Synthetic biology (Oxford, England)最新文献

New gene sensors enable precise cell monitoring and control without altering gene sequence. 新型基因传感器能够在不改变基因序列的情况下对细胞进行精确监测和控制。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2024-10-29 eCollection Date: 2024-01-01 DOI: 10.1093/synbio/ysae014

Tea Crnković

引用次数: 0

In vitro transcription-based biosensing of glycolate for prototyping of a complex enzyme cascade. 基于体外转录的乙醇酸生物传感技术，用于复杂酶级联的原型开发。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2024-09-20 eCollection Date: 2024-01-01 DOI: 10.1093/synbio/ysae013

Sebastian Barthel, Luca Brenker, Christoph Diehl, Nitin Bohra, Simone Giaveri, Nicole Paczia, Tobias J Erb

{"title":"In vitro transcription-based biosensing of glycolate for prototyping of a complex enzyme cascade.","authors":"Sebastian Barthel, Luca Brenker, Christoph Diehl, Nitin Bohra, Simone Giaveri, Nicole Paczia, Tobias J Erb","doi":"10.1093/synbio/ysae013","DOIUrl":"10.1093/synbio/ysae013","url":null,"abstract":"In vitro metabolic systems allow the reconstitution of natural and new-to-nature pathways outside of their cellular context and are of increasing interest in bottom-up synthetic biology, cell-free manufacturing, and metabolic engineering. Yet, the analysis of the activity of such in vitro networks is very often restricted by time- and cost-intensive methods. To overcome these limitations, we sought to develop an in vitro transcription (IVT)-based biosensing workflow that is compatible with the complex conditions of in vitro metabolism, such as the crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle, a 27-component in vitro metabolic system that converts CO2 into glycolate. As proof of concept, we constructed a novel glycolate sensor module that is based on the transcriptional repressor GlcR from Paracoccus denitrificans and established an IVT biosensing workflow that allows us to quantify glycolate from CETCH samples in the micromolar to millimolar range. We investigate the influence of 13 (shared) cofactors between the two in vitro systems to show that Mg2+, adenosine triphosphate , and other phosphorylated metabolites are critical for robust signal output. Our optimized IVT biosensor correlates well with liquid chromatography-mass spectrometry-based glycolate quantification of CETCH samples, with one or multiple components varying (linear correlation 0.94-0.98), but notably at ∼10-fold lowered cost and ∼10 times faster turnover time. Our results demonstrate the potential and challenges of IVT-based systems to quantify and prototype the activity of complex reaction cascades and in vitro metabolic networks.","PeriodicalId":74902,"journal":{"name":"Synthetic biology (Oxford, England)","volume":"9 1","pages":"ysae013"},"PeriodicalIF":2.6,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11470758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cell-free synthesis of infective phages from in vitro assembled phage genomes for efficient phage engineering and production of large phage libraries. 从体外组装的噬菌体基因组中无细胞合成感染性噬菌体，用于高效的噬菌体工程和大型噬菌体文库的生产。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2024-08-24 eCollection Date: 2024-01-01 DOI: 10.1093/synbio/ysae012

Camilla S Kristensen, Anders Ø Petersen, Mogens Kilstrup, Eric van der Helm, Adam Takos

引用次数: 0

Data hazards in synthetic biology. 合成生物学中的数据危害。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2024-06-21 eCollection Date: 2024-01-01 DOI: 10.1093/synbio/ysae010

Natalie R Zelenka, Nina Di Cara, Kieren Sharma, Seeralan Sarvaharman, Jasdeep S Ghataora, Fabio Parmeggiani, Jeff Nivala, Zahraa S Abdallah, Lucia Marucci, Thomas E Gorochowski

{"title":"Data hazards in synthetic biology.","authors":"Natalie R Zelenka, Nina Di Cara, Kieren Sharma, Seeralan Sarvaharman, Jasdeep S Ghataora, Fabio Parmeggiani, Jeff Nivala, Zahraa S Abdallah, Lucia Marucci, Thomas E Gorochowski","doi":"10.1093/synbio/ysae010","DOIUrl":"10.1093/synbio/ysae010","url":null,"abstract":"Data science is playing an increasingly important role in the design and analysis of engineered biology. This has been fueled by the development of high-throughput methods like massively parallel reporter assays, data-rich microscopy techniques, computational protein structure prediction and design, and the development of whole-cell models able to generate huge volumes of data. Although the ability to apply data-centric analyses in these contexts is appealing and increasingly simple to do, it comes with potential risks. For example, how might biases in the underlying data affect the validity of a result and what might the environmental impact of large-scale data analyses be? Here, we present a community-developed framework for assessing data hazards to help address these concerns and demonstrate its application to two synthetic biology case studies. We show the diversity of considerations that arise in common types of bioengineering projects and provide some guidelines and mitigating steps. Understanding potential issues and dangers when working with data and proactively addressing them will be essential for ensuring the appropriate use of emerging data-intensive AI methods and help increase the trustworthiness of their applications in synthetic biology.","PeriodicalId":74902,"journal":{"name":"Synthetic biology (Oxford, England)","volume":"9 1","pages":"ysae010"},"PeriodicalIF":2.6,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11227101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141556148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Navigating the 'moral hazard' argument in synthetic biology's application. 引导合成生物学应用中的 "道德风险 "论点。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2024-05-23 eCollection Date: 2024-01-01 DOI: 10.1093/synbio/ysae008

Christopher Hunter Lean

引用次数: 0

Screening putative polyester polyurethane degrading enzymes with semi-automated cell-free expression and nitrophenyl probes. 利用半自动无细胞表达和硝基苯探针筛选假定的聚酯聚氨酯降解酶。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2024-02-13 eCollection Date: 2024-01-01 DOI: 10.1093/synbio/ysae005

Afrin Ahsan, Dominique Wagner, Vanessa A Varaljay, Victor Roman, Nancy Kelley-Loughnane, Nigel F Reuel

{"title":"Screening putative polyester polyurethane degrading enzymes with semi-automated cell-free expression and nitrophenyl probes.","authors":"Afrin Ahsan, Dominique Wagner, Vanessa A Varaljay, Victor Roman, Nancy Kelley-Loughnane, Nigel F Reuel","doi":"10.1093/synbio/ysae005","DOIUrl":"10.1093/synbio/ysae005","url":null,"abstract":"Cell-free expression (CFE) has shown recent utility in prototyping enzymes for discovery efforts. In this work, CFE is demonstrated as an effective tool to screen putative polyester polyurethane degrading enzyme sequences sourced from metagenomic analysis of biofilms prospected on aircraft and vehicles. An automated fluid handler with a controlled temperature block is used to assemble the numerous 30 µL CFE reactions to provide more consistent results over human assembly. In sum, 13 putative hydrolase enzymes from the biofilm organisms as well as a previously verified, polyester-degrading cutinase were expressed using in-house E. coli extract and minimal linear templates. The enzymes were then tested for esterase activity directly in extract using nitrophenyl conjugated substrates, showing highest sensitivity to shorter substrates (4-nitrophenyl hexanoate and 4-nNitrophenyl valerate). This screen identified 10 enzymes with statistically significant activities against these substrates; however, all were lower in measured relative activity, on a CFE volume basis, to the established cutinase control. This approach portends the use of CFE and reporter probes to rapidly prototype, screen and design for synthetic polymer degrading enzymes from environmental consortia. Graphical Abstract.","PeriodicalId":74902,"journal":{"name":"Synthetic biology (Oxford, England)","volume":"9 1","pages":"ysae005"},"PeriodicalIF":2.6,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10898825/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139984743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Preparing for the future of precision medicine: synthetic cell drug regulation. 为未来的精准医疗做准备：合成细胞药物调控。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2024-01-27 eCollection Date: 2024-01-01 DOI: 10.1093/synbio/ysae004

Kira Sampson, Carlise Sorenson, Katarzyna P Adamala

引用次数: 0

The naringenin-dependent regulator FdeR can be applied as a NIMPLY gate controlled by naringenin and arabinose. 柚皮苷依赖性调节器 FdeR 可用作由柚皮苷和阿拉伯糖控制的 NIMPLY 门。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2024-01-16 eCollection Date: 2024-01-01 DOI: 10.1093/synbio/ysae001

Fernanda Miyuki Kashiwagi, Brenno Wendler Miranda, Emanuel Maltempi de Souza, Marcelo Müller-Santos

{"title":"The naringenin-dependent regulator FdeR can be applied as a NIMPLY gate controlled by naringenin and arabinose.","authors":"Fernanda Miyuki Kashiwagi, Brenno Wendler Miranda, Emanuel Maltempi de Souza, Marcelo Müller-Santos","doi":"10.1093/synbio/ysae001","DOIUrl":"10.1093/synbio/ysae001","url":null,"abstract":"The FdeR regulator has been reported as a transcriptional activator dependent on the interaction with naringenin. Previously, FdeR and its cognate promoter were used to construct naringenin-sensitive sensors, though no correlation was associated between the FdeR level of expression and outputs. Therefore, to understand this correlation, we constructed a circuit with FdeR expression adjusted by the arabinose concentration through an AraC-PBAD system and the FdeR-regulated promoter controlling the expression of GFP. We observed a significant reduction in the activity of the target promoter by increasing FdeR expression, indicating that although FdeR has been primarily classified as a transcriptional activator, it also represses transcription. Leveraging the bifunctional feature of FdeR, acting as both transcriptional activator and repressor, we demonstrated that this genetic circuit, when previously switched on by naringenin, can be switched off by inducing an increased FdeR expression level. This engineered system functioned as a NIMPLY gate, effectively decreasing GFP expression by 50% when arabinose was added without removing naringenin from the medium. Exploiting FdeR versatility, this study demonstrates an innovative application of this transcriptional factor for developing novel NIMPLY gates activated by a molecule with low toxicity and nutraceutical properties that may be important for several applications. Graphical Abstract.","PeriodicalId":74902,"journal":{"name":"Synthetic biology (Oxford, England)","volume":"9 1","pages":"ysae001"},"PeriodicalIF":2.6,"publicationDate":"2024-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10799723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139514515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cell-free expression of RuBisCO for ATP production in the synthetic cells. 在合成细胞中无细胞表达 RuBisCO 以产生 ATP。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2023-12-20 eCollection Date: 2023-01-01 DOI: 10.1093/synbio/ysad016

Shugo Sugii, Katsumi Hagino, Ryo Mizuuchi, Norikazu Ichihashi

引用次数: 0

Special issue: reproducibility in synthetic biology. 特刊:合成生物学的可重复性。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2023-11-16 eCollection Date: 2023-01-01 DOI: 10.1093/synbio/ysad015

Matthew W Lux, Elizabeth A Strychalski, Gary J Vora

引用次数: 0