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IF 2.5 3区生物学

Biotechnology Progress Pub Date : 2024-06-24 DOI: 10.1002/btpr.3488

Hong Li, Patricia Rose, Patricia Rowicki, Collette Cutler, Jeffrey T. McPhee, Claudia Frey, Linda Lemieux, Gerald Pelette, Joo Kok Ang, Ren Liu, Douglas D. Richardson

引用次数: 0

Primary clarification of mammalian cell culture fluid using enhanced sedimentation on inclined surfaces inside the single-use disposable Sudhin BioSettler150 利用一次性使用的 Sudhin BioSettler150 内倾斜表面上的增强沉降功能，对哺乳动物细胞培养液进行初级澄清。

IF 2.5 3区生物学

Biotechnology Progress Pub Date : 2024-06-19 DOI: 10.1002/btpr.3489

Christopher B. Glascock, Dhinakar S. Kompala

{"title":"Primary clarification of mammalian cell culture fluid using enhanced sedimentation on inclined surfaces inside the single-use disposable Sudhin BioSettler150","authors":"Christopher B. Glascock, Dhinakar S. Kompala","doi":"10.1002/btpr.3489","DOIUrl":"10.1002/btpr.3489","url":null,"abstract":"The first downstream processing step in the purification of a biopharmaceutical protein secreted into mammalian cell culture fluid is the primary clarification of the culture fluid. As cell densities in the fed-batch and increasingly more common perfusion bioreactors have increased over last two decades through intensified upstream bioreactor production processes, the traditional primary clarification unit operations of centrifugation and/or microfiltration become more challenging with issues like frequent desludging, cell disruption due to shear damage and quick fouling of membranes. We have developed a novel compact cell settler device exploiting the enhanced sedimentation on inclined surfaces and demonstrated that this settler device can be adapted easily to remove and contain cells or cell clumps from the clarified supernatant collected via the top effluent of the settler. In this work, we present high product recovery results during primary clarification of mammalian cell culture supernatant using our novel single-use disposable BioSettler150 while processing about 10 L of cell culture broth within short processing times of about 4 h.","PeriodicalId":8856,"journal":{"name":"Biotechnology Progress","volume":"40 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evaluation of TrpM and PsiD substrate promiscuity reveals new biocatalytic capabilities 对 TrpM 和 PsiD 底物杂交性的评估揭示了新的生物催化能力。

IF 2.5 3区生物学

Biotechnology Progress Pub Date : 2024-06-18 DOI: 10.1002/btpr.3492

Fiona C. Kanis, Caroline N. Broude, Elle B. Hellwarth, William J. Gibbons Jr, Abhishek K. Sen, Alexandra M. Adams, Xin Wang, J. Andrew Jones

{"title":"Evaluation of TrpM and PsiD substrate promiscuity reveals new biocatalytic capabilities","authors":"Fiona C. Kanis, Caroline N. Broude, Elle B. Hellwarth, William J. Gibbons Jr, Abhishek K. Sen, Alexandra M. Adams, Xin Wang, J. Andrew Jones","doi":"10.1002/btpr.3492","DOIUrl":"10.1002/btpr.3492","url":null,"abstract":"N-methylated tryptamines, such as the hallucinogenic natural products, psilocybin and N,N-dimethyltryptamine (DMT), are gaining interest from the medical community due to their potential as next generation treatments for mental health disorders. The clinical relevance of these compounds has driven scientists to develop biosynthetic production routes to a number of tryptamine drug candidates, and efforts are ongoing to expand and further develop these biosynthetic capabilities. To that end, we have further characterized the substrate preferences of two enzymes involved in tryptamine biosynthesis: TrpM, a tryptophan N-methyltransferase from Psilocybe serbica, and PsiD, the gateway decarboxylase of the psilocybin biosynthesis pathway. Here, we show that TrpM can N-methylate the non-native amino acid substrate, 4-hydroxytryptophan, a key intermediate in the Escherichia coli-based recombinant psilocybin biosynthesis pathway. However, the ability to incorporate TrpM into a functional psilocybin biosynthesis pathway was thwarted by PsiD's inability to use N,N-dimethyl-4-hydroxytryptophan as substrate, under the culturing conditions tested, despite demonstrating activity on N-methylated and 4-hydroxylated tryptophan derivatives individually. Taken together, this work expands upon the known substrates for TrpM and PsiD, further increasing the diversity of tryptamine biosynthetic products.","PeriodicalId":8856,"journal":{"name":"Biotechnology Progress","volume":"40 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/btpr.3492","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141417537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

The development of an automated microscope image tracking and analysis system 开发自动显微镜图像跟踪和分析系统。

IF 2.5 3区生物学

Biotechnology Progress Pub Date : 2024-06-18 DOI: 10.1002/btpr.3490

Lillian McAfee, Zach Heath, William Anderson, Marvin Hozi, John Walker Orr, Youngbok (Abraham) Kang

{"title":"The development of an automated microscope image tracking and analysis system","authors":"Lillian McAfee, Zach Heath, William Anderson, Marvin Hozi, John Walker Orr, Youngbok (Abraham) Kang","doi":"10.1002/btpr.3490","DOIUrl":"10.1002/btpr.3490","url":null,"abstract":"Microscopy image analysis plays a crucial role in understanding cellular behavior and uncovering important insights in various biological and medical research domains. Tracking cells within the time-lapse microscopy images is a fundamental technique that enables the study of cell dynamics, interactions, and migration. While manual cell tracking is possible, it is time-consuming and prone to subjective biases that impact results. In order to solve this issue, we sought to create an automated software solution, named cell analyzer, which is able to track cells within microscopy images with minimal input required from the user. The program of cell analyzer was written in Python utilizing the open source computer vision (OpenCV) library and featured a graphical user interface that makes it easy for users to access. The functions of all codes were verified through closeness, area, centroid, contrast, variance, and cell tracking test. Cell analyzer primarily utilizes image preprocessing and edge detection techniques to isolate cell boundaries for detection and analysis. It uniquely recorded the area, displacement, speed, size, and direction of detected cell objects and visualized the data collected automatically for fast analysis. Our cell analyzer provides an easy-to-use tool through a graphical user interface for tracking cell motion and analyzing quantitative cell images.","PeriodicalId":8856,"journal":{"name":"Biotechnology Progress","volume":"40 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141417538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Metagenomics analysis yields assembled genomes from prokaryotic anaerobes with polymer-degrading potential 元基因组学分析产生了具有聚合物降解潜力的原核厌氧菌的组装基因组。

IF 2.5 3区生物学

Biotechnology Progress Pub Date : 2024-06-17 DOI: 10.1002/btpr.3484

Elaina M. Blair, Jennifer L. Brown, Dong Li, Patricia A. Holden, Michelle A. O'Malley

{"title":"Metagenomics analysis yields assembled genomes from prokaryotic anaerobes with polymer-degrading potential","authors":"Elaina M. Blair, Jennifer L. Brown, Dong Li, Patricia A. Holden, Michelle A. O'Malley","doi":"10.1002/btpr.3484","DOIUrl":"10.1002/btpr.3484","url":null,"abstract":"Anaerobic microbial communities are often highly degradative, such as those found in the herbivore rumen and large-scale anaerobic digesters. Since the microbial communities in these systems degrade recalcitrant organic polymers, we hypothesize that some microbes in anaerobic environments may be involved in man-made plastic association, deformation, or even breakdown. While efforts have been put toward characterizing microbial communities, many microbes remain unidentified until they can be sufficiently cultivated to generate enough genetic material to assemble high-quality metagenome assemblies and reference genomes. In this study, microbial consortia from goat fecal pellets and anaerobic digester sludge were cultivated for over 6 weeks to assemble metagenomes from novel anaerobic taxa with potential degradative activity. To select for microbes with potential plastic-degrading abilities, plastic strips were included in culture, though the presence of plastic did not appear to enrich for particularly degradative consortia, yet it did select for novel species that otherwise may not have been characterized. Whole-genome shotgun sequencing enabled assembly of 72 prokaryotic metagenome-assembled genomes (MAGs) with >90% completion, <5% contamination, and an N50 >10,000 bp; 17 of these MAGs are classified as novel species given their lack of similarity to publicly available genomes and MAGs. These 72 MAGs vary in predicted carbohydrate-degrading abilities, with genes predicted to encode fewer than 10 or up to nearly 400 carbohydrate-active enzymes. Overall, this enrichment strategy enables characterization of less abundant MAGs in a community, and the MAGs identified here can be further mined to advance understanding of degradative anaerobic microbial consortia.","PeriodicalId":8856,"journal":{"name":"Biotechnology Progress","volume":"40 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/btpr.3484","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141330307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

High-throughput in silico workflow for optimization and characterization of multimodal chromatographic processes 优化和表征多模式色谱过程的高通量硅学工作流程。

IF 2.5 3区生物学

Biotechnology Progress Pub Date : 2024-06-10 DOI: 10.1002/btpr.3483

Scott H. Altern, Jessica Y. Lyall, John P. Welsh, Sean Burgess, Vijesh Kumar, Chris Williams, Abraham M. Lenhoff, Steven M. Cramer

{"title":"High-throughput in silico workflow for optimization and characterization of multimodal chromatographic processes","authors":"Scott H. Altern, Jessica Y. Lyall, John P. Welsh, Sean Burgess, Vijesh Kumar, Chris Williams, Abraham M. Lenhoff, Steven M. Cramer","doi":"10.1002/btpr.3483","DOIUrl":"10.1002/btpr.3483","url":null,"abstract":"While high-throughput (HT) experimentation and mechanistic modeling have long been employed in chromatographic process development, it remains unclear how these techniques should be used in concert within development workflows. In this work, a process development workflow based on HT experiments and mechanistic modeling was constructed. The integration of HT and modeling approaches offers improved workflow efficiency and speed. This high-throughput in silico (HT-IS) workflow was employed to develop a Capto MMC polishing step for mAb aggregate removal. High-throughput batch isotherm data was first generated over a range of mobile phase conditions and a suite of analytics were employed. Parameters for the extended steric mass action (SMA) isotherm were regressed for the multicomponent system. Model validation was performed using the extended SMA isotherm in concert with the general rate model of chromatography using the CADET modeling software. Here, step elution profiles were predicted for eight RoboColumn runs across a range of ionic strength, pH, and load density. Optimized processes were generated through minimization of a complex objective function based on key process metrics. Processes were evaluated at lab-scale using two feedstocks, differing in composition. The results confirmed that both processes obtained high monomer yield (>85%) and removed <math>\u0000 <mrow>\u0000 <mo>∼</mo>\u0000 <mn>50</mn>\u0000 <mo>%</mo>\u0000 </mrow></math> of aggregate species. Column simulations were then carried out to determine sensitivity to a wide range of process inputs. Elution buffer pH was found to be the most critical process parameter, followed by resin ionic capacity. Overall, this study demonstrated the utility of the HT-IS workflow for rapid process development and characterization.","PeriodicalId":8856,"journal":{"name":"Biotechnology Progress","volume":"40 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141295496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to “Soluble production and function of vascular endothelial growth factor/basic fibroblast growth factor complex peptide” 更正 "血管内皮生长因子/碱性成纤维细胞生长因子复合肽的可溶性产生和功能"。

IF 2.5 3区生物学

Biotechnology Progress Pub Date : 2024-05-27 DOI: 10.1002/btpr.3455

引用次数: 0

Buffer effects on protein sieving losses in ultrafiltration and their relationship to biophysical properties 缓冲液对超滤中蛋白质筛分损失的影响及其与生物物理特性的关系。

IF 2.5 3区生物学

Biotechnology Progress Pub Date : 2024-05-23 DOI: 10.1002/btpr.3481

Aylin Mohammadzadehmarandi, Andrew L. Zydney

引用次数: 0

Effect of culture hydrodynamics on Arthrospira platensis production using a single-use photobioreactor system through a CFD supported approach 通过 CFD 支持方法研究培养液流体力学对使用一次性光生物反应器系统生产节肢动物的影响。

IF 2.5 3区生物学

Biotechnology Progress Pub Date : 2024-05-20 DOI: 10.1002/btpr.3480

S. Furkan Demirden, Barıs Erdogan, Deniz Şenyay Öncel, Suphi S. Oncel

{"title":"Effect of culture hydrodynamics on Arthrospira platensis production using a single-use photobioreactor system through a CFD supported approach","authors":"S. Furkan Demirden, Barıs Erdogan, Deniz Şenyay Öncel, Suphi S. Oncel","doi":"10.1002/btpr.3480","DOIUrl":"10.1002/btpr.3480","url":null,"abstract":"Laboratory scale conventional single-use bioreactor was used to investigate the effect of different stirrer speeds on the Arthrospira platensis (Spirulina platensis) culture. Experiments were handled in two steps. First step was the selection of the stirring speeds, which was simulated via using CFD, and the second was the long term cultivation with the selected speed. During 10 days of batches as the first step, under identical culture conditions, stirrer speed of 230 rpm gave higher results, compared to 130 and 70 rpm, with respect to dry biomass weight, absorbance value (AB) and chlorophyll-a concentration. Volumetric productivity during the growth phase of the cultures were calculated as 0.39 ± 0.03, 0.28 ± 0.01, and 0.19 ± 0.02 g L−1 d−1, from the fast to the slower speeds. According to the results a 17 day batch was handled with 230 rpm in order to monitor the effects on the culture. The culture reached a volumetric productivity of 0.33 ± 0.04 g L−1 d−1. Statistical analysis showed the significance of the parameters related with the stirring speed.","PeriodicalId":8856,"journal":{"name":"Biotechnology Progress","volume":"40 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141065370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A strategy for successful dual-species protein expression of genes with non-optimal codon usage destined for bacterial and yeast cell factories 成功表达细菌和酵母细胞工厂非最佳密码子使用基因的双物种蛋白质的策略。

IF 2.5 3区生物学

Biotechnology Progress Pub Date : 2024-05-17 DOI: 10.1002/btpr.3482

Marcus Wäneskog, Trine Bertram Rasmussen, Emil D. Jensen

{"title":"A strategy for successful dual-species protein expression of genes with non-optimal codon usage destined for bacterial and yeast cell factories","authors":"Marcus Wäneskog, Trine Bertram Rasmussen, Emil D. Jensen","doi":"10.1002/btpr.3482","DOIUrl":"10.1002/btpr.3482","url":null,"abstract":"Recombinant protein expression on an industrial scale traditionally utilizes one of two microbial workhorses: Escherichia coli or Saccharomyces cerevisiae. Additionally, random protein engineering of enzymes and proteins aimed for expression in S. cerevisiae are often mutagenized and pre-screened in E. coli before expression in yeast. This introduces artificial bottlenecks as the bacterial expression vector needs to be substituted for a yeast expression vector via sub-cloning, and the new library re-evaluated before a final screening in yeast. Here, we put forward a protein expression and engineering strategy that involves the use of a dual-host shuttle vector (pYB-Dual) designed with both a strong inducible yeast promoter (pGAL1), and a strong inducible bacterial promoter (pT7-RNAP), which allows for inducible protein expression in both species. Additionally, we demonstrate that by transforming the pYB-Dual vector into the E. coli strain Rosetta 2, which has elevated levels of 7 rare tRNAs, we can achieve high-level protein expression in both yeast and bacteria, even when using a mNeonGreen gene codon optimized for yeast. This dual expression vector is expected to remove bottlenecks during protein engineering of commercially important enzymes destined for high-titer expression in yeast.","PeriodicalId":8856,"journal":{"name":"Biotechnology Progress","volume":"40 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/btpr.3482","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140955525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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