Biotechnology and Bioengineering最新文献_第9页

Cover Image, Volume 121, Number 8, August 2024 封面图片，第 121 卷，第 8 号，2024 年 8 月

IF 3.5 2区生物学

Biotechnology and Bioengineering Pub Date : 2024-07-24 DOI: 10.1002/bit.28809

引用次数: 0

Biotechnology and Bioengineering: Volume 121, Number 8, August 2024 生物技术与生物工程第 121 卷第 8 号，2024 年 8 月

IF 3.5 2区生物学

Biotechnology and Bioengineering Pub Date : 2024-07-24 DOI: 10.1002/bit.28803

引用次数: 0

ProteinFlow: An advanced framework for feature engineering in protein data analysis ProteinFlow：蛋白质数据分析特征工程的高级框架。

IF 3.5 2区生物学

Biotechnology and Bioengineering Pub Date : 2024-07-23 DOI: 10.1002/bit.28812

Yanlin Mi, Stefan-Bogdan Marcu, Venkata V. B. Yallapragada, Sabin Tabirca

{"title":"ProteinFlow: An advanced framework for feature engineering in protein data analysis","authors":"Yanlin Mi, Stefan-Bogdan Marcu, Venkata V. B. Yallapragada, Sabin Tabirca","doi":"10.1002/bit.28812","DOIUrl":"10.1002/bit.28812","url":null,"abstract":"In the burgeoning field of proteins, the effective analysis of intricate protein data remains a formidable challenge, necessitating advanced computational tools for data processing, feature extraction, and interpretation. This study introduces ProteinFlow, an innovative framework designed to revolutionize feature engineering in protein data analysis. ProteinFlow stands out by offering enhanced efficiency in data collection and preprocessing, along with advanced capabilities in feature extraction, directly addressing the complexities inherent in multidimensional protein data sets. Through a comparative analysis, ProteinFlow demonstrated a significant improvement over traditional methods, notably reducing data preprocessing time and expanding the scope of biologically significant features identified. The framework's parallel data processing strategy and advanced algorithms ensure not only rapid data handling but also the extraction of comprehensive, meaningful insights from protein sequences, structures, and interactions. Furthermore, ProteinFlow exhibits remarkable scalability, adeptly managing large-scale data sets without compromising performance, a crucial attribute in the era of big data.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 11","pages":"3563-3571"},"PeriodicalIF":3.5,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bit.28812","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141751082","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}

引用次数: 0

In-situ biological biogas upgrading using upflow anaerobic polyfoam bioreactor: Operational and biological aspects 利用上流式厌氧聚脂生物反应器进行原位生物沼气升级：操作和生物方面。

IF 3.5 2区生物学

Biotechnology and Bioengineering Pub Date : 2024-07-22 DOI: 10.1002/bit.28811

Katie Baransi-Karkaby, Keren Yanuka-Golub, Mahdi Hassanin, Nedal Massalha, Isam Sabbah

{"title":"In-situ biological biogas upgrading using upflow anaerobic polyfoam bioreactor: Operational and biological aspects","authors":"Katie Baransi-Karkaby, Keren Yanuka-Golub, Mahdi Hassanin, Nedal Massalha, Isam Sabbah","doi":"10.1002/bit.28811","DOIUrl":"10.1002/bit.28811","url":null,"abstract":"A high rate upflow anaerobic polyfoam-based bioreactor (UAPB) was developed for lab-scale in-situ biogas upgrading by H2 injection. The reactor, with a volume of 440 mL, was fed with synthetic wastewater at an organic loading rate (OLR) of 3.5 g COD/L·day and a hydraulic retention time (HRT) of 7.33 h. The use of a porous diffuser, alongside high gas recirculation, led to a higher H2 liquid mass transfer, and subsequently to a better uptake for high CH4 content of 56% (starting from 26%). Our attempts to optimize both operational parameters (H2 flow rate and gas recirculation ratio, which is the total flow rate of recirculated gas over the total outlet of gas flow rate) were not initially successful, however, at a very high recirculation ratio (32) and flow rate (54 mL/h), a significant improvement of the hydrogen consumption was achieved. These operational conditions have in turn driven the methanogenic community toward the dominance of Methanosaetaceae, which out-competed Methanosarcinaceae. Nevertheless, highly stable methane production rates of 1.4–1.9 L CH4/Lreactor.day were observed despite the methanogenic turnover. During the different applied operational conditions, the bacterial community was especially impacted, resulting in substantial shifts of taxonomic groups. Notably, Aeromonadaceae was the only bacterial group positively correlated with increasing hydrogen consumption rates. The capacity of Aeromonadaceae to extracellularly donate electrons suggests that direct interspecies electron transfer (DIET) enhanced biogas upgrading. Overall, the proposed innovative biological in-situ biogas upgrading technology using the UAPB configuration shows promising results for stable, simple, and effective biological biogas upgrading.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 11","pages":"3471-3483"},"PeriodicalIF":3.5,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bit.28811","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141733631","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}

引用次数: 0

Engineering xylose induction in Vibrio natriegens for biomanufacturing applications 在纳氏弧菌中进行木糖诱导工程，促进生物制造应用

IF 3.5 2区生物学

Biotechnology and Bioengineering Pub Date : 2024-07-19 DOI: 10.1002/bit.28804

Eric VanArsdale, Erin Kelly, Cameron V. Sayer, Gary J. Vora, Tanya Tschirhart

{"title":"Engineering xylose induction in Vibrio natriegens for biomanufacturing applications","authors":"Eric VanArsdale, Erin Kelly, Cameron V. Sayer, Gary J. Vora, Tanya Tschirhart","doi":"10.1002/bit.28804","DOIUrl":"10.1002/bit.28804","url":null,"abstract":"Xylose is an abundant, inexpensive and readily available carbohydrate common in minimally processed feedstocks such as seaweed and algae. While a wide variety of marine microbes have evolved to utilize seaweed and algae, only a few currently have the requisite characteristics and genetic engineering tools necessary to entertain the use of these underutilized feedstocks. The rapidly growing Gram-negative halophilic bacterium Vibrio natriegens is one such chassis. In this study, we engineered and tested xylose induction in V. natriegens as a tool for scalable bioproduction applications. First, we created a sensing construct based on the xylose operon from Escherichia coli MG1665 and measured its activity using a fluorescent reporter and identified that cellular import plays a key role in induction strength and that expression required the XylR transcription factor. Next, we identified that select deletions of the promoter region enhance gene expression, limiting the effect of carbohydrate repression when xylose is used as an inducer in the presence of industrially relevant carbon sources. Lastly, we used the optimized constructs to produce the biopolymer melanin using seawater mimetic media. One of these formulations utilized a nori-based seaweed extract as an inducer and demonstrated melanin yields comparable to previously optimized methods using a more traditional and costly inducer. Together, the results demonstrate that engineering xylose induction in V. natriegens can provide an effective and lower cost option for timed biosynthesis in scalable biomanufacturing applications using renewable feedstocks.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 11","pages":"3572-3581"},"PeriodicalIF":3.5,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bit.28804","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141730634","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}

引用次数: 0

Substrate and nutrient manipulation during continuous cultivation of extremophilic algae, Galdieria spp. RTK 37.1, substantially impacts biomass productivity and composition 在连续培养嗜极藻类 Galdieria spp. RTK 37.1 的过程中，对底质和营养物质的操作会对生物量的生产率和组成产生重大影响。

IF 3.5 2区生物学

Biotechnology and Bioengineering Pub Date : 2024-07-19 DOI: 10.1002/bit.28814

Emma Buckeridge, Carlos C. Caballero, Daniel H. Smith, Matthew B. Stott, Carlo R. Carere

{"title":"Substrate and nutrient manipulation during continuous cultivation of extremophilic algae, Galdieria spp. RTK 37.1, substantially impacts biomass productivity and composition","authors":"Emma Buckeridge, Carlos C. Caballero, Daniel H. Smith, Matthew B. Stott, Carlo R. Carere","doi":"10.1002/bit.28814","DOIUrl":"10.1002/bit.28814","url":null,"abstract":"The extremophilic nature and metabolic flexibility of Galdieria spp. highlights their potential for biotechnological application. However, limited research into continuous cultivation of Galdieria spp. has slowed progress towards the commercialization of these algae. The objective of this research was to investigate biomass productivity and growth yields during continuous photoautotrophic, mixotrophic and heterotrophic cultivation of Galdieria sp. RTK371; a strain recently isolated from within the Taupō Volcanic Zone in Aotearoa-New Zealand. Results indicate Galdieria sp. RTK371 grows optimally at pH 2.5 under warm white LED illumination. Photosynthetic O2 production was dependent on lighting intensity with a maximal value of (133.5 ± 12.1 nmol O2 mgbiomass−1 h−1) achieved under 100 μmol m−2 s−1 illumination. O2 production rates slowed significantly to 42 ± 1 and <0.01 nmol O2 mgbiomass−1 h−1 during mixotrophic and heterotrophic growth regimes respectively. Stable, long-term chemostat growth of Galdieria sp. RTK371 was achieved during photoautotrophic, mixotrophic and heterotrophic growth regimes. During periods of ammonium limitation, Galdieria sp. RTK371 increased its intracellular carbohydrate content (up to 37% w/w). In contrast, biomass grown in ammonium excess was composed of up to 65% protein (w/w). Results from this study demonstrate that the growth of Galdieria sp. RTK371 can be manipulated during continuous cultivation to obtain desired biomass and product yields over long cultivation periods.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 11","pages":"3428-3439"},"PeriodicalIF":3.5,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bit.28814","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141731000","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}

引用次数: 0

Optimizing the production of dsRNA biocontrols in microbial systems using multiple transcriptional terminators 利用多种转录终止子优化微生物系统中 dsRNA 生物控制的生产

IF 3.5 2区生物学

Biotechnology and Bioengineering Pub Date : 2024-07-18 DOI: 10.1002/bit.28805

Sebastian J. Ross, Gareth R. Owen, James Hough, Annelies Philips, Wendy Maddelein, John Ray, Peter M. Kilby, Mark J. Dickman

{"title":"Optimizing the production of dsRNA biocontrols in microbial systems using multiple transcriptional terminators","authors":"Sebastian J. Ross, Gareth R. Owen, James Hough, Annelies Philips, Wendy Maddelein, John Ray, Peter M. Kilby, Mark J. Dickman","doi":"10.1002/bit.28805","DOIUrl":"10.1002/bit.28805","url":null,"abstract":"Crop pests and pathogens annually cause over $220 billion in global crop damage, with insects consuming 5%–20% of major grain crops. Current crop pest and disease control strategies rely on insecticidal and fungicidal sprays, plant genetic resistance, transgenes, and agricultural practices. Double-stranded RNA (dsRNA) is emerging as a novel sustainable method of plant protection as an alternative to traditional chemical pesticides. Successful commercialization of dsRNA-based biocontrols requires the economical production of large quantities of dsRNA combined with suitable delivery methods to ensure RNAi efficacy against the target pest. In this study, we have optimized the design of plasmid DNA constructs to produce dsRNA biocontrols in Escherichia coli, by employing a wide range of alternative synthetic transcriptional terminators before measurement of dsRNA yield. We demonstrate that a 7.8-fold increase of dsRNA was achieved using triple synthetic transcriptional terminators within a dual T7 dsRNA production system compared to the absence of transcriptional terminators. Moreover, our data demonstrate that batch fermentation production dsRNA using multiple transcriptional terminators is scalable and generates significantly higher yields of dsRNA generated in the absence of transcriptional terminators at both small-scale batch culture and large-scale fermentation. In addition, we show that application of these dsRNA biocontrols expressed in E. coli cells results in increased insect mortality. Finally, novel mass spectrometry analysis was performed to determine the precise sites of transcriptional termination at the different transcriptional terminators providing important further mechanistic insight.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 11","pages":"3582-3599"},"PeriodicalIF":3.5,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bit.28805","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141730635","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}

引用次数: 0

Predictive modeling for cell culture in commercial manufacturing of biotherapeutics 生物治疗商业化生产中的细胞培养预测模型。

IF 3.5 2区生物学

Biotechnology and Bioengineering Pub Date : 2024-07-18 DOI: 10.1002/bit.28813

Shyam Panjwani, Alice Almazan, Rubin Hille, Konstantinos Spetsieris

引用次数: 0

A computational model for single cell Lamin-A structural organization after microfluidic compression 微流体压缩后单细胞 Lamin-A 结构组织的计算模型。

IF 3.5 2区生物学

Biotechnology and Bioengineering Pub Date : 2024-07-17 DOI: 10.1002/bit.28810

Maria Isabella Maremonti, Filippo Causa

{"title":"A computational model for single cell Lamin-A structural organization after microfluidic compression","authors":"Maria Isabella Maremonti, Filippo Causa","doi":"10.1002/bit.28810","DOIUrl":"10.1002/bit.28810","url":null,"abstract":"In recent years, nuclear mechanobiology gained a lot of attention for the study of cell responses to external cues like adhesive forces, applied compression, and/or shear-stresses. In details, the Lamin-A protein—as major constituent of the cell nucleus structure—plays a crucial role in the overall nucleus mechanobiological response. However, modeling and analysis of Lamin-A protein organization upon rapid compression conditions in microfluidics are still difficult to be performed. Here, we introduce the possibility to control an applied microfluidic compression on single cells, deforming them up to the nucleus level. In a wide range of stresses (~1–102 kPa) applied on healthy and cancer cells, we report increasing Lamin-A intensities which scale as a power law with the applied compression. Then, an increase up to two times of the nuclear viscosity is measured in healthy cells, due to the modified Lamin-A organization. This is ascribable to the increasing assembly of Lamin-A filament-like branches which increment both in number and elongation (up to branches four-time longer). Moreover, the solution of a computational model of differential equations is presented as a powerful tool for a single cell prediction of the Lamin-A assembly as a function of the applied compression.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 11","pages":"3551-3562"},"PeriodicalIF":3.5,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bit.28810","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632670","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}

引用次数: 0

Reducing the degree of crosslinking of peptidoglycan in Listeria monocytogenes promoted the secretion of membrane vesicles 降低李斯特菌肽聚糖的交联度可促进膜囊泡的分泌。

IF 3.5 2区生物学

Biotechnology and Bioengineering Pub Date : 2024-07-16 DOI: 10.1002/bit.28807

Mingyuan Tang, Yao Lei, Kehan Chen, Mingming Ding, Qian Ou, Jing Tang, Yunwen Zhang, Tian Tang, Chuan Wang

{"title":"Reducing the degree of crosslinking of peptidoglycan in Listeria monocytogenes promoted the secretion of membrane vesicles","authors":"Mingyuan Tang, Yao Lei, Kehan Chen, Mingming Ding, Qian Ou, Jing Tang, Yunwen Zhang, Tian Tang, Chuan Wang","doi":"10.1002/bit.28807","DOIUrl":"10.1002/bit.28807","url":null,"abstract":"Listeria monocytogenes (LM) is a Gram-positive (G+) bacterium that secretes nanoscale membrane vesicles (MVs). LM MVs comprise various bacterial components and may have potential as an antigen or drug-delivery vehicle; however, the low yield of the LM MVs limits related research. G+-bacterial MVs germinate from the bacterial plasma membrane and must pass through a thick crosslinked peptidoglycan layer for release. Herein, we aimed to increase the release of MVs by reducing the degree of crosslinking of peptidoglycan. We knocked out two genes related to the longitudinal crosslinking of peptidoglycan, dal and dat, and supplemented the knocked-out dal gene through plasmid expression to obtain a stably inherited recombinant strain LMΔdd::pCW633. The structure, particle size, and main protein components of MVs secreted by this recombinant strain were consistent with those secreted from the wild strain, but the yield of MVs was considerably increased (p < 0.05). Furthermore, Listeria ivanovii (LI) was found to secrete MVs that differed in the composition of the main proteins compared with those of LM MVs. The abovementioned method was also feasible for promoting the secretion of MVs from the attenuated LM strain and LI wild-type and attenuated strains. Our study provides a new method to increase the secretion of MVs derived from Listeria that could be extended to other G+ bacteria.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"121 11","pages":"3629-3641"},"PeriodicalIF":3.5,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141625999","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}

引用次数: 0