Journal of Biological Engineering最新文献

{"title":"Promoting osteogenesis and bone regeneration employing icariin-loaded nanoplatforms","authors":"Mahsa Mohammadzadeh, Masoud Zarei, Hossein Abbasi, Thomas J. Webster, Nima Beheshtizadeh","doi":"10.1186/s13036-024-00425-4","DOIUrl":"https://doi.org/10.1186/s13036-024-00425-4","url":null,"abstract":"There is an increasing demand for innovative strategies that effectively promote osteogenesis and enhance bone regeneration. The critical process of bone regeneration involves the transformation of mesenchymal stromal cells into osteoblasts and the subsequent mineralization of the extracellular matrix, making up the complex mechanism of osteogenesis. Icariin’s diverse pharmacological properties, such as anti-inflammatory, anti-oxidant, and osteogenic effects, have attracted considerable attention in biomedical research. Icariin, known for its ability to stimulate bone formation, has been found to encourage the transformation of mesenchymal stromal cells into osteoblasts and improve the subsequent process of mineralization. Several studies have demonstrated the osteogenic effects of icariin, which can be attributed to its hormone-like function. It has been found to induce the expression of BMP-2 and BMP-4 mRNAs in osteoblasts and significantly upregulate Osx at low doses. Additionally, icariin promotes bone formation by stimulating the expression of pre-osteoblastic genes like Osx, RUNX2, and collagen type I. However, icariin needs to be effectively delivered to bone to perform such promising functions. Encapsulating icariin within nanoplatforms holds significant promise for promoting osteogenesis and bone regeneration through a range of intricate biological effects. When encapsulated in nanofibers or nanoparticles, icariin exerts its effects directly at the cellular level. Recalling that inflammation is a critical factor influencing bone regeneration, icariin's anti-inflammatory effects can be harnessed and amplified when encapsulated in nanoplatforms. Also, while cell adhesion and cell migration are pivotal stages of tissue regeneration, icariin-loaded nanoplatforms contribute to these processes by providing a supportive matrix for cellular attachment and movement. This review comprehensively discusses icariin-loaded nanoplatforms used for bone regeneration and osteogenesis, further presenting where the field needs to go before icariin can be used clinically.","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"27 1","pages":""},"PeriodicalIF":5.6,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140635813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recent advances in nanomaterial-based biosensor for periodontitis detection","authors":"Mohammad Hosseini Hooshiar, Masoud Amiri Moghaddam, Mohammad Kiarashi, Athraa Y. Al-Hijazi, Abbas Fadel Hussein, Hareth A.Alrikabi, Sara Salari, Samar Esmaelian, Hassan Mesgari, Saman Yasamineh","doi":"10.1186/s13036-024-00423-6","DOIUrl":"https://doi.org/10.1186/s13036-024-00423-6","url":null,"abstract":"Periodontitis, a chronic inflammatory condition caused by bacteria, often causes gradual destruction of the components that support teeth, such as the alveolar bone, cementum, periodontal ligament, and gingiva. This ultimately results in teeth becoming loose and eventually falling out. Timely identification has a crucial role in preventing and controlling its progression. Clinical measures are used to diagnose periodontitis. However, now, there is a hunt for alternative diagnostic and monitoring methods due to the progress of technology. Various biomarkers have been assessed using multiple bodily fluids as sample sources. Furthermore, conventional periodontal categorization factors do not provide significant insights into the present disease activity, severity and amount of tissue damage, future development, and responsiveness to treatment. In recent times, there has been a growing utilization of nanoparticle (NP)-based detection strategies to create quick and efficient detection assays. Every single one of these platforms leverages the distinct characteristics of NPs to identify periodontitis. Plasmonic NPs include metal NPs, quantum dots (QDs), carbon base NPs, and nanozymes, exceptionally potent light absorbers and scatterers. These find application in labeling, surface-enhanced spectroscopy, and color-changing sensors. Fluorescent NPs function as photostable and sensitive instruments capable of labeling various biological targets. This article presents a comprehensive summary of the latest developments in the effective utilization of various NPs to detect periodontitis. ","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"83 1","pages":""},"PeriodicalIF":5.6,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140625695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chitosan modified with PAP as a promising delivery system for melatonin in the treatment of osteoporosis: targeting the divalent metal transporter 1","authors":"Weilin Zhang, Hongrui Rong, Jinguo Liang, Chao Mao, Zhencong Li, Zhiwen Dai, Dingbin Li, Weixiong Guo, Siyuan Chen, Zhongwei Wang, Jinsong Wei","doi":"10.1186/s13036-024-00422-7","DOIUrl":"https://doi.org/10.1186/s13036-024-00422-7","url":null,"abstract":"The demands for novel and efficient therapies have gradually increased with the rising concerns of osteoporosis (OP). The most popular method in promoting bone regeneration during osteoporotic conditions consists of loading bioactive materials with different drugs to treat osteoporotic bones by either promoting the process of osteogenesis, or by inhibiting the activity of osteoclasts. By analyzing single cell sequencing results, we found that divalent metal transporter 1 (DMT1) played a role in OP. Based on our previous results, we found that melatonin (MT) suppressed expression of DMT1 induced by high glucose during OP, so we determined the efficacy of MT for the treatment of OP. However, the clinical effects of MT on OP were unsatisfactory. To enhance its biological efficacy, we combined MT with porous gelatin chitosan (chitosan) and the conductive material, PLA-b-AP-b-PLA (PAP), then determined how MT incorporation in chitosan@PAP nanoparticles affected the ability to promote MC3T3-E1 osteogenesis and mineralization, both in vitro and in vivo. The results confirmed the effect of MT on DMT1. We then prepared and characterized composites prepared as nanofibers, and determined the efficacy of MT combined with chitosan-PAP modified hydrogels as a slow-release system in a femur model of osteoporosis mice, with associated properties suitable for bone tissue engineering. The results indicated that MT-loaded chitosan@PAP nanospheres showed favorable osteogenic functions, both in vivo and in vitro, providing a practical solution for bone regeneration for OP patients.","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"25 1","pages":""},"PeriodicalIF":5.6,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140567948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fluorescent tools for the standardized work in Gram-negative bacteria","authors":"Mario Delgadillo-Guevara, Manuel Halte, Marc Erhardt, Philipp F. Popp","doi":"10.1186/s13036-024-00420-9","DOIUrl":"https://doi.org/10.1186/s13036-024-00420-9","url":null,"abstract":"Standardized and thoroughly characterized genetic tools are a prerequisite for studying cellular processes to ensure the reusability and consistency of experimental results. The discovery of fluorescent proteins (FPs) represents a milestone in the development of genetic reporters for monitoring transcription or protein localization in vivo. FPs have revolutionized our understanding of cellular dynamics by enabling the real-time visualization and tracking of biological processes. Despite these advancements, challenges remain in the appropriate use of FPs, specifically regarding their proper application, protein turnover dynamics, and the undesired disruption of cellular functions. Here, we systematically compared a comprehensive set of 15 FPs and assessed their performance in vivo by focusing on key parameters, such as signal over background ratios and protein stability rates, using the Gram-negative model organism Salmonella enterica as a representative host. We evaluated four protein degradation tags in both plasmid- and genome-based systems and our findings highlight the necessity of introducing degradation tags to analyze time-sensitive cellular processes. We demonstrate that the gain of dynamics mediated by the addition of degradation tags impacts the cell-to-cell heterogeneity of plasmid-based but not genome-based reporters. Finally, we probe the applicability of FPs for protein localization studies in living cells using standard and super-resolution fluorescence microscopy. In summary, our study underscores the importance of careful FP selection and paves the way for the development of improved genetic reporters to enhance the reproducibility and reliability of fluorescence-based research in Gram-negative bacteria and beyond.","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"26 1","pages":""},"PeriodicalIF":5.6,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140567989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of viscoelasticity in the appearance of low-Reynolds turbulence: considerations for modelling","authors":"Ivana Pajic-Lijakovic, Milan Milivojevic, Peter V. E. McClintock","doi":"10.1186/s13036-024-00415-6","DOIUrl":"https://doi.org/10.1186/s13036-024-00415-6","url":null,"abstract":"Inertial effects caused by perturbations of dynamical equilibrium during the flow of soft matter constitute a hallmark of turbulence. Such perturbations are attributable to an imbalance between energy storage and energy dissipation. During the flow of Newtonian fluids, kinetic energy can be both stored and dissipated, while the flow of viscoelastic soft matter systems, such as polymer fluids, induces the accumulation of both kinetic and elastic energies. The accumulation of elastic energy causes local stiffening of stretched polymer chains, which can destabilise the flow. Migrating multicellular systems are hugely complex and are capable of self-regulating their viscoelasticity and mechanical stress generation, as well as controlling their energy storage and energy dissipation. Since the flow perturbation of viscoelastic systems is caused by the inhomogeneous accumulation of elastic energy, rather than of kinetic energy, turbulence can occur at low Reynolds numbers. This theoretical review is focused on clarifying the role of viscoelasticity in the appearance of low-Reynolds turbulence. Three types of system are considered and compared: (1) high-Reynolds turbulent flow of Newtonian fluids, (2) low and moderate-Reynolds flow of polymer solutions, and (3) migration of epithelial collectives, discussed in terms of two model systems. The models considered involve the fusion of two epithelial aggregates, and the free expansion of epithelial monolayers on a substrate matrix.","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"39 1","pages":""},"PeriodicalIF":5.6,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140567733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Eggshell waste bioprocessing for sustainable acid phosphatase production and minimizing environmental hazards","authors":"Soad Abubakr Abdelgalil, Mohamed Mohamed Yousri Kaddah, Gaber Attia Abo-Zaid","doi":"10.1186/s13036-024-00421-8","DOIUrl":"https://doi.org/10.1186/s13036-024-00421-8","url":null,"abstract":"The Environmental Protection Agency has listed eggshell waste as the 15th most significant food industry pollution hazard. Using eggshell waste as a renewable energy source has been a hot topic recently. Therefore, finding a sustainable solution for the recycling and valorization of eggshell waste by investigating its potential to produce acid phosphatase (ACP) and organic acids by the newly-discovered B. sonorensis was the target of the current investigation. Drawing on both molecular and morphological characterizations, the most potent ACP-producing B. sonorensis strain ACP2, was identified as a local bacterial strain obtained from the effluent of the paper and pulp industries. The use of consecutive statistical experimental approaches of Plackett–Burman Design (PBD) and Orthogonal Central Composite Design (OCCD), followed by pH-uncontrolled cultivation conditions in a 7 L bench-top bioreactor, revealed an innovative medium formulation that substantially improved ACP production, reaching 216 U L−1 with an ACP yield coefficient Yp/x of 18.2 and a specific growth rate (µ) of 0.1 h−1. The metals Ag+, Sn+, and Cr+ were the most efficiently released from eggshells during the solubilization process by B. sonorensis. The uncontrolled pH culture condition is the most suitable and favoured setting for improving ACP and organic acids production. Quantitative and qualitative analyses of the produced organic acids were carried out using liquid chromatography-tandem mass spectrometry (LC–MS/MS). Lactic acid, citric acid, and hydroxybenzoic acid isomer were the most common organic acids produced throughout the cultivation process. The findings of TGA, DSC, SEM, EDS, FTIR, and XRD analysis emphasize the significant influence of organic acids and ACP activity on the solubilization of eggshell particles. This study emphasized robust microbial engineering approaches for the large-scale production of a newly discovered acid phosphatase, accompanied by organic acids production from B. sonorensis. The biovalorization of the eggshell waste and the production of cost-effective ACP and organic acids were integrated into the current study, and this was done through the implementation of a unique and innovative medium formulation design for eggshell waste management, as well as scaling up ACP production on a bench-top scale.","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"77 1","pages":""},"PeriodicalIF":5.6,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140567975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhanced therapeutic potential of antibody fragment via IEDDA-mediated site-specific albumin conjugation","authors":"Eun Byeol Go, Jae Hun Lee, Jeong Haeng Cho, Na Hyun Kwon, Jong-il Choi, Inchan Kwon","doi":"10.1186/s13036-024-00418-3","DOIUrl":"https://doi.org/10.1186/s13036-024-00418-3","url":null,"abstract":"The use of single-chain variable fragments (scFvs) for treating human diseases, such as cancer and immune system disorders, has attracted significant attention. However, a critical drawback of scFv is its extremely short serum half-life, which limits its therapeutic potential. Thus, there is a critical need to prolong the serum half-life of the scFv for clinical applications. One promising serum half-life extender for therapeutic proteins is human serum albumin (HSA), which is the most abundant protein in human serum, known to have an exceptionally long serum half-life. However, conjugating a macromolecular half-life extender to a small protein, such as scFv, often results in a significant loss of its critical properties. In this study, we conjugated the HSA to a permissive site of scFv to improve pharmacokinetic profiles. To ensure minimal damage to the antigen-binding capacity of scFv upon HSA conjugation, we employed a site-specific conjugation approach using a heterobifunctional crosslinker that facilitates thiol-maleimide reaction and inverse electron-demand Diels-Alder reaction (IEDDA). As a model protein, we selected 4D5scFv, derived from trastuzumab, a therapeutic antibody used in human epithermal growth factor 2 (HER2)-positive breast cancer treatment. We introduced a phenylalanine analog containing a very reactive tetrazine group (frTet) at conjugation site candidates predicted by computational methods. Using the linker TCO-PEG4-MAL, a single HSA molecule was site-specifically conjugated to the 4D5scFv (4D5scFv-HSA). The 4D5scFv-HSA conjugate exhibited HER2 binding affinity comparable to that of unmodified 4D5scFv. Furthermore, in pharmacokinetic profile in mice, the serum half-life of 4D5scFv-HSA was approximately 12 h, which is 85 times longer than that of 4D5scFv. The antigen binding results and pharmacokinetic profile of 4D5scFv-HSA demonstrate that the site-specifically albumin-conjugated scFv retained its binding affinity with a prolonged serum half-life. In conclusion, we developed an effective strategy to prepare site-specifically albumin-conjugated 4D5scFv, which can have versatile clinical applications with improved efficacy.","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"25 1","pages":""},"PeriodicalIF":5.6,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140567979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"3D-printed nanohydroxyapatite/methylacrylylated silk fibroin scaffold for repairing rat skull defects.","authors":"Wu Huiwen, Liang Shuai, Xie Jia, Deng Shihao, Wei Kun, Yang Runhuai, Qian Haisheng, Li Jun","doi":"10.1186/s13036-024-00416-5","DOIUrl":"10.1186/s13036-024-00416-5","url":null,"abstract":"<p><p>The repair of bone defects remains a major challenge in the clinic, and treatment requires bone grafts or bone replacement materials. Existing biomaterials have many limitations and cannot meet the various needs of clinical applications. To treat bone defects, we constructed a nanohydroxyapatite (nHA)/methylacrylylated silk fibroin (MASF) composite biological scaffold using photocurable 3D printing technology. In this study, scanning electron microscopy (SEM) was used to detect the changes in the morphological structure of the composite scaffold with different contents of nanohydroxyapatite, and FTIR was used to detect the functional groups and chemical bonds in the composite scaffold to determine the specific components of the scaffold. In in vitro experiments, bone marrow mesenchymal stem cells from SD rats were cocultured with scaffolds soaking solution, and the cytotoxicity, cell proliferation, Western blot analysis, Quantitative real-time PCR analysis, bone alkaline phosphatase activity and alizarin red staining of scaffolds were detected to determine the biocompatibility of scaffolds and the effect of promoting proliferation and osteogenesis of bone marrow mesenchymal stem cells in vitro. In the in vivo experiment, the skull defect was constructed by adult SD rats, and the scaffold was implanted into the skull defect site. After 4 weeks and 8 weeks of culture, the specific osteogenic effect of the scaffold in the skull defect site was detected by animal micro-CT, hematoxylin and eosin (HE) staining and Masson's staining. Through the analysis of the morphological structure of the scaffold, we found that the frame supported good retention of the lamellar structure of silk fibroin, when mixed with nHA, the surface of the stent was rougher, the cell contact area increased, and cell adhesion and lamellar microstructure for cell migration and proliferation of the microenvironment provided a better space. FTIR results showed that the scaffold completely retained the β -folded structure of silk fibroin, and the scaffold composite was present without obvious impurities. The staining results of live/dead cells showed that the constructed scaffolds had no significant cytotoxicity, and thw CCK-8 assay also showed that the constructed scaffolds had good biocompatibility. The results of osteogenic induction showed that the scaffold had good osteogenic induction ability. Moreover, the results also showed that the scaffold with a MASF: nHA ratio of 1: 0.5 (SFH) showed better osteogenic ability. The micro-CT and bone histometric results were consistent with the in vitro results after stent implantation, and there was more bone formation at the bone defect site in the SFH group.This research used photocurable 3D printing technology to successfully build an osteogenesis bracket. The results show that the constructed nHA/MASF biological composite material, has good biocompatibility and good osteogenesis function. At the same time, in the microenvironment","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"18 1","pages":"22"},"PeriodicalIF":5.6,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10956317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140184544","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":"Construction and applications of the EOMA spheroid model of Kaposiform hemangioendothelioma.","authors":"Yanan Li, Xinglong Zhu, Li Li, Chunjuan Bao, Qin Liu, Ning Zhang, Ziyan He, Yi Ji, Ji Bao","doi":"10.1186/s13036-024-00417-4","DOIUrl":"10.1186/s13036-024-00417-4","url":null,"abstract":"<p><strong>Background: </strong>Kaposiform hemangioendothelioma (KHE) is a rare intermediate vascular tumor with unclear pathogenesis. Recently, three dimensional (3D) cell spheroids and organoids have played an indispensable role in the study of many diseases, such as infantile hemangioma and non-involuting congenital hemangiomas. However, few research on KHE are based on the 3D model. This study aims to evaluate the 3D superiority, the similarity with KHE and the ability of drug evaluation of EOMA spheroids as an in vitro 3D KHE model.</p><p><strong>Results: </strong>After two days, relatively uniform morphology and high viability of EOMA spheroids were generated by the rotating cell culture system (RCCS). Through transcriptome analysis, compared with 2D EOMA cells, focal adhesion-related genes such as Itgb4, Flt1, VEGFC, TNXB, LAMA3, VWF, and VEGFD were upregulated in EOMA spheroids. Meanwhile, the EOMA spheroids injected into the subcutaneous showed more obvious KMP than 2D EOMA cells. Furthermore, EOMA spheroids possessed the similar characteristics to the KHE tissues and subcutaneous tumors, such as diagnostic markers (CD31 and LYVE-1), cell proliferation (Ki67), hypoxia (HIF-1α) and cell adhesion (E-cadherin and N-cadherin). Based on the EOMA spheroid model, we discovered that sirolimus, the first-line drug for treating KHE, could inhibit EOMA cell proliferation and downregulate the VEGFC expression. Through the extra addition of VEGFC, the effect of sirolimus on EOMA spheroid could be weakened.</p><p><strong>Conclusion: </strong>With a high degree of similarity of the KHE, 3D EOMA spheroids generated by the RCCS can be used as a in vitro model for basic researches of KHE, generating subcutaneous tumors and drug screening.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"18 1","pages":"21"},"PeriodicalIF":5.6,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941415/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140131533","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":"Structural and practical identifiability analysis in bioengineering: a beginner's guide.","authors":"Linda Wanika, Joseph R Egan, Nivedhitha Swaminathan, Carlos A Duran-Villalobos, Juergen Branke, Stephen Goldrick, Mike Chappell","doi":"10.1186/s13036-024-00410-x","DOIUrl":"10.1186/s13036-024-00410-x","url":null,"abstract":"<p><p>Advancements in digital technology have brought modelling to the forefront in many disciplines from healthcare to architecture. Mathematical models, often represented using parametrised sets of ordinary differential equations, can be used to characterise different processes. To infer possible estimates for the unknown parameters, these models are usually calibrated using associated experimental data. Structural and practical identifiability analyses are a key component that should be assessed prior to parameter estimation. This is because identifiability analyses can provide insights as to whether or not a parameter can take on single, multiple, or even infinitely or countably many values which will ultimately have an impact on the reliability of the parameter estimates. Also, identifiability analyses can help to determine whether the data collected are sufficient or of good enough quality to truly estimate the parameters or if more data or even reparameterization of the model is necessary to proceed with the parameter estimation process. Thus, such analyses also provide an important role in terms of model design (structural identifiability analysis) and the collection of experimental data (practical identifiability analysis). Despite the popularity of using data to estimate the values of unknown parameters, structural and practical identifiability analyses of these models are often overlooked. Possible reasons for non-consideration of application of such analyses may be lack of awareness, accessibility, and usability issues, especially for more complicated models and methods of analysis. The aim of this study is to introduce and perform both structural and practical identifiability analyses in an accessible and informative manner via application to well established and commonly accepted bioengineering models. This will help to improve awareness of the importance of this stage of the modelling process and provide bioengineering researchers with an understanding of how to utilise the insights gained from such analyses in future model development.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"18 1","pages":"20"},"PeriodicalIF":5.7,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11465550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140028058","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}