New biotechnology最新文献

{"title":"Using control bias to identify initial targets for bioproduction improvement","authors":"Michael Binns ,&nbsp;Pedro de Atauri ,&nbsp;Marta Cascante ,&nbsp;Constantinos Theodoropoulos","doi":"10.1016/j.nbt.2025.07.008","DOIUrl":"10.1016/j.nbt.2025.07.008","url":null,"abstract":"<div><div>Sensitivity analysis of bioprocess metabolic reaction networks analysis allows the prediction of system parameters such as those associated with the enzyme activity of certain reaction steps which significantly affect the overall production. However, uncertainties in kinetic rate expressions and in the resulting steady-state flux distributions limit the accuracy of these predictions. Starting from minimal information (reaction stoichiometry, and external fluxes in/out of the system and potentially identification of steps at equilibrium) a new preliminary method is proposed using sampling of elasticities and metabolic fluxes to calculate the control bias. The calculated control bias identifies steps which are likely to have positive control, negative control or negligible/uncertain control. This is intended to give initial guidance before further detailed investigation is carried out, identifying targets for any organism to enhance production of valuable chemicals. As a case study, this methodology is applied to succinic acid bioproduction using <em>Actinobacillus succinogenes</em> and analysis successfully reveals the reaction steps having the greatest positive and negative influence on biosuccinic acid production.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"89 ","pages":"Pages 130-140"},"PeriodicalIF":4.9,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144718160","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":"Improving PHB production in cyanobacteria: Modeling the optimal light regime for growth","authors":"I. Perez Couñago ,&nbsp;J.M. Fernandez Montenegro ,&nbsp;S. Iglesias Moreira ,&nbsp;F. Rodriguez Lorenzo ,&nbsp;M. Placer Lorenzo ,&nbsp;P. Villar Sola ,&nbsp;E. Pancorbo González ,&nbsp;J. Illade Quinteiro ,&nbsp;L. Herrero Castilla ,&nbsp;J.A. Álvarez Rodríguez ,&nbsp;B. Altamira Algarra ,&nbsp;E. Gonzalez Flo ,&nbsp;J. Garcia ,&nbsp;F. Guedes ,&nbsp;M. Lopez-Garcia ,&nbsp;S. Muiños-Landin","doi":"10.1016/j.nbt.2025.05.005","DOIUrl":"10.1016/j.nbt.2025.05.005","url":null,"abstract":"<div><div>The production of bioplastics, such as polyhydroxybutyrate (PHB), using cyanobacteria offers a sustainable alternative to conventional plastics. However, achieving economically viable production requires optimizing biomass growth. This study examined four growth models: Gompertz (empirical growth), Baranyi-Roberts (biologically dependent), Monod (nutrient dependent), and Aiba (irradiance dependent). The results indicate that a light-based model more accurately describes cyanobacterial growth and shows potential for optimizing light regimes. Additionally, an estimator was proposed to assess the potential PHB yield within the given biomass. Experiments were conducted to correlate photosynthetic efficiency with biomass production, providing deeper insights into the effects of light on growth. These findings support the development of optimized cultivation strategies, ultimately improving the economic viability of cyanobacteria-based bioplastics.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"89 ","pages":"Pages 73-81"},"PeriodicalIF":4.5,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485268","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":"Model-based engineering of Bacillus methanolicus towards de novo polyamine bioproduction from methanol","authors":"Luciana Fernandes Brito ,&nbsp;Adshaha Arampu ,&nbsp;Fernando Pérez-García ,&nbsp;Fatma Ece Altınışık Kaya ,&nbsp;Nihat Alpagu Sayar ,&nbsp;Berna Sariyar Akbulut ,&nbsp;Trygve Brautaset","doi":"10.1016/j.nbt.2025.07.001","DOIUrl":"10.1016/j.nbt.2025.07.001","url":null,"abstract":"<div><div>This study explores the one-carbon feedstock methanol to bolster sustainable bioproduction of valuable polyamines. <em>Bacillus methanolicus</em> MGA3, a methylotroph, stands out as a promising host due to its aptitude for employing methanol to synthesize various chemicals. Our approach used flux balance analysis (FBA) to leverage native <em>B. methanolicus</em> pathways for biosynthesis of the polyamines putrescine and spermidine. Despite possessing the genetic repertoire required for their production, <em>B. methanolicus</em> naturally secretes spermidine but not putrescine. Therefore, we created recombinant strains overexpressing endogenous and heterologous genes for putrescine biosynthesis via the arginine decarboxylase pathway, including arginine decarboxylase (<em>speA</em>) and agmatinase (<em>speB</em>). The <em>B. methanolicus</em> strain PUTEc, overexpressing <em>speAB</em> from <em>Escherichia coli</em> rather than native ones, achieved putrescine production of 47.5 ± 0.8 μM in shake flasks. Towards spermidine production, FBA pointed to overexpressing <em>S</em>-adenosylmethionine decarboxylase (<em>speH</em>) and spermidine synthase (<em>speE</em>) in the PUTEc strain. As a result, production of 83.9 ± 2.7 μM spermidine was achieved from methanol. Subsequently, the PUTEc strain underwent FBA-based screening involving precursor supplementation extracellularly in the growth medium or intracellularly by gene co-overexpression to enhance putrescine production. Overexpression of the endogenous ornithine biosynthesis pathway in the PUTEc strain yielded the highest methanol-based polyamine production in this study: 137.7 ± 1.8 μM putrescine in small-scale shake flask conditions. With further improvements in titer towards several grams per litre, this sustainable bioprocess could supply the steadily growing ∼ $500 M putrescine market. To our knowledge, this is the first proof-of-concept study towards production of putrescine and spermidine from methanol.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"89 ","pages":"Pages 91-104"},"PeriodicalIF":4.5,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144626786","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":"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":"2025-11-25","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":"Biology-aware machine learning for culture medium optimization","authors":"Takamasa Hashizume ,&nbsp;Bei-Wen Ying","doi":"10.1016/j.nbt.2025.07.006","DOIUrl":"10.1016/j.nbt.2025.07.006","url":null,"abstract":"<div><div>Cell culture technologies are widely used in academia and industry, yet optimizing culture media remains an art due to the complexity of cell-medium interactions. Machine learning has emerged as a promising solution, but it is hindered by biological fluctuations and experimental errors. To address these issues, we developed a medium optimization platform that integrates simplified and effective experimental manipulation, error-aware data processing for model training, predictive model construction to enhance accuracy and avoid local optimization, and an efficient optimization framework of active learning. Using this approach, we fine-tuned a 57-component serum-free medium for CHO-K1 cells, in which a total of 364 media were experimentally tested. The reformulated medium achieved approximately 60 % higher cell concentration than commercial alternatives. The improved cell culture is definitive toward CHO-K1, underscoring the platform's precision in targeted cell culture optimization. Our approach offers a robust tool for optimizing complex systems in cell culture and broader experimental studies, as well as in biomedical engineering applications.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"89 ","pages":"Pages 141-151"},"PeriodicalIF":4.9,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144721105","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":"Effect of operating conditions on the microbial selection of P(3HB-co-3HV) producers in open continuous culture","authors":"Matteo Castiello ,&nbsp;Laetitia Cavaillé ,&nbsp;Mansour Bounouba ,&nbsp;Simon Dubos ,&nbsp;Claire Dumas ,&nbsp;Etienne Paul","doi":"10.1016/j.nbt.2025.06.001","DOIUrl":"10.1016/j.nbt.2025.06.001","url":null,"abstract":"<div><div>From the perspective of producing P(3HB-co-3HV), the selection of PHA accumulating organisms from activated sludge with a feeding incorporating propionate was investigated in open continuous culture under dual carbon and phosphorus limitation conditions. The selected consortia were then harvested in batch cultures with phosphorus (P) deficiency to evaluate their PHA storage potential. Microbial selection exhibited consistent functional stability of PHA production, emphasizing the robustness of this enrichment strategy. A comparison with previous studies revealed that at a given degree of P limitation, the distribution of carbon consumption between cell growth, PHA storage and maintenance reactions was conditioned by the nature of the carbon source. The combination of the nature of the carbon substrate, the degree of P limitation and the dilution rate governs microbial competition. The dominant bacterial genera showed very heterogeneous PHA production capacities. <em>Acinetobacte</em>r spp., whose establishment was favored by the presence of acetate, a high dilution rate, and a low C/P ratio, was found to be a poor producer. In contrast, <em>Malikia</em> spp. and <em>Zoogloea</em> spp., mostly selected with butyrate, a lower dilution rate, and strong P limitation, exhibited high specific PHA production rates.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"89 ","pages":"Pages 40-50"},"PeriodicalIF":4.5,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144302586","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":"Single-cell proteins polyhydroxyalkanoates-rich microbial biomass from municipal and winery waste as potential additive for aquafeeds","authors":"Giulia Adele Tuci ,&nbsp;Marco Gottardo ,&nbsp;Aditi Parmar Chitharanjan ,&nbsp;Gloriana Cardinaletti ,&nbsp;Giulia Pascon ,&nbsp;Paolo Pavan ,&nbsp;Francesco Valentino","doi":"10.1016/j.nbt.2025.06.003","DOIUrl":"10.1016/j.nbt.2025.06.003","url":null,"abstract":"<div><div>This study evaluated single-cell protein production from PHA-rich mixed microbial cultures obtained from fermentation and subsequent PHA storage, using urban (namely food waste and municipal sewage sludge; FW-MSS) and agricultural waste (namely wine lees; WL) streams as substrates. FW-MSS fermentation achieved stable short-chain fatty acid (SCFA) production and a high COD_SCFA/COD_SOL ratio of 0.77 ± 0.01, which allowed to select a mixed microbial culture (MMC) with intracellular PHA content of 15.1 wt%, which aligns with fish dietary standards and yielded a MMC biomass with a protein level of 55.1 wt% and a balanced essential amino acid (EAA) profile. In contrast, WL fermentation showed lower SCFA content and stability, yielding a MMC with 45.8 wt% of protein along with a high non-conformance rate (53.65 %), and 7.2 wt% PHA, making the resulting MMC more suited as a supplemental protein source. Distinct microbial communities developed in the two SBRs due to different feedstocks, influencing the abundance of PHA-storing bacteria, with no known fish pathogens detected in either sample. Statistical analysis confirmed FW-MSS’s superior product consistency, supporting its potential as a good quality SCP for aquafeed, especially for rainbow trout, as confirmed by its high essential amino acid index (EAAI).</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"89 ","pages":"Pages 29-39"},"PeriodicalIF":4.5,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144366897","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":"Conditional guide RNA deactivation by mRNA and small molecule triggers in Saccharomyces cerevisiae","authors":"Chenggang Xi ,&nbsp;Stephen Chiu ,&nbsp;William E. Voje ,&nbsp;James M. Carothers ,&nbsp;Tae Seok Moon","doi":"10.1016/j.nbt.2025.07.004","DOIUrl":"10.1016/j.nbt.2025.07.004","url":null,"abstract":"<div><div>CRISPR interference (CRISPRi) technologies have revolutionized bioengineering by providing precise tools for gene expression modulation, enabling targeted gene perturbation and metabolic pathway optimization. Despite these advances, achieving dynamic control over gene expression by CRISPR-based regulation remains a challenge due to its inherently static nature. Utilizing toehold-mediated strand displacement and ligand-responsive ribozymes (aptazymes), this study introduces switchable guide RNAs (gRNAs) that facilitate tunable gene expression mediated by mRNA or small molecule signals. We demonstrate complete silencing of gRNA via strategically designed 5’ or 3’ extensions that impede the gRNA spacer or the dCas9 handle, with subsequent restoration of function through sequestration or cleavage of the obstructive sequence. The resulting toehold-embedded or aptazyme-embedded gRNAs can be deactivated by specific signals, including two full-length translatable mRNAs and two small molecule triggers, thereby lifting CRISPRi repression on targeted genes. This modular approach allows for gRNA-based biocomputing through multi-layer or multi-input genetic logic gates in <em>Saccharomyces cerevisiae</em>. Offering a versatile strategy for post-CRISPR regulation in response to environmental signals or cellular states, this methodology expands the toolkit in eukaryotic systems for reversible control of gene expression.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"89 ","pages":"Pages 105-118"},"PeriodicalIF":4.5,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668090","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":"Hac1p-based inverse secretory pathway engineering (Hi-SPE) of Pichia pastoris for improved glucose oxidase production","authors":"Xinyu Zhao ,&nbsp;Jiayu Fang ,&nbsp;Sijie Yu ,&nbsp;Guoxia Liu ,&nbsp;Yanping Zhang ,&nbsp;Yin Li ,&nbsp;Taicheng Zhu","doi":"10.1016/j.nbt.2025.07.002","DOIUrl":"10.1016/j.nbt.2025.07.002","url":null,"abstract":"<div><div>Secretion and folding are common bottlenecks in protein expression using eukaryotic systems, and engineering the secretory pathway to enhance host cell capabilities is a key strategy for improving protein secretion. However, secretion is a very complex process, making the identification of likely targets for engineering a formidable task. In this study, using glucose oxidase (GOX) expression in <em>Pichia pastoris</em> (<em>Komagataella phaffii</em>) as a model, we introduce a strategy called Hac1p-based inverse secretory pathway engineering (Hi-SPE). This strategy leverages Hac1p, the actuator of the unfolded protein response, which is a naturally evolved mechanism to cope with protein overload in endoplasmic reticulum (ER) of eukaryotic cells. When combined with comparative transcriptomics, Hi-SPE narrows down the target from several hundred genes in traditional approaches to 20 secretion-related protein genes. Results showed that overexpression of six out of seven selected genes improved GOX secretion, including the co-chaperone, JEM1, which increased GOX expression per OD₆₀₀ by 147.6 %. Further optimization through combinatorial expression of secretion-related proteins led to a strain co-expressing <em>JEM1</em>, <em>KAR2</em>, and <em>CNE1</em>, achieving a GOX titer of 1903.2 U/mL in 1-L fed-batch fermentation. Additionally, transcriptomic analysis revealed the physiological effects of <em>JEM1</em> overexpression on <em>P</em>. <em>pastoris</em>. This study highlights Hi-SPE as a powerful strategy for improving protein secretion in eukaryotic systems.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"89 ","pages":"Pages 82-90"},"PeriodicalIF":4.5,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144619442","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":"PHB in cyanobacteria: analyzing production through images processing and FT-IR techniques.","authors":"Paula Villar Sola ,&nbsp;Juan Fernández Montenegro ,&nbsp;Sandra Iglesias Moreira ,&nbsp;Francisco Rodríguez Lorenzo ,&nbsp;Philippe Vandervorst ,&nbsp;Erika Pancorbo González ,&nbsp;Miguel Placer Lorenzo ,&nbsp;Inés Pérez Couñago ,&nbsp;Santiago Muíños Landín ,&nbsp;Luz Herrero Castilla ,&nbsp;Julio Illade Quinteiro ,&nbsp;Juan A. Álvarez Rodríguez ,&nbsp;Beatriz Altamira Algarra ,&nbsp;Eva Gonzalez Flo ,&nbsp;Joan García","doi":"10.1016/j.nbt.2025.07.003","DOIUrl":"10.1016/j.nbt.2025.07.003","url":null,"abstract":"<div><div>Cyanobacteria have gained significant attention in recent years due to their ability to produce a variety of valuable compounds. One such compound is polyhydroxybutyrate (PHB), a biodegradable polymer with immense potential in various industrial applications. Given that PHB is stored intracellularly, a dedicated process is needed to extract and measure the biopolymer content. Nevertheless, this process is time consuming and requires environmental hazardous chemicals, such as chloroform. In the present work, we present two complementary methods developed to analyze and quantify PHB production in cyanobacteria microbiomes. The first one consists in an image processing applied on images obtained from Transmission Electronic Microscope (TEM), that can potentially be applied to others type of microscope images as confocal, for qualitative assessment. In this case, a segmentation process allows differentiating PHB grains inside cyanobacteria cells. A metric is then established by computing pixels area taken up by PHB in the whole image and in cyanobacteria cells. A good correlation (higher than 0.65) is observed for all indicators as regard to PHB content. The second method relies on Fourier-transform infrared (FTIR) spectroscopy, as a non-destructive and rapid method to analyze PHB. Absorption peaks due to carbonyl, and Amide I and II group characteristics of monomer structure in PHB and cyanobacteria´s protein are observed. A correlation coefficient r² of 0.96 is reached with the linear regression. A comparison between the two techniques is presented and their main advantages for PHB production optimization are explained.</div><div>-------------------------------------------------------------------------------------------------------------------------</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"89 ","pages":"Pages 119-129"},"PeriodicalIF":4.5,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668091","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}