ACS Synthetic Biology最新文献_第7页

CRISPR-GEM: A Novel Machine Learning Model for CRISPR Genetic Target Discovery and Evaluation CRISPR-GEM：用于发现和评估 CRISPR 基因靶标的新型机器学习模型

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-10-07 DOI: 10.1021/acssynbio.4c0047310.1021/acssynbio.4c00473

Joshua P. Graham, Yu Zhang, Lifang He and Tomas Gonzalez-Fernandez*,

{"title":"CRISPR-GEM: A Novel Machine Learning Model for CRISPR Genetic Target Discovery and Evaluation","authors":"Joshua P. Graham, Yu Zhang, Lifang He and Tomas Gonzalez-Fernandez*, ","doi":"10.1021/acssynbio.4c0047310.1021/acssynbio.4c00473","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00473https://doi.org/10.1021/acssynbio.4c00473","url":null,"abstract":"CRISPR gene editing strategies are shaping cell therapies through precise and tunable control over gene expression. However, limitations in safely delivering high quantities of CRISPR machinery demand careful target gene selection to achieve reliable therapeutic effects. Informed target gene selection requires a thorough understanding of the involvement of target genes in gene regulatory networks (GRNs) and thus their impact on cell phenotype. Effective decoding of these complex networks has been achieved using machine learning models, but current techniques are limited to single cell types and focus mainly on transcription factors, limiting their applicability to CRISPR strategies. To address this, we present CRISPR-GEM, a multilayer perceptron (MLP) based synthetic GRN constructed to accurately predict the downstream effects of CRISPR gene editing. First, input and output nodes are identified as differentially expressed genes between defined experimental and target cell/tissue types, respectively. Then, MLP training learns regulatory relationships in a black-box approach allowing accurate prediction of output gene expression using only input gene expression. Finally, CRISPR-mimetic perturbations are made to each input gene individually, and the resulting model predictions are compared to those for the target group to score and assess each input gene as a CRISPR candidate. The top scoring genes provided by CRISPR-GEM therefore best modulate experimental group GRNs to motivate transcriptomic shifts toward a target group phenotype. This machine learning model is the first of its kind for predicting optimal CRISPR target genes and serves as a powerful tool for enhanced CRISPR strategies across a range of cell therapies.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acssynbio.4c00473","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142450353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An Automated Cell-Free Workflow for Transcription Factor Engineering 转录因子工程的无细胞自动工作流程

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-10-07 DOI: 10.1021/acssynbio.4c0047110.1021/acssynbio.4c00471

Holly M. Ekas, Brenda Wang, Adam D. Silverman, Julius B. Lucks, Ashty S. Karim and Michael C. Jewett*,

{"title":"An Automated Cell-Free Workflow for Transcription Factor Engineering","authors":"Holly M. Ekas, Brenda Wang, Adam D. Silverman, Julius B. Lucks, Ashty S. Karim and Michael C. Jewett*, ","doi":"10.1021/acssynbio.4c0047110.1021/acssynbio.4c00471","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00471https://doi.org/10.1021/acssynbio.4c00471","url":null,"abstract":"The design and optimization of metabolic pathways, genetic systems, and engineered proteins rely on high-throughput assays to streamline design-build-test-learn cycles. However, assay development is a time-consuming and laborious process. Here, we create a generalizable approach for the tailored optimization of automated cell-free gene expression (CFE)-based workflows, which offers distinct advantages over in vivo assays in reaction flexibility, control, and time to data. Centered around designing highly accurate and precise transfers on the Echo Acoustic Liquid Handler, we introduce pilot assays and validation strategies for each stage of protocol development. We then demonstrate the efficacy of our platform by engineering transcription factor-based biosensors. As a model, we rapidly generate and assay libraries of 127 MerR and 134 CadR transcription factor variants in 3682 unique CFE reactions in less than 48 h to improve limit of detection, selectivity, and dynamic range for mercury and cadmium detection. This was achieved by assessing a panel of ligand conditions for sensitivity (to 0.1, 1, 10 μM Hg and 0, 1, 10, 100 μM Cd for MerR and CadR, respectively) and selectivity (against Ag, As, Cd, Co, Cu, Hg, Ni, Pb, and Zn). We anticipate that our Echo-based, cell-free approach can be used to accelerate multiple design workflows in synthetic biology.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acssynbio.4c00471","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142450494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bacterial Living Therapeutics with Engineered Protein Secretion Circuits to Eliminate Breast Cancer Cells 利用工程化蛋白质分泌回路消灭乳腺癌细胞的细菌活体疗法

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-10-05 DOI: 10.1021/acssynbio.3c0072310.1021/acssynbio.3c00723

Gozeel Binte Shahid, Recep Erdem Ahan, Julian Ostaku and Urartu Ozgur Safak Seker*,

{"title":"Bacterial Living Therapeutics with Engineered Protein Secretion Circuits to Eliminate Breast Cancer Cells","authors":"Gozeel Binte Shahid, Recep Erdem Ahan, Julian Ostaku and Urartu Ozgur Safak Seker*, ","doi":"10.1021/acssynbio.3c0072310.1021/acssynbio.3c00723","DOIUrl":"https://doi.org/10.1021/acssynbio.3c00723https://doi.org/10.1021/acssynbio.3c00723","url":null,"abstract":"Cancer therapy can be limited by potential side effects, and bacteria-based living cancer therapeutics have gained scientific interest in recent years. However, the full potential of bacteria as therapeutics has yet to be explored due to engineering challenges. In this study, we present a bacterial device designed to specifically target and eliminate breast cancer cells. We have engineered Escherichia coli (E. coli) to bind to HER2 receptors on breast cancer cells while also secreting a toxin, HlyE, which is a pore-forming protein. The binding of E. coli to HER2 is facilitated by a nanobody expressed on the bacteria’s surface via the Ag43 autotransporter protein system. Our findings demonstrate that the nanobody efficiently binds to HER2+ cells in vitro, and we have utilized the YebF secretion tag to secrete HlyE and kill the target cancer cells. Overall, our results highlight the potential of our engineered bacteria as an innovative strategy for breast cancer treatment.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142450779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Efficient Strategy for Synthesizing Vector-Free and Oncolytic Herpes Simplex Type 1 Viruses 合成无载体和溶瘤型 1 型单纯疱疹病毒的高效策略

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-10-02 DOI: 10.1021/acssynbio.4c0036010.1021/acssynbio.4c00360

Han Xiao, Hengrui Hu, Yijia Guo, Jiang Li, Wen-Bo Zeng*, Min-Hua Luo, Manli Wang* and Zhihong Hu*,

{"title":"Efficient Strategy for Synthesizing Vector-Free and Oncolytic Herpes Simplex Type 1 Viruses","authors":"Han Xiao, Hengrui Hu, Yijia Guo, Jiang Li, Wen-Bo Zeng*, Min-Hua Luo, Manli Wang* and Zhihong Hu*, ","doi":"10.1021/acssynbio.4c0036010.1021/acssynbio.4c00360","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00360https://doi.org/10.1021/acssynbio.4c00360","url":null,"abstract":"Synthesizing viral genomes plays an important role in fundamental virology research and in the development of vaccines and antiviral drugs. Herpes simplex virus type 1 (HSV-1) is a large DNA virus widely used in oncolytic virotherapy. Although de novo synthesis of the HSV-1 genome has been previously reported, the synthetic procedure is still far from efficient, and the synthesized genome contains a vector sequence that may affect its replication and application. In the present study, we developed an efficient vector-free strategy for synthesis and rescue of synthetic HSV-1. In contrast to the conventional method of transfecting mammalian cells with a completely synthesized genome containing a vector, overlapping HSV-1 fragments synthesized by transformation-associated recombination (TAR) in yeast were linearized and cotransfected into mammalian cells to rescue the synthetic virus. Using this strategy, a synthetic virus, F-Syn, comprising the complete genome of the HSV-1 F strain, was generated. The growth curve and electron microscopy of F-Syn confirmed that its replication dynamics and morphogenesis are similar to those of the parental virus. In addition, by combining TAR with in vitro CRISPR/Cas9 editing, an oncolytic virus, F-Syn-O, with deleted viral genes ICP6, ICP34.5, and ICP47 was generated. The antitumor effect of F-Syn-O was tested in vitro. F-Syn-O established a successful infection and induced dose-dependent cytotoxic effects in various human tumor cell lines. These strategies will facilitate convenient and systemic manipulation of HSV-1 genomes and could be further applied to the design and construction of oncolytic herpesviruses.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142450830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

One-Pot Assay for Rapid Detection of Stenotrophomonas maltophilia by RPA-CRISPR/Cas12a 利用 RPA-CRISPR/Cas12a 快速检测嗜麦芽僵菌的单锅测定法

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-10-02 DOI: 10.1021/acssynbio.4c0048110.1021/acssynbio.4c00481

Jiangli Zhang, Ling Qin, Yingying Chang, Yulong He, Weichao Zhao, Yongyou Zhao, Yanan Ding, Jin Gao* and Xiting Zhao*,

{"title":"One-Pot Assay for Rapid Detection of Stenotrophomonas maltophilia by RPA-CRISPR/Cas12a","authors":"Jiangli Zhang, Ling Qin, Yingying Chang, Yulong He, Weichao Zhao, Yongyou Zhao, Yanan Ding, Jin Gao* and Xiting Zhao*, ","doi":"10.1021/acssynbio.4c0048110.1021/acssynbio.4c00481","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00481https://doi.org/10.1021/acssynbio.4c00481","url":null,"abstract":"Stenotrophomonas maltophilia (S. maltophilia, SMA) is a common opportunistic pathogen that poses a serious threat to the food industry and human health. Traditional detection methods for SMA are time-consuming, have low detection rates, require complex and expensive equipment and professional technical personnel for operation, and are unsuitable for on-site detection. Therefore, establishing an efficient on-site detection method has great significance in formulating appropriate treatment strategies and ensuring food safety. In the present study, a rapid one-pot detection method was established for SMA using a combination of Recombinase Polymerase Amplification (RPA) and CRISPR/Cas12a, referred to as ORCas12a-SMA (one-pot RPA-CRISPR/Cas12a platform). In the ORCas12a-SMA detection method, all components were added into a single tube simultaneously to achieve one-pot detection and address the problems of nucleic acid cross-contamination and reduced sensitivity caused by frequent cap opening during stepwise detection. The ORCas12a-SMA method could detect at least 3 × 10° copies·μL–1 of SMA genomic DNA within 30 min at 37 °C. Additionally, this method exhibited sensitivity compared to the typical two-step RPA-CRISPR/Cas12a method. Overall, the ORCas12a-SMA detection offered the advantages of rapidity, simplicity, high sensitivity and specificity, and decreased need for complex large-scale instrumentation. This assay is the first application of the one-pot platform based on the combination of RPA and CRISPR/Cas12a in SMA detection and is highly suitable for point-of-care testing. It helps reduce losses in the food industry and provides assistance in formulating timely and appropriate antimicrobial treatment plans.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142450329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Potential of Artificial Cells Functioning under In Situ Deep-Sea Conditions 人造细胞在原位深海条件下发挥作用的潜力

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-10-01 DOI: 10.1021/acssynbio.4c0044110.1021/acssynbio.4c00441

Yutetsu Kuruma*, Hidetaka Nomaki, Noriyuki Isobe, Daisuke Matsuoka and Yasuhiro Shimane,

{"title":"The Potential of Artificial Cells Functioning under In Situ Deep-Sea Conditions","authors":"Yutetsu Kuruma*, Hidetaka Nomaki, Noriyuki Isobe, Daisuke Matsuoka and Yasuhiro Shimane, ","doi":"10.1021/acssynbio.4c0044110.1021/acssynbio.4c00441","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00441https://doi.org/10.1021/acssynbio.4c00441","url":null,"abstract":"Artificial cells with reconstructed cellular functions could serve as practical protocell models for studying the early cellular life on the Earth. Investigating the viability of protocell models in extreme environments where life may have arisen is important for advancing origin-of-life research. Here, we tested the survivability of lipid membrane vesicles in deep-sea environments. The vesicles were submerged in the deep-sea floor with a human-occupied vehicle. Although most of the vesicles were broken, some vesicles maintained a spherical shape after the dives. When a cell-free protein synthesis system was encapsulated inside, a few vesicles remained even after a 1,390 m depth dive. Interestingly, such artificial cells could subsequently synthesize protein in a nutrient-rich buffer solution. Together with on shore experiments showing artificial cells synthesized protein under high pressure, our results suggest artificial cells may be able to express genes in deep-sea environments where thermal energy is available from hydrothermal vents.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acssynbio.4c00441","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142450464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to “Cell-Free Gene Expression Dynamics in Synthetic Cell Populations” 对 "合成细胞群中的无细胞基因表达动态 "的更正

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-10-01 DOI: 10.1021/acssynbio.4c0058310.1021/acssynbio.4c00583

David T. Gonzales, Naresh Yandrapalli, Tom Robinson, Christoph Zechner* and T-Y. Dora Tang*,

引用次数: 0

Disentangling the Regulatory Response of Agrobacterium tumefaciens CHLDO to Glyphosate for Engineering Whole-Cell Phosphonate Biosensors 厘清农杆菌 CHLDO 对草甘膦的调控响应以设计全细胞膦酸盐生物传感器

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-30 DOI: 10.1021/acssynbio.4c0049710.1021/acssynbio.4c00497

Fiorella Masotti, Nicolas Krink, Nicolas Lencina, Natalia Gottig, Jorgelina Ottado* and Pablo I. Nikel*,

{"title":"Disentangling the Regulatory Response of Agrobacterium tumefaciens CHLDO to Glyphosate for Engineering Whole-Cell Phosphonate Biosensors","authors":"Fiorella Masotti, Nicolas Krink, Nicolas Lencina, Natalia Gottig, Jorgelina Ottado* and Pablo I. Nikel*, ","doi":"10.1021/acssynbio.4c0049710.1021/acssynbio.4c00497","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00497https://doi.org/10.1021/acssynbio.4c00497","url":null,"abstract":"Phosphonates (PHTs), organic compounds with a stable C–P bond, are widely distributed in nature. Glyphosate (GP), a synthetic PHT, is extensively used in agriculture and has been linked to various human health issues and environmental damage. Given the prevalence of GP, developing cost-effective, on-site methods for GP detection is key for assessing pollution and reducing exposure risks. We adopted Agrobacterium tumefaciens CHLDO, a natural GP degrader, as a host and the source of genetic parts for constructing PHT biosensors. In this bacterial species, the phn gene cluster, encoding the C–P lyase pathway, is regulated by the PhnF transcriptional repressor. We selected the phnG promoter, which displays a dose-dependent response to GP, to build a set of whole-cell biosensors. Through stepwise genetic optimization of the transcriptional cascade, we created a whole-cell biosensor capable of detecting GP in the 0.25–50 μM range in various samples, including soil and water.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acssynbio.4c00497","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142450316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bioproduction of 3-Hydroxypropionic Acid by Enhancing the Precursor Supply with a Hybrid Pathway and Cofactor Regeneration 利用混合途径和辅助因子再生技术加强前体供应，实现 3-羟基丙酸的生物生产

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-25 DOI: 10.1021/acssynbio.4c0042710.1021/acssynbio.4c00427

Tingting Chen, Yufei Zhang, Junhua Yun, Mei Zhao, Cunsheng Zhang, Ziwei Chen, Hossain M. Zabed*, Wenjing Sun* and Xianghui Qi*,

{"title":"Bioproduction of 3-Hydroxypropionic Acid by Enhancing the Precursor Supply with a Hybrid Pathway and Cofactor Regeneration","authors":"Tingting Chen, Yufei Zhang, Junhua Yun, Mei Zhao, Cunsheng Zhang, Ziwei Chen, Hossain M. Zabed*, Wenjing Sun* and Xianghui Qi*, ","doi":"10.1021/acssynbio.4c0042710.1021/acssynbio.4c00427","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00427https://doi.org/10.1021/acssynbio.4c00427","url":null,"abstract":"3-Hydroxypropionic acid (3-HP) is one of the 12 valuable platform chemicals with versatile applications in the chemical, food, and cosmetic industries. However, the biosynthesis of 3-HP faces challenges due to the lack of robust chassis and the high costs associated with the fermentation process. To address these challenges, we made efforts to augment the robustness of 3-HP-producing chassis by exploiting metabolic regulation, controlling carbon flux, balancing cofactor generation, and optimizing fermentation conditions. First, the malonyl-CoA (MCA) pathway was recruited and rebalanced in Escherichia coli. Subsequently, a hybrid pathway integrating the Embden–Meyerhof–Parnas pathway with the nonoxidative glycolysis pathway was systematically modulated to enhance carbon flux to the MCA pathway, followed by fine-tuning NADPH regeneration. Then, by optimizing the fermentation conditions, 3-HP production was significantly improved, reaching 6.8 g/L. Finally, in a fed-batch experiment, the final chassis produced 42.8 g/L 3-HP, corresponding to a 0.4 mol/mol yield and 0.6 g/(L·h) productivity.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142450527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Efficient Simulation of Viral Transduction and Propagation for Biomanufacturing 高效模拟生物制造中的病毒转导和传播

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-24 DOI: 10.1021/acssynbio.4c0022710.1021/acssynbio.4c00227

Francesco Destro, and , Richard D. Braatz*,

{"title":"Efficient Simulation of Viral Transduction and Propagation for Biomanufacturing","authors":"Francesco Destro,  and , Richard D. Braatz*, ","doi":"10.1021/acssynbio.4c0022710.1021/acssynbio.4c00227","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00227https://doi.org/10.1021/acssynbio.4c00227","url":null,"abstract":"The design of biomanufacturing platforms based on viral transduction and/or propagation poses significant challenges at the intersection between synthetic biology and process engineering. This paper introduces vitraPro, a software toolkit composed of a multiscale model and an efficient numeric technique that can be leveraged for determining genetic and process designs that optimize transduction-based biomanufacturing platforms and viral amplification processes. Viral infection and propagation for up to two viruses simultaneously can be simulated through the model, considering viruses in either the lytic or lysogenic stage, during batch, perfusion, or continuous operation. The model estimates the distribution of the viral genome(s) copy number in the cell population, which is an indicator of transduction efficiency and viral genome stability. The infection age distribution of the infected cells is also calculated, indicating how many cells are in an infection stage compatible with recombinant product expression or viral amplification. The model can also consider the presence of defective interfering particles in the system, which can severely compromise the productivity of biomanufacturing processes. Model benchmarking and validation are demonstrated for case studies of the baculovirus expression vector system and influenza A propagation in suspension cultures.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142450536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0