Journal of Biological Engineering最新文献

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Glutathione peroxidase 4 overexpression induces anomalous subdiffusion and impairs glioblastoma cell growth.
IF 5.7 3区 生物学
Journal of Biological Engineering Pub Date : 2024-12-21 DOI: 10.1186/s13036-024-00472-x
Nahom Teferi, Akalanka Ekanayake, Stephenson B Owusu, Thomas O Moninger, Jann N Sarkaria, Alexei V Tivanski, Michael S Petronek
{"title":"Glutathione peroxidase 4 overexpression induces anomalous subdiffusion and impairs glioblastoma cell growth.","authors":"Nahom Teferi, Akalanka Ekanayake, Stephenson B Owusu, Thomas O Moninger, Jann N Sarkaria, Alexei V Tivanski, Michael S Petronek","doi":"10.1186/s13036-024-00472-x","DOIUrl":"https://doi.org/10.1186/s13036-024-00472-x","url":null,"abstract":"<p><p>Glioblastoma tumors are the most common and aggressive adult central nervous system malignancy. Nearly all patients experience disease progression, which significantly contributes to disease mortality. Recently, it has been suggested that recurrent tumors may be characterized by a ferroptosis-prone phenotype with a significant decrease in glutathione peroxidase 4 (GPx4) expression. This led to the hypothesis that GPx4 expression negatively influences GBM cell growth. This study utilizes a doxycycline inducible GPx4 overexpression model to test this hypothesis. Consistently, the overexpression of GPx4 significantly impairs cell growth and colony formation while also causing an accumulation of cells in G1/G0 phase of the cell cycle. From a biophysical perspective, GPx4 overexpressing cells have significantly greater surface area, increased Young's modulus, and experience anomalous sub-diffusion as opposed to normal diffusion associated with Brownian motion. Moreover, analysis of patient derived GBM cells reveal that cell growth rates, plating efficiency, and Young's modulus are all inversely proportional to GPx4 expression. Therefore, GPx4 appears to be a biophysical regulator of GBM cell growth that warrants further mechanistic investigation in its role in GBM progression.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"18 1","pages":"72"},"PeriodicalIF":5.7,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Dynamic control of the plasmid copy number maintained without antibiotics in Escherichia coli.
IF 5.7 3区 生物学
Journal of Biological Engineering Pub Date : 2024-12-19 DOI: 10.1186/s13036-024-00460-1
Geunyung Park, Jina Yang, Sang Woo Seo
{"title":"Dynamic control of the plasmid copy number maintained without antibiotics in Escherichia coli.","authors":"Geunyung Park, Jina Yang, Sang Woo Seo","doi":"10.1186/s13036-024-00460-1","DOIUrl":"https://doi.org/10.1186/s13036-024-00460-1","url":null,"abstract":"<p><strong>Background: </strong>Manipulating the gene expression is the key strategy to optimize the metabolic flux. Not only transcription, translation, and post-translation level control, but also the dynamic plasmid copy number (PCN) control has been studied. The dynamic PCN control systems that have been developed to date are based on the understanding of origin replication mechanisms, which limits their application to specific origins of replication and requires the use of antibiotics for plasmid maintenance. In this study, we developed a dynamic PCN control system for Escherichia coli that is maintained without antibiotics. This is achieved by regulating the transcription level of the translation initiation factor IF-1 (infA), an essential gene encoded on the plasmid, while deleting it from the plasmid-bearing host cell.</p><p><strong>Results: </strong>When validated using GFP as a reporter protein, our system demonstrated a 22-fold dynamic range in PCN within the CloDF13 origin. The system was employed to determine the optimal copy number of the plasmid carrying the cad gene, which converts an intermediate of the tricarboxylic acid cycle (TCA cycle) to itaconic acid. By optimizing the PCN, we could achieve an itaconic acid titer of 3 g/L, which is 5.3-fold higher than the control strain.</p><p><strong>Conclusions: </strong>Our system offers a strategy to identify the optimal expression level of genes that have a competitive relationship with metabolic pathways crucial for the growth of the host organism. This approach can potentially be applied to other bacterial hosts by substituting the sensing module or the essential gene.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"18 1","pages":"71"},"PeriodicalIF":5.7,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Identification and verification of diagnostic biomarkers for deep infiltrating endometriosis based on machine learning algorithms. 基于机器学习算法的深部浸润性子宫内膜异位症诊断生物标志物的识别与验证。
IF 5.7 3区 生物学
Journal of Biological Engineering Pub Date : 2024-11-25 DOI: 10.1186/s13036-024-00466-9
Shanping Shi, Chao Huang, Xiaojian Tang, Hua Liu, Weiwei Feng, Chen Chen
{"title":"Identification and verification of diagnostic biomarkers for deep infiltrating endometriosis based on machine learning algorithms.","authors":"Shanping Shi, Chao Huang, Xiaojian Tang, Hua Liu, Weiwei Feng, Chen Chen","doi":"10.1186/s13036-024-00466-9","DOIUrl":"10.1186/s13036-024-00466-9","url":null,"abstract":"<p><p>This study addresses the challenges in the early diagnosis of deep infiltrating endometriosis (DIE) by exploring the potential role of the deubiquitinating enzyme USP14. By analyzing the GSE141549 dataset from the Gene Expression Omnibus (GEO) database, using bioinformatics methods and three machine learning algorithms (LASSO, Random Forest, and Support Vector Machine), the key feature gene USP14 was identified. The results indicated that USP14 is significantly upregulated in DIE and exhibits good predictive value (AUC = 0.786). Further analysis revealed the important role of USP14 in muscle function, cellular growth factor response, and maintenance of chromosome structure, and its close association with various immune cell functions. Immunohistochemical staining confirmed the high expression of USP14 in DIE tissues. This study provides a new molecular target for the early diagnosis of DIE, which holds significant clinical implications and potential application value.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"18 1","pages":"70"},"PeriodicalIF":5.7,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11590220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142715772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Engineering Saccharomyces cerevisiae for the production of natural osmolyte glucosyl glycerol from sucrose and glycerol through Ccw12-based surface display of sucrose phosphorylase. 通过基于 Ccw12 的蔗糖磷酸化酶表面展示工程化酿酒酵母,从蔗糖和甘油中生产天然渗透溶质葡萄糖基甘油。
IF 5.7 3区 生物学
Journal of Biological Engineering Pub Date : 2024-11-22 DOI: 10.1186/s13036-024-00468-7
Tea Martinić Cezar, Nenad Marđetko, Antonija Trontel, Antonia Paić, Anita Slavica, Renata Teparić, Bojan Žunar
{"title":"Engineering Saccharomyces cerevisiae for the production of natural osmolyte glucosyl glycerol from sucrose and glycerol through Ccw12-based surface display of sucrose phosphorylase.","authors":"Tea Martinić Cezar, Nenad Marđetko, Antonija Trontel, Antonia Paić, Anita Slavica, Renata Teparić, Bojan Žunar","doi":"10.1186/s13036-024-00468-7","DOIUrl":"10.1186/s13036-024-00468-7","url":null,"abstract":"<p><strong>Background: </strong>Yeast Saccharomyces cerevisiae is widely recognised as a versatile chassis for constructing microbial cell factories. However, producing chemicals from toxic, highly concentrated, or cell-impermeable substrates, or chemicals dependent on enzymatic reactions incompatible with the yeast's intracellular environment, remains challenging. One such chemical is 2-O-(α-D-glucopyranosyl)-sn-glycerol (glucosyl glycerol, αGG), a natural osmolyte used in the cosmetics and healthcare industries. This compound can be synthesised in a one-enzyme reaction from sucrose and glycerol by Leuconostoc mesenteroides sucrose phosphorylase (SucP), an enzyme which, in a low-water, glycerol-rich, phosphate-free environment, transfers the glucosyl moiety from sucrose to glycerol.</p><p><strong>Results: </strong>In this study, we engineered a yeast microbial cell factory for αGG production. For this purpose, we first focused on the abundant yeast GPI-anchored cell wall protein Ccw12 and used our insights to develop a miniature Ccw12-tag, which adds only 1.1 kDa to the enzyme of interest while enabling its covalent attachment to the cell wall. Next, we Ccw12-tagged SucP and expressed it in an invertase-negative strain of yeast S. cerevisiae from the PHO5 promoter, i.e., promoter strongly induced under phosphate-free conditions. Such SucP isoform, covalently C-terminally anchored to the outer cell surface, produced extracellularly 37.3 g l<sup>- 1</sup> (146 mM) of αGG in five days, while the underlying chassis metabolised reaction by-products, thereby simplifying downstream processing.</p><p><strong>Conclusions: </strong>The here-described S. cerevisiae strain, displaying C-terminally anchored sucrose phosphorylase on its cell surface, is the first eukaryotic microbial cell factory capable of a one-step αGG production from the readily available substrates sucrose and glycerol.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"18 1","pages":"69"},"PeriodicalIF":5.7,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11583750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
A dual-inducible control system for multistep biosynthetic pathways. 多步生物合成途径的双诱导控制系统。
IF 5.7 3区 生物学
Journal of Biological Engineering Pub Date : 2024-11-20 DOI: 10.1186/s13036-024-00462-z
Andrés Felipe Carrillo Rincón, Alexandra J Cabral, Andras Gyorgy, Natalie G Farny
{"title":"A dual-inducible control system for multistep biosynthetic pathways.","authors":"Andrés Felipe Carrillo Rincón, Alexandra J Cabral, Andras Gyorgy, Natalie G Farny","doi":"10.1186/s13036-024-00462-z","DOIUrl":"10.1186/s13036-024-00462-z","url":null,"abstract":"<p><strong>Background: </strong>The successful production of industrially relevant natural products hinges on two key factors: the cultivation of robust microbial chassis capable of synthesizing the desired compounds, and the availability of reliable genetic tools for expressing target genes. The development of versatile and portable genetic tools offers a streamlined pathway to efficiently produce a variety of compounds in well-established chassis organisms. The σ<sup>70</sup>lac and tet expression systems - adaptations of the widely used lac and tet regulatory systems developed in our laboratory - have shown effective regulation and robust expression of recombinant proteins in various Gram-negative bacteria. Understanding the strengths and limitations of these regulatory systems in controlling recombinant protein production is essential for progress in this area.</p><p><strong>Results: </strong>To assess their capacity for combinatorial control, both the σ<sup>70</sup>lac and tet expression systems were combined into a single plasmid and assessed for their performance in producing fluorescent reporters as well as the terpenoids lycopene and β-carotene. We thoroughly characterized the induction range, potential for synergistic effects, and metabolic costs of our dual σ<sup>70</sup>lac and tet expression system in the well-established microorganisms Escherichia coli, Pseudomonas putida, and Vibrio natriegens using combinations of fluorescent reporters. The dynamic range and basal transcriptional control of the σ<sup>70</sup> expression systems were further improved through the incorporation of translational control mechanisms via toehold switches. This improvement was assessed using the highly sensitive luciferase reporter system. The improvement in control afforded by the integration of the toehold switches enabled the accumulation of a biosynthetic intermediate (lycopene) in the β-carotene synthesis pathway.</p><p><strong>Conclusion: </strong>This study presents the development and remaining challenges of a set of versatile genetic tools that are portable across well-established gammaproteobacterial chassis and capable of controlling the expression of multigene biosynthetic pathways. The enhanced σ<sup>70</sup> expression systems, combined with toehold switches, facilitate the biosynthesis and study of enzymes, recombinant proteins, and natural products, thus providing a valuable resource for producing a variety of compounds in microbial cell factories.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"18 1","pages":"68"},"PeriodicalIF":5.7,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11580509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
A rotenone organotypic whole hemisphere slice model of mitochondrial abnormalities in the neonatal brain. 新生儿大脑线粒体异常的鱼藤酮器官型全半球切片模型。
IF 5.7 3区 生物学
Journal of Biological Engineering Pub Date : 2024-11-14 DOI: 10.1186/s13036-024-00465-w
Brendan Butler, Malcolm Renney, Kristin Bennett, Gisele Charpentier, Elizabeth Nance
{"title":"A rotenone organotypic whole hemisphere slice model of mitochondrial abnormalities in the neonatal brain.","authors":"Brendan Butler, Malcolm Renney, Kristin Bennett, Gisele Charpentier, Elizabeth Nance","doi":"10.1186/s13036-024-00465-w","DOIUrl":"10.1186/s13036-024-00465-w","url":null,"abstract":"<p><p>Mitochondrial abnormalities underscore a variety of neurologic injuries and diseases and are well-studied in adult populations. Clinical studies identify critical roles of mitochondria in a wide range of developmental brain injuries, but models that capture mitochondrial abnormalities in systems representative of the neonatal brain environment are lacking. Here, we develop an organotypic whole-hemisphere (OWH) brain slice model of mitochondrial dysfunction in the neonatal brain. We extended the utility of complex I inhibitor rotenone (ROT), canonically used in models of adult neurodegenerative diseases, to inflict mitochondrial damage in OWH slices from term-equivalent rats. We quantified whole-slice health over 6 days of exposure for a range of doses represented in ROT literature. We identified 50 nM ROT as a suitable exposure level for OWH slices to inflict injury without compromising viability. At the selected exposure level, we confirmed exposure- and time-dependent mitochondrial responses showing differences in mitochondrial fluorescence and nuclear localization using MitoTracker imaging in live OWH slices and dysregulated mitochondrial markers via RT-qPCR screening. We leveraged the regional structures present in OWH slices to quantify cell density and cell death in the cortex and the midbrain regions, observing higher susceptibilities to damage in the midbrain as a function of exposure and culture time. We supplemented these findings with analysis of microglia and mature neurons showing time-, region-, and exposure-dependent differences in microglial responses. We demonstrated changes in tissue microstructure as a function of region, culture time, and exposure level using live-video epifluorescence microscopy of extracellularly diffusing nanoparticle probes in live OWH slices. Our results highlight severity-, time-, and region-dependent responses and establish a complimentary model system of mitochondrial abnormalities for high-throughput or live-tissue experimental needs.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"18 1","pages":"67"},"PeriodicalIF":5.7,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11566268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Thermo-amplifier circuit in probiotic E. coli for stringently temperature-controlled release of a novel antibiotic. 益生大肠杆菌中的热放大器电路,用于严格温控新型抗生素的释放。
IF 5.7 3区 生物学
Journal of Biological Engineering Pub Date : 2024-11-12 DOI: 10.1186/s13036-024-00463-y
Sourik Dey, Carsten E Seyfert, Claudia Fink-Straube, Andreas M Kany, Rolf Müller, Shrikrishnan Sankaran
{"title":"Thermo-amplifier circuit in probiotic E. coli for stringently temperature-controlled release of a novel antibiotic.","authors":"Sourik Dey, Carsten E Seyfert, Claudia Fink-Straube, Andreas M Kany, Rolf Müller, Shrikrishnan Sankaran","doi":"10.1186/s13036-024-00463-y","DOIUrl":"10.1186/s13036-024-00463-y","url":null,"abstract":"<p><p>Peptide drugs have seen rapid advancement in biopharmaceutical development, with over 80 candidates approved globally. Despite their therapeutic potential, the clinical translation of peptide drugs is hampered by challenges in production yields and stability. Engineered bacterial therapeutics is a unique approach being explored to overcome these issues by using bacteria to produce and deliver therapeutic compounds at the body site of use. A key advantage of this technology is the possibility to control drug delivery within the body in real time using genetic switches. However, the performance of such genetic switches suffers when used to control drugs that require post-translational modifications or are toxic to the host. In this study, these challenges were experienced when attempting to establish a thermal switch for the production of a ribosomally synthesized and post-translationally modified peptide antibiotic, darobactin, in probiotic E. coli. These challenges were overcome by developing a thermo-amplifier circuit that combined the thermal switch with a T7 RNA Polymerase. Due to the orthogonality of the Polymerase, this strategy overcame limitations imposed by the host transcriptional machinery. This circuit enabled production of pathogen-inhibitory levels of darobactin at 40 °C while maintaining leakiness below the detection limit at 37 °C. Furthermore, the thermo-amplifier circuit sustained gene expression beyond the thermal induction duration such that with only 2 h of induction, the bacteria were able to produce pathogen-inhibitory levels of darobactin. This performance was maintained even in physiologically relevant simulated conditions of the intestines that include bile salts and low nutrient levels.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"18 1","pages":"66"},"PeriodicalIF":5.7,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142620955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
High-throughput proliferation and activation of NK-92MI cell spheroids via a homemade one-step closed bioreactor in pseudostatic cultures for immunocellular therapy. 通过自制的假静态培养一步式封闭生物反应器高通量增殖和激活 NK-92MI 细胞球,用于免疫细胞疗法。
IF 5.7 3区 生物学
Journal of Biological Engineering Pub Date : 2024-11-12 DOI: 10.1186/s13036-024-00461-0
Jhih-Ni Lin, Che-Yung Kuan, Chia-Ting Chang, Zhi-Yu Chen, Wei-Ting Kuo, Jason Lin, Yu-Ying Lin, I-Hsuan Yang, Feng-Huei Lin
{"title":"High-throughput proliferation and activation of NK-92MI cell spheroids via a homemade one-step closed bioreactor in pseudostatic cultures for immunocellular therapy.","authors":"Jhih-Ni Lin, Che-Yung Kuan, Chia-Ting Chang, Zhi-Yu Chen, Wei-Ting Kuo, Jason Lin, Yu-Ying Lin, I-Hsuan Yang, Feng-Huei Lin","doi":"10.1186/s13036-024-00461-0","DOIUrl":"10.1186/s13036-024-00461-0","url":null,"abstract":"<p><p>The NK-92MI cell line has displayed significant promise in clinical trials for cancer treatment. However, challenges persist in obtaining sufficient cell quantities and achieving optimal cytotoxicity. The proliferation of natural killer (NK) cells involves the formation of cell aggregates, but excessively large aggregates can impede nutrient and waste transport, leading to reduced cell survival rates. In this study, a custom bioreactor was designed to mimic pseudostatic culture conditions by integrating brief mechanical rotation during a 6-h static culture period. This method aimed to achieve an optimal aggregate size while improving cell viability. The findings revealed a 144-fold expansion of 3D NK-92MI cell aggregates, reaching an ideal size of 80-150 µm, significantly increasing both cell proliferation and survival rates. After 14 days of culture, the NK-92MI cells maintained their phenotype during the subsequent phase of cell activation. Moreover, these cells presented elevated levels of IFN-γ expression after IL-18 activation, resulting in enhanced NK cell-mediated cytotoxicity against K562 cells. This innovative strategy, which uses a closed suspension-based culture system, presents a promising approach for improving cell expansion and activation techniques in immunocellular therapy.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"18 1","pages":"65"},"PeriodicalIF":5.7,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11555828/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142620954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Evaluating ATP testing for distribution system monitoring: comparison to HPC, impact of chlorine quenching, and hold time dependency. 评估用于配电系统监控的 ATP 测试:与 HPC 的比较、氯淬火的影响以及保持时间的依赖性。
IF 5.7 3区 生物学
Journal of Biological Engineering Pub Date : 2024-11-05 DOI: 10.1186/s13036-024-00446-z
William S Chen, Leili Abkar, Madjid Mohseni
{"title":"Evaluating ATP testing for distribution system monitoring: comparison to HPC, impact of chlorine quenching, and hold time dependency.","authors":"William S Chen, Leili Abkar, Madjid Mohseni","doi":"10.1186/s13036-024-00446-z","DOIUrl":"10.1186/s13036-024-00446-z","url":null,"abstract":"<p><p>Adenosine triphosphate (ATP) assays have a faster turnaround time and higher sensitivity than traditional cultivation methods for microbial monitoring. Challenges implementing ATP testing include incompatibility with chlorine quenching agents and hold time sensitivity, which are not well-studied. Chlorinated distribution system samples were collected from two Canadian utilities, Metro Vancouver (n = 40 samples) and Halifax Water (n = 283). No significant correlations were observed between heterotrophic cell count (HPC) and cellular ATP, suggesting these do not correlate well in waters with low biological activity (median HPC < 2 CFU/mL). However, interpretation of HPC and cATP results (based on the HPC guideline of 100 CFU/mL and cATP of 10 pg/mL) yielded the same conclusion for 95% of samples, suggesting a potential decision-making framework to replace HPC with cATP. Moreover, cATP correlates better with free chlorine (p < 0.04) compared with HPC for one of the studied systems. Importantly, adding chlorine quench (10% sodium thiosulfate) did not produce significantly different cATP results, nor did analyzing at various hold times of 4-, 6-, and 24-h. This study supports the integration of ATP testing into existing sampling procedures for water utilities, as a sensitive, fast, and reliable monitoring method.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"18 1","pages":"63"},"PeriodicalIF":5.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536932/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Construction of multilayered gene circuits using de-novo-designed synthetic transcriptional regulators in cell-free systems. 在无细胞系统中利用重新设计的合成转录调节因子构建多层基因回路。
IF 5.7 3区 生物学
Journal of Biological Engineering Pub Date : 2024-11-05 DOI: 10.1186/s13036-024-00459-8
Mingming Zhao, Jeongwon Kim, Jiayan Jiao, Yelin Lim, Xianai Shi, Shaobin Guo, Jongmin Kim
{"title":"Construction of multilayered gene circuits using de-novo-designed synthetic transcriptional regulators in cell-free systems.","authors":"Mingming Zhao, Jeongwon Kim, Jiayan Jiao, Yelin Lim, Xianai Shi, Shaobin Guo, Jongmin Kim","doi":"10.1186/s13036-024-00459-8","DOIUrl":"10.1186/s13036-024-00459-8","url":null,"abstract":"<p><strong>Background: </strong>De-novo-designed synthetic transcriptional regulators have great potential as the genetic parts for constructing complex multilayered gene circuits. The design flexibility afforded by advanced nucleic acid sequence design tools vastly expands the repertoire of regulatory elements for circuit design. In principle, the design space of synthetic regulators should allow for the construction of regulatory circuits of arbitrary complexity; still, the orthogonality and robustness of such components have not been fully elucidated, thereby limiting the depth and width of synthetic circuits.</p><p><strong>Results: </strong>In this work, we systematically explored the design strategy of synthetic transcriptional regulators, termed switchable transcription terminators. Specifically, by redesigning key sequence domains, we created a high-performance switchable transcription terminator with a maximum fold change of 283.11 upon activation by its cognate input RNA. Further, an automated design algorithm was developed for these elements to improve orthogonality for a complex multi-layered circuit construction. The resulting orthogonal switchable transcription terminators could be used to construct a three-layer cascade circuit and a two-input three-layer OR gate.</p><p><strong>Conclusions: </strong>We demonstrated a practical strategy for designing standardized regulatory elements and assembling modular gene circuits, ultimately laying the foundation for the streamlined construction of complex synthetic gene circuits.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"18 1","pages":"64"},"PeriodicalIF":5.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11539451/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
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