ACS Synthetic Biology最新文献

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.4c00227

Francesco Destro, Richard D Braatz

{"title":"Efficient Simulation of Viral Transduction and Propagation for Biomanufacturing.","authors":"Francesco Destro, Richard D Braatz","doi":"10.1021/acssynbio.4c00227","DOIUrl":"https://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":"142306534","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

Impact of Chromatin Organization and Epigenetics on CRISPR-Cas and TALEN Genome Editing. 染色质组织和表观遗传学对 CRISPR-Cas 和 TALEN 基因组编辑的影响。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-24 DOI: 10.1021/acssynbio.4c00099

Surbhi Jain, Guanhua Xun, Huimin Zhao

{"title":"Impact of Chromatin Organization and Epigenetics on CRISPR-Cas and TALEN Genome Editing.","authors":"Surbhi Jain, Guanhua Xun, Huimin Zhao","doi":"10.1021/acssynbio.4c00099","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00099","url":null,"abstract":"DNA lies at the heart of the central dogma of life. Altering DNA can modify the flow of information in fundamental cellular processes such as transcription and translation. The ability to precisely manipulate DNA has led to remarkable advances in treating incurable human genetic ailments and has changed the landscape of biological research. Genome editors such as CRISPR-Cas nucleases and TALENs have become ubiquitous tools in basic and applied biological research and have been translated to the clinic to treat patients. The specificity and modularity of these genome editors have made it possible to efficiently engineer genomic DNA; however, underlying principles governing editing outcomes in eukaryotes are still being uncovered. Editing efficiency can vary from cell type to cell type for the same DNA target sequence, necessitating de novo design and validation efforts. Chromatin structure and epigenetic modifications have been shown to affect the activity of genome editors because of the role they play in hierarchical organization of the underlying DNA. Understanding the nuclear search mechanism of genome editors and their molecular interactions with higher order chromatin will lead to improved models for predicting precise genome editing outcomes. Insights from such studies will unlock the entire genome to be engineered for the creation of novel therapies to treat critical illnesses.","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":"142306535","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

Implementing Optogenetic-Controlled Bacterial Systems in Drosophila melanogaster for Alleviation of Heavy Metal Poisoning. 在黑腹果蝇体内实施光遗传学控制细菌系统以缓解重金属中毒。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-23 DOI: 10.1021/acssynbio.4c00409

Junyi Wang, Ying Li, Dawei Sun, Jingyi Li, Lianyue Li, Xinyu Zhang, Xinyu Liu, Zhijie Feng, Huimin Xue, Yuhui Cui, Yiwen Wang, Duo Liu, Hanjie Wang

{"title":"Implementing Optogenetic-Controlled Bacterial Systems in Drosophila melanogaster for Alleviation of Heavy Metal Poisoning.","authors":"Junyi Wang, Ying Li, Dawei Sun, Jingyi Li, Lianyue Li, Xinyu Zhang, Xinyu Liu, Zhijie Feng, Huimin Xue, Yuhui Cui, Yiwen Wang, Duo Liu, Hanjie Wang","doi":"10.1021/acssynbio.4c00409","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00409","url":null,"abstract":"Drosophila melanogaster (fruit fly) is an animal model chassis in biological and genetic research owing to its short life cycle, ease of cultivation, and acceptability to genetic modification. While the D. melanogaster chassis offers valuable insights into drug efficacy, toxicity, and mechanisms, several obvious challenges such as dosage control and drug resistance still limit its utility in pharmacological studies. Our research combines optogenetic control with engineered gut bacteria to facilitate the precise delivery of therapeutic substances in D. melanogaster for biomedical research. We have shown that the engineered bacteria can be orally administered to D. melanogaster to get a stable density of approximately 28,000 CFUs/per fly, leading to no detectable negative effects on the growth of D. melanogaster. In a model of D. melanogaster exposure to heavy metal, these orally administered bacteria uniformly express target genes under green light control to produce MtnB protein for binding and detoxifying lead, which significantly reduces the level of oxidative stress in the intestinal tract of Pb-treated flies. This pioneering study lays the groundwork for using optogenetic-controlled bacteria in the model chassis D. melanogaster to advance biomedical applications.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306536","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

Construction of Whole Cell Bacterial Biosensors as an Alternative Environmental Monitoring Technology to Detect Naphthenic Acids in Oil Sands Process-Affected Water. 构建全细胞细菌生物传感器，作为检测油砂加工影响水中环烷酸的替代环境监测技术。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-23 DOI: 10.1021/acssynbio.4c00260

Tyson Bookout, Steve Shideler, Evan Cooper, Kira Goff, John V Headley, Lisa M Gieg, Shawn Lewenza

{"title":"Construction of Whole Cell Bacterial Biosensors as an Alternative Environmental Monitoring Technology to Detect Naphthenic Acids in Oil Sands Process-Affected Water.","authors":"Tyson Bookout, Steve Shideler, Evan Cooper, Kira Goff, John V Headley, Lisa M Gieg, Shawn Lewenza","doi":"10.1021/acssynbio.4c00260","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00260","url":null,"abstract":"After extraction of bitumen from oil sands deposits, the oil sand process-affected water (OSPW) is stored in tailings ponds. Naphthenic acids (NA) in tailings ponds have been identified as the primary contributor to toxicity to aquatic life. As an alternative to other analytical methods, here we identify bacterial genes induced after growth in naphthenic acids and use synthetic biology approaches to construct a panel of candidate biosensors for NA detection in water. The main promoters of interest were the atuAR promoters from a naphthenic acid degradation operon and upstream TetR regulator, the marR operon which includes a MarR regulator and downstream naphthenic acid resistance genes, and a hypothetical gene with a possible role in fatty acid biology. Promoters were printed and cloned as transcriptional lux reporter plasmids that were introduced into a tailings pond-derived Pseudomonas species. All candidate biosensor strains were tested for transcriptional responses to naphthenic acid mixtures and individual compounds. The three priority promoters respond in a dose-dependent manner to simple, acyclic, and complex NA mixtures, and each promoter has unique NA specificities. The limits of NA detection from the various NA mixtures ranged between 1.5 and 15 mg/L. The atuA and marR promoters also detected NA in small volumes of OSPW samples and were induced by extracts of the panel of OSPW samples. While biosensors have been constructed for other hydrocarbons, here we describe a biosensor approach that could be employed in environmental monitoring of naphthenic acids in oil sands mining wastewater.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306532","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

Design and Characterization of a Transcriptional Repression Toolkit for Plants. 植物转录抑制工具包的设计和特征描述

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-23 DOI: 10.1021/acssynbio.4c00404

Kasey Markel, Jean Sabety, Shehan Wijesinghe, Patrick M Shih

{"title":"Design and Characterization of a Transcriptional Repression Toolkit for Plants.","authors":"Kasey Markel, Jean Sabety, Shehan Wijesinghe, Patrick M Shih","doi":"10.1021/acssynbio.4c00404","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00404","url":null,"abstract":"Regulation of gene expression is essential for all life. Tools to manipulate the gene expression level have therefore proven to be very valuable in efforts to engineer biological systems. However, there are few well-characterized genetic parts that reduce gene expression in plants, commonly known as transcriptional repressors. We characterized the repression activity of a library consisting of repression motifs from approximately 25% of the members of the largest known family of repressors. Combining sequence information with our trans-regulatory function data, we next generated a library of synthetic transcriptional repression motifs with function predicted in advance. After characterizing our synthetic library, we demonstrated not only that many of our synthetic constructs were functional as repressors but also that our advance predictions of repression strength were better than random guesses. Finally, we assessed the functionality of known transcriptional repression motifs from a wide range of eukaryotes. Our study represents the largest plant repressor motif library experimentally characterized to date, providing unique opportunities for tuning transcription in plants.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306533","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

Fundamentals and Exceptions of the LysR-type Transcriptional Regulators. LysR 型转录调控因子的基本原理与例外。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-22 DOI: 10.1021/acssynbio.4c00219

Wouter Demeester, Brecht De Paepe, Marjan De Mey

{"title":"Fundamentals and Exceptions of the LysR-type Transcriptional Regulators.","authors":"Wouter Demeester, Brecht De Paepe, Marjan De Mey","doi":"10.1021/acssynbio.4c00219","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00219","url":null,"abstract":"LysR-type transcriptional regulators (LTTRs) are emerging as a promising group of macromolecules for the field of biosensors. As the largest family of bacterial transcription factors, the LTTRs represent a vast and mostly untapped repertoire of sensor proteins. To fully harness these regulators for transcription factor-based biosensor development, it is crucial to understand their underlying mechanisms and functionalities. In the first part, this Review discusses the established model and features of LTTRs. As dual-function regulators, these inducible transcription factors exude precise control over their regulatory targets. In the second part of this Review, an overview is given of the exceptions to the \"classic\" LTTR model. While a general regulatory mechanism has helped elucidate the intricate regulation performed by LTTRs, it is essential to recognize the variations within the family. By combining this knowledge, characterization of new regulators can be done more efficiently and accurately, accelerating the expansion of transcriptional sensors for biosensor development. Unlocking the pool of LTTRs would significantly expand the currently limited range of detectable molecules and regulatory functions available for the implementation of novel synthetic genetic circuitry.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142277245","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

Modular Cloning Tools for Streptomyces spp. and Application to the De Novo Biosynthesis of Flavokermesic Acid. 链霉菌的模块化克隆工具及其在黄腐酸新生物合成中的应用。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-22 DOI: 10.1021/acssynbio.4c00412

Jean-Malo Massicard, Delphine Noel, Andrea Calderari, André Le Jeune, Cyrille Pauthenier, Kira J Weissman

引用次数: 0

Adeno-Associated Virus 5 Protein Particles Produced by E. coli Cell-Free Protein Synthesis. 大肠杆菌细胞自由蛋白质合成产生的腺相关病毒 5 蛋白颗粒。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-20 Epub Date: 2024-08-23 DOI: 10.1021/acssynbio.4c00403

Danielle Deuker, Ernest Asilonu, Daniel G Bracewell, Stefanie Frank

{"title":"Adeno-Associated Virus 5 Protein Particles Produced by E. coli Cell-Free Protein Synthesis.","authors":"Danielle Deuker, Ernest Asilonu, Daniel G Bracewell, Stefanie Frank","doi":"10.1021/acssynbio.4c00403","DOIUrl":"10.1021/acssynbio.4c00403","url":null,"abstract":"Recombinant adeno-associated viruses (rAAVs) have emerged as important tools for gene therapy and, more recently, vaccine development. Nonetheless, manufacturing can be costly and time-consuming, emphasizing the importance of alternative production platforms. We investigate the potential of E. coli-based cell-free protein synthesis (CFPS) to produce recombinant AAV5 virus-like particles (VLPs). AAV5 virus protein 3 (VP3) constructs, both with and without Strep-tag II, were expressed with CFPS. Lower reaction temperatures resulted in increased solubility, with the untagged variant containing nearly 90% more soluble VLP VP3 protein at 18 °C than at 37 °C. Affinity chromatography of N-terminally Strep(II)-tagged VP3 enabled successful isolation with minimal processing. DLS and TEM confirmed the presence of ∼20 nm particles. Furthermore, the N-terminally tagged AAV5 VP3 VLPs were biologically active, successfully internalizing into HeLa cells. This study describes an innovative approach to AAV VLP production using E. coli-based CFPS, demonstrating its potential for rapid and biologically active AAV VLP synthesis.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142043776","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

Algorithms for Autonomous Formation of Multicellular Shapes from Single Cells. 单细胞自主形成多细胞形状的算法。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-20 Epub Date: 2024-08-28 DOI: 10.1021/acssynbio.4c00037

Evan Appleton, Noushin Mehdipour, Tristan Daifuku, Demarcus Briers, Iman Haghighi, Michaël Moret, George Chao, Timothy Wannier, Anush Chiappino-Pepe, Jeremy Huang, Calin Belta, George M Church

引用次数: 0

Approaching Optimal pH Enzyme Prediction with Large Language Models. 利用大型语言模型接近最佳 pH 值酶预测。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-20 Epub Date: 2024-08-28 DOI: 10.1021/acssynbio.4c00465

Mark Zaretckii, Pavel Buslaev, Igor Kozlovskii, Alexander Morozov, Petr Popov

{"title":"Approaching Optimal pH Enzyme Prediction with Large Language Models.","authors":"Mark Zaretckii, Pavel Buslaev, Igor Kozlovskii, Alexander Morozov, Petr Popov","doi":"10.1021/acssynbio.4c00465","DOIUrl":"10.1021/acssynbio.4c00465","url":null,"abstract":"Enzymes are widely used in biotechnology due to their ability to catalyze chemical reactions: food making, laundry, pharmaceutics, textile, brewing─all these areas benefit from utilizing various enzymes. Proton concentration (pH) is one of the key factors that define the enzyme functioning and efficiency. Usually there is only a narrow range of pH values where the enzyme is active. This is a common problem in biotechnology to design an enzyme with optimal activity in a given pH range. A large part of this task can be completed in silico, by predicting the optimal pH of designed candidates. The success of such computational methods critically depends on the available data. In this study, we developed a language-model-based approach to predict the optimal pH range from the enzyme sequence. We used different splitting strategies based on sequence similarity, protein family annotation, and enzyme classification to validate the robustness of the proposed approach. The derived machine-learning models demonstrated high accuracy across proteins from different protein families and proteins with lower sequence similarities compared with the training set. The proposed method is fast enough for the high-throughput virtual exploration of protein space for the search for sequences with desired optimal pH levels.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142085835","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