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Comprehensive rheological analysis of structurally related acetan-like heteroexopolysaccharides from two Kozakia baliensis strains in surfactants and galactomannan blends 对表面活性剂和半乳甘露聚糖混合物中来自两种巴厘岛楮树菌株的结构相关的类乙缩醛杂多糖进行综合流变学分析。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-05-13 DOI: 10.1016/j.nbt.2024.05.003
Julia Schilling, Jochen Schmid
{"title":"Comprehensive rheological analysis of structurally related acetan-like heteroexopolysaccharides from two Kozakia baliensis strains in surfactants and galactomannan blends","authors":"Julia Schilling,&nbsp;Jochen Schmid","doi":"10.1016/j.nbt.2024.05.003","DOIUrl":"10.1016/j.nbt.2024.05.003","url":null,"abstract":"<div><p>Natural biopolymers become increasingly attractive as bio-based alternatives to petrol-based rheological modifiers, especially in personal care applications. However, many polysaccharides exhibit undesired properties in cosmetic applications such as limited viscosifying characteristics, unpleasant sensory properties, or incompatibility with certain formulation compounds. Here, a comprehensive rheological analysis of non-decorated acetan-like heteroexopolysaccharides derived from two <em>Kozakia baliensis</em> strains was performed in selected surfactant formulations. The results were compared to native xanthan gum and a genetically engineered xanthan variant, Xan∆<em>gumFGL</em>, which lacks any acetyl- and pyruvyl moieties and whose rheological properties are unaffected by saline environments. All four polysaccharides displayed a highly similar rheological performance in the non-ionic surfactant lauryl glucoside, while the rheological properties differed in amphoteric and anionic surfactants cocamidopropyl betaine and sodium laureth sulfate due to minor changes in side chain composition. Polysaccharide precipitation was observed in the presence of the cationic surfactant. Nevertheless, the native heteroexopolysaccharide derived from <em>K. baliensis</em> LMG 27018 shows significant potential as a salt-independent rheological modifier compared to the genetically engineered Xan∆<em>gumFGL</em> variant. In addition, blends of heteroexopolysaccharides from <em>K. baliensis</em> and several galactomannans displayed synergistic effects which were comparable to native xanthan gum-galactomannan blends. This study shows that heteroexopolysaccharides of <em>K. baliensis</em> are capable of further extending the portfolio of bio-based rheological modifiers.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000177/pdfft?md5=43daa64bf5b6e893faf2f82fc9f11b40&pid=1-s2.0-S1871678424000177-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140945229","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
Extracellular Vesicles based STAT3 delivery as innovative therapeutic approach to restore STAT3 signaling deficiency 基于细胞外囊泡的 STAT3 递送是恢复 STAT3 信号缺乏的创新治疗方法。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-05-09 DOI: 10.1016/j.nbt.2024.05.001
Ilaria Bettin , Martina Brattini , Elham Ataie Kachoie , Stefano Capaldi , Muhammed Ashiq Thalappil , Paolo Bernardi , Isacco Ferrarini , Gregor Fuhrmann , Sofia Mariotto , Elena Butturini
{"title":"Extracellular Vesicles based STAT3 delivery as innovative therapeutic approach to restore STAT3 signaling deficiency","authors":"Ilaria Bettin ,&nbsp;Martina Brattini ,&nbsp;Elham Ataie Kachoie ,&nbsp;Stefano Capaldi ,&nbsp;Muhammed Ashiq Thalappil ,&nbsp;Paolo Bernardi ,&nbsp;Isacco Ferrarini ,&nbsp;Gregor Fuhrmann ,&nbsp;Sofia Mariotto ,&nbsp;Elena Butturini","doi":"10.1016/j.nbt.2024.05.001","DOIUrl":"10.1016/j.nbt.2024.05.001","url":null,"abstract":"<div><p>Extracellular Vesicles (EVs) have been proposed as a promising tool for drug delivery because of their natural ability to cross biological barriers, protect their cargo, and target specific cells. Moreover, EVs are not recognized by the immune system as foreign, reducing the risk of an immune response and enhancing biocompatibility. Herein, we proposed an alternative therapeutic strategy to restore STAT3 signaling exploiting STAT3 loaded EVs. This approach could be useful in the treatment of Autosomal Dominant Hyper-IgE Syndrome (AD-HIES), a rare primary immunodeficiency and multisystem disorder due to the presence of mutations in <em>STAT3</em> gene. These mutations alter the signal transduction of STAT3, thereby impeding Th17 CD4<sup>+</sup> cell differentiation that leads to the failure of immune response. We set up a simple and versatile method in which EVs were loaded with fully functional STAT3 protein. Moreover, our method allows to follow the uptake of STAT3 loaded vesicles inside cells due to the presence of EGFP in the EGFP-STAT3 fusion protein construct. Taken together, the data presented in this study could provide the scientific background for the development of new therapeutic strategy aimed to restore STAT3 signaling in STAT3 misfunction associated diseases like AD-HIES. In the future, the administration of fully functional wild type STAT3 to CD4+ T cells of AD-HIES patients might compensate its loss of function and would be beneficial for these patients, lowering the risk of infections, the use of medications, and hospitalizations.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000165/pdfft?md5=538c798d7d3902f2878350ac26fadfb7&pid=1-s2.0-S1871678424000165-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140909156","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
Semi-continuous cultivation of EPS-producing marine cyanobacteria: A green biotechnology to remove dissolved metals obtaining metal-organic materials 半连续培养产生 EPS 的海洋蓝藻:从金属有机材料中去除溶解金属的绿色生物技术。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-05-05 DOI: 10.1016/j.nbt.2024.04.004
Matilde Ciani , Francesca Decorosi , Claudio Ratti , Roberto De Philippis , Alessandra Adessi
{"title":"Semi-continuous cultivation of EPS-producing marine cyanobacteria: A green biotechnology to remove dissolved metals obtaining metal-organic materials","authors":"Matilde Ciani ,&nbsp;Francesca Decorosi ,&nbsp;Claudio Ratti ,&nbsp;Roberto De Philippis ,&nbsp;Alessandra Adessi","doi":"10.1016/j.nbt.2024.04.004","DOIUrl":"10.1016/j.nbt.2024.04.004","url":null,"abstract":"<div><p>Given the necessity for bioprocesses scaling-up, the present study aims to explore the potential of three marine cyanobacteria and a consortium, cultivated in semi-continuous mode, as a green approach for <em>i</em>) continuous exopolysaccharide-rich biomass production and <em>ii</em>) removal of positively charged metals (Cu, Ni, Zn) from mono and multi-metallic solutions. To ensure the effectiveness of both cellular and released exopolysaccharides, weekly harvested whole cultures were confined in dialysis tubings. The results revealed that all the tested cyanobacteria have a stronger affinity towards Cu in mono and three-metal systems. Despite the amount of metals removed per gram of biomass decreased with higher biosorbent dosage, the more soluble carbohydrates were produced, the greater was the metal uptake, underscoring the pivotal role of released exopolysaccharides in metal biosorption. According to this, <em>Dactylococcopsis salina</em> 16Som2 showed the highest carbohydrate productivity (142 mg L<sup>−1</sup> d<sup>−1</sup>) and metal uptake (84 mg Cu g<sup>−1</sup> biomass) representing a promising candidate for further studies. The semi-continuous cultivation of marine cyanobacteria here reported assures a schedulable production of exopolysaccharide-rich biosorbents with high metal removal and recovery potential, even from multi-metallic solutions, as a step forward in the industrial application of cyanobacteria.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000153/pdfft?md5=342442f2d0004a74744e55543fceb17d&pid=1-s2.0-S1871678424000153-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140876907","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
Analysis of the molecular basis for the non-amylolytic and non-proteolytic nature of Aspergillus vadensis CBS 113365 瓦登曲霉(Aspergillus vadensis)CBS 113365 非甲酰溶解和非蛋白溶解性质的分子基础分析
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-05-01 DOI: 10.1016/j.nbt.2024.04.003
Dujuan Liu , Sandra Garrigues , Helena Culleton , Vincent A. McKie , Ronald P. de Vries
{"title":"Analysis of the molecular basis for the non-amylolytic and non-proteolytic nature of Aspergillus vadensis CBS 113365","authors":"Dujuan Liu ,&nbsp;Sandra Garrigues ,&nbsp;Helena Culleton ,&nbsp;Vincent A. McKie ,&nbsp;Ronald P. de Vries","doi":"10.1016/j.nbt.2024.04.003","DOIUrl":"https://doi.org/10.1016/j.nbt.2024.04.003","url":null,"abstract":"<div><p><em>Aspergillus vadensis</em> CBS 113365, a close relative of <em>A. niger</em>, has been suggested as a more favourable alternative for recombinant protein production as it does not acidify the culture medium and produces very low levels of extracellular proteases. The aim of this study was to investigate the underlying cause of the non-amylolytic and non-proteolytic phenotype of <em>A. vadensis</em> CBS 113365. Our results demonstrate that the non-functionality of the amylolytic transcription factor AmyR in <em>A. vadensis</em> CBS 113365 is primarily attributed to the lack of functionality of its gene’s promoter sequence. In contrast, a different mechanism is likely causing the lack of PrtT activity, which is the main transcriptional regulator of protease production. The findings presented here not only expand our understanding of the genetic basis behind the distinct characteristics of <em>A. vadensis</em> CBS 113365, but also underscore its potential as a favourable alternative for recombinant protein production.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000141/pdfft?md5=5eda25cb7805f55b9da5e9cc3e40155a&pid=1-s2.0-S1871678424000141-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140825359","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
Genomic mining of Geobacillus stearothermophilus GF16 for xylose production from hemicellulose-rich biomasses using secreted enzymes 利用分泌酶从富含半纤维素的生物质中生产木糖的嗜热地衣芽孢杆菌 GF16 基因组挖掘
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-04-28 DOI: 10.1016/j.nbt.2024.04.002
Miriam Carbonaro , Martina Aulitto , Scott Mazurkewich , Alessia Di Fraia , Patrizia Contursi , Danila Limauro , Johan Larsbrink , Gabriella Fiorentino
{"title":"Genomic mining of Geobacillus stearothermophilus GF16 for xylose production from hemicellulose-rich biomasses using secreted enzymes","authors":"Miriam Carbonaro ,&nbsp;Martina Aulitto ,&nbsp;Scott Mazurkewich ,&nbsp;Alessia Di Fraia ,&nbsp;Patrizia Contursi ,&nbsp;Danila Limauro ,&nbsp;Johan Larsbrink ,&nbsp;Gabriella Fiorentino","doi":"10.1016/j.nbt.2024.04.002","DOIUrl":"https://doi.org/10.1016/j.nbt.2024.04.002","url":null,"abstract":"<div><p>The valorization of lignocellulosic biomass, derived from various bio-waste materials, has received considerable attention as a sustainable approach to improve production chains while reducing environmental impact. Microbial enzymes have emerged as key players in the degradation of polysaccharides, offering versatile applications in biotechnology and industry. Among these enzymes, glycoside hydrolases (GHs) play a central role. Xylanases, in particular, are used in a wide range of applications and are essential for the production of xylose, which can be fermented into bioethanol or find use in many other industries. Currently, fungal secretomes dominate as the main reservoir of lignocellulolytic enzymes, but thermophilic microorganisms offer notable advantages in terms of enzyme stability and production efficiency. Here we present the genomic characterization of <em>Geobacillus stearothermophilus</em> GF16 to identify genes encoding putative enzymes involved in lignocellulose degradation. Thermostable GHs secreted by <em>G. stearothermophilus</em> GF16 were investigated and found to be active on different natural polysaccharides and synthetic substrates, revealing an array of inducible GH activities. In particular, the concentrated secretome possesses significant thermostable xylanase and β-xylosidase activities (5 ×10<sup>3</sup> U/L and 1.7 ×10<sup>5</sup> U/L, respectively), highlighting its potential for application in biomass valorization. We assessed the hemicellulose hydrolysis capabilities of various agri-food wastes using the concentrated secretome of the strain cultivated on xylan. An impressive 300-fold increase in xylose release compared to a commercially available cocktail was obtained with the secretome, underscoring the remarkable efficacy of this approach.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S187167842400013X/pdfft?md5=d59b9f12440fce19aea3e8fecc147964&pid=1-s2.0-S187167842400013X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140816337","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
A novel data-driven model for prediction and adaptive control of pH in raceway reactor for microalgae cultivation 用于预测和自适应控制微藻培养赛道反应器 pH 值的新型数据驱动模型
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-04-12 DOI: 10.1016/j.nbt.2024.04.001
M. Caparroz , J.L. Guzmán , M. Berenguel , F.G. Acién
{"title":"A novel data-driven model for prediction and adaptive control of pH in raceway reactor for microalgae cultivation","authors":"M. Caparroz ,&nbsp;J.L. Guzmán ,&nbsp;M. Berenguel ,&nbsp;F.G. Acién","doi":"10.1016/j.nbt.2024.04.001","DOIUrl":"10.1016/j.nbt.2024.04.001","url":null,"abstract":"<div><p>This work proposes a new data-driven model to estimate and predict pH dynamics in freshwater raceway photobioreactors. The resulting model is based purely on data measured from the reactor and divides the pH dynamics into two different behaviors. One behavior is described by the variation of pH due to the photosynthesis phenomena made by microalgae; and the other comes from the effect of CO<sub>2</sub> injections into the medium for control purposes. Moreover, it was observed that the model parameters vary throughout the day depending on the weather conditions and reactor status. Thus, a decision tree algorithm is also developed to capture the parameter variation based on measured variables of the system, such as solar radiation, medium temperature, and medium level. The proposed model has been validated for a data set of more than 100 days during 10 months in a semi-industrial raceway reactor, covering a wide range of weather and system scenarios. Additionally, the proposed model was used to design an adaptive control algorithm which was also experimentally tested and compared with a classical fixed parameter control approach.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000128/pdfft?md5=571f8dcc323cebe03d51d6b8ec1c7fa8&pid=1-s2.0-S1871678424000128-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140616273","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
Complete genome sequence and transcriptome response to vitamin C supplementation of Novacetimonas hansenii SI1 - producer of highly-stretchable cellulose 高弹性纤维素生产者 Novacetimonas hansenii SI1 的完整基因组序列和转录组对维生素 C 补充的反应。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-03-24 DOI: 10.1016/j.nbt.2024.03.004
Małgorzata Ryngajłło , Izabela Cielecka , Maurycy Daroch
{"title":"Complete genome sequence and transcriptome response to vitamin C supplementation of Novacetimonas hansenii SI1 - producer of highly-stretchable cellulose","authors":"Małgorzata Ryngajłło ,&nbsp;Izabela Cielecka ,&nbsp;Maurycy Daroch","doi":"10.1016/j.nbt.2024.03.004","DOIUrl":"10.1016/j.nbt.2024.03.004","url":null,"abstract":"<div><p><em>Novacetimonas hansenii</em> SI1, previously known as <em>Komagataeibacter hansenii</em>, produces bacterial nanocellulose (BNC) with unique ability to stretch. The addition of vitamin C in the culture medium increases the porosity of the membranes and their stretchability making them highly moldable. To better understand the genetic background of this strain, we obtained its complete genome sequence using a hybrid sequencing and assembly strategy. We described the functional regions in the genome which are important for the synthesis of BNC and acetan-like II polymer. We next investigated the effect of 1% vitamin C supplementation on the global gene expression profile using RNA sequencing. Our transcriptomic readouts imply that vitamin C functions mainly as a reducing agent. We found that the changes in cellular redox status are balanced by strong repression of the sulfur assimilation pathway. Moreover, in the reduced conditions, glucose oxidation is decreased and alternative pathways for energy generation, such as acetate accumulation, are activated. The presence of vitamin C negatively influences acetan-like II polymer biosynthesis, which may explain the lowered yield and changed mechanical properties of BNC. The results of this study enrich the functional characteristics of the genomes of the efficient producers of the <em>N. hansenii</em> species. Improved understanding of the adaptation to the presence of vitamin C at the molecular level has important guiding significance for influencing the biosynthesis of BNC and its morphology.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000116/pdfft?md5=5fb3e469f4ec4a21d4468ea9cded0349&pid=1-s2.0-S1871678424000116-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140294116","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
Food and human health applications of edible mushroom by-products 食用菌副产品在食品和人类健康方面的应用。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-03-22 DOI: 10.1016/j.nbt.2024.03.003
Pablo Navarro-Simarro , Lourdes Gómez-Gómez , Oussama Ahrazem , Ángela Rubio-Moraga
{"title":"Food and human health applications of edible mushroom by-products","authors":"Pablo Navarro-Simarro ,&nbsp;Lourdes Gómez-Gómez ,&nbsp;Oussama Ahrazem ,&nbsp;Ángela Rubio-Moraga","doi":"10.1016/j.nbt.2024.03.003","DOIUrl":"10.1016/j.nbt.2024.03.003","url":null,"abstract":"<div><p>Mushroom waste can account for up to 50% of the total mushroom mass. Spent mushroom substrate, misshapen mushrooms, and mushroom stems are examples of mushroom byproducts. In ancient cultures, fungi were prized for their medicinal properties. Aqueous extracts containing high levels of β-glucans as functional components capable of providing prebiotic polysaccharides and improved texture to foods have been widely used and new methods have been tested to improve extraction yields. Similarly, the addition of insoluble polysaccharides controls the glycemic index, counteracting the effects of increasingly high-calorie diets. Numerous studies support these benefits <em>in vitro</em>, but evidence <em>in vivo</em> is scarce. Nonetheless, many authors have created a variety of functional foods, ranging from yogurt to noodles. In this review, we focus on the pharmacological properties of edible mushroom by-products, and the possible risks derived from its consumption. By incorporating these by-products into human or animal feed formulations, mushroom producers will be able to fully optimize crop use and pave the way for the industry to move toward a zero-waste paradigm.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000104/pdfft?md5=2d7ef8c186d307246adff8c25d489f3e&pid=1-s2.0-S1871678424000104-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140194282","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
A monodispersed metal-complexing peptide-based polymer for mass cytometry enabling spectral applications 向《新生物技术》杂志投稿的全文 一种单分散金属络合肽基聚合物,可用于质谱分析。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-03-16 DOI: 10.1016/j.nbt.2024.03.002
Jan Verhoeff , Saskia van Asten , Lisan Kuijper , Marlous van den Braber , Erika Amstalden-van Hove , Rob Haselberg , Hakan Kalay , Juan J. Garcia-Vallejo
{"title":"A monodispersed metal-complexing peptide-based polymer for mass cytometry enabling spectral applications","authors":"Jan Verhoeff ,&nbsp;Saskia van Asten ,&nbsp;Lisan Kuijper ,&nbsp;Marlous van den Braber ,&nbsp;Erika Amstalden-van Hove ,&nbsp;Rob Haselberg ,&nbsp;Hakan Kalay ,&nbsp;Juan J. Garcia-Vallejo","doi":"10.1016/j.nbt.2024.03.002","DOIUrl":"10.1016/j.nbt.2024.03.002","url":null,"abstract":"<div><p>We report the synthesis of a novel class of metal-complexing peptide-based polymers, which we name HyperMAPs (<strong>Hyper</strong>-loaded <strong>M</strong>et<strong>A</strong>l-complexed <strong>P</strong>olymers). The controlled solid-phase synthesis of HyperMAPs’ scaffold peptide provides our polymer with a well-defined molecular structure that allows for an accurate on-design assembly of a wide variety of metals. The peptide-scaffold features a handle for direct conjugation to antibodies or any other biomolecules by means of a thiol-maleimide-click or aldehyde-oxime reaction, a fluorogenic moiety for biomolecule conjugation tracking, and a well-defined number of functional groups for direct incorporation of metal-chelator complexes. Since metal-chelator complexes are prepared in a separate reaction prior to incorporation to the peptide scaffold, polymers can be designed to contain specific ratios of metal isotopes, providing each polymer with a unique CyTOF spectral fingerprint. We demonstrate the complexing of 21 different metals using two different chelators and provide evidence of the application of HyperMAPs on a 13 parameter CyTOF panel and compare its performance to monoisotopic metal-conjugated antibodies.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000098/pdfft?md5=f176ca2f30fe15394a5e0e05ea56bde6&pid=1-s2.0-S1871678424000098-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140143910","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
Learning vs. understanding: When does artificial intelligence outperform process-based modeling in soil organic carbon prediction? 学习与理解:在土壤有机碳预测中,人工智能何时才能胜过基于过程的建模?
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-03-08 DOI: 10.1016/j.nbt.2024.03.001
Luca G. Bernardini , Christoph Rosinger , Gernot Bodner , Katharina M. Keiblinger , Emma Izquierdo-Verdiguier , Heide Spiegel , Carl O. Retzlaff , Andreas Holzinger
{"title":"Learning vs. understanding: When does artificial intelligence outperform process-based modeling in soil organic carbon prediction?","authors":"Luca G. Bernardini ,&nbsp;Christoph Rosinger ,&nbsp;Gernot Bodner ,&nbsp;Katharina M. Keiblinger ,&nbsp;Emma Izquierdo-Verdiguier ,&nbsp;Heide Spiegel ,&nbsp;Carl O. Retzlaff ,&nbsp;Andreas Holzinger","doi":"10.1016/j.nbt.2024.03.001","DOIUrl":"10.1016/j.nbt.2024.03.001","url":null,"abstract":"<div><p>In recent years, machine learning (ML) algorithms have gained substantial recognition for ecological modeling across various temporal and spatial scales. However, little evaluation has been conducted for the prediction of soil organic carbon (SOC) on small data sets commonly inherent to long-term soil ecological research. In this context, the performance of ML algorithms for SOC prediction has never been tested against traditional process-based modeling approaches. Here, we compare ML algorithms, calibrated and uncalibrated process-based models as well as multiple ensembles on their performance in predicting SOC using data from five long-term experimental sites (comprising 256 independent data points) in Austria. Using all available data, the ML-based approaches using Random forest and Support vector machines with a polynomial kernel were superior to all process-based models. However, the ML algorithms performed similar or worse when the number of training samples was reduced or when a leave-one-site-out cross validation was applied. This emphasizes that the performance of ML algorithms is strongly dependent on the data-size related quality of learning information following the well-known curse of dimensionality phenomenon, while the accuracy of process-based models significantly relies on proper calibration and combination of different modeling approaches. Our study thus suggests a superiority of ML-based SOC prediction at scales where larger datasets are available, while process-based models are superior tools when targeting the exploration of underlying biophysical and biochemical mechanisms of SOC dynamics in soils. Therefore, we recommend applying ensembles of ML algorithms with process-based models to combine advantages inherent to both approaches.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000086/pdfft?md5=63bda49e4bb9729283361b81ea4e3f0f&pid=1-s2.0-S1871678424000086-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140094397","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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