New biotechnology最新文献

{"title":"Sprinkling in extra validation for high-value PTMs and therapeutic Abs with MILKSHAKE Western blots and Sundae ELISAs","authors":"Qiana Mendez ,&nbsp;Srinivas S. Thota ,&nbsp;Jason J. Oliveira ,&nbsp;Hannah J. Crary ,&nbsp;Suchetana Saha ,&nbsp;Kezzia S. Jones ,&nbsp;Lourdes Perez ,&nbsp;Felicity Acca ,&nbsp;Cassandra D. Chapados ,&nbsp;Holland A. Driscoll ,&nbsp;Xiaofeng Li ,&nbsp;Gregory R. Mirando ,&nbsp;Mikhail A. Kostylev ,&nbsp;Erik C. Gunther ,&nbsp;Brian K. Kay ,&nbsp;Michael P. Weiner ,&nbsp;Mary R. Ferguson","doi":"10.1016/j.nbt.2025.05.007","DOIUrl":"10.1016/j.nbt.2025.05.007","url":null,"abstract":"<div><div>Thoroughly validated antibodies (Abs) are crucial for the generation of meaningful scientific data. Abs for post translationally modified (PTM) protein targets in particular pose added validation challenges. The MILKSHAKE method employs surrogate proteins which are either modified or non-modified at a specific site. Western blot is used to observe the binding of PTM Abs to the surrogate proteins, indicating the specificity of the PTM Ab under test. In this study, we expand the utility of MILKSHAKE by validating acetyl and methyl specific Abs and by introducing another surrogate protein antigen based on cellulose binding domain (CBD) to evaluate Abs in a single western blot lane. This study also explores the use of ‘Sundae’ surrogate protein ELISA specifically for therapeutic Ab evaluation.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"89 ","pages":"Pages 11-19"},"PeriodicalIF":4.5,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144248903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial synthesis of polyhydroxyalkanoate blends with engineered Pseudomonas putida","authors":"Minglong Li ,&nbsp;Khalid Doudin ,&nbsp;David B. Robins ,&nbsp;Georgios Tetradis-Mairis ,&nbsp;Tuck Seng Wong ,&nbsp;Kang Lan Tee","doi":"10.1016/j.nbt.2025.05.004","DOIUrl":"10.1016/j.nbt.2025.05.004","url":null,"abstract":"<div><div>Polyhydroxyalkanoates (PHAs) are biopolymers naturally produced by various microorganisms and offer a sustainable alternative to fossil fuel-derived plastics. They can be synthesized from diverse feedstock, including waste biomass such as lignocellulose, municipal waste, sludge, and industrial by-products. To tailor their properties for specific applications, PHAs are typically blended post synthesis. An alternative approach is the direct synthesis of PHA blends in a single fermentation, which can reduce the need for multiple separate fermentations and extractions. In this study, we engineered <em>Pseudomonas putida</em> to synthesize PHA blends composed of poly-3-hydroxybutyrate [P3(HB)] and medium-chain-length PHA (mcl-PHA). Through using different promoters, blends with 3HB monomer content ranging from 17.9 mol% to 99.6 mol% were produced. Optimizing cultivation conditions yielded a maximum PHA production of 1.48 ± 0.15 g/L, with a PHA content of 52.2 ± 4.3 wt% of cell dry weight. A combination of gel permeation chromatography, nuclear magnetic resonance and diffusion ordered spectroscopy were employed to determine the molecular weight and confirm the identity of the PHA blend, revealing in all cases, a higher molecular weight P(3HB) than mcl-PHA. The blends produced had thermal properties comparable to PHA blends produced by post synthesis melt compounding. This work demonstrates the microbial synthesis of PHA blends in <em>P. putida</em> and is the first instance of blend composition control via promoter selection, paving the way for the one-step biomanufacturing of customizable PHA blends.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"88 ","pages":"Pages 161-170"},"PeriodicalIF":4.5,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144226063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Establishment of a cell-free multi-enzyme cascade for the synthesis of UDP-GalNAc","authors":"Tuan Son Hoang ,&nbsp;Sara-Theres Wormstall ,&nbsp;Nam-Hai Hoang ,&nbsp;Udo Reichl ,&nbsp;Thomas F.T. Rexer","doi":"10.1016/j.nbt.2025.05.003","DOIUrl":"10.1016/j.nbt.2025.05.003","url":null,"abstract":"<div><div>UDP-<em>N</em>-acetylgalactosamine (UDP-GalNAc) is an essential building block in the synthesis of glycans including <em>O</em>-glycans and glycosaminoglycans. For the latter, enzymatic synthesis is often a promising approach for producing multi-gram amounts. However, the high cost of UDP-GalNAc has limited this approach. This study reports on the development and optimization of a multi-enzyme cascade for synthesizing UDP-GalNAc from inexpensive substrates. Consisting of six recombinant enzymes, the cascade converts uridine (Uri) and GalNAc to UDP-GalNAc with <em>in situ</em> ATP regeneration using polyphosphate (PolyP_n). Two rounds of Design of Experiments (DoE) optimization were performed to systematically evaluate and optimize reaction parameters including pH, temperature, MgCl₂, ATP, and PolyP_n concentrations. The established cascade achieved a percentage yield of 95 % and an UDP-GalNAc titer of 46.1 mM (28 g/L). This represented a 19-fold improvement over the initial conditions. Purification by anion-exchange chromatography yielded a maximum recovery of 89 % and a purity of 90 %. Overall, this scalable, low-cost enzymatic synthesis of UDP-GalNAc overcomes current limitations in availability and cost, potentially enabling new applications in the field of glycobiotechnology.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"89 ","pages":"Pages 20-28"},"PeriodicalIF":4.5,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144199706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MutS-mediated rapid and cost-effective error correction in in vitro DNA synthesis","authors":"Liting Jia ,&nbsp;Shuang Wang ,&nbsp;Dongmei Wang ,&nbsp;Xingjiang Li ,&nbsp;Jiong Hong","doi":"10.1016/j.nbt.2025.05.002","DOIUrl":"10.1016/j.nbt.2025.05.002","url":null,"abstract":"<div><div>The <em>in vitro</em> synthesis of DNA oligonucleotides and their subsequent assembly into longer target molecules represents a pivotal technique within the field of synthetic biology. However, the occurrence of side reactions and the inherent coupling efficiency of the synthesis process lead to the unavoidable introduction of errors into the resulting DNA. Consequently, there is a pressing demand for a straightforward, cost-effective, and efficient method for error correction. In this study, eleven Cbm3-Egfp-MutS fusion proteins were recombinantly expressed and purified, and their capacity to bind heteroduplex DNA was assessed. Among the MutS proteins, TaMutS and TtMutS exhibited thermal stability and effectively distinguished DNA containing mismatches. Following this, a simple, rapid, efficient, and economical error correction method was devised utilizing a homemade spin column composed of amorphous cellulose and a filter tip. The quantitative affinity of EcMutS, TaMutS, and TtMutS for all conceivable single-base errors was determined, and the efficacy of combining MutS proteins for error correction was evaluated. The error rate in synthesized DNA was reduced by a factor ranging from 2.15--8.17, with the material cost for a single reaction amounting to $0.032. The reaction volume was limited to 10 μL, and the reaction could be completed within 20 minutes.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"88 ","pages":"Pages 150-160"},"PeriodicalIF":4.5,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144187442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancement of glutathione production in Saccharomyces cerevisiae through inverse metabolic engineering","authors":"Soo Bin Nho ,&nbsp;Sang-Hun Do ,&nbsp;Young-Oh Lee ,&nbsp;Chan-Hong Ahn ,&nbsp;Jong Myoung Park ,&nbsp;Sun-Ki Kim","doi":"10.1016/j.nbt.2025.05.001","DOIUrl":"10.1016/j.nbt.2025.05.001","url":null,"abstract":"<div><div>Glutathione is an important tripeptide with a variety of health-promoting effects. Currently, glutathione is produced industrially through a fermentation process using <em>Saccharomyces cerevisiae</em> with high glutathione content. However, the glutathione production yield and titer are relatively low compared to using bacteria as a host strain. The underlying reason for this limitation is that previous studies have mainly focused on gene targets directly related to glutathione production. To overcome this limitation, we aimed to identify novel gene targets capable of enhancing glutathione production in <em>S. cerevisiae</em>. To this end, the #ACR3–12 mutant, exhibiting 1.8-fold higher glutathione content than the wild-type D452–2 strain, was isolated after two rounds of acrolein resistance-mediated screening. Next, the genes responsible for the increased glutathione production were identified by analyzing mutations that occurred in the #ACR3–12 mutant. Notably, the <em>SSD1</em> and <em>YBL100W-B</em> genes, which encode a translational repressor of cell wall protein synthesis and a <em>Ty2</em> retrotransposon, respectively, played a crucial role in enhancing glutathione production efficiency. In particular, the D452–2 strain overexpressing the <em>YBL100W-B</em> gene exhibited 1.6- and 2.1-fold higher maximum dry cell weight and glutathione concentration than the wild-type D452–2 strain.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"88 ","pages":"Pages 142-149"},"PeriodicalIF":4.5,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144143049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Retraction notice to \"Continuous H-B-E fermentation by Clostridium carboxidivorans: CO vs syngas\" [New Biotechnol 1495 2024;81(July):1–9]","authors":"F. Lanzillo ,&nbsp;S. Pisacane ,&nbsp;M. Capilla ,&nbsp;F. Raganati ,&nbsp;M.E. Russo ,&nbsp;P. Salatino ,&nbsp;A. Marzocchella","doi":"10.1016/j.nbt.2025.04.005","DOIUrl":"10.1016/j.nbt.2025.04.005","url":null,"abstract":"","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"88 ","pages":"Page 141"},"PeriodicalIF":4.5,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143942070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Value-added utilisation of industrial by-products from bioenergy processes for growth of the PHB synthesising bacterium Cupriavidus necator","authors":"Felix Berthold,&nbsp;York Chiduch,&nbsp;Marco Lederer,&nbsp;Christian Schlenk,&nbsp;Christian Hausmann,&nbsp;Stephanie Christine Stute","doi":"10.1016/j.nbt.2025.04.012","DOIUrl":"10.1016/j.nbt.2025.04.012","url":null,"abstract":"<div><div>The utilisation of low-value by-products derived from the production of bioenergy as nutrient media for microbial growth was investigated using the polyhydroxybutyrate (PHB) synthesising bacterium <em>Cupriavidus necator</em> as a case study. The potentially suitable by-products crude glycerol (derived from biodiesel production as carbon source) and digestate (resulting from biogas production as source for nitrogen and other nutrients) contain significant amounts of nutrients but also dissolved and solid impurities. In order to minimise negative effects such as clogging in bioreactor infrastructure and complications during product recovery in a future industrial production scale, the amount of solids was reduced by filtration and centrifugation. In addition, the treatment of the liquid anaerobic digestate (LAD) included dilution and pH stabilisation in order to reduce growth inhibition due to excessive concentrations of compounds in the digestate and an unsuitable pH. Experiments were carried out in a stirred tank bioreactor comparing growth on a medium consisting only of treated LAD and crude glycerol with growth on a reference media containing crude glycerol but mineral salts instead of LAD. Fermentation with crude glycerol and LAD showed slightly reduced specific growth rates (0.1 1/h) but a similar cell dry weight (8.8 g_CDW/L) compared to the reference media with crude glycerol and mineral salts (0.14 1/h and 9.5 g_CDW/L). As no specific conditions were set to promote PHB accumulation, only low levels of PHA of 5,45w_PHB/w_CDW-% ( ± 1,5) were observed for both medium variations at the end of growth.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"88 ","pages":"Pages 132-140"},"PeriodicalIF":4.5,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143942069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenotypic and genomic characterization of bacteriocin-producing lactic acid bacteria with probiotic and biotechnological potential for pathogen control in animal production","authors":"Pamela Oliveira de Souza de Azevedo ,&nbsp;Mauro de Medeiros Oliveira ,&nbsp;Taís Mayumi Kuniyoshi ,&nbsp;Carlos Emilio Cabrera Matajira ,&nbsp;Elionio Galvão Frota ,&nbsp;Meriellen Dias ,&nbsp;Sebastián Armando Bermúdez-Puga ,&nbsp;Amanda Romana Santos Pessoa ,&nbsp;Anna Carolina Meireles Piazentin ,&nbsp;Carlos Miguel Nóbrega Mendonça ,&nbsp;Wellison Amorim Pereira ,&nbsp;Attilio Converti ,&nbsp;José Manuel Domínguez ,&nbsp;Martin Gierus ,&nbsp;Alessandro M. Varani ,&nbsp;Ricardo Pinheiro de Souza Oliveira","doi":"10.1016/j.nbt.2025.04.008","DOIUrl":"10.1016/j.nbt.2025.04.008","url":null,"abstract":"<div><div>The emergence of antibiotic-resistant pathogens has raised significant concerns in the poultry industry, driving the search for alternatives to antibiotics as growth promoters in animal feed. Probiotics, particularly those belonging to the Lactic Acid Bacteria (LAB) group, represent a promising solution by mitigating the risk of infectious disease. However, a uniform concentration of probiotic LAB is not suitable for feed additives due to varying growth kinetics. Additionally, the genomic and physiological profiles of the LAB strains involved must be thoroughly evaluated. In this study, we provide an analytical framework to comprehensively assess LAB as potential antibiotic alternatives in poultry farming. Three LAB strains – <em>Pediococcus pentosaceus</em> (isolated from corn silage), <em>Ligilactobacillus salivarius</em> (from the poultry gut) and <em>Lactococcus lactis</em> (from the gut of rainbow trout) – were sequenced and characterized, with a focus on evaluating their probiotic potential and safety at the genomic level. The analyses included co-culturing LAB with pathogens, assessing viable cells, and determining the minimum inhibitory concentration of bacteriocin-like inhibitory substances (BLIS). In addition to demonstrating effective antimicrobial activity against avian pathogens (<em>Salmonella</em> spp., <em>Clostridium</em> spp. and <em>Campylobacter coli</em>), the results revealed notable probiotic traits in all three LAB strains, such as tolerance to bile salts and acidic environment and adhesion to intestinal cells. In conclusion, our analytical framework and results highlighted the potential of the tested LAB strains as biotechnological tools for developing zootechnical additives. These probiotics show promise as viable alternatives to antibiotics for enhancing poultry health and productivity.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"88 ","pages":"Pages 114-131"},"PeriodicalIF":4.5,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143936653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Valorization of prosecco wine lees for sustainable polyhydroxyalkanoates production by Cupriavidus necator DSM 545 and Hydrogenophaga pseudoflava DSM 1034","authors":"Viola Caminiti ,&nbsp;Ameya Pankaj Gupte ,&nbsp;Lorenzo Favaro ,&nbsp;Sergio Casella ,&nbsp;Marina Basaglia","doi":"10.1016/j.nbt.2025.04.009","DOIUrl":"10.1016/j.nbt.2025.04.009","url":null,"abstract":"<div><div>Nowadays, in the agricultural and agro-industrial sectors, there is increasing attention on the wine industry. The environmental impact of wine production, particularly in terms of residues generation, is a growing concern. Among generated residues, wine lees, rich in organic matter, phenols compounds, and with low pH, pose environmental challenges due to their disposal requirements. Despite their usage for biogas production and extraction of compounds, such as antioxidants, tartaric acid and ethanol, their potential in bioplastic production, specifically polyhydroxyalkanoates (PHAs), remains largely untapped. This study aims to evaluate the potential use of wine lees as a medium sustaining bacterial growth and PHAs accumulation. Specifically, <em>Cupriavidus necator</em> DSM 545 and <em>Hydrogenophaga pseudoflava</em> DSM 1034, were cultivated in the liquid phase of wine lees obtained from the Prosecco winemaking. On pure distilled wine lees, after mild feedstock pre-treatments, <em>C. necator</em> DSM 545 reached a CDW (cell dry weight) of 2.97 g/L and accumulated PHAs was 1.27 g/L, pair to 42.90 % of CDW. On the same substrate, CDW for <em>H. pseudoflava</em> DSM 1034 was 3.96 g/L and PHAs reached values of 1.60 g/L and 40.42 % CDW. These results obtained on wine lees are similar or even better than those achieved in the control growths of the two strains on pure glucose.</div><div>This is the first approach for the utilization of wine lees for PHAs production, highlighting their potential use in the PHAs industry, and offering a sustainable alternative for both residues management and bioplastic production.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"88 ","pages":"Pages 73-82"},"PeriodicalIF":4.5,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143888060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Addressing semantic ambiguity in biotechnology: Proposals from the European research infrastructure IBISBA","authors":"Marie Ancelin ,&nbsp;Vitor A.P. Martins dos Santos ,&nbsp;John P. Morrissey ,&nbsp;Michael J. O’Donohue ,&nbsp;Merja Penttilä ,&nbsp;James C. Philp","doi":"10.1016/j.nbt.2025.04.010","DOIUrl":"10.1016/j.nbt.2025.04.010","url":null,"abstract":"<div><div>Driven by numerous scientific discoveries in biology in the second half of the last century, biotechnology is now set to play an important role as a driver for advanced manufacturing, leveraging the power of living organisms to produce a range of goods and services. Considering this prospect, it is vital that terminology surrounding biotechnology is sufficiently clear to provide a basis for efficient regulation and public buy-in. Despite the apparent clarity of the term biotechnology, its definition is the subject of a longstanding debate and liberal interpretations. Likewise, other more recent terms such as biomanufacturing, synthetic biology and engineering biology also lack consensual definitions despite their use in both scientific and secular circles. Additionally, new terms such as precision fermentation and cellular agriculture, recently introduced in the framework of business-to-business exchanges, appear to call upon imaginaries rather than scientific facts. Herein, we examine the lexical complexity of the biotechnology field and argue that, for the sake of efficient policymaking, it is vital to harmonise the definitions of some core terms, including biotechnology, biomanufacturing, engineering biology and synthetic biology. With this aim in mind, this discussion paper is intended to be useful to policymakers and science communicators, whether in the media or in professional settings.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"88 ","pages":"Pages 83-88"},"PeriodicalIF":4.5,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143890890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}