Nagdeve, Baviththira Suganthan, Ramaraja P Ramasamy","doi":"10.1186/s13036-025-00492-1","DOIUrl":"10.1186/s13036-025-00492-1","url":null,"abstract":"<p><p>Oral cancer presents substantial challenges to global health due to its elevated mortality rates. Approximately 90% of these malignancies are oral squamous cell carcinoma (OSCC). A significant contributor to the prevalence of oral cancer is the difficulty in detecting cancerous biomarkers, further exacerbated by socioeconomic disadvantages and late-stage diagnoses. Given the critical nature of oral cancer, the early detection of biomarkers is essential for reducing mortality rates. This study investigates the application of microRNA-31 (miRNA-31) as a biomarker for the electrochemical detection of oral cancer, recognizing the considerable potential that microRNAs have demonstrated in cancer screening and diagnosis. The methodology employed includes the use of a glassy carbon electrode modified with graphene and a molecular tethering agent designed to enhance sensitivity and specificity. The biosensor exhibited a limit of detection of 10^- 11 M (70 pg/mL or 6.022 × 10⁶ copies/µL) in buffer and 10^- 10 M (700 pg/mL or 6.022 × 10⁷ copies/µL) in diluted serum for the complementary target miRNA-31 using the Six Sigma method. The efficacy of this biosensor was further validated through specificity studies utilizing a non-complementary miRNA in both buffer and human serum samples. The electrochemical biosensor displayed exceptional performance and high sensitivity in detecting miRNA-31, confirming its role as an innovative sensor for the non-invasive diagnosis of oral cancer. Furthermore, the proposed biosensor demonstrates several advantages over current methodologies, including reduced detection time, and cost-effective reagents.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"24"},"PeriodicalIF":5.7,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11938787/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143709616","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":"Rapid osteoinduction of human adipose-derived stem cells grown on bioactive surfaces and stimulated by chemically modified media flow.","authors":"Karolina Truchan, Barbara Zagrajczuk, Katarzyna Cholewa-Kowalska, Anna Maria Osyczka","doi":"10.1186/s13036-025-00491-2","DOIUrl":"10.1186/s13036-025-00491-2","url":null,"abstract":"<p><p>Adipose-derived stem cells (ASCs) provide an ample, easily accessible source of multipotent cells, an alternative to bone marrow-derived stromal cells (BMSCs), capable of differentiating into osteoblasts. However, the osteogenic potential of ASCs is reportedly lower than that of BMSCs and protocols to effectively differentiate ASCs into osteoblasts are in high demand. Here, we present novel strategies for effective osteogenic differentiation of human ASCs by combining their culture on bioactive growth surfaces with their treatment with specific supplements in osteogenic medium and application of fluid shear stress. Human ASCs were cultured on PLGA-based composites containing 50 wt% sol-gel bioactive glasses (SBGs) from the SiO₂-CaO±P₂O₅ system, either unmodified or modified with 5 wt% ZnO or SrO. The osteogenic medium was supplemented with recombinant human bone morphogenetic protein 2 (BMP-2), MEK1/2 kinase inhibitor (PD98059) and indirect Smurf1 inhibitor (Phenamil). Fluid shear stress was applied with a standard horizontal rocker. ASC culture on SBG-PLGA composites along with the osteogenic medium supplements enhanced the expression of both early and late osteogenic markers. Modification of SBG with either SrO or ZnO further enhanced osteogenic gene expression compared to ASCs cultured on composites containing unmodified SBGs. Notably, the application of fluid shear stress synergistically strengthened the osteogenic effects of bioactive composites and medium supplements. We also show that the presented culture strategies can drive ASCs toward osteoblastic cells in a 3-day culture period and provide mineralizing osteoblasts through a short, 7-day ASC preculture on bioactive composites. Our results also indicate that the applied osteogenic treatment leads to the phosphorylation of β-catenin and CREB or the COX-2 expression. We believe the presented strategies are feasible for rapid ASC differentiation to early osteoblasts or mineralizing osteoblastic cells for various potential cell-based bone regeneration therapies.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"23"},"PeriodicalIF":5.7,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634044","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":"Correction: Treatment of effluents from Food services establishment (FSEs) by physico-chemical processes: a case study for Trinidad & Tobago.","authors":"Cudjoe Shamika, Banerjee Goutam, Cooper Vincent","doi":"10.1186/s13036-024-00474-9","DOIUrl":"10.1186/s13036-024-00474-9","url":null,"abstract":"","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"22"},"PeriodicalIF":5.7,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11895273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143596972","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":"CRISPR/Cas12a-mediated gene silencing across diverse functional genes demonstrates single gene-specific spacer efficacy in Mycobacterium smegmatis.","authors":"Megha Sodani, Chitra S Misra, Savita Kulkarni, Devashish Rath","doi":"10.1186/s13036-025-00490-3","DOIUrl":"10.1186/s13036-025-00490-3","url":null,"abstract":"<p><strong>Background: </strong>Tuberculosis, a persistent global health threat, necessitates a comprehensive understanding of the genes and pathways crucial for the survival and virulence of the causative pathogen, Mycobacterium tuberculosis. Working with M. tuberculosis (M.tb) presents significant challenges; therefore, the use of M. smegmatis as a surrogate system for conducting genetic studies of M.tb has proven to be highly valuable. Development of novel genetic tools to probe cellular processes accelerates the progress in the field of drug development and also helps in understanding the basic physiology of the bacterium.</p><p><strong>Results: </strong>This study reports the successful implementation and evaluation of the CRISPR-Cas12a system for gene repression in Mycobacterium smegmatis, a surrogate for M. tuberculosis. We engineered a Cas12a-based CRISPR interference (CRISPRi) system and assessed its functionality. Targeting 45 genes with a single sgRNA per gene, we achieved efficient gene repression, leading to marked phenotypic changes. Each knockdown strain was evaluated individually for growth phenotypes, and a comparison of the results with the reported essential gene library probed with dCas9 demonstrated congruous results across diverse gene categories. The study shows that CRISPR/Cas12a system can be effectively utilised with a single gene specific target for efficient silencing of the gene and highlights the importance of subsequent growth assays required to evaluate the vulnerability of targeted gene silencing.</p><p><strong>Conclusion: </strong>Our findings reveal the robustness and versatility of the dCas12a-CRISPRi system in M. smegmatis, providing a valuable tool for functional genomics research. This work showcases the potential of the dCas12a-CRISPRi system in investigating essential genes, enabling a deeper understanding of the biology and potential therapeutic targets in mycobacterium species.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"21"},"PeriodicalIF":5.7,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11871654/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531447","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":"Carbon fluxes rewiring in engineered E. coli via reverse tricarboxylic acid cycle pathway under chemolithotrophic condition.","authors":"Jian-Hau Peng, Shou-Chen Lo, Yu-Ning Yu, Ya-Tang Yang, Yu-Chieh Chen, An-I Tsai, Dong-Yan Wu, Chu-Han Huang, Tien-Tsai Su, Chieh-Chen Huang, En-Pei Isabel Chiang","doi":"10.1186/s13036-025-00489-w","DOIUrl":"10.1186/s13036-025-00489-w","url":null,"abstract":"<p><strong>Background: </strong>A transgenic strain of Escherichia coli has been engineered to directly assimilate gaseous CO₂ into its biomass through hydrogen-powered anaerobic respiration. This was achieved by expressing key components of the reverse tricarboxylic acid (rTCA) cycle, including genes encoding α-ketoglutarate: ferredoxin oxidoreductase (KOR) and ATP-dependent citrate lyase (ACL) from Chlorobium tepidum. These enzymes were selected for their essential roles in enabling CO₂ fixation and integration into central metabolism.</p><p><strong>Results: </strong>This study found that KOR alone can support cellular maintenance under chemolithotrophic conditions, while additional expression of ACL enhances CO₂ assimilation. Using isotopic ¹³CO₂ tracing, it was demonstrated that KOR alone facilitates CO₂ assimilation into TCA metabolites. However, co-expression of ACL with KOR redirected carbon fluxes from TCA cycle toward essential metabolic pathways, particularly those involved in protein and nucleotide biosynthesis. Compared to KOR alone, ACL co-expression significantly increased isotopic enrichments in amino acids (e.g., methionine, threonine, glycine) and nucleotides (e.g., deoxythymidine, deoxycytidine). These results suggest that ACL supports the synthesis of nitrogen-containing metabolites when inorganic nitrogen is sufficient, while KOR alone sustains core metabolic functions under chemolithotrophic conditions.</p><p><strong>Conclusions: </strong>This study demonstrates a novel strategy to engineer E. coli for CO₂ fixation using only one or two heterologous enzymes under chemolithotrophic conditions. These findings reveal the minimal genetic and nutritional requirements for CO₂ assimilation and provide insights into metabolic flux partitioning in engineered strains. This research paves the way for sustainable applications in carbon fixation and biotechnological innovation.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"20"},"PeriodicalIF":5.7,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11863533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143500858","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":"Metabolic engineering of Komagataella phaffii for enhanced 3-hydroxypropionic acid (3-HP) production from methanol.","authors":"Sílvia Àvila-Cabré, Joan Albiol, Pau Ferrer","doi":"10.1186/s13036-025-00488-x","DOIUrl":"10.1186/s13036-025-00488-x","url":null,"abstract":"<p><strong>Background: </strong>Bioconversion of methanol derived from CO₂ reduction into value-added chemicals provides a unique approach for mitigating global warming and reducing fossil fuels dependence. Production of 3-hydroxypropionic acid (3-HP), a key building block for the development of biobased products such as acrylates and 1,3-propanediol, has been successfully achieved using methanol as the sole carbon and energy source in the methylotrophic yeast Komagataella phaffii (syn. Pichia pastoris). However, challenges remain in meeting commercially relevant concentrations, yields and productivities of 3-HP, prompting further strain optimization. In the present study, we have combined metabolic engineering strategies aiming at increasing metabolic precursors supply and redirecting carbon flux towards 3-HP production.</p><p><strong>Results: </strong>A combinatorial metabolic engineering strategy targeting precursors supply and 3-HP export was applied to the original 3-HP producing K. phaffii strain harboring the synthetic β-alanine pathway and a mutated NADP-dependent formate dehydrogenase from Pseudomonas sp. 101 (PseFDH(V9)). To do so, several genes encoding enzymes catalyzing reactions immediately upstream of the β-alanine pathway were overexpressed to enhance precursors availability. However, only the overexpression of the pyruvate carboxylase PYC2 gene significantly increased the 3-HP yield on biomass (Y_P/X) in small-scale cultivations. Co-overexpression of PYC2 and the lactate permeases ESBP6 and JEN1 genes led to a 55% improvement in 3-HP titer and product yield in methanol deep-well plate cultures compared to the reference strain, mostly due to Esbp6 activity, proving its effectiveness as a 3-HP transporter. Deletion of the native formate dehydrogenase gene FDH1 did not increase methanol flux entering the assimilatory pathway. Instead, knockout strains showed severe growth defects due to toxic intermediates accumulation. Co-expression of the PseFDH(V9) encoding gene in these strains failed to compensate for the loss of the native FDH. The strain combining PYC2, ESBP6, and JEN1 overexpression was further tested in fed-batch cultures at pH 5, achieving a 3-HP concentration of 27.0 g l^- 1, with a product yield of 0.19 g g^- 1, and a volumetric productivity of 0.56 g l^- 1 h^- 1 for the methanol feeding phase of the cultivations. These results represent a 42% increase in final concentration and over 20% improvement in volumetric productivity compared to the original 3-HP-producing strain. Furthermore, bioreactor-scale cultivations at pH 3.5 revealed increased robustness of the strains overexpressing monocarboxylate transporters.</p><p><strong>Conclusions: </strong>Our results point out the potential of lactate transporters to efficiently drive 3-HP export in K. phaffii, leading to higher titers, yields, and productivities, even at lower pH conditions.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"19"},"PeriodicalIF":5.7,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11844118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468194","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":"Bioelectric profiling of Rickettsia montanensis in Vero cells utilizing dielectrophoresis.","authors":"Negar Farhang Doost, Sai Deepika Reddy Yaram, Kayla Wagner, Harshit Garg, Soumya K Srivastava","doi":"10.1186/s13036-025-00487-y","DOIUrl":"10.1186/s13036-025-00487-y","url":null,"abstract":"<p><p>Rickettsia is an intracellular bacteria transmitted to humans through ticks, lice, fleas, or their feces, causing acute symptoms such as fever, headache, rashes, and muscle aches. Detecting rickettsial diseases is challenging due to limitations in current methods such as negative results, low sensitivity, and high cost. These limitations highlight the need for improved detection methods. Dielectrophoresis (DEP) offers a promising alternative to develop a point-of-care economical, label-free, and sensitive diagnostic tool. By exposing cells to non-uniform electric fields one can measure the electrical properties of the cells which are different and unique based on the cell type. By comparing the dielectric profiles of healthy and infected cells, DEP could be utilized to design a rapid, cost-effective diagnostic tool. Initial steps involve characterizing the electrophysiological properties of Vero cells infected with Rickettsia montanensis to develop this new detection tool. This study found significant differences in electrical parameters between healthy and Rickettsia spp. infected Vero cells, particularly at a medium conductivity of 500 µS/cm. Moreover, we found that the dielectric spectrum showed the greatest differences between healthy and Rickettsia spp. infected Vero cells at medium conductivity of 500 µS/cm, with significantly different dielectrophoretic crossover frequencies (no DEP force region). These findings suggest that dielectrophoretic detection of infected cells could serve as a quick, cost-effective, label-free, and sensitive alternative for developing a point-of-care diagnostic tool for Rickettsial infections.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"18"},"PeriodicalIF":5.7,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837300/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449060","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":"Reversible fluorescent solid porous films for detection of zinc ions in biological media.","authors":"Alessandro Gandin, Laura Brigo, Sujatha Giacomazzo, Veronica Torresan, Giovanna Brusatin, Alfredo Franco","doi":"10.1186/s13036-025-00484-1","DOIUrl":"10.1186/s13036-025-00484-1","url":null,"abstract":"<p><p>The need for a sensitive, selective, non-invasive and reversible fluorescent sensor for Zn²⁺ monitoring is addressed in this work. A novel guest-host system is developed, including a Zn²⁺ sensitive fluorescent probe, Zinpyr-1, embedded in a porous optically transparent hybrid film. The entrapped probe molecules are accessible and can interact with the external analyte. The immobilized Zinpyr-1 confirms its specificity and selectivity for Zn²⁺, as shown by sensing tests conducted in buffer solutions that mimic the ionic composition of biological media. The uniqueness of the developed sensor system lies in its reversibility, combined with a fast and selective response, allowing dynamic measurements of zinc concentrations in the 1 µM to 1 mM range within few tens of seconds. Unlike most Zn²⁺ sensors, this system is a film-based sensor, making it an interesting minimally invasive tool for future studies on how live cells cultured on it dynamically regulate the Zn²⁺ concentration under controlled physiological conditions.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"17"},"PeriodicalIF":5.7,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449062","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":"The stability and self-assembly of tri-calcium silicate and hydroxyapatite scaffolds in bone tissue engineering applications.","authors":"Nima Beheshtizadeh, Amir Abbas Seraji, Behnam Azadpour, Sima Rezvantalab","doi":"10.1186/s13036-025-00481-4","DOIUrl":"10.1186/s13036-025-00481-4","url":null,"abstract":"<p><p>The fabrication of scaffolds for bone tissue engineering (BTE) applications often involves the utilization of two distinct categories of biomaterials, namely calcium phosphates and calcium silicates. The selection of these materials is based on their biocompatibility, bioactivity, and mechanical characteristics that closely resemble those of natural bone. The present research examined the utilization of hydroxyapatite (HAP) and tri-calcium silicate (TCS), which are among the most commonly utilized materials in calcium phosphates and calcium silicates, in the context of bone scaffolding applications. A molecular dynamics simulation was conducted to investigate the impact of different concentrations of ceramic nanoparticles, when combined with sodium alginate (SA) hydrogel, on the fabrication of bone scaffolds.The stability and self-assembly were assessed through several parameters, such as the solvent-accessible surface area (SASA), radius of gyration (Rg), radial distribution function (g(r)), root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), hydrogen bonding, van der Waals, electrostatic, and total energies. The findings indicate that the addition of 10 wt% HAP and TCS to the SA hydrogel matrix results in a more compact, stable, and potentially less hydrated structure. Accordingly, the experimental validation of these simulation approved our in silico findings. Experimental rheology and mechanical properties evaluation validate our simulation results, indicating a superior characteristic of TCS10 and HAP10 inks and 3D-printed scaffolds among other composition ratios. This could potentially benefit the in vitro and in vivo performance of the scaffold and its interaction with cells. The aforementioned traits are considered fundamental for the successful execution of the scaffold in the field of BTE. The findings indicate that TCS samples exhibit superior properties when compared to HAP samples, specifically in terms of composition with SA hydrogel.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"16"},"PeriodicalIF":5.7,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143440781","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}