Biotechnology and Bioengineering最新文献

{"title":"Alterations in Protein Phosphorylation and Arginine Biosynthesis Metabolism Confer β-Phenylethanol Tolerance in Saccharomyces cerevisiae","authors":"Chenghan Yang,&nbsp;Yilin Ren,&nbsp;Li Zhang,&nbsp;Yina Li,&nbsp;Chunxia Wang,&nbsp;Haifeng Hang,&nbsp;Xiwei Tian,&nbsp;Ali Mohsin,&nbsp;Ju Chu,&nbsp;Yingping Zhuang","doi":"10.1002/bit.28936","DOIUrl":"10.1002/bit.28936","url":null,"abstract":"<div>\u0000 \u0000 <p>The aromatic compound β-phenylethanol (2-PE) is inherently toxic and can inhibit cell activity in <i>Saccharomyces cerevisiae</i>, making it highly challenging to enhance strain tolerance through rational design due to the lack of reliable connections between tolerance phenotype and genetic loci. This study employed adaptive laboratory evolution strategy to investigate the tolerance characteristics of <i>S. cerevisiae</i> S288C under inhibitory concentrations of 2-PE. The tolerant mutant SEC4.0 was characterized through comprehensive analysis of whole genome sequence, transcriptome, and phosphoproteome. The findings revealed that the high resistance of SEC4.0 was not primarily due to large-scale transcriptional upregulation of stress response genes, but rather through alterations in the phosphorylation levels of lipid-related pathways. <i>PKC1</i> mutations that affect stress signal transduction and <i>SPT3</i> mutations that affect arginine biosynthesis have been shown to significantly enhance 2-PE resistance. This study also investigated the effects of exogenous amino acid addition and synergistic effects with two key mutanted genes on 2-PE resistance. This study provides a foundation for enhancing yeast tolerance to this aromatic compound through rational design strategies.</p></div>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"122 5","pages":"1174-1189"},"PeriodicalIF":3.5,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063718","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":"A New Modeling Approach for Predicting the Growth of Filamentous Algae in Outdoor Algae-Based Wastewater Treatment Systems","authors":"Sulochana Pitawala,&nbsp;Peter J. Scales,&nbsp;Gregory J. O. Martin","doi":"10.1002/bit.28941","DOIUrl":"10.1002/bit.28941","url":null,"abstract":"<p>Filamentous algae (FA) can form readily harvestable floating mats or attached turfs that facilitate their application in wastewater treatment systems. However, large-scale implementation is hindered by our inability to predict performance as a function of key operational parameters. A predictive mathematical model would be a valuable tool for designing efficient FA-based systems. Developing accurate models is challenging due to dynamic environmental conditions and the spatial complexities of FA cultures. In this work, a model was developed to mathematically describe the biomass productivity of static FA cultures (mats and turfs) in relation to the incident light intensity and temperature. The model was validated against published data to investigate the influence of time-dependent inhibition (inhibition from sustained light exposure) on productivity. When time-dependent inhibition was included in the model, predictions were within ~10% of experimental values, however, without including time-dependent inhibition there was a sixfold overestimation of biomass productivity. The model could also generate predictions of the effects of time-dependent inhibition during diurnal light fluctuations using experimentally determined rate constants. The model represents a powerful tool for optimizing the design and operational parameters in FA cultures that could be further expanded to incorporate the influence of nutrient and CO₂ availability.</p>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"122 5","pages":"1202-1217"},"PeriodicalIF":3.5,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bit.28941","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063717","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}

{"title":"Effectively Guiding Cell Elongation and Alignment by Constructing Micro/Nano Hierarchical Patterned Titania on Titanium Substrate","authors":"Feng-Jiao Bai,&nbsp;Hui Wang,&nbsp;Yu-Qing Hu,&nbsp;Yun-Fei Shao,&nbsp;Yi-Ran Zhu,&nbsp;Yu-Lin Jiang,&nbsp;Jian-Chen Hu,&nbsp;Hui-Jing Zhao,&nbsp;Ke-Qin Zhang","doi":"10.1002/bit.28934","DOIUrl":"10.1002/bit.28934","url":null,"abstract":"<div>\u0000 \u0000 <p>Based on the innate sensitivity of cell to substrate topographical cues, modulating cell-directed growth behavior is crucial for promoting tissue repair and reconstruction. Although photolithography technology has been extensively employed to fabricate a variety of anisotropic patterned structures to guide cell growth, it remains a great challenge to design high-resolution micro/nano hierarchical structures directly onto medical titanium (Ti)-based implants. Herein, we present a rapid, reliable and reproducible approach combining photolithography and hydrothermal technology to construct a micro/nano hierarchical structure including anisotropic micro-strips and a porous structure composed of TiO₂ nanotubes features. In vitro biological and physicochemical analyses revealed that the micro/nano hierarchical structures not only efficiently facilitate the localization and adsorption of BSA molecules, but also enhances the control of cell growth behavior. The synergistic effect between the physical limitation for organizing cellular cytoskeleton at micropattern and the control of focal adhesion sits at the nanoscale can effectively guide cells to maintain stable elongation and alignment, even at large micro-stripe width of 100 μm. This study presents a promising strategy to precisely construct micro/nano multi-level patterned structure on Ti substrate using biomaterials with excellent biocompatibility. These functional micro/nano hybrid micropatterns offer a powerful platform for regulating bioreagent localization and cell behaviors in various applications including tissue engineering, regenerative medicine, drug screening, and biosensors.</p></div>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"122 5","pages":"1272-1283"},"PeriodicalIF":3.5,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057115","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":"Proteo-Transcriptomic Analysis Reveals the Mechanisms Underlying Escherichia coli Phenotypic Shifts Under Blue Light","authors":"Shuqi Shi,&nbsp;Wenlu Qi,&nbsp;Jinming Zhang,&nbsp;Caice Liang,&nbsp;Wei Liu,&nbsp;Hui Han,&nbsp;Wei Zhuang,&nbsp;Tianpeng Chen,&nbsp;Wenjun Sun,&nbsp;Yong Chen","doi":"10.1002/bit.28939","DOIUrl":"10.1002/bit.28939","url":null,"abstract":"<div>\u0000 \u0000 <p>Bacteria can adapt their lifestyles, including microbial growth, metabolism, and biofilm formation, in response to light signaling. However, the molecular pathways through which blue light affects the lifestyle of <i>Escherichia coli</i> (<i>E. coli</i>) remain incomplete and poorly understood. To address this gap, transcriptomic and proteomic approaches were employed to analyze the physiological differences of <i>E. coli</i> under dark and blue light conditions. Our results indicate that, compared to dark conditions, blue light attenuates flagellar assembly, reduces cell motility and communication, and decreases biofilm formation in <i>E. coli</i>. In addition, this study elucidates the signaling pathways involved in the blue light-mediated regulation of <i>E. coli</i> behavior, providing a theoretical framework for understanding how <i>E. coli</i> responds to blue light signaling to modulate biofilm formation for the production of food chemicals.</p></div>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"122 5","pages":"1258-1271"},"PeriodicalIF":3.5,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055191","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":"High-Efficiency CRISPR-Cas9 Genome Editing Unveils Biofilm Insights and Enhances Antimicrobial Activity in Bacillus velezensis FZB42","authors":"Na Guo,&nbsp;Shangjun Wang,&nbsp;Christopher Tyler Whitfield,&nbsp;William D. Batchelor,&nbsp;Yifen Wang,&nbsp;David Blersch,&nbsp;Brendan T. Higgins,&nbsp;Yucheng Feng,&nbsp;Mark R. Liles,&nbsp;Luz E. de-Bashan,&nbsp;Yi Wang,&nbsp;Yuechao Ma","doi":"10.1002/bit.28933","DOIUrl":"10.1002/bit.28933","url":null,"abstract":"<div>\u0000 \u0000 <p><i>Bacillus velezensis</i> FZB42 is a prominent plant growth-promoting rhizobacterium and biocontrol agent known for producing a wide array of antimicrobial compounds. The capability to genetically manipulate this strain would facilitate understanding its metabolism and enhancing its sustainable agriculture applications. In this study, we report the first successful implementation of high-efficiency CRISPR-Cas9 genome editing in <i>B. velezensis</i> FZB42, enabling targeted genetic modifications to gain insights into its plant growth-promotion and biocontrol properties. Deletion of the <i>slrR</i> gene, a key regulator of biofilm formation, resulted in significant alterations in biofilm structure and development, as demonstrated by scanning electron microscopy and quantitative biofilm assays. These findings provide valuable insights into the mechanisms of biofilm formation, which are critical for root colonization and plant growth promotion. Additionally, we overexpressed the <i>bac</i> gene cluster responsible for bacilysin biosynthesis by replacing its native promoter with the strong constitutive promoter P43 and integrating an additional copy of the <i>bacG</i> gene. This genetic manipulation led to a 2.7-fold increase in <i>bacB</i> gene expression and significantly enhanced antibacterial activity against <i>Escherichia coli</i> and <i>Lactobacillus diolivorans</i>. The successful implementation of the CRISPR-Cas9 system for genome editing in FZB42 provides a valuable tool for genetic engineering, with the potential to improve its biocontrol efficacy and broaden its applications in agriculture and other biotechnology areas. Our principles and procedures are broadly applicable to other agriculturally significant microorganisms.</p></div>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"122 4","pages":"983-994"},"PeriodicalIF":3.5,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143050932","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":"Graphene Oxide-Assisted Tapered Microfiber Super-Sensor for Rapid Detection of Mycobacterium tuberculosis Antigens","authors":"Ren Liu,&nbsp;Tianhuan Song,&nbsp;Xiaolin Chen,&nbsp;Zhiheng Yu,&nbsp;Cunliang Yang,&nbsp;Xianchao Zhang,&nbsp;Fengli Huang,&nbsp;Hao Jia,&nbsp;Jijun Feng,&nbsp;Yujiong Wang","doi":"10.1002/bit.28929","DOIUrl":"10.1002/bit.28929","url":null,"abstract":"<div>\u0000 \u0000 <p>Tuberculosis (TB), caused by <i>Mycobacterium tuberculosis</i> (MTB), is one of the most widespread infectious diseases, with nearly 2 billion people infected globally. We present an innovative approach for the real-time detection of TB antigens Mpt64 and Ag85B using DNA aptamers in combination with a graphene oxide (GO)-assisted optical microfiber super-sensor. The high surface-to-volume ratio and superior properties of the GO layer significantly enhance the microfiber's fixation capabilities. To validate the clinical applicability of this sensing method, we employed the optical sensor to successfully detect Mpt64 and Ag85B in serum samples within 10 s, achieving limits of detection of 4.23 × 10⁻²⁰ M and 3.11 × 10⁻¹⁹ M, respectively. Due to the high conservation of Mpt64 and Ag85B in human and bovine MTB strains, our detection system can be used to identify MTB in both humans and bovine. These results demonstrate the sensor's high sensitivity for quantifying MTB particles, enabling rapid identification of infected individuals or bovine. Overall, the optical microfiber sensor system offers a promising platform for diagnosing MTB due to its straightforward detection scheme and potential for miniaturization.</p></div>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"122 4","pages":"1025-1034"},"PeriodicalIF":3.5,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044204","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":"A Dive Into Yeast's Sugar Diet—Comparing the Metabolic Response of Glucose, Fructose, Sucrose, and Maltose Under Dynamic Feast/Famine Conditions","authors":"Koen Johannes Anthonius Verhagen,&nbsp;Ilse Henrike Pardijs,&nbsp;Hendrik Matthijs van Klaveren,&nbsp;Sebastian Aljoscha Wahl","doi":"10.1002/bit.28935","DOIUrl":"10.1002/bit.28935","url":null,"abstract":"<p>Microbes experience dynamic conditions in natural habitats as well as in engineered environments, such as large-scale bioreactors, which exhibit increased mixing times and inhomogeneities. While single perturbations have been studied for several organisms and substrates, the impact of recurring short-term perturbations remains largely unknown. In this study, we investigated the response of <i>Saccharomyces cerevisiae</i> to repetitive gradients of four different sugars: glucose, fructose, sucrose, and maltose. Due to different transport mechanisms and metabolic routes, nonglucose sugars lead to varied intracellular responses. To characterize the impact of the carbon sources and the dynamic substrate gradients, we applied both steady-state and dynamic cultivation conditions, comparing the physiology, intracellular metabolome, and proteome. For maltose, the repeated concentration gradients led to a significant decrease in biomass yield. Under glucose, fructose, and sucrose conditions, <i>S. cerevisiae</i> maintained the biomass yield observed under steady-state conditions. Although the physiology was very similar across the different sugars, the intracellular metabolome and proteome were clearly differentiated. Notably, the concentration of upper glycolytic enzymes decreased for glucose and maltose (up to −60% and −40%, respectively), while an increase was observed for sucrose and fructose when exposed to gradients. Nevertheless, for all sugar gradient conditions, a stable energy charge was maintained, ranging between 0.78 and 0.89. This response to maltose is particularly distinct compared to previous single-substrate pulse experiments or limitation to excess shifts, which led to maltose-accelerated death in earlier studies. At the same time, enzymes of lower glycolysis were elevated. Interestingly, common stress-related proteins (GO term: cellular response to oxidative stress) decreased during dynamic conditions.</p>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"122 4","pages":"1035-1050"},"PeriodicalIF":3.5,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bit.28935","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044275","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}

{"title":"Application of Multiple Base-Editing Mediated by Polycistronic tRNA-gRNA-Processing System in Pig Cells","authors":"Wudi Zhao,&nbsp;Xiangxing Zhu,&nbsp;Guobin Huang,&nbsp;Hao Gu,&nbsp;Yanzhen Bi,&nbsp;Dongsheng Tang,&nbsp;Hongyan Ren","doi":"10.1002/bit.28931","DOIUrl":"10.1002/bit.28931","url":null,"abstract":"<div>\u0000 \u0000 <p>Gene edited pigs have extensive and important application value in the fields of agriculture and biomedicine. With the increasing demand in medical research and agricultural markets, more and more application scenarios require gene edited pigs to possess two or even more advantageous phenotypes simultaneously. The current production of multi gene edited pigs is inefficient, time-consuming, and costly, and there is an urgent need to develop efficient and accurate multi gene editing application technologies. The polycistronic tRNA-gRNA-processing system (PTG), developed based on endogenous tRNA self-processing systems, has been shown to exhibit efficient multi gene editing in plants. This study aims to combine a PTG strategy with multiple gRNA production functions with an adenine base editor (ABE) to test its feasibility for efficient and precise multi gene base editing in pig cells. The results indicate that the PTG based integrated ABE plasmid can perform efficient base editing at multiple gene loci in pig cells. And while the gene editing efficiency was significantly improved, no indel and sgRNA dependent off target effects caused by DSB were detected. This work permit will provide a solid foundation for the production of multi gene edited pigs with agricultural and medical applications.</p></div>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"122 4","pages":"779-791"},"PeriodicalIF":3.5,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143020979","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":"Real-Time Auto Controlling of Viable Cell Density in Perfusion Cultivation Aided by In-Line Dielectric Spectroscopy With Segmented Adaptive PLS Model","authors":"Yunpeng Sun,&nbsp;Qiongqiong Zhang,&nbsp;Yunfei He,&nbsp;Dongliang Chen,&nbsp;Zheyu Wang,&nbsp;Xiang Zheng,&nbsp;Mingyue Fang,&nbsp;Hang Zhou","doi":"10.1002/bit.28930","DOIUrl":"10.1002/bit.28930","url":null,"abstract":"<div>\u0000 \u0000 <p>Serving as a dedicated process analytical technology (PAT) tool for biomass monitoring and control, the capacitance probe, or dielectric spectroscopy, is showing great potential in robust pharmaceutical manufacturing, especially with the growing interest in integrated continuous bioprocessing. Despite its potential, challenges still exist in terms of its accuracy and applicability, particularly when it is used to monitor cells during stationary and decline phases. In this study, data pre-processing methods were first evaluated through cross-validation, where the first-order derivative emerged as the most effective method to diminish variability in prediction accuracy across different training datasets. Subsequently, a segmented adaptive partial least squares (SA-PLS) model was developed, and its accuracy and universality were demonstrated through several validation studies using different clones and culture processes. Furthermore, a real-time viable cell density (VCD) auto-control system in perfusion culture was established, where the VCD was maintained around the target with notable precision and robustness. This model enhanced the monitoring capabilities of capacitance-based PAT tools throughout the cultivation, expanded their application in cell-specific automatic control strategies, and contributed vitally to the advancement of continuous manufacturing paradigms.</p></div>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"122 4","pages":"858-869"},"PeriodicalIF":3.5,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142989318","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":"Reducing Structural Nonidentifiabilities in Upstream Bioprocess Models Using Profile-Likelihood","authors":"Heiko Babel,&nbsp;Ola Omar,&nbsp;Albert Paul,&nbsp;Joachim Bär","doi":"10.1002/bit.28922","DOIUrl":"10.1002/bit.28922","url":null,"abstract":"<div>\u0000 \u0000 <p>Process models are increasingly used to support upstream process development in the biopharmaceutical industry for process optimization, scale-up and to reduce experimental effort. Parametric unstructured models based on biological mechanisms are highly promising, since they do not require large amounts of data. The critical part in the application is the certainty of the parameter estimates, since uncertainty of the parameter estimates propagates to model predictions and can increase the risk associated with those predictions. Currently Fisher-Information-Matrix based approximations or Monte-Carlo approaches are used to estimate parameter confidence intervals and regularization approaches to decrease parameter uncertainty. Here we apply profile likelihood to determine parameter identifiability of a recent upstream process model. We have investigated the effect of data amount on identifiability and found out that addition of data reduces non-identifiability. The likelihood profiles of nonidentifiable parameters were then used to uncover structural model changes. These changes effectively alleviate the remaining non-identifiabilities except for a single parameter out of 21 total parameters. We present the first application of profile likelihood to a complete upstream process model. Profile likelihood is a highly suitable method to determine parameter confidence intervals in upstream process models and provides reliable estimates even with nonlinear models and limited data.</p></div>","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"122 4","pages":"833-845"},"PeriodicalIF":3.5,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142989317","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}