Biotechnology Progress最新文献_第4页

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 2.9 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":"https://doi.org/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":null,"pages":null},"PeriodicalIF":2.9,"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 2.9 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":"https://doi.org/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":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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 2.9 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":"https://doi.org/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> <semantics><mrow><mo>∼</mo> <mn>50</mn> <mo>%</mo></mrow> <annotation>$$ sim 50% $$</annotation></semantics> </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":null,"pages":null},"PeriodicalIF":2.9,"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 2.9 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 2.9 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":"https://doi.org/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":null,"pages":null},"PeriodicalIF":2.9,"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 2.9 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":"https://doi.org/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":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Targeted delivery of interleukin-12 plasmid into HepG2 cells through folic acid conjugated graphene oxide nanocarrier 通过叶酸共轭氧化石墨烯纳米载体向 HepG2 细胞靶向递送白细胞介素-12 质粒。

IF 2.5 3区生物学

Biotechnology Progress Pub Date : 2024-05-16 DOI: 10.1002/btpr.3473

Farshad Safari, Hassan Bardania, Ali Dehshahri, Somayeh Hallaj-Nezhadi, Arash Asfaram, Vahid Mohammadi, Marzieh Baneshi, Sima Bahramianpour, Negar Akrami, Bahman Khalvati, Ali Mirzaei

{"title":"Targeted delivery of interleukin-12 plasmid into HepG2 cells through folic acid conjugated graphene oxide nanocarrier","authors":"Farshad Safari, Hassan Bardania, Ali Dehshahri, Somayeh Hallaj-Nezhadi, Arash Asfaram, Vahid Mohammadi, Marzieh Baneshi, Sima Bahramianpour, Negar Akrami, Bahman Khalvati, Ali Mirzaei","doi":"10.1002/btpr.3473","DOIUrl":"10.1002/btpr.3473","url":null,"abstract":"Successful gene therapy relies on carriers to transfer genetic materials with high efficiency and low toxicity in a targeted manner. To enhance targeted cell binding and uptake, we developed and synthesized a new gene delivery vector based on graphene oxide (GO) modified by branched polyethyleneimine (BPEI) and folic acid (FA). The GO-PEI-FA nanocarriers exhibit lower toxicity compared to unmodified PEI, as well as having the potential to efficiently condense and protect pDNA. Interestingly, increasing the polymer content in the polyplex formulation improved plasmid transfer ability. Substituting graphene oxide for PEI at an N/P ratio of 10 in the HepG2 and THP1 cell lines improved hIL-12 expression by up to approximately eightfold compared to simple PEI, which is twice as high as GO-PEI-FA in Hek293 at the same N/P ratio. Therefore, the GO-PEI-FA described in this study may serve as a targeting nanocarrier for the delivery of the hIL-12 plasmid into cells overexpressing folic acid receptors, such as those found in hepatocellular carcinoma.","PeriodicalId":8856,"journal":{"name":"Biotechnology Progress","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140955629","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

SPEED-MODE cell line development (CLD): Reducing Chinese hamster ovary (CHO) CLD timelines via earlier suspension adaptation and maximizing time spent in the exponential growth phase 快速模式细胞系开发（CLD）：通过提前悬浮适应和最大限度地延长指数生长阶段的时间，缩短中国仓鼠卵巢 (CHO) 细胞系开发 (CLD) 的时间。

IF 2.5 3区生物学

Biotechnology Progress Pub Date : 2024-05-08 DOI: 10.1002/btpr.3479

Kavya Ganapathy, Cynthia Lam, Joni Tsukuda, Alyssa Sargon, Adrian Nava, Peter Harms, Amy Shen, Gavin Barnard, Shahram Misaghi

{"title":"SPEED-MODE cell line development (CLD): Reducing Chinese hamster ovary (CHO) CLD timelines via earlier suspension adaptation and maximizing time spent in the exponential growth phase","authors":"Kavya Ganapathy, Cynthia Lam, Joni Tsukuda, Alyssa Sargon, Adrian Nava, Peter Harms, Amy Shen, Gavin Barnard, Shahram Misaghi","doi":"10.1002/btpr.3479","DOIUrl":"10.1002/btpr.3479","url":null,"abstract":"Chinese hamster ovary (CHO) cells are the preferred system for expression of therapeutic proteins and the majority of all biotherapeutics are being expressed by these cell lines. CHO expression systems are readily scalable, resistant to human adventitious agents, and have desirable post-translational modifications, such as glycosylation. Regardless, drug development as a whole is a very costly, complicated, and time-consuming process. Therefore, any improvements that result in reducing timelines are valuable and can provide patients with life-saving drugs earlier. Here we report an effective method (termed SPEED-MODE, herein) to speed up the Cell line Development (CLD) process in a targeted integration (TI) CHO CLD system. Our findings show that (1) earlier single cell cloning (SCC) of transfection pools, (2) speeding up initial titer screening turnaround time, (3) starting suspension adaptation of cultures sooner, and (4) maximizing the time CHO cultures spend in the exponential growth phase can reduce CLD timelines from ~4 to ~3 months. Interestingly, SPEED-MODE timelines closely match the theoretical minimum timeline for CHO CLD assuming that CHO cell division is the rate limiting factor. Clones obtained from SPEED-MODE CLD yielded comparable titer and product quality to those obtained via a standard CLD process. Hence, SPEED-MODE CLD is advantageous for manufacturing biotherapeutics in an industrial setting as it can significantly reduce CLD timelines without compromising titer or product quality.","PeriodicalId":8856,"journal":{"name":"Biotechnology Progress","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140875739","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

Developing tardigrade-inspired material: Track membranes functionalized with Dsup protein for cell-free DNA isolation 开发受 Tardigrade 启发的材料：用于无细胞 DNA 分离的 Dsup 蛋白功能化轨道膜

IF 2.5 3区生物学

Biotechnology Progress Pub Date : 2024-05-03 DOI: 10.1002/btpr.3478

Mikhail Zarubin, Evgeny Andreev, Elena Kravchenko, Uliana Pinaeva, Alexander Nechaev, Pavel Apel

{"title":"Developing tardigrade-inspired material: Track membranes functionalized with Dsup protein for cell-free DNA isolation","authors":"Mikhail Zarubin, Evgeny Andreev, Elena Kravchenko, Uliana Pinaeva, Alexander Nechaev, Pavel Apel","doi":"10.1002/btpr.3478","DOIUrl":"10.1002/btpr.3478","url":null,"abstract":"When developing functionalized biomaterials, the proteins from extremophilic organisms, in particular unique tardigrade disordered proteins, are of great value. The damage suppressor protein (Dsup), initially discovered in the tardigrade Ramazzottius varieornatus and found to be an efficient DNA protector under oxidative and irradiation stress, has been hypothesized to possess a good potential for the development of the material, which can isolate cell-free DNA. With this in mind, DNA-nonadsorbing polyethylene terephthalate track membranes have been functionalized using the Dsup protein via covalent bonding with glutaraldehyde. The filtration experiments have verified the ability of track membranes with the immobilized Dsup protein to adsorb cell-free DNA, with an accumulation capacity of 70 ± 19 mg m−2. The resulting track membrane-based biomaterial might be used in various devices for filtration and separation of cell-free DNA molecules from biological solutions and environmental samples, and also for their accumulation, storage, and further manipulation.","PeriodicalId":8856,"journal":{"name":"Biotechnology Progress","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140831906","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