New biotechnology最新文献

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Improved taxadiene production by optimizing DXS expression and fusing short-chain prenyltransferases 通过优化 DXS 表达和融合短链前炔基转移酶提高紫杉二烯的产量。
IF 4.5 2区 生物学
New biotechnology Pub Date : 2024-07-01 DOI: 10.1016/j.nbt.2024.06.007
Siqi He, Anne-Sophie M.W. Bekhof, Eli Z. Popova, Ronald van Merkerk, Wim J. Quax
{"title":"Improved taxadiene production by optimizing DXS expression and fusing short-chain prenyltransferases","authors":"Siqi He,&nbsp;Anne-Sophie M.W. Bekhof,&nbsp;Eli Z. Popova,&nbsp;Ronald van Merkerk,&nbsp;Wim J. Quax","doi":"10.1016/j.nbt.2024.06.007","DOIUrl":"10.1016/j.nbt.2024.06.007","url":null,"abstract":"<div><p>This study highlights the significance of overexpressing 1-deoxy-d-xylulose-5-phosphate synthase (DXS) from the MEP (methylerythritol 4-phosphate) pathway, in addition to short-chain prenyltransferase fusions for the improved production of the diterpene, taxa-4,11-diene, the first committed intermediate in the production of anti-cancer drug paclitaxel. The results showed that the strain which has (i) the taxadiene synthase (<em>txs</em>) gene integrated into the genome, (ii) the MEP pathway genes overexpressed, (iii) the <em>fpps-crtE</em> prenyltransferases fusion protein and (iv) additional expression of 1-deoxy-d-xylulose-5-phosphate synthase (DXS), yielded the highest production of taxa-4,11-diene at 390 mg/L (26 mg/L/OD<sub>600</sub>). This represents a thirteen-fold increase compared to the highest reported concentration in <em>B. subtilis</em>. The focus on additional overexpression of DXS and utilizing short-chain prenyltransferase fusions underscores their pivotal role in achieving significant titer improvements in terpene biosynthesis.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000281/pdfft?md5=52241de28f4d51e9aed7fbdd0b4196f5&pid=1-s2.0-S1871678424000281-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141498559","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
Ectoine enhances recombinant antibody production in Chinese hamster ovary cells by promoting cell cycle arrest 辛胺通过促进细胞周期停滞来提高中国仓鼠卵巢细胞重组抗体的产生。
IF 4.5 2区 生物学
New biotechnology Pub Date : 2024-06-28 DOI: 10.1016/j.nbt.2024.06.006
Salinthip Jarusintanakorn , Enrico Mastrobattista , Montarop Yamabhai
{"title":"Ectoine enhances recombinant antibody production in Chinese hamster ovary cells by promoting cell cycle arrest","authors":"Salinthip Jarusintanakorn ,&nbsp;Enrico Mastrobattista ,&nbsp;Montarop Yamabhai","doi":"10.1016/j.nbt.2024.06.006","DOIUrl":"10.1016/j.nbt.2024.06.006","url":null,"abstract":"<div><p>Chinese hamster ovary (CHO) cells represent the most preferential host cell system for therapeutic monoclonal antibody (mAb) production. Enhancing mAb production in CHO cells can be achieved by adding chemical compounds that regulate the cell cycle and cell survival pathways. This study investigated the impact of ectoine supplementation on mAb production in CHO cells. The results showed that adding ectoine at a concentration of 100 mM on the 3<sup>rd</sup> day of cultivation improved mAb production by improving cell viability and extending the culture duration. RNA sequencing analysis revealed differentially expressed genes associated with cell cycle regulation, cell proliferation, and cellular homeostasis, in particular promotion of cell cycle arrest, which was then confirmed by flow cytometry analysis. Ectoine-treated CHO cells exhibited an increase in the number of cells in the G0/G1 phase. In addition, the cell diameter was also increased. These findings support the hypothesis that ectoine enhances mAb production in CHO cells through mechanisms involving cell cycle arrest and cellular homeostasis. Overall, this study highlights the potential of ectoine as a promising supplementation strategy to enhance mAb production not only in CHO cells but also in other cell lines.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S187167842400027X/pdfft?md5=cb3f4933fc0dfa4065d22ad81d6ee85d&pid=1-s2.0-S187167842400027X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141469696","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
Biosynthesis of D-1,2,4-butanetriol promoted by a glucose-xylose dual metabolic channel system in engineered Escherichia coli 在工程大肠杆菌中通过葡萄糖-木糖双代谢通道系统促进 D-1,2,4-丁三醇的生物合成。
IF 4.5 2区 生物学
New biotechnology Pub Date : 2024-06-25 DOI: 10.1016/j.nbt.2024.06.003
Lu Zhang , Jinbao Wang , Songhe Gu , Xuedan Liu , Miao Hou , Jing Zhang , Ge Yang , Dongxu Zhao , Runan Dong , Haijun Gao
{"title":"Biosynthesis of D-1,2,4-butanetriol promoted by a glucose-xylose dual metabolic channel system in engineered Escherichia coli","authors":"Lu Zhang ,&nbsp;Jinbao Wang ,&nbsp;Songhe Gu ,&nbsp;Xuedan Liu ,&nbsp;Miao Hou ,&nbsp;Jing Zhang ,&nbsp;Ge Yang ,&nbsp;Dongxu Zhao ,&nbsp;Runan Dong ,&nbsp;Haijun Gao","doi":"10.1016/j.nbt.2024.06.003","DOIUrl":"10.1016/j.nbt.2024.06.003","url":null,"abstract":"<div><p>D-1,2,4-butanetriol (BT) is a widely used fine chemical that can be manufactured by engineered <em>Escherichia coli</em> expressing heterologous pathways and using xylose as a substrate. The current study developed a glucose-xylose dual metabolic channel system in an engineered <em>E. coli</em> and Combinatorially optimized it using multiple strategies to promote BT production. The carbon catabolite repression effects were alleviated by deleting the gene <em>ptsG</em> that encodes the major glucose transporter IICB<sup>Glc</sup> and mutating the gene <em>crp</em> that encodes the catabolite repressor protein, thereby allowing C-fluxes of both glucose and xylose into their respective metabolic channels separately and simultaneously, which increased BT production by 33% compared with that of the original MJ133K-1 strain. Then, the branch metabolic pathways of intermediates in the BT channel were investigated, the transaminase HisC, the ketoreductases DlD, OLD, and IlvC, and the aldolase MhpE and YfaU were identified as the enzymes for the branched metabolism of 2-keto-3-deoxy-xylonate, deletion of the gene <em>hisC</em> increased BT titer by 21.7%. Furthermore, the relationship between BT synthesis and the intracellular NADPH level was examined, and deletion of the gene <em>pntAB</em> that encodes a transhydrogenase resulted in an 18.1% increase in BT production. The combination of the above approaches to optimize the metabolic network increased BT production by 47.5%, resulting in 2.67 g/L BT in 24 deep-well plates. This study provides insights into the BT biosynthesis pathway and demonstrates effective strategies to increase BT production, which will promote the industrialization of the biosynthesis of BT.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000244/pdfft?md5=dc531489f5bb939dcea255ee0eded361&pid=1-s2.0-S1871678424000244-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141469697","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
Nucleic acid aptamers protect against lead (Pb(II)) toxicity 核酸适配体能抵御铅(Pb(II)毒性。
IF 4.5 2区 生物学
New biotechnology Pub Date : 2024-06-24 DOI: 10.1016/j.nbt.2024.06.004
Afreen Anwar , Solimar Ramis De Ayreflor Reyes , Aijaz Ahmad John , Erik Breiling , Abigail M. O’Connor , Stephanie Reis , Jae-Hyuck Shim , Ali Asghar Shah , Jagan Srinivasan , Natalie G. Farny
{"title":"Nucleic acid aptamers protect against lead (Pb(II)) toxicity","authors":"Afreen Anwar ,&nbsp;Solimar Ramis De Ayreflor Reyes ,&nbsp;Aijaz Ahmad John ,&nbsp;Erik Breiling ,&nbsp;Abigail M. O’Connor ,&nbsp;Stephanie Reis ,&nbsp;Jae-Hyuck Shim ,&nbsp;Ali Asghar Shah ,&nbsp;Jagan Srinivasan ,&nbsp;Natalie G. Farny","doi":"10.1016/j.nbt.2024.06.004","DOIUrl":"10.1016/j.nbt.2024.06.004","url":null,"abstract":"<div><p>Lead (Pb(II)) is a pervasive heavy metal toxin with many well-established negative effects on human health. Lead toxicity arises from cumulative, repeated environmental exposures. Thus, prophylactic strategies to protect against the bioaccumulation of lead could reduce lead-associated human pathologies. Here we show that DNA and RNA aptamers protect <em>C. elegans</em> from toxic phenotypes caused by lead. Reproductive toxicity, as measured by brood size assays, is prevented by co-feeding of animals with DNA or RNA aptamers. Similarly, lead-induced neurotoxicity, measured by behavioral assays, are also normalized by aptamer feeding. Further, cultured human HEK293 and primary murine osteoblasts are protected from lead toxicity by transfection with DNA aptamers. The osteogenic development, which is decreased by lead exposure, is maintained by prior transfection of lead-binding DNA aptamers. Aptamers may be an effective strategy for the protection of human health in the face of increasing environmental toxicants.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000256/pdfft?md5=e9d83be5b6e972b815981e815414d398&pid=1-s2.0-S1871678424000256-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141458372","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
Soft sensor for viable cell counting by measuring dynamic oxygen uptake rate 通过测量动态摄氧量进行存活细胞计数的软传感器。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-06-13 DOI: 10.1016/j.nbt.2024.06.001
M. Winter , L. Achleitner , P. Satzer
{"title":"Soft sensor for viable cell counting by measuring dynamic oxygen uptake rate","authors":"M. Winter ,&nbsp;L. Achleitner ,&nbsp;P. Satzer","doi":"10.1016/j.nbt.2024.06.001","DOIUrl":"10.1016/j.nbt.2024.06.001","url":null,"abstract":"<div><p>Regulatory authorities in biopharmaceutical industry emphasize process design by process understanding but applicable tools that are easy to implement are still missing. Soft sensors are a promising tool for the implementation of the Quality by Design (QbD) approach and Process Analytical Technology (PAT). In particular, the correlation between viable cell counting and oxygen consumption was investigated, but problems remained: Either the process had to be modified for excluding CO<sub>2</sub> in pH control, or complex <span><math><mrow><msub><mrow><mi>k</mi></mrow><mrow><mi>L</mi></mrow></msub><mi>a</mi></mrow></math></span> models had to be set up for specific processes. In this work, a non-invasive soft sensor for simplified on-line cell counting based on dynamic oxygen uptake rate was developed with no need of special equipment. The dynamic oxygen uptake rates were determined by automated and periodic interruptions of gas supply in DASGIP® bioreactor systems, realized by a programmed Visual Basic script in the DASware® control software. With off-line cell counting, the two parameters were correlated based on linear regression and led to a robust model with a correlation coefficient of 0.92. Avoidance of oxygen starvation was achieved by gas flow reactivation at a certain minimum dissolved oxygen concentration. The soft sensor model was established in the exponential growth phase of a Chinese Hamster Ovary fed-batch process. Control studies showed no impact on cell growth by the discontinuous gas supply. This soft sensor is the first to be presented that does not require any specialized additional equipment as the methodology relies solely on the direct measurement of oxygen consumed by the cells in the bioreactor.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000220/pdfft?md5=09591024f36230ef7931545d7fac7e72&pid=1-s2.0-S1871678424000220-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141327715","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
Autotrophic adaptive laboratory evolution of the acetogen Clostridium autoethanogenum delivers the gas-fermenting strain LAbrini with superior growth, products, and robustness 乙酸梭菌的自养自适应实验室进化产生了气体发酵菌株 LAbrini,其生长、产品和稳健性都非常出色。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-06-11 DOI: 10.1016/j.nbt.2024.06.002
Henri Ingelman , James K. Heffernan , Audrey Harris , Steven D. Brown , Kurshedaktar Majibullah Shaikh , Asfand Yar Saqib , Marina J. Pinheiro , Lorena Azevedo de Lima , Karen Rodriguez Martinez , Ricardo A. Gonzalez-Garcia , Grant Hawkins , Jim Daleiden , Loan Tran , Hunter Zeleznik , Rasmus O. Jensen , Vinicio Reynoso , Heidi Schindel , Jürgen Jänes , Séan D. Simpson , Michael Köpke , Kaspar Valgepea
{"title":"Autotrophic adaptive laboratory evolution of the acetogen Clostridium autoethanogenum delivers the gas-fermenting strain LAbrini with superior growth, products, and robustness","authors":"Henri Ingelman ,&nbsp;James K. Heffernan ,&nbsp;Audrey Harris ,&nbsp;Steven D. Brown ,&nbsp;Kurshedaktar Majibullah Shaikh ,&nbsp;Asfand Yar Saqib ,&nbsp;Marina J. Pinheiro ,&nbsp;Lorena Azevedo de Lima ,&nbsp;Karen Rodriguez Martinez ,&nbsp;Ricardo A. Gonzalez-Garcia ,&nbsp;Grant Hawkins ,&nbsp;Jim Daleiden ,&nbsp;Loan Tran ,&nbsp;Hunter Zeleznik ,&nbsp;Rasmus O. Jensen ,&nbsp;Vinicio Reynoso ,&nbsp;Heidi Schindel ,&nbsp;Jürgen Jänes ,&nbsp;Séan D. Simpson ,&nbsp;Michael Köpke ,&nbsp;Kaspar Valgepea","doi":"10.1016/j.nbt.2024.06.002","DOIUrl":"10.1016/j.nbt.2024.06.002","url":null,"abstract":"<div><p>Microbes able to convert gaseous one-carbon (C1) waste feedstocks are increasingly important to transition to the sustainable production of renewable chemicals and fuels. Acetogens are interesting biocatalysts since gas fermentation using <em>Clostridium autoethanogenum</em> has been commercialised. However, most acetogen strains need complex nutrients, display slow growth, and are not robust for bioreactor fermentations. In this work, we used three different and independent adaptive laboratory evolution (ALE) strategies to evolve the wild-type <em>C. autoethanogenum</em> to grow faster, without yeast extract and to be robust in operating continuous bioreactor cultures. Multiple evolved strains with improved phenotypes were isolated on minimal media with one strain, named “LAbrini”, exhibiting superior performance regarding the maximum specific growth rate, product profile, and robustness in continuous cultures. Whole-genome sequencing of the evolved strains identified 25 mutations. Of particular interest are two genes that acquired seven different mutations across the three ALE strategies, potentially as a result of convergent evolution. Reverse genetic engineering of mutations in potentially sporulation-related genes CLAU_3129 (<em>spo0A</em>) and CLAU_1957 recovered all three superior features of our ALE strains through triggering significant proteomic rearrangements. This work provides a robust <em>C. autoethanogenum</em> strain “LAbrini” to accelerate phenotyping and genetic engineering and to better understand acetogen metabolism.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000232/pdfft?md5=fc2d46fc08743b866ad6843bc29bb71f&pid=1-s2.0-S1871678424000232-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141317854","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
Modifying flavor profiles of Saccharomyces spp. for industrial brewing using FIND-IT, a non-GMO approach for metabolic engineering of yeast 利用 FIND-IT(一种用于酵母代谢工程的非转基因方法)改变酵母菌的风味特征,用于工业酿造。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-05-22 DOI: 10.1016/j.nbt.2024.05.006
Vratislav Stovicek , Klaus B. Lengeler , Toni Wendt , Magnus Rasmussen , Michael Katz , Jochen Förster
{"title":"Modifying flavor profiles of Saccharomyces spp. for industrial brewing using FIND-IT, a non-GMO approach for metabolic engineering of yeast","authors":"Vratislav Stovicek ,&nbsp;Klaus B. Lengeler ,&nbsp;Toni Wendt ,&nbsp;Magnus Rasmussen ,&nbsp;Michael Katz ,&nbsp;Jochen Förster","doi":"10.1016/j.nbt.2024.05.006","DOIUrl":"10.1016/j.nbt.2024.05.006","url":null,"abstract":"<div><p>Species of <em>Saccharomyces</em> genus have played an irreplaceable role in alcoholic beverage and baking industry for centuries. <em>S. cerevisiae</em> has also become an organism of choice for industrial production of alcohol and other valuable chemicals and a model organism shaping the rise of modern genetics and genomics in the past few decades. Today´s brewing industry faces challenges of decreasing consumption of traditional beer styles and increasing consumer demand for new styles, flavors and aromas. The number of currently used brewer’s strains and their genetic diversity is yet limited and implementation of more genetic and phenotypic variation is seen as a solution to cope with the market challenges. This requires modification of current production strains or introduction of novel strains from other settings, e.g. industrial or wild habitats into the brewing industry. Due to legal regulation in many countries and negative customer perception of GMO organisms, the production of food and beverages requires non-GMO production organisms, whose development can be difficult and time-consuming. Here, we apply FIND-IT (Fast Identification of Nucleotide variants by DigITal PCR), an ultrafast genome-mining method, for isolation of novel yeast variants with varying flavor profiles. The FIND-IT method uses combination of random mutagenesis, droplet digital PCR with probes that target a specific desired mutation and a sub-isolation of the mutant clone. Such an approach allows the targeted identification and isolation of specific mutant strains with eliminated production of certain flavor and off-flavors and/or changes in the strain metabolism. We demonstrate that the technology is useful for the identification of loss-of function or gain of function mutations in unrelated industrial and wild strains differing in ploidy. Where no other phenotypic selection exists, this technology serves together with standard breeding techniques as a modern tool facilitating a modification of (brewer’s) yeast strains leading to diversification of the product portfolio.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000219/pdfft?md5=65af89520016d881c562a548639f24e5&pid=1-s2.0-S1871678424000219-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141094047","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 gradient phage-assisted continuous evolution method for screening suppressor tRNAs in Escherichia coli 梯度噬菌体辅助连续进化法筛选大肠杆菌中的抑制性 tRNA
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-05-20 DOI: 10.1016/j.nbt.2024.05.005
Fan Wang , Li-Hua Liu , Zhenyu Wang , Ao Jiang , Yi-Rui Wu
{"title":"A gradient phage-assisted continuous evolution method for screening suppressor tRNAs in Escherichia coli","authors":"Fan Wang ,&nbsp;Li-Hua Liu ,&nbsp;Zhenyu Wang ,&nbsp;Ao Jiang ,&nbsp;Yi-Rui Wu","doi":"10.1016/j.nbt.2024.05.005","DOIUrl":"https://doi.org/10.1016/j.nbt.2024.05.005","url":null,"abstract":"<div><p>Suppressor tRNAs, notable for their capability of reading through the stop codon while maintaining normal peptide synthesis, are promising in treating diseases caused by premature termination codons (PTC). However, the lack of effective engineering methods for suppressor tRNAs has curtailed their application potential. Here, we introduce a directed evolution technology that employs phage-assisted continuous evolution (PACE), combined with gradient biosensors featuring various PTCs in the M13 gene <em>III</em>. Utilizing this novel methodology, we have successfully evolved tRNA<sup>Trp (UGG)</sup> reading through the UGA stop codon in <em>Escherichia coli</em>. Massively parallel sequencing revealed that these mutations predominantly occurred in the anticodon loop. Finally, two suppressor tRNA<sup>Trp (UGA)</sup> mutants exhibited over fivefold increases in readthrough efficiency.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000207/pdfft?md5=8e4e7ecb0eeb6a0348b77f3619864be1&pid=1-s2.0-S1871678424000207-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141078468","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
Split fluorescent protein-mediated multimerization of cell wall binding domain for highly sensitive and selective bacterial detection 分裂荧光蛋白介导的细胞壁结合域多聚化,用于高灵敏度和选择性细菌检测。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-05-13 DOI: 10.1016/j.nbt.2024.05.004
Shirley Xu , Inseon Lee , Seok-Joon Kwon , Eunsol Kim , Liv Nevo , Lorelli Straight , Hironobu Murata , Krzysztof Matyjaszewski , Jonathan S. Dordick
{"title":"Split fluorescent protein-mediated multimerization of cell wall binding domain for highly sensitive and selective bacterial detection","authors":"Shirley Xu ,&nbsp;Inseon Lee ,&nbsp;Seok-Joon Kwon ,&nbsp;Eunsol Kim ,&nbsp;Liv Nevo ,&nbsp;Lorelli Straight ,&nbsp;Hironobu Murata ,&nbsp;Krzysztof Matyjaszewski ,&nbsp;Jonathan S. Dordick","doi":"10.1016/j.nbt.2024.05.004","DOIUrl":"10.1016/j.nbt.2024.05.004","url":null,"abstract":"<div><p>Cell wall peptidoglycan binding domains (CBDs) of cell lytic enzymes, including bacteriocins, autolysins and bacteriophage endolysins, enable highly selective bacterial binding, and thus, have potential as biorecognition molecules for nondestructive bacterial detection. Here, a novel design for a self-complementing split fluorescent protein (FP) complex is proposed, where a multimeric FP chain fused with specific CBDs ((FP-CBD)<sub>n</sub>) is assembled inside the cell, to improve sensitivity by enhancing the signal generated upon <em>Staphylococcus aureus</em> or <em>Bacillus anthracis</em> binding. Flow cytometry shows enhanced fluorescence on the cell surface with increasing FP stoichiometry and surface plasmon resonance reveals nanomolar binding affinity to isolated peptidoglycan. The breadth of function of these complexes is demonstrated through the use of CBD modularity and the ability to attach enzymatic detection modalities. Horseradish peroxidase-coupled (FP-CBD)<sub>n</sub> complexes generate a catalytic amplification, with the degree of amplification increasing as a function of FP length, reaching a limit of detection (LOD) of 10<sup>3</sup> cells/droplet (approximately 0.1 ng <em>S. aureus</em> or <em>B. anthracis</em>) within 15 min on a polystyrene surface. These fusion proteins can be multiplexed for simultaneous detection. Multimeric split FP-CBD fusions enable use as a biorecognition molecule with enhanced signal for use in bacterial biosensing platforms.</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/S1871678424000190/pdfft?md5=1e6e8acca5df87aa829e6b86cb7e6301&pid=1-s2.0-S1871678424000190-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140945306","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
Bulking agent in dry anaerobic digestion as a key factor for the enhancement of biogas production 干式厌氧消化中的膨化剂是提高沼气产量的关键因素。
IF 5.4 2区 生物学
New biotechnology Pub Date : 2024-05-13 DOI: 10.1016/j.nbt.2024.05.002
Andrea Carvajal , Claudio Sepúlveda , Daniel Navia , Ignacio Poblete-Castro , Fernanda Pinto-Ibieta , Antonio Serrano
{"title":"Bulking agent in dry anaerobic digestion as a key factor for the enhancement of biogas production","authors":"Andrea Carvajal ,&nbsp;Claudio Sepúlveda ,&nbsp;Daniel Navia ,&nbsp;Ignacio Poblete-Castro ,&nbsp;Fernanda Pinto-Ibieta ,&nbsp;Antonio Serrano","doi":"10.1016/j.nbt.2024.05.002","DOIUrl":"10.1016/j.nbt.2024.05.002","url":null,"abstract":"<div><p>Dry anaerobic digestion (dry-AD) is an attractive process for solid wastes such as agri-food waste. However, some limitations mainly associated to lack of effective mixing, can hinder the methane production capacity of the systems. Bulking agent (BA) has been proposed as a solution to the compaction issues in systems without mechanical agitation, such as leaching bed reactors. However, effects of BA are still not clear, and, thus, the factors to consider for its dose has not been optimized yet. This work studies the effect of BA in dry-AD. Two substrates with different characteristics were proposed as models, bean peel as a lignocellulosic substrate and a mixture of food waste as a readily biodegradable substrate. Inert plastic rings were used as BA at different BA:S ratios. Assessed BA:S ratio did not affect the performance of methane production for the lignocellulosic waste, but it did significantly affect to the easily biodegradable substrate, showing up to a 28% of methane production increase. This result could be due to the presence of lignocellulosic compounds in the bean peel, behaving like a natural BA. In assays with an increased bed height, the compaction of the system was more severe, resulting in the rapid acidification of the processes. At these conditions, the positive effect of BA addition was more marked, allowing methane production and no acidification of the system. Thus, the addition of BA is a suitable strategy for improving methane production or stability in dry-AD systems without requiring the stirring of the systems.</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/S1871678424000189/pdfft?md5=76996e52212f0013441d1bb761b59fea&pid=1-s2.0-S1871678424000189-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140945266","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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