BioDesign Research最新文献

Biodetoxification of lignocellulose hydrolysate for direct use in succinic acid production 生物解毒木质纤维素水解物，直接用于琥珀酸生产

BioDesign Research Pub Date : 2024-07-26 DOI: 10.34133/bdr.0044

Wankui Jiang, Zhixiao Lei, Haiyan Gao, Yujia Jiang, Carol Sze Ki Lin, Wenming Zhang, Fengxue Xin, Min Jiang

引用次数: 0

CRISPR-Cas13: Pioneering RNA Editing for Nucleic Acid Therapeutics CRISPR-Cas13：开创核酸治疗的 RNA 编辑技术

BioDesign Research Pub Date : 2024-07-26 DOI: 10.34133/bdr.0041

Guanglin Zhu, Xinzhi Zhou, Mingzhang Wen, Jianjun Qiao, Guo Li, Yuan-Feng Yao

引用次数: 0

Harnessing a T1 phage-derived spanin for developing phage-based antimicrobial development 利用 T1 噬菌体衍生的 spanin 开发基于噬菌体的抗微生物开发项目

BioDesign Research Pub Date : 2024-01-08 DOI: 10.34133/bdr.0028

Wakana Yamashita, Shinjiro Ojima, Azumi Tamura, A. Azam, Kohei Kondo, Yuancheng Zhang, Longzhu Cui, Masaki Shintani, Masato Suzuki, Yoshimasa Takahashi, Koichi Watashi, Satoshi Tsuneda, Kotaro Kiga

引用次数: 0

Microbial upcycling of depolymerized lignin into value-added chemicals 通过微生物将解聚木质素转化为高附加值化学品

BioDesign Research Pub Date : 2023-12-28 DOI: 10.34133/bdr.0027

Yang Zhang, Cheng Cheng, Bixia Fu, Teng Long, Ning He, Jianqiang Fan, Zheyong Xue, Anqi Chen, Jifeng Yuan

引用次数: 0

Multidimensional Optimization of Saccharomyces cerevisiae for Carotenoid Overproduction 多维优化酿酒酵母，促进类胡萝卜素的过度生产

BioDesign Research Pub Date : 2023-12-18 DOI: 10.34133/bdr.0026

Jian Fan, Yang Zhang, Wenhao Li, Zhizhen Li, Danli Zhang, Qiwen Mo, Mingfeng Cao, Jifeng Yuan

引用次数: 0

A MoClo-compatible toolbox of ECF sigma factor-based regulatory switches for proteobacterial chassis 与 MoClo 兼容的基于 ECF 西格玛因子的蛋白细菌底盘调控开关工具箱

BioDesign Research Pub Date : 2023-12-12 DOI: 10.34133/bdr.0025

Doreen Meier, Christian Rauch, Marcel Wagner, Paul Klemm, Patrick Blumenkamp, Raphael Müller, Eric Ellenberger, Kinnari M. Karia, Stefano Vecchione, Javier Serranía, Marcus Lechner, Georg Fritz, Alexander Goesmann, Anke Becker

引用次数: 0

Production of Volatile Moth Sex Pheromones in Transgenic Nicotiana benthamiana Plants 转基因烟叶中飞蛾性信息素的产生

BioDesign Research Pub Date : 2021-04-21 DOI: 10.1101/2021.03.31.437903

Rubén Mateos-Fernández, Elena Moreno-Giménez, S. Gianoglio, Alfredo Quijano-Rubio, Jose Gavaldá-García, Lucía Estellés, A. Rubert, J. Rambla, M. Vazquez-Vilar, E. Huet, Asun Fernández-del-Carmen, A. Espinosa-Ruiz, Mojca Juteršek, S. Vacas, I. Navarro, V. Navarro‑Llopis, J. Primo-Millo, D. Orzáez

{"title":"Production of Volatile Moth Sex Pheromones in Transgenic Nicotiana benthamiana Plants","authors":"Rubén Mateos-Fernández, Elena Moreno-Giménez, S. Gianoglio, Alfredo Quijano-Rubio, Jose Gavaldá-García, Lucía Estellés, A. Rubert, J. Rambla, M. Vazquez-Vilar, E. Huet, Asun Fernández-del-Carmen, A. Espinosa-Ruiz, Mojca Juteršek, S. Vacas, I. Navarro, V. Navarro‑Llopis, J. Primo-Millo, D. Orzáez","doi":"10.1101/2021.03.31.437903","DOIUrl":"https://doi.org/10.1101/2021.03.31.437903","url":null,"abstract":"Plant-based bio-production of insect sex pheromones has been proposed as an innovative strategy to increase the sustainability of pest control in agriculture. Here we describe the engineering of transgenic plants producing (Z)-11-hexadecen-1-ol (Z11-16OH) and (Z)-11-hexadecenyl acetate (Z11-16OAc), two main volatile components in many Lepidoptera sex pheromone blends. We assembled multigene DNA constructs encoding the pheromone biosynthetic pathway and stably transformed them in Nicotiana benthamiana plants. The constructs comprised the Amyelois transitella AtrΔ11 desaturase gene, the Helicoverpa armigera farnesyl reductase HarFAR gene, and the Euonymus alatus diacylglycerol acetyltransferase EaDAct gene in different configurations. All the pheromone-producing plants showed dwarf phenotypes, whose severity correlated with pheromone levels. All but one of the recovered lines produced high levels of Z11-16OH but very low levels of Z11-16OAc, probably as a result of recurrent truncations at the level of the EaDAct gene. Only one plant line (SxPv1.2) was recovered harbouring an intact pheromone pathway and producing moderate levels of Z11-16OAc (11.8 µg g-1 FW), next to high levels of Z11-16OH (111.4 µg g-1). Z11-16OAc production was accompanied in SxPv1.2 by a partial recovery of the dwarf phenotype. SxPv1.2 was used to estimate the rates of volatile pheromone release, which resulted in 8.48 ng g-1 FW per day for Z11-16OH and 9.44 ng g-1 FW per day for Z11-16OAc. Our results suggest that pheromone release acts as a limiting factor in pheromone bio-dispenser strategies and establish a roadmap for biotechnological improvements.","PeriodicalId":324993,"journal":{"name":"BioDesign Research","volume":"52 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124941675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

Phagocytosed Polyhedrin-Cytokine Cocrystal Nanoparticles Provide Sustained Secretion of Bioactive Cytokines from Macrophages 吞噬多面蛋白-细胞因子共晶纳米颗粒提供巨噬细胞持续分泌生物活性细胞因子

BioDesign Research Pub Date : 2021-02-17 DOI: 10.1101/2021.02.17.431660

A. Wendler, N. James, Michael H. Jones, C. Pernstich

{"title":"Phagocytosed Polyhedrin-Cytokine Cocrystal Nanoparticles Provide Sustained Secretion of Bioactive Cytokines from Macrophages","authors":"A. Wendler, N. James, Michael H. Jones, C. Pernstich","doi":"10.1101/2021.02.17.431660","DOIUrl":"https://doi.org/10.1101/2021.02.17.431660","url":null,"abstract":"Many cells possess the ability to engulf and incorporate particles by phagocytosis. This active process is characteristic of microorganisms as well as higher order species. In mammals, monocytes, macrophages and microglia are among so-called professional phagocytes. In addition, cells such as fibroblast and chondrocytes are classified as non-professional phagocytes. Professional phagocytes play important roles in both the innate and adaptive immune response, wound healing and tissue homeostasis. Consequently, these cells are increasingly studied as targets and vectors of therapeutic intervention to treat a range of diseases. Professional phagocytes are notoriously difficult to transfect limiting their study and manipulation. Consequently, efforts have shifted towards the development of nanoparticles to deliver a cargo to phagocytic cells via phagocytosis. However, this approach carries significant technical challenges, particularly for protein cargos. We have focused on the development of nanoscale co-crystalline protein depots, known as PODS®, that contain protein cargos, including cytokines. Here, we show that PODS are readily phagocytosed by non-professional as well as professional phagocytic cells and have attributes, such as highly sustained release of cargo, that suggest potential utility for the study and exploitation of phagocytic cells for drug delivery. Monocytes and macrophages that ingest PODS retain normal characteristics including a robust chemotactic response. Moreover, the PODS-cytokine cargo is secreted by the loaded cell at a level sufficient to modulate the behavior of surrounding non-phagocytic cells. The results presented here demonstrate the potential of PODS nanoparticles as a novel molecular tool for the study and manipulation of phagocytic cells and for the development of Trojan horse immunotherapy strategies to treat cancer and other diseases.","PeriodicalId":324993,"journal":{"name":"BioDesign Research","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116815844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

In-Depth Computational Analysis of Natural and Artificial Carbon Fixation Pathways 自然和人工碳固定途径的深入计算分析

BioDesign Research Pub Date : 2021-01-06 DOI: 10.1101/2021.01.05.425423

Hannes Löwe, A. Kremling

{"title":"In-Depth Computational Analysis of Natural and Artificial Carbon Fixation Pathways","authors":"Hannes Löwe, A. Kremling","doi":"10.1101/2021.01.05.425423","DOIUrl":"https://doi.org/10.1101/2021.01.05.425423","url":null,"abstract":"In the recent years, engineering new-to-nature CO2 and C1 fixing metabolic pathways made a leap forward. These new, artificial pathways promise higher yields and activity than natural ones like the Calvin-Benson-Bassham cycle. The question remains how to best predict their in vivo performance and what actually makes one pathway “better” than another. In this context, we explore aerobic carbon fixation pathways by a computational approach and compare them based on their ATP-efficiency and specific activity considering the kinetics and thermodynamics of the reactions. Beside natural pathways, this included the artificial Reductive Glycine Pathway, the CETCH cycle and two completely new cycles with superior stoichiometry: The Reductive Citramalyl-CoA cycle and the 2-Hydroxyglutarate-Reverse Tricarboxylic Acid cycle. A comprehensive kinetic data set was collected for all enzymes of all pathways and missing kinetic data was sampled with the Parameter Balancing algorithm. Kinetic and thermodynamic data were fed to the Enzyme Cost Minimization algorithm to check for respective inconsistencies and calculate pathway specific activities. We found that the Reductive Glycine Pathway, the CETCH cycle and the new Reductive Citramalyl-CoA cycle were predicted to have higher ATP-efficiencies and specific activities than the natural cycles. The Calvin Cycle performed better than previously thought, however. It can be concluded that the weaker overall characteristics in the design of the Calvin Cycle might be compensated by other benefits like robustness, low nutrient demand and a good compatibility with the host’s physiological requirements. Nevertheless, the artificial carbon fixation cycles hold great potential for future applications in Industrial Biotechnology and Synthetic Biology.","PeriodicalId":324993,"journal":{"name":"BioDesign Research","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116732067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 19