bioRxiv - Bioengineering最新文献

{"title":"Direct Nuclear Delivery of Proteins on Living Plant via Partial Enzymatic Cell Wall Digestion","authors":"Qufei Gu, Nathan Ming, Yalikunjiang Aizezi, Xiaoyang Wei, Yizhong Yuan, Brian Esquivel, Zhi-Yong Wang","doi":"10.1101/2024.09.03.611064","DOIUrl":"https://doi.org/10.1101/2024.09.03.611064","url":null,"abstract":"While many variations of protein delivery methods have been described, it can still be difficult or inefficient to introduce exogenous proteins into plants. A major barrier to progress is the cell wall which is primarily composed of polysaccharides and thus only permeable to small molecules. Here, we report a partial enzymatic cell wall digestion-mediated uptake method that efficiently delivers protein into the nucleus of plant cells. Such a method allowed efficient nuclear delivery of GFP proteins into Arabidopsis root cells throughout all cell layers. This study establishes that a partial enzymatic cell wall degradation could enable a myriad of plant biotechnology applications that rely on functional protein delivery into walled plant cells.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"72 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216642","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}

{"title":"Enhanced Ultrasound Image Formation with Computationally Efficient Cross-Angular Delay Multiply and Sum Beamforming","authors":"Cameron A. B. Smith, Matthieu Toulemonde, Marcelo Lerendegui, Kai Riemer, Dina Malounda, Peter D. Weinberg, Mikhail G. Shapiro, Meng-Xing Tang","doi":"10.1101/2024.09.03.611015","DOIUrl":"https://doi.org/10.1101/2024.09.03.611015","url":null,"abstract":"Ultrasound imaging is a valuable clinical tool. It is commonly achieved using the delay and sum beamformer algorithm, which takes the signals received by an array of sensors and generates an image estimating the spatial distribution of the signal sources. This algorithm, while computationally efficient, has limited resolution and suffers from high side lobes. Nonlinear processing has proven to be an effective way to enhance the image quality produced by beamforming in a computationally efficient manner. In this work, we describe a new beamforming algorithm called Cross-Angular Delay Multiply and Sum, which takes advantage of nonlinear compounding to enhance contrast and resolution. This is then implemented with a mathematical reformulation to produce images with tighter point spread functions and enhanced contrast at a low computational cost. We tested this new algorithm over a range of in vitro and in vivo scenarios for both conventional B-Mode and amplitude modulation imaging, and for two types of ultrasound contrast agents, demonstrating its potential for clinical settings.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216643","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}

{"title":"Self-driving development of perfusion processes for monoclonal antibody production","authors":"Claudio Mueller, Thomas Vuillemin, Chethana Janardhana Gadiyar, Jonathan Souquet, Jean Marc Bielser, Alessandro Fagnani, Michae Sokolov, Moritz von Stosch, Fabian Feidl, Alessandro Butte, Mariano Nicolas Cruz Bournazou","doi":"10.1101/2024.09.03.610922","DOIUrl":"https://doi.org/10.1101/2024.09.03.610922","url":null,"abstract":"It is essential to increase the number of autonomous agents bioprocess development for biopharma innovation to shorten time and resource utilization in the path from product to process. While robotics and machine learning have significantly accelerated drug discovery and initial screening, the later stages of development have seen improvement only in the experimental automation but lack advanced computational tools for experimental planning and execution. For instance, during development of new monoclonal antibodies, the search for optimal upstream conditions (feeding strategy, pH, temperature, media composition, etc.) is often performed in highly advanced high-throughput (HT) mini-bioreactor systems. However, the integration of machine learning tools for experiment design and operation in these systems remains underdeveloped. In this study, we introduce an integrated framework composed by a Bayesian experimental design algorithm, a cognitive digital twin of the cultivation system, and an advanced 24 parallel mini-bioreactor perfusion experimental setup. The result is an autonomous experimental machine capable of 1. embedding existing process knowledge, 2. learning during experimentation, 3. Using information from similar processes, 4. Notifying events in the near future, and 5. Autonomously operating the parallel cultivation setup to reach challenging objectives. As a proof of concept, we present experimental results of 27 days long cultivations operated by an autonomous software agent reaching challenging goals as are increasing the VCV and maximizing the viability of the cultivation up to its end.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216648","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}

{"title":"NIRSTORM: a Brainstorm extension dedicated to functional Near Infrared Spectroscopy (fNIRS) data analysis, advanced 3D reconstructions, and optimal probe design.","authors":"Édouard Delaire, Thomas Vincent, Zhengchen Cai, Alexis Machado, Laurent hugueville, Denis Schwartz, Francois Tadel, Raymundo Cassani, Louis Bherer, jean-marc JM Lina, Mélanie Pélégrini-Issac, Christophe Grova","doi":"10.1101/2024.09.05.611463","DOIUrl":"https://doi.org/10.1101/2024.09.05.611463","url":null,"abstract":"Significance: We propose NIRSTORM, a software package built within Brainstorm environment, enabling full data analysis of functional Near InfraRed Spectroscopy (fNIRS) data from experiment planning to 3D reconstruction of hemodynamic fluctuations on the cortical surface using optical tomographic approaches. NIRSTORM enables the integration of fNIRS analysis within a multimodal setup making it easy to study fNIRS in combination with other multimodal data such as electroencephalography (EEG) or magnetic resonance imaging (MRI). Aim: NIRSTORM aims to provide an easy-to-use and fully modular toolbox for fNIRS analysis from experimental planning to optical tomography 3D reconstruction extending Brainstorm capacity for multimodal analysis.\u0000Approach: NIRSTORM was developed in MATLAB ® and integrated as a plugin of the software Brainstorm. Brainstorm is a GUI-oriented, widely used software originally dedicated to statistical analysis and source imaging of EEG and magnetoencephalography (MEG) data. Results: In addition to conventional fNIRS preprocessing steps, including standard channel space and statistical analyses, NIRSTORM provides advanced methods dedicated to optimal probe placement, allowing personalized fNIRS study designs and accurate near-infrared optical tomography within the Maximum Entropy on the Mean (MEM) framework. Conclusion: NIRSTORM is an open-access, user-friendly plugin extending the capacity of Brainstorm, for fNIRS analysis, therefore narrowing the gap between EEG/MEG and hemodynamics.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216660","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}

{"title":"Olfactory Mucosa-Derived Mesenchymal Stem Cells Differentiate Towards a Schwann Cell-Like Phenotype Towards Sourcing for Peripheral Nerve Regeneration","authors":"Katelyn Neuman, Abigail N Koppes, Ryan A Koppes","doi":"10.1101/2024.09.03.611001","DOIUrl":"https://doi.org/10.1101/2024.09.03.611001","url":null,"abstract":"Mesenchymal stem cells (MSCs) are a promising source of stem cells for treating peripheral nerve injuries. Here, we present the first investigation of differentiation of olfactory mucosa-derived MSC (OM-MSC) towards a Schwann Cell (SC)-like phenotype. OM-MSCs are an advantageous potential source of SCs for peripheral nerve repair, as isolation can be accomplished with a minimally invasive procedure compared to autologous nerve harvest and isolation. Here, Schwann Cell Conditioned Media (SCCM) or a defined growth factor supplemented media (GF) was applied to OM-MSC for twenty-one days. The differentiation process and resulting populations were characterized by immunocytochemistry and RT-qPCR. Functionality of differentiated populations was assessed in an in vitro co-culture model to evaluate interaction with sensory neurons (dorsal root ganglia) juxtaposed to native SCs. Compared to undifferentiated MSCs, differentiation protocols resulted in significant changes in morphology, gene expression, and functionality using SCCM and GF media, representing key characteristics of SCs. Specifically, differentiated populations exhibit elongated, spindle-like morphologies, a high degree of eccentricity, increased S-100, CD44, and NGF expression, and colocalization of myelin basic proteins with neurites in the co-culture model. In conclusion, this work highlights the potential of OM-MSCs to be expanded and differentiated to SCs to improve synthetic scaffolds or for use in decellularized allografts for nerve repair.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"39 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216645","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}

{"title":"Evaluating Physiological Indicators in Detecting Deception using the Comparison Question Test (CQT)","authors":"A M Shahruj Rashid, Bryan Carmichael, Charlize Su, Keming Shi, Keefe Lim, Poorvika Senthil Kumar, Ngok Jeun Wan, Eshaan Govil, Dennis Yap","doi":"10.1101/2024.09.01.609623","DOIUrl":"https://doi.org/10.1101/2024.09.01.609623","url":null,"abstract":"Despite significant advancements in deception detection, traditional methods often fall short in real-world applications. This study addresses these limitations by evaluating the effectiveness of various physiological measures Pupil Response, Electrodermal Activity (EDA), Heart Rate (HR), and facial temperature changes in predicting deception using the Comparison Question Test (CQT). It also fills a critical research gap by validating these methods within an Asian context. Employing a between-subjects design, data was collected from a diverse sample of 118 participants from Singapore, including Chinese, Indian, and Malay individuals. The research aims to identify which physiological indicators, in combination, offer the most robust predictions of deceptive behavior. Key innovations include the adaptation of the CQT with a modified directed lie paradigm and an expanded sample size to assess the relative importance of each physiological measure. The study's findings reveal that Pupil Response is the most significant predictor of deception, with EDA enhancing the model's explanatory power. HR, while relevant, adds limited value when combined with Pupil Response and EDA, and facial temperature changes were statistically non-significant. The study highlights the need for further research into the interactions among physiological measures and their application in varied contexts. This research contributes valuable insights into improving deception detection methodologies and sets the stage for future investigations that could incorporate additional physiological indicators and explore real-world applications.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"283 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216647","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}

{"title":"Synchrotron Tomography-Based Finite Element Analysis of Vertebral Endplate Loading Reveals Functional Roles for Architectural Features","authors":"Jishizhan Chen, Alissa L Parmenter, Aikta Sharma, Elis Newham, Eral Bele, Sebastian Marussi, Andrew A Pitsillides, Nick J Terrill, Himadri S Gupta, Peter D Lee","doi":"10.1101/2024.09.03.610954","DOIUrl":"https://doi.org/10.1101/2024.09.03.610954","url":null,"abstract":"Lower back pain is linked to vertebral biomechanics, with vertebral endplates (VEPs) playing a key role in vertebral load transfer and distribution. Synchrotron computed tomography (sCT) allows for detailed visualisation of the microstructure of intact VEPs under near-physiological loads and, when coupled with digital volume correlation (DVC), can be used to quantify three-dimensional (3D) strain fields with nanoscale resolution. Herein, we spatially couple DVC data and an image-based finite element model (FEM) to determine the material properties of murine VEPs. This model was then extended to investigate VEP biomechanics under different motions and disease conditions to reveal that VEP protrusions are important for load absorption and redistribution under different motions and predicted that abnormal intervertebral disc (IVD) stress may underpin osteoporosis- and pycnodysostosis-related IVD degeneration. Our study validates the efficacy of using DVC to increase the accuracy of FEM predictions and highlights that these methodologies may be scalable to large animals and humans.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142227037","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}

{"title":"T cell correction pipeline for Inborn Errors of Immunity","authors":"Katariina Mamia, Solrun Kolbeinsdottir, Zhuokun Li, Kornel Labun, Anna Komisarczuk, Salla Keskitalo, Ganna Reint, Frida Hosoien Haugen, Britt Olaug Lindestad, Thea Johanne Gjerdingen, Antti Tuhkala, Carolina Wieczorek Ervik, Pavel Kopcil, Nail Fatkhutdinov, Monika Szymanska, Eero Tolo, Virpi Glumoff, Janna Saarela, Trond Melbye Michelsen, Camilla Schalin-Jantti, Johanna Olweus, Eira Leinonen, Markku Varjosalo, Eivind Valen, Timo Hautala, Martin Enge, Timi Martelius, Shiva Dahal-Koirala, Emma Haapaniemi","doi":"10.1101/2024.09.03.610811","DOIUrl":"https://doi.org/10.1101/2024.09.03.610811","url":null,"abstract":"CRISPR/Cas9 gene editing technology is a promising tool for correcting pathogenic variants for autologous cell therapies for Inborn Errors of Immunity (IEI). The present IEI correction strategies mainly focus on the knock-in of therapeutic cDNAs, or knockout of the disease-causing gene when feasible. These strategies address many single-gene defects but may disrupt gene expression and require significant optimization for each newly discovered IEI-causing gene, highlighting the need for complementary platforms that can precisely correct diverse pathogenic variants. Here, we present a safe and efficient T cell single nucleotide variant (SNV) correction pipeline based on homology-directed repair (HDR), suitable for diverse monogenic mutations. By using founder mutations of Deficiency of ADA2 (DADA2), Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) and Cartilage Hair Hypoplasia (CHH) as IEI models, we show that our pipeline can achieve up to 80% bi-allelic editing, with resultant functional correction of the disease phenotype in patient T cells. We do not find detectable pre-malignant off-target effects or karyotypic, transcriptomic or proteomic aberrations upon profiling patient T cells with GUIDE-seq, single cell RNA sequencing, PacBio based long-read whole genome sequencing, and high-throughput proteomics. This study demonstrates that HDR-based SNV editing is a safe and effective option for IEI T cell correction and that it could be developed to an autologous T cell therapy, as the presented protocol is scalable for a GMP-compatible workflow. This study is a step towards the development of gene correction platform that targets a broad number of monogenic mutations.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"106 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216665","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}

{"title":"In vivo Imaging and Pharmacokinetics of Percutaneously Injected Ultrasound and X-ray Imageable Thermosensitive Hydrogel loaded with Doxorubicin versus Free Drug in Swine","authors":"Jose F Delgado, Ayele H Negussie, Nicole A Varble, Andrew S Mikhail, Antonio Arrichiello, Tabea Borde, Laetitia Saccenti, Ivane Bakhutashvili, Robert Morhard, Joshua W Owen, John W Karanian, William F Pritchard, Bradford J Wood","doi":"10.1101/2024.09.01.610710","DOIUrl":"https://doi.org/10.1101/2024.09.01.610710","url":null,"abstract":"Intratumoral injections often lack visibility, leading to unpredictable outcomes such as incomplete tumor coverage, off-target drug delivery and systemic toxicities. This study investigated an ultrasound (US) and x-ray imageable thermosensitive hydrogel based on poloxamer 407 (POL) percutaneously delivered in a healthy swine model. The primary objective was to assess the 2D and 3D distribution of the hydrogel within tissue across three different needle devices and injection sites: liver, kidney, and intercostal muscle region. Secondly, pharmacokinetics of POL loaded with doxorubicin (POLDOX) were evaluated and compared to free doxorubicin injection (DOXSoln) with a Single End Hole Needle. Utilizing 2D and 3D morphometrics from US and x-ray imaging techniques such as Computed Tomography (CT) and Cone Beam CT (CBCT), we monitored the localization and leakage of POLDOX over time. Relative iodine concentrations measured with CBCT following incorporation of an iodinated contrast agent in POL indicated potential drug diffusion and advection transport. Furthermore, US imaging revealed temporal changes, suggesting variations in acoustic intensity, heterogeneity, and echotextures. Notably, 3D reconstruction of the distribution of POL and POLDOX from 2D ultrasound frames was achieved and morphometric data obtained. Pharmacokinetic analysis revealed lower systemic exposure of the drug in various organs with POLDOX formulation compared to DOXSoln formulation. This was demonstrated by a lower area under the curve (852.1 ± 409.1 ng/mL·h vs 2283.4 ± 377.2 ng/mL·h) in the plasma profile, suggesting a potential reduction in systemic toxicity. Overall, the use of POL formulation offers a promising strategy for precise and localized drug delivery, that may minimize adverse effects. Dual modality POL imaging enabled analysis of patterns of gel distribution and morphology, alongside of pharmacokinetics of local delivery. Incorporating hydrogels into drug delivery systems holds significant promise for improving the predictability of the delivered drug and enhancing spatial conformability. These advancements can potentially enhance the safety and precision of anticancer therapy.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216658","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}

{"title":"Tissue-specific modulation of CRISPR activity by miRNA-sensing guide RNAs","authors":"Antonio Garcia Guerra, Chaitra Sathyaprakash, Olivier Gerrit de Jong, Wooi Lim, Pieter Vader, Samir EL Andaloussi, Jonathan Bath, Jesus Reine, Yoshitsugu Aoki, Andrew Turberfield, Matthew Wood, Carlo Rinaldi","doi":"10.1101/2024.08.09.605335","DOIUrl":"https://doi.org/10.1101/2024.08.09.605335","url":null,"abstract":"Nucleic acid nanostructures offer unique opportunities for biomedical applications due to their sequence-programmable structures and functions, which enable the design of complex responses to molecular cues. Control of the biological activity of therapeutic cargoes based on endogenous molecular signatures holds the potential to overcome major hurdles in translational research: cell specificity and off-target effects. Endogenous microRNAs can be used to profile cell type and cell state and are ideal inputs for RNA nanodevices. Here we present CRISPR MiRAGE (miRNA-activated genome editing), a tool comprising a dynamic single-guide RNA that senses miRNA complexed with Argonaute proteins and controls downstream CRISPR activity based on the detected miRNA signature. We study the operation of the miRNA-sensing single-guide RNA and attain muscle-specific activation of gene editing through CRISPR MiRAGE in models of Duchenne muscular dystrophy. By enabling RNA-controlled gene editing activity, this technology creates opportunities to advance tissue-specific CRISPR treatments for human diseases.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"82 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941666","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}