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Inter-patient heterogeneity in the hepatic ischemia-reperfusion injury transcriptome: Implications for research and diagnostics 肝缺血再灌注损伤转录组的患者间异质性:对研究和诊断的影响
IF 5.4 2区 生物学
New biotechnology Pub Date : 2023-12-10 DOI: 10.1016/j.nbt.2023.12.001
Silvia Groiss , Christian Viertler , Marcel Kap , Gerwin Bernhardt , Hans-Jörg Mischinger , Anieta Sieuwerts , Cees Verhoef , Peter Riegman , Mogens Kruhøffer , David Svec , Sjoback Robert Sjöback , Karl-Friedrich Becker , Kurt Zatloukal
{"title":"Inter-patient heterogeneity in the hepatic ischemia-reperfusion injury transcriptome: Implications for research and diagnostics","authors":"Silvia Groiss ,&nbsp;Christian Viertler ,&nbsp;Marcel Kap ,&nbsp;Gerwin Bernhardt ,&nbsp;Hans-Jörg Mischinger ,&nbsp;Anieta Sieuwerts ,&nbsp;Cees Verhoef ,&nbsp;Peter Riegman ,&nbsp;Mogens Kruhøffer ,&nbsp;David Svec ,&nbsp;Sjoback Robert Sjöback ,&nbsp;Karl-Friedrich Becker ,&nbsp;Kurt Zatloukal","doi":"10.1016/j.nbt.2023.12.001","DOIUrl":"10.1016/j.nbt.2023.12.001","url":null,"abstract":"<div><p>Cellular responses induced by surgical procedure or ischemia-reperfusion injury (IRI) may severely alter transcriptome profiles and complicate molecular diagnostics. To investigate this effect, we characterized such pre-analytical effects in 143 non-malignant liver samples obtained from 30 patients at different time points of ischemia during surgery from two individual cohorts treated either with the Pringle manoeuvre or total vascular exclusion. Transcriptomics profiles were analyzed by Affymetrix microarrays and expression of selected mRNAs was validated by RT-PCR. We found 179 mutually deregulated genes which point to elevated cytokine signaling with NFκB as a dominant pathway in ischemia responses. In contrast to ischemia, reperfusion induced pro-apoptotic and pro-inflammatory cascades involving TNF, NFκB and MAPK pathways. <em>FOS</em> and <em>JUN</em> were down-regulated in steatosis compared to their up-regulation in normal livers. Surprisingly, molecular signatures of underlying primary and secondary cancers were present in non-tumor tissue. The reported inter-patient variability might reflect differences in individual stress responses and impact of underlying disease conditions. Furthermore, we provide a set of 230 pre-analytically highly robust genes identified from histologically normal livers (&lt;2% covariation across both cohorts) that might serve as reference genes and could be particularly suited for future diagnostic applications.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678423000699/pdfft?md5=4b881c8fd8540c502613033c766653cc&pid=1-s2.0-S1871678423000699-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138580831","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
Insights into the effects of anthropogenic activities on oil reservoir microbiome and metabolic potential 人类活动对油藏微生物群和代谢势的影响。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2023-11-30 DOI: 10.1016/j.nbt.2023.11.004
Fatou T. Mbow , Ali Akbari , Nicole Dopffel , Konstantin Schneider , Soujatya Mukherjee , Rainer U. Meckenstock
{"title":"Insights into the effects of anthropogenic activities on oil reservoir microbiome and metabolic potential","authors":"Fatou T. Mbow ,&nbsp;Ali Akbari ,&nbsp;Nicole Dopffel ,&nbsp;Konstantin Schneider ,&nbsp;Soujatya Mukherjee ,&nbsp;Rainer U. Meckenstock","doi":"10.1016/j.nbt.2023.11.004","DOIUrl":"10.1016/j.nbt.2023.11.004","url":null,"abstract":"<div><p>Microbial communities have long been observed in oil reservoirs, where the subsurface conditions are major drivers shaping their structure and functions. Furthermore, anthropogenic activities such as water flooding during oil production can affect microbial activities and community compositions in oil reservoirs through the injection of recycled produced water, often associated with biocides. However, it is still unclear to what extent the introduced chemicals and microbes influence the metabolic potential of the subsurface microbiome. Here we investigated an onshore oilfield in Germany (Field A) that undergoes secondary oil production along with biocide treatment to prevent souring and microbially induced corrosion (MIC). With the integrated approach of 16 S rRNA gene amplicon and shotgun metagenomic sequencing of water-oil samples from 4 production wells and 1 injection well, we found differences in microbial community structure and metabolic functions. In the injection water samples, amplicon sequence variants (ASVs) belonging to families such as <em>Halanaerobiaceae</em>, <em>Ectothiorhodospiraceae, Hydrogenophilaceae, Halobacteroidaceae, Desulfohalobiaceae,</em> and <em>Methanosarcinaceae</em> were dominant, while in the production water samples, ASVs of families such as <em>Thermotogaceae, Nitrospiraceae, Petrotogaceae, Syntrophaceae, Methanobacteriaceae,</em> and <em>Thermoprotei</em> were also dominant. The metagenomic analysis of the injection water sample revealed the presence of C1-metabolism, namely, genes involved in formaldehyde oxidation. Our analysis revealed that the microbial community structure of the production water samples diverged slightly from that of injection water samples. Additionally, a metabolic potential for oxidizing the applied biocide clearly occurred in the injection water samples indicating an adaptation and buildup of degradation capacity or resistance against the added biocide.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678423000675/pdfft?md5=0e53fd8641140d7b1fa1b284d4afb038&pid=1-s2.0-S1871678423000675-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138470632","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
Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control 操纵哺乳动物细胞工厂中的基因表达水平:实现多路控制的合成分子工具箱概述。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2023-11-30 DOI: 10.1016/j.nbt.2023.11.003
Peter Eisenhut , Nicolas Marx , Giulia Borsi , Maja Papež , Caterina Ruggeri , Martina Baumann , Nicole Borth
{"title":"Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control","authors":"Peter Eisenhut ,&nbsp;Nicolas Marx ,&nbsp;Giulia Borsi ,&nbsp;Maja Papež ,&nbsp;Caterina Ruggeri ,&nbsp;Martina Baumann ,&nbsp;Nicole Borth","doi":"10.1016/j.nbt.2023.11.003","DOIUrl":"10.1016/j.nbt.2023.11.003","url":null,"abstract":"<div><p>Mammalian cells have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell’s phenotype. Modulating cellular phenotypes is of major interest to study their role in disease or to reprogram cells for the manufacturing of recombinant products, such as biopharmaceuticals. Cells of mammalian origin, for example Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Early genetic engineering approaches to alter their phenotype have often been attempted by “uncontrolled” overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, highlight that rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much more precision than such “uncontrolled” approaches. To this end, synthetic biology tools have been generated that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools used in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678423000663/pdfft?md5=3605aabf6c33227befedf2475e1ecaa6&pid=1-s2.0-S1871678423000663-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138470640","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
Artificial intelligence / machine-learning tool for post-market surveillance of in vitro diagnostic assays 用于体外诊断检测上市后监测的人工智能/机器学习工具。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2023-11-29 DOI: 10.1016/j.nbt.2023.11.005
Joanna Reniewicz , Vinay Suryaprakash , Justyna Kowalczyk , Anna Blacha , Greg Kostello , Haiming Tan , Yan Wang , Patrick Reineke , Davide Manissero
{"title":"Artificial intelligence / machine-learning tool for post-market surveillance of in vitro diagnostic assays","authors":"Joanna Reniewicz ,&nbsp;Vinay Suryaprakash ,&nbsp;Justyna Kowalczyk ,&nbsp;Anna Blacha ,&nbsp;Greg Kostello ,&nbsp;Haiming Tan ,&nbsp;Yan Wang ,&nbsp;Patrick Reineke ,&nbsp;Davide Manissero","doi":"10.1016/j.nbt.2023.11.005","DOIUrl":"10.1016/j.nbt.2023.11.005","url":null,"abstract":"<div><p>The study compares an artificial intelligence technology with traditional manual search of literature databases to assess the accuracy and efficiency of retrieving relevant articles for post-market surveillance of in vitro diagnostic and medical devices under the Medical Device Regulation and In Vitro Diagnostic Medical Device Regulation. Over a 3-year period, literature searches and technical assessment searches were performed manually or using the Huma.AI platform to retrieve relevant articles related to the safety and performance of selected in vitro diagnostic and medical devices. The manual search involved refined keyword searches, screening of titles/abstracts / full text, and extraction of relevant information. The Huma.AI search utilized advanced caching techniques and a natural language processing system to identify relevant reports. Searches were conducted on PubMed and PubMed Central. The number of identified relevant reports, precision rates, and time requirements for each approach were analyzed. The Huma.AI system outperformed the manual search in terms of the number of identified relevant articles in almost all cases. The average precision rates per year were significantly higher and more consistent with the Huma.AI search compared with the manual search. The Huma.AI system also took significantly less time to perform the searches and analyze the outputs than the manual search. The study demonstrated that the Huma.AI platform was more effective and efficient in identifying relevant articles compared with the manual approach.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678423000687/pdfft?md5=7d7dc7859aecbb377dbb37507f5cc0ed&pid=1-s2.0-S1871678423000687-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138470631","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
Effect of seawater on the biomass composition of Spirulina produced at a pilot-scale 海水对利用海水生产的螺旋藻生物量组成的影响。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2023-11-14 DOI: 10.1016/j.nbt.2023.11.002
Silvia Villaró , Marco García-Vaquero , Lara Morán , Carlos Álvarez , Eduarda Melo Cabral , Tomas Lafarga
{"title":"Effect of seawater on the biomass composition of Spirulina produced at a pilot-scale","authors":"Silvia Villaró ,&nbsp;Marco García-Vaquero ,&nbsp;Lara Morán ,&nbsp;Carlos Álvarez ,&nbsp;Eduarda Melo Cabral ,&nbsp;Tomas Lafarga","doi":"10.1016/j.nbt.2023.11.002","DOIUrl":"10.1016/j.nbt.2023.11.002","url":null,"abstract":"<div><p>The microalga <em>Arthrospira platensis</em> BEA 005B was produced in 11.4 m<sup>3</sup> raceway photobioreactors and a culture medium based on commercial fertilisers and either freshwater or seawater. The biomass productivity of the reactors operated at a fixed dilution rate of 0.3 day<sup>−1</sup> decreased from 22.9 g·m<sup>−2</sup>·day<sup>−1</sup> when operated using freshwater to 16.3 g·m<sup>−2</sup>·day<sup>−1</sup> when the biomass was produced using seawater. The protein content of the biomass produced in seawater was lower; however, the content of essential amino acids including valine, leucine and isoleucine was higher. Seawater also triggered the production of carotenoids and altered the synthesis and accumulation of fatty acids. For example, the biomass produced using seawater showed a 319% and 210% higher content of oleic and eicosenoic acid, respectively. The results demonstrate that it is possible to produce the selected microalga using seawater after an adaptation period and that the composition of the produced biomass is suitable for food applications.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678423000651/pdfft?md5=7f3640af8e127bde72d260631449bbdb&pid=1-s2.0-S1871678423000651-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134649442","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
Significance of poly(ethylene terephthalate) (PET) substrate crystallinity on enzymatic degradation 聚对苯二甲酸乙二醇酯(PET)基质结晶度对酶降解的意义。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2023-11-07 DOI: 10.1016/j.nbt.2023.11.001
Thore Bach Thomsen , Kristoffer Almdal , Anne S. Meyer
{"title":"Significance of poly(ethylene terephthalate) (PET) substrate crystallinity on enzymatic degradation","authors":"Thore Bach Thomsen ,&nbsp;Kristoffer Almdal ,&nbsp;Anne S. Meyer","doi":"10.1016/j.nbt.2023.11.001","DOIUrl":"10.1016/j.nbt.2023.11.001","url":null,"abstract":"<div><p>Poly(ethylene terephthalate) (PET) is a semi-crystalline plastic polyester material with a global production volume of 83 Mt/year. PET is mainly used in textiles, but also widely used for packaging materials, notably plastic bottles, and is a major contributor to environmental plastic waste accumulation. Now that enzymes have been demonstrated to catalyze PET degradation, new options for sustainable bio-recycling of PET materials via enzymatic catalysis have emerged. The enzymatic degradation rate is strongly influenced by the properties of PET, notably the degree of crystallinity, <em>X</em><sub>C</sub>. The higher the <em>X</em><sub>C</sub> of the PET material, the slower the enzymatic rate. Crystallization of PET, resulting in increased <em>X</em><sub>C</sub>, is induced thermally (via heating) and/or mechanically (via stretching), and the <em>X</em><sub>C</sub> of most PET plastic bottles and microplastics exceeds what currently known enzymes can readily degrade. The enzymatic action occurs at the surface of the insoluble PET material and improves when the polyester chain mobility increases. The chain mobility increases drastically when the temperature exceeds the glass transition temperature, <em>T</em><sub>g</sub>, which is ∼40 °C at the surface layer of PET. Since PET crystallization starts at 70 °C, the ideal temperature for enzymatic degradation is just below 70 °C to balance high chain mobility and enzymatic reaction activation without inducing crystal formation. This paper reviews the current understanding on the properties of PET as an enzyme substrate and summarizes the most recent knowledge of how the crystalline and amorphous regions of PET form, and how the <em>X</em><sub>C</sub> and the <em>T</em><sub>g</sub> impact the efficiency of enzymatic PET degradation.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S187167842300064X/pdfft?md5=752cdfce83c04e5ab776cda7c4bbcc56&pid=1-s2.0-S187167842300064X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71522196","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
Effective application of immobilized second generation industrial Saccharomyces cerevisiae strain on consolidated bioprocessing 固定化第二代工业酿酒酵母菌株在联合生物加工中的有效应用。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2023-10-31 DOI: 10.1016/j.nbt.2023.10.011
Márcio D.N. Ramos , Juliana P. Sandri , Arne Claes , Bruna T. Carvalho , Johan M. Thevelein , Teresa C. Zangirolami , Thais S. Milessi
{"title":"Effective application of immobilized second generation industrial Saccharomyces cerevisiae strain on consolidated bioprocessing","authors":"Márcio D.N. Ramos ,&nbsp;Juliana P. Sandri ,&nbsp;Arne Claes ,&nbsp;Bruna T. Carvalho ,&nbsp;Johan M. Thevelein ,&nbsp;Teresa C. Zangirolami ,&nbsp;Thais S. Milessi","doi":"10.1016/j.nbt.2023.10.011","DOIUrl":"10.1016/j.nbt.2023.10.011","url":null,"abstract":"<div><p>Integrated bioprocessing strategies can facilitate ethanol production from both cellulose and hemicellulose fractions of lignocellulosic biomass. Consolidated bioprocessing (CBP) is an approach that combines enzyme production, biomass hydrolysis and sugar fermentation in a single step. However, technologies that propose the use of microorganisms together with solid biomass present the difficulty of the recovery and reuse of the biocatalyst, which can be overcome by cell immobilization. In this regard, this work applied immobilized cells of AC14 yeast, a recombinant yeast that secretes 7 hydrolytic enzymes, in the CBP process in a successful proof-of-concept for the enzyme access to the substrate polymers. The most appropriate cell load for CBP under the conditions studied with immobilized cells was selected among three optical densities (OD) 10, 55 and 100. These experiments were performed with free cells to ensure that the results were not biased by mass limitations effects. OD 10 achieved 100% of the sugar consumption and the higher specific production of enzymes, being selected for further studies. Diffusional effects were observed with immobilized cells under static conditions. However, mass transfer limitations were mitigated under agitation, with an 18.5% increase in substrate consumption rate (from 2.7 to 3.5 g/L/h), reaching the same substrate uptake rates as free cells. In addition, immobilized cells achieved 100% hydrolysis and consumption of all substrates offered within only 12 h. Overall, this is the first report of a successful application of immobilized yeast cells in CBP processes for bioethanol production, a promising technology that can be extended to other biorefinery bioproducts.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678423000626/pdfft?md5=8495c29f29896b578dc0d94f203cf8f1&pid=1-s2.0-S1871678423000626-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71425457","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: 1
EBRC: Enhancing bioeconomy through research and communication 欧洲复兴开发银行:通过研究和交流增强生物经济。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2023-10-31 DOI: 10.1016/j.nbt.2023.10.012
Tae Seok Moon
{"title":"EBRC: Enhancing bioeconomy through research and communication","authors":"Tae Seok Moon","doi":"10.1016/j.nbt.2023.10.012","DOIUrl":"10.1016/j.nbt.2023.10.012","url":null,"abstract":"<div><p>On September 12, 2022, President Biden issued Executive Order 14081 to enable the progress of biomanufacturing and biotechnology. This timely initiative will help overcome many challenging issues, and its potential impacts will be huge. This article discusses eight recommendations to make this US national initiative successful, encourage other nations to consider similar initiatives, and create a better world for the next generations.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678423000638/pdfft?md5=1e7c672316fcf9314010a863f7578597&pid=1-s2.0-S1871678423000638-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71425456","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
The stressostat: A novel approach in adaptive laboratory evolution to improve end-product resistance 应力稳定仪:一种在适应性实验室进化中提高最终产品抵抗力的新方法。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2023-10-23 DOI: 10.1016/j.nbt.2023.10.010
Sylviani Hartono, Marlisa F.A. Meijerink, Tjakko Abee, Eddy J. Smid, Oscar van Mastrigt
{"title":"The stressostat: A novel approach in adaptive laboratory evolution to improve end-product resistance","authors":"Sylviani Hartono,&nbsp;Marlisa F.A. Meijerink,&nbsp;Tjakko Abee,&nbsp;Eddy J. Smid,&nbsp;Oscar van Mastrigt","doi":"10.1016/j.nbt.2023.10.010","DOIUrl":"10.1016/j.nbt.2023.10.010","url":null,"abstract":"<div><p>End-product inhibition in pH-controlled batch cultures, is the major limiting factor for bacterial biomass formation in the starter culture industry as well as in many other biotechnological processes. Adaptive laboratory evolution (ALE) has emerged over the past decades as a powerful tool for phenotype optimization, but none of the existing ALE methods could select for improved end-product resistance. Therefore, we developed the stressostat (STress Resistance Evolution in Substrate Surplus) as a novel continuous ALE method. Stressostat cultivation applies end-product concentrations as constant evolutionary pressure on microorganisms in the presence of substrate surplus. In this study, we improved the lactate resistance of <em>Lactococcus lactis</em> FM03P in 35 days of stressostat cultivations. The lactate concentrations increased over time from 530 to 675 mM, indicating the successful selection for variants with improved lactate resistance. Thirty-four variants were isolated and grouped into four clusters based on their growth rates at high lactate concentrations. In the high-throughput screening without pH control, most isolated variants could grow at high lactate concentrations (870–928 mM), while the wild type was completely inhibited. The variants grew slower than wild type at low lactate media indicating possible evolutionary trade-off. However, in pH-controlled batch cultivations, most variants produced more biomass than the wild type. In conclusion, stressostat cultivation is a valuable method to obtain <em>L. lactis</em> variants with improved end-product resistance and further characterization is needed to elucidate underlying resistance mechanisms and potential industrial applications.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678423000614/pdfft?md5=cad7fdcb13716ed1fadfd8cbe1be8a8f&pid=1-s2.0-S1871678423000614-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50162341","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
Effects of municipal waste compost on microbial biodiversity and energy production in terrestrial microbial fuel cells 城市垃圾堆肥对陆生微生物燃料电池微生物多样性和能量产生的影响。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2023-10-22 DOI: 10.1016/j.nbt.2023.10.009
Gian Luigi Garbini , Anna Barra Caracciolo , Ludovica Rolando , Andrea Visca , Domenico Borello , Carlotta Cosentini , Gabriele Gagliardi , Ioannis Ieropoulos , Paola Grenni
{"title":"Effects of municipal waste compost on microbial biodiversity and energy production in terrestrial microbial fuel cells","authors":"Gian Luigi Garbini ,&nbsp;Anna Barra Caracciolo ,&nbsp;Ludovica Rolando ,&nbsp;Andrea Visca ,&nbsp;Domenico Borello ,&nbsp;Carlotta Cosentini ,&nbsp;Gabriele Gagliardi ,&nbsp;Ioannis Ieropoulos ,&nbsp;Paola Grenni","doi":"10.1016/j.nbt.2023.10.009","DOIUrl":"10.1016/j.nbt.2023.10.009","url":null,"abstract":"<div><p>Microbial Fuel Cells (MFCs) transform organic matter into electricity through microbial electrochemical reactions catalysed on anodic and cathodic half-cells. Terrestrial MFCs (TMFCs) are a bioelectrochemical system for bioelectricity production as well as soil remediation. In TMFCs, the soil is the ion-exchange electrolyte, whereas a biofilm on the anode oxidises organic matter through electroactive bacteria. Little is known of the overall microbial community composition in a TMFC, which impedes complete exploitation of the potential to generate energy in different soil types. In this context, an experiment was performed to reveal the prokaryotic community structure in single chamber TMFCs with soil in the presence and absence of a municipal waste compost (3% w/v). The microbial community was assessed on the anode and cathode and in bulk soil at the end of the experiment (54 days). Moreover, TMFC electrical performance (voltage and power) was also evaluated over the experimental period, varying the external resistance to improve performance. Compost stimulated soil microbial activity, in line with a general increase in voltage and power. Significant differences were observed in the microbial communities between initial soil conditions and TMFCs, and between the anode, cathode and bulk soil in the presence of the compost. Several electroactive genera (<em>Bacillus</em>, <em>Fulvivirga</em>, <em>Burkholdeira</em> and <em>Geobacter</em>) were found at the anode in the presence of compost. Overall, the use of municipal waste compost significantly increased the performance of the MFCs in terms of electrical power and voltage generated, not least thanks to the selective pressure towards electroactive bacteria on the anode.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678423000602/pdfft?md5=293557ae0fb4e64303b7c80988bfbb03&pid=1-s2.0-S1871678423000602-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50158441","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}
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