bioRxiv - Bioengineering最新文献

Single unit electrophysiology recordings and computational modeling can predict octopus arm movement 单体电生理学记录和计算建模可预测章鱼的手臂运动

bioRxiv - Bioengineering Pub Date : 2024-09-19 DOI: 10.1101/2024.09.13.612676

Nitish Satya Sai Gedela, Sachin Salim, Ryan D Radawiec, Julianna Marie Richie, Cynthia A Chestek, Anne Draelos, Galit Pelled

{"title":"Single unit electrophysiology recordings and computational modeling can predict octopus arm movement","authors":"Nitish Satya Sai Gedela, Sachin Salim, Ryan D Radawiec, Julianna Marie Richie, Cynthia A Chestek, Anne Draelos, Galit Pelled","doi":"10.1101/2024.09.13.612676","DOIUrl":"https://doi.org/10.1101/2024.09.13.612676","url":null,"abstract":"The octopus simplified nervous system holds the potential to reveal principles of motor circuits and improve brain-machine interface devices through computational modeling with machine learning and statistical analysis. Here, an array of carbon electrodes providing single-unit electrophysiology recordings were implanted into the octopus anterior nerve cord. The number of spikes and arm movements in response to stimulation at different locations along the arm were recorded. We observed that the number of spikes occurring within the first 100ms after stimulation were predictive of the resultant movement response. Computational models showed that temporal electrophysiological features could be used to predict whether an arm movement occurred with 88.64% confidence, and if it was a lateral arm movement or a grasping motion with 75.45% confidence. Both supervised and unsupervised methods were applied to gain streaming measurements of octopus arm movements and how their motor circuitry produces rich movement types in real time. Deep learning models and unsupervised dimension reduction identified a consistent set of features that could be used to distinguish different types of arm movements. These models generated predictions for how to evoke a particular, complex movement in an orchestrated sequence for an individual motor circuit.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"60 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PiggyBac mediated transgenesis and CRISPR/Cas9 knockout in the greater waxmoth, Galleria mellonella PiggyBac 介导的大蜡蛾转基因和 CRISPR/Cas9 基因敲除技术

bioRxiv - Bioengineering Pub Date : 2024-09-18 DOI: 10.1101/2024.09.17.613535

James C Pearce, Jennie Samantha Campbell, Joann L Prior, Richard W Titball, James G Wakefield

引用次数: 0

Investigating the right heart hemodynamics in the Tetralogy of Fallot: a computational study 调查法洛氏四联症的右心血流动力学：一项计算研究

bioRxiv - Bioengineering Pub Date : 2024-09-18 DOI: 10.1101/2024.09.13.612742

Francesca Renzi, Giovanni Puppini, Giovanni Battista Luciani, Christian Vergara

{"title":"Investigating the right heart hemodynamics in the Tetralogy of Fallot: a computational study","authors":"Francesca Renzi, Giovanni Puppini, Giovanni Battista Luciani, Christian Vergara","doi":"10.1101/2024.09.13.612742","DOIUrl":"https://doi.org/10.1101/2024.09.13.612742","url":null,"abstract":"Characterizing flow within the right heart (RH) is particularly challenging due to its complex geometries.\u0000However, gaining insight into RH fluid dynamics is of extreme diagnostic importance given the high prevalence of acquired and congenital heart diseases with impaired RH functionality. In this study, we present a comprehensive, patient-specific, image-based computational analysis of the hemodynamics of the RH in healthy and repaired-ToF (ToF) cases. From multi-series cine-MTRI, we reconstruct the geometry and motion of the patient's right atrium, ventricle, and pulmonary and tricuspid valves. For this purpose, we develop a novel and flexible reconstruction procedure that enables us, for the first time, to integrate fully patient-specific tricuspid valve dynamics into a computational model, enhancing the accuracy of our RH blood flow simulations. This work provides novel insight into the altered hemodynamics of repaired-ToF RH with severe pulmonary regurgitation and into the hemodynamics changes induced by the pulmonary valve replacement intervention. Modelling the whole RH enables us to understand the contribution of the superior and inferior vena cava inflows to the ventricular filling, as well as the impact of the impaired right atrial function on the ventricular diastole. We analyze the turbulent and transitional behaviour by including the Large-Eddies Simulation sigma model in our computational framework. This highlights how the contribution of the smallest scales in the dissipation of the turbulent energy changes among health and disease.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"54 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A microinjection protocol for the greater waxworm moth, Galleria mellonella 大蜡蛾的显微注射方案

bioRxiv - Bioengineering Pub Date : 2024-09-18 DOI: 10.1101/2024.09.17.613528

James C Pearce, Amy Housden, Nicola J Senior, Olivia L Champion, Joann L Prior, Richard W Titball, James G Wakefield

引用次数: 0

Engineered Receptors for Soluble Cell-to-Cell Communication 用于细胞间可溶性通信的工程受体

bioRxiv - Bioengineering Pub Date : 2024-09-18 DOI: 10.1101/2024.09.17.613377

Dan Ilya Piraner, Mohamad H Abedi, Maria J Duran Gonzalez, Adam Chazin-Gray, Iowis Zhu, Pavithran T Ravindran, Thomas Schlichthaerle, Buwei Huang, David Lee, David Baker, Kole T Roybal

{"title":"Engineered Receptors for Soluble Cell-to-Cell Communication","authors":"Dan Ilya Piraner, Mohamad H Abedi, Maria J Duran Gonzalez, Adam Chazin-Gray, Iowis Zhu, Pavithran T Ravindran, Thomas Schlichthaerle, Buwei Huang, David Lee, David Baker, Kole T Roybal","doi":"10.1101/2024.09.17.613377","DOIUrl":"https://doi.org/10.1101/2024.09.17.613377","url":null,"abstract":"Despite recent advances in mammalian synthetic biology, there remains a lack of modular synthetic receptors that can robustly respond to soluble ligands and in turn activate cellular functions. Such receptors would have extensive clinical potential to regulate the activity of engineered therapeutic cells, but to date only receptors against cell surface targets have approached clinical translation. To address this gap, we developed a receptor based on SynNotch, called synthetic intramembrane proteolysis receptors (SNIPRs), that have the added ability to be activated by soluble ligands, both natural and synthetic, with remarkably low baseline activity and high fold activation. SNIPRs are able to access an endocytic, pH-dependent cleavage mechanism to achieve soluble ligand sensing, in addition to employing a canonical-like pathway for detecting surface-bound ligands. We demonstrate the therapeutic capabilities of the receptor platform by localizing the activity of CAR T-cells to solid tumors where soluble disease-associated factors are expressed, bypassing the major hurdle of on-target off-tumor toxicity in bystander organs. We further applied the SNIPR platform to engineer fully synthetic signaling networks between cells orthogonal to natural signaling pathways, expanding the scope of synthetic biology. Our design framework enables cellular communication and environmental interactions, extending the capabilities of synthetic cellular networking in clinical and research contexts.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Synthesis and mechanical characterization of polyacrylamide (PAAm) hydrogels with different stiffnesses for large-batch cell culture applications 用于大批量细胞培养的具有不同硬度的聚丙烯酰胺（PAAm）水凝胶的合成与力学性能分析

bioRxiv - Bioengineering Pub Date : 2024-09-18 DOI: 10.1101/2024.09.17.613503

Charlotte Cresens, Samet Aytekin, Behrad Shaghaghi, Lotte Gerrits, Ana Montero-Calle, Rodrigo Barderas, Paul Kouwer, Susana Rocha

引用次数: 0

Capturing sclera anisotropy using direct collagen fiber models. Linking microstructure to macroscopic mechanical properties. 利用直接胶原纤维模型捕捉巩膜各向异性。将微观结构与宏观机械性能联系起来。

bioRxiv - Bioengineering Pub Date : 2024-09-17 DOI: 10.1101/2024.09.12.612702

Fengting Ji, Mohammad R. Islam, Frederick Sebastian, Hannah Schilpp, Bingrui Wang, Yi Hua, Rouzbeh Amini, Ian A Sigal

{"title":"Capturing sclera anisotropy using direct collagen fiber models. Linking microstructure to macroscopic mechanical properties.","authors":"Fengting Ji, Mohammad R. Islam, Frederick Sebastian, Hannah Schilpp, Bingrui Wang, Yi Hua, Rouzbeh Amini, Ian A Sigal","doi":"10.1101/2024.09.12.612702","DOIUrl":"https://doi.org/10.1101/2024.09.12.612702","url":null,"abstract":"Because of the crucial role of collagen fibers on soft tissue mechanics, there is great interest in techniques to incorporate them in computational models. Recently we introduced a direct fiber modeling approach for sclera based on representing the long interwoven fibers. Our method differs from the conventional continuum approach to modeling sclera that homogenizes the fibers and describes them as statistical distributions for each element. At large scale our method captured gross collagen fiber bundle architecture from histology and experimental intraocular pressure-induced deformations. At small scale, a direct fiber model of a sclera sample reproduced equi-biaxial experimental behavior from the literature. In this study our goal was a much more challenging task for the direct fiber modeling: to capture specimen-specific 3D fiber architecture and anisotropic mechanics of four sclera samples tested under equibiaxial and four non-equibiaxial loadings. Samples of sclera from three eyes were isolated and tested in five biaxial loadings following an approach previously reported. Using microstructural architecture from polarized light microscopy we then created specimen-specific direct fiber models. Model fiber orientations agreed well with the histological information (adjusted R2's>0.89). Through an inverse-fitting process we determined model characteristics, including specimen-specific fiber mechanical properties to match equibiaxial loading. Interestingly, the equibiaxial properties also reproduced all the non-equibiaxial behaviors. These results indicate that the direct fiber modeling method naturally accounted for tissue anisotropy within its fiber structure. Direct fiber modeling is therefore a promising approach to understand how macroscopic behavior arises from microstructure.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Precision Repair of Zone-Specific Meniscal Injuries Using a Tunable Extracellular Matrix-Based Hydrogel System 利用可调细胞外基质水凝胶系统精确修复特定区域的半月板损伤

bioRxiv - Bioengineering Pub Date : 2024-09-17 DOI: 10.1101/2024.09.12.612723

Se-Hwan Lee, Zizhao Li, Ellen Y Zhang, Dong Hwa Kim, Ziqi Huang, Sang Jin Lee, Hyun-Wook Kang, Jason A Burdick, Robert L Mauck, Su Chin Heo

{"title":"Precision Repair of Zone-Specific Meniscal Injuries Using a Tunable Extracellular Matrix-Based Hydrogel System","authors":"Se-Hwan Lee, Zizhao Li, Ellen Y Zhang, Dong Hwa Kim, Ziqi Huang, Sang Jin Lee, Hyun-Wook Kang, Jason A Burdick, Robert L Mauck, Su Chin Heo","doi":"10.1101/2024.09.12.612723","DOIUrl":"https://doi.org/10.1101/2024.09.12.612723","url":null,"abstract":"Meniscus injuries present significant therapeutic challenges due to their limited self-healing capacity and diverse biological and mechanical properties across meniscal tissue. Conventional repair strategies neglect to replicate the complex zonal characteristics within the meniscus, resulting in suboptimal outcomes. In this study, we introduce an innovative, age- and stiffness-tunable meniscus decellularized extracellular matrix (DEM)-based hydrogel system designed for precision repair of heterogeneous, zonal-dependent meniscus injuries. By synthesizing age-dependent DEM hydrogels, we identified distinct cellular responses: fetal bovine meniscus-derived DEM promoted chondrogenic differentiation, while adult meniscus-derived DEM supported fibrochondrogenic phenotypes. The incorporation of methacrylate hyaluronic acid (MeHA) further refined the mechanical properties and injectability of the DEM-based hydrogels. The combination of age-dependent DEM with MeHA allowed for precise stiffness tuning, influencing cell differentiation and closely mimicking native tissue environments. In vivo tests confirmed the biocompatibility of hydrogels and their integration with native meniscus tissues. Furthermore, advanced 3D bioprinting techniques enabled the fabrication of hybrid hydrogels with biomaterial and mechanical gradients, effectively emulating the zonal properties of meniscus tissue and enhancing cell integration. This study represents a significant advancement in meniscus tissue engineering, providing a promising platform for customized regenerative therapies across a range of heterogeneous fibrous connective tissues.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"75 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Interpenetrating networks of fibrillar and amorphous collagen promote cell spreading and hydrogel stability 纤维状胶原蛋白和无定形胶原蛋白的相互渗透网络促进了细胞扩散和水凝胶的稳定性

bioRxiv - Bioengineering Pub Date : 2024-09-16 DOI: 10.1101/2024.09.11.612534

Lucia G. Brunel, Chris M. Long, Fotis Christakopoulos, Betty Cai, Patrik K. Johansson, Diya Singhal, Annika Enejder, David Myung, Sarah C Heilshorn

{"title":"Interpenetrating networks of fibrillar and amorphous collagen promote cell spreading and hydrogel stability","authors":"Lucia G. Brunel, Chris M. Long, Fotis Christakopoulos, Betty Cai, Patrik K. Johansson, Diya Singhal, Annika Enejder, David Myung, Sarah C Heilshorn","doi":"10.1101/2024.09.11.612534","DOIUrl":"https://doi.org/10.1101/2024.09.11.612534","url":null,"abstract":"Hydrogels composed of collagen, the most abundant protein in the human body, are widely used as scaffolds for tissue engineering due to their ability to support cellular activity. However, collagen hydrogels with encapsulated cells often experience bulk contraction due to cell-generated forces, and conventional strategies to mitigate this undesired deformation often compromise either the fibrillar microstructure or cytocompatibility of the collagen. To support the spreading of encapsulated cells while preserving the structural integrity of the gels, we present an interpenetrating network (IPN) of two distinct collagen networks with different crosslinking mechanisms and microstructures. First, a physically self-assembled collagen network preserves the fibrillar microstructure and enables the spreading of encapsulated human corneal mesenchymal stromal cells. Second, an amorphous collagen network covalently crosslinked with bioorthogonal chemistry fills the voids between fibrils and stabilizes the gel against cell-induced contraction. This collagen IPN balances the biofunctionality of natural collagen with the stability of covalently crosslinked, engineered polymers. Taken together, these data represent a new avenue for maintaining both the fiber-induced spreading of cells and the structural integrity of collagen hydrogels by leveraging an IPN of fibrillar and amorphous collagen networks.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Contributions of mechanical loading and hormonal changes to eccentric hypertrophy during volume overload: a Bayesian analysis using logic-based network models. 机械负荷和荷尔蒙变化对体积超负荷时偏心肥大的贡献：利用基于逻辑的网络模型进行的贝叶斯分析。

bioRxiv - Bioengineering Pub Date : 2024-09-16 DOI: 10.1101/2024.09.12.612768

Johane H. Bracamonte, Lionel Watkins, Betty Pat, Louis J. Dell'Italia, Jeffrey J. Saucerman, Jeffrey W. Holmes

{"title":"Contributions of mechanical loading and hormonal changes to eccentric hypertrophy during volume overload: a Bayesian analysis using logic-based network models.","authors":"Johane H. Bracamonte, Lionel Watkins, Betty Pat, Louis J. Dell'Italia, Jeffrey J. Saucerman, Jeffrey W. Holmes","doi":"10.1101/2024.09.12.612768","DOIUrl":"https://doi.org/10.1101/2024.09.12.612768","url":null,"abstract":"Primary mitral regurgitation (MR) is a pathology that alters mechanical loading on the left ventricle and induces a distinctive ventricular remodeling response known as eccentric hypertrophy. Drug therapies may alleviate symptoms, but only mitral valve repair can provide significant recovery of cardiac function and dimensions. However, 20% of patients still develop systolic dysfunction post-operatively despite being treated according to the current guidelines. Thus, better understanding of the hypertrophic process in the setting of ventricular volume overload (VO) is needed to improve and better personalize the management of MR. To address this knowledge gap, we employ a Bayesian approach to combine data from 70 studies on experimental volume overload in dogs and rats and use it to calibrate a logic-based network model of hypertrophic signaling in myocytes. The calibrated model suggests that growth in experimental VO is mostly driven by the neurohormonal response, with an initial increase in myocardial tissue stretch being compensated by subsequent remodeling fairly early in the time course of VO. This observation contrasts with a common perception that volume-overload hypertrophy is driven primarily by increased myocyte strain. The model suggests that Endothelin1 receptor activity plays a central role in driving hypertrophic responses and the activation of the fetal gene program. The model reproduces a number of responses to drug therapy not used in its calibration, and predicts that a combination of endothelin receptor antagonist and angiotensin receptor blockers would have the greatest potential to dampen cardiomyocyte hypertrophy and dysfunction in VO.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"202 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0