生物设计研究(英文)最新文献_第3页

SLICER: A Seamless Gene Deletion Method for Deinococcus radiodurans. SLICER:一种针对耐辐射球菌的无缝基因缺失方法。

生物设计研究(英文) Pub Date : 2023-03-15 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0009

Stephanie L Brumwell, Katherine D Van Belois, Daniel P Nucifora, Bogumil J Karas

{"title":"SLICER: A Seamless Gene Deletion Method for Deinococcus radiodurans.","authors":"Stephanie L Brumwell, Katherine D Van Belois, Daniel P Nucifora, Bogumil J Karas","doi":"10.34133/bdr.0009","DOIUrl":"10.34133/bdr.0009","url":null,"abstract":"Deinococcus radiodurans' high resistance to various stressors combined with its ability to utilize sustainable carbon sources makes it an attractive bacterial chassis for synthetic biology and industrial bioproduction. However, to fully harness the capabilities of this microbe, further strain engineering and tool development are required. Methods for creating seamless genome modifications are an essential part of the microbial genetic toolkit to enable strain engineering. Here, we report the development of the SLICER method, which can be used to create seamless gene deletions in D. radiodurans. This process involves (a) integration of a seamless deletion cassette replacing a target gene, (b) introduction of the pSLICER plasmid to mediate cassette excision by I-SceI endonuclease cleavage and homologous recombination, and (c) curing of the helper plasmid. We demonstrate the utility of SLICER for creating multiple gene deletions in D. radiodurans by sequentially targeting 5 putative restriction-modification system genes, recycling the same selective and screening markers for each subsequent deletion. While we observed no significant increase in transformation efficiency for most of the knockout strains, we demonstrated SLICER as a promising method to create a fully restriction-minus strain to expand the synthetic biology applications of D. radiodurans, including its potential as an in vivo DNA assembly platform.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"5 ","pages":"0009"},"PeriodicalIF":0.0,"publicationDate":"2023-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10085245/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Peptide Variant Detection by a Living Yeast Biosensor via an Epitope-Selective Protease. 活酵母生物传感器通过表位选择性蛋白酶检测肽变体。

生物设计研究(英文) Pub Date : 2023-03-15 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0003

Tea Crnković, Benjamin J Bokor, Mead E Lockwood, Virginia W Cornish

{"title":"Peptide Variant Detection by a Living Yeast Biosensor via an Epitope-Selective Protease.","authors":"Tea Crnković, Benjamin J Bokor, Mead E Lockwood, Virginia W Cornish","doi":"10.34133/bdr.0003","DOIUrl":"https://doi.org/10.34133/bdr.0003","url":null,"abstract":"We previously demonstrated that we could hijack the fungal pheromone signaling pathway to provide a living yeast biosensor where peptide biomarkers were recognized by G-protein-coupled receptors and engineered to transcribe a readout. Here, we demonstrated that the protease could be reintroduced to the biosensor to provide a simple mechanism for distinguishing single-amino-acid changes in peptide ligands that, otherwise, would likely be difficult to detect using binding-based assays. We characterized the dose-response curves for five fungal pheromone G-protein-coupled receptors, peptides, and proteases-Saccharomyces cerevisiae, Candida albicans, Schizosaccharomyces pombe, Schizosaccharomyces octosporus, and Schizosaccharomyces japonicus. Alanine scanning was carried out for the most selective of these-S. cerevisiae and C. albicans-with and without the protease. Two peptide variants were discovered, which showed diminished cleavage by the protease (CaPep2A and CaPep2A13A). Those peptides were then distinguished by utilizing the biosensor strains with and without the protease, which selectively cleaved and altered the apparent concentration of peptide required for half-maximal activation for 2 peptides-CaPep and CaPep13A, respectively-by more than one order of magnitude. These results support the hypothesis that the living yeast biosensor with a sequence-specific protease can translate single-amino-acid changes into more than one order of magnitude apparent shift in the concentration of peptide required for half-maximal activation. With further engineering by computational modeling and directed evolution, the biosensor could likely distinguish a wide variety of peptide sequences beyond the alanine scanning carried out here. In the future, we envision incorporating proteases into our living yeast biosensor for use as a point of care diagnostic, a scalable communication language, and other applications.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"5 ","pages":"0003"},"PeriodicalIF":0.0,"publicationDate":"2023-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10084949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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 Need for Biosecurity Education in Biotechnology Curricula. 生物技术课程中生物安全教育的必要性。

生物设计研究(英文) Pub Date : 2023-03-14 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0008

Ying-Chiang J Lee, Xuanqi Chen, Siddharth Marwaha

引用次数: 0

Engineering Nitrogenases for Synthetic Nitrogen Fixation: From Pathway Engineering to Directed Evolution. 用于合成固氮的工程固氮酶：从路径工程到定向进化。

生物设计研究(英文) Pub Date : 2023-02-07 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0005

Emily M Bennett, James W Murray, Mark Isalan

引用次数: 5

De Novo Design and Synthesis of Polypeptide Immunomodulators for Resetting Macrophage Polarization. 用于重置巨噬细胞极化的多肽免疫调节剂的De Novo设计和合成。

生物设计研究(英文) Pub Date : 2023-02-07 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0006

Na Kong, Hongru Ma, Zhongji Pu, Fengju Wan, Dongfang Li, Lei Huang, Jiazhang Lian, Xingxu Huang, Shengjie Ling, Haoran Yu, Yuan Yao

{"title":"De Novo Design and Synthesis of Polypeptide Immunomodulators for Resetting Macrophage Polarization.","authors":"Na Kong, Hongru Ma, Zhongji Pu, Fengju Wan, Dongfang Li, Lei Huang, Jiazhang Lian, Xingxu Huang, Shengjie Ling, Haoran Yu, Yuan Yao","doi":"10.34133/bdr.0006","DOIUrl":"10.34133/bdr.0006","url":null,"abstract":"Modulating the extracellular matrix microenvironment is critical for achieving the desired macrophage phenotype in immune investigations or tumor therapy. Combining de novo protein design and biosynthesis techniques, herein, we designed a biomimetic polypeptide self-assembled nano-immunomodulator to trigger the activation of a specific macrophage phenotype. It was intended to be made up of (GGSGGPGGGPASAAANSASRATSNSP)n, the RGD motif from collagen, and the IKVAV motif from laminin. The combination of these domains allows the biomimetic polypeptide to assemble into extracellular matrix-like nanofibrils, creating an extracellular matrix-like milieu for macrophages. Furthermore, changing the concentration further provides a facile route to fine-tune macrophage polarization, which enhances antitumor immune responses by precisely resetting tumor-associated macrophage immune responses into an M1-like phenotype, which is generally considered to be tumor-killing macrophages, primarily antitumor, and immune-promoting. Unlike metal or synthetic polymer-based nanoparticles, this polypeptide-based nanomaterial exhibits excellent biocompatibility, high efficacy, and precise tunability in immunomodulatory effectiveness. These encouraging findings motivate us to continue our research into cancer immunotherapy applications in the future.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"5 ","pages":"0006"},"PeriodicalIF":0.0,"publicationDate":"2023-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521685/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

qSanger: Quantification of Genetic Variants in Bacterial Cultures by Sanger Sequencing. qSanger：通过Sanger测序对细菌培养物中的遗传变异进行量化。

生物设计研究(英文) Pub Date : 2023-02-07 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0007

Satya Prakash, Adrian Racovita, Teresa Petrucci, Roberto Galizi, Alfonso Jaramillo

{"title":"qSanger: Quantification of Genetic Variants in Bacterial Cultures by Sanger Sequencing.","authors":"Satya Prakash, Adrian Racovita, Teresa Petrucci, Roberto Galizi, Alfonso Jaramillo","doi":"10.34133/bdr.0007","DOIUrl":"10.34133/bdr.0007","url":null,"abstract":"Genetic variations such as mutations and recombinations arise spontaneously in all cultured organisms. Although it is possible to identify nonneutral mutations by selection or counterselection, the identification of neutral mutations in a heterogeneous population usually requires expensive and time-consuming methods such as quantitative or droplet polymerase chain reaction and high-throughput sequencing. Neutral mutations could even become dominant under changing environmental conditions enforcing transitory selection or counterselection. We propose a novel method, which we called qSanger, to quantify DNA using amplitude ratios of aligned electropherogram peaks from mixed Sanger sequencing reads. Plasmids expressing enhanced green fluorescent protein and mCherry fluorescent markers were used to validate qSanger both in vitro and in cotransformed Escherichia coli via quantitative polymerase chain reaction and fluorescence quantifications. We show that qSanger allows the quantification of genetic variants, including single-base natural polymorphisms or de novo mutations, from mixed Sanger sequencing reads, with substantial reduction of labor and costs compared to canonical approaches.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"5 ","pages":"0007"},"PeriodicalIF":0.0,"publicationDate":"2023-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521659/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Phages and Nanotechnology: New Insights against Multidrug-Resistant Bacteria. 噬菌体和纳米技术：对抗多药耐药细菌的新见解。

生物设计研究(英文) Pub Date : 2023-01-16 eCollection Date: 2023-01-01 DOI: 10.34133/bdr.0004

Marco Pardo-Freire, Pilar Domingo-Calap

{"title":"Phages and Nanotechnology: New Insights against Multidrug-Resistant Bacteria.","authors":"Marco Pardo-Freire, Pilar Domingo-Calap","doi":"10.34133/bdr.0004","DOIUrl":"10.34133/bdr.0004","url":null,"abstract":"Bacterial infections are a major threat to the human healthcare system worldwide, as antibiotics are becoming less effective due to the emergence of multidrug-resistant strains. Therefore, there is a need to explore nontraditional antimicrobial alternatives to support rapid interventions and combat the spread of pathogenic bacteria. New nonantibiotic approaches are being developed, many of them at the interface of physics, nanotechnology, and microbiology. While physical factors (e.g., pressure, temperature, and ultraviolet light) are typically used in the sterilization process, nanoparticles and phages (bacterial viruses) are also applied to combat pathogenic bacteria. Particularly, phage-based therapies are rising due to the unparalleled specificity and high bactericidal activity of phages. Despite the success of phages mostly as compassionate use in clinical cases, some drawbacks need to be addressed, mainly related to their stability, bioavailability, and systemic administration. Combining phages with nanoparticles can improve their performance in vivo. Thus, the combination of nanotechnology and phages might provide tools for the rapid and accurate detection of bacteria in biological samples (diagnosis and typing), and the development of antimicrobials that combine the selectivity of phages with the efficacy of targeted therapy, such as photothermal ablation or photodynamic therapies. In this review, we aim to provide an overview of how phage-based nanotechnology represents a step forward in the fight against multidrug-resistant bacteria.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"5 ","pages":"0004"},"PeriodicalIF":0.0,"publicationDate":"2023-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521656/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

The Obstacles and Potential Solution Clues of Prime Editing Applications in Tomato. 番茄Prime编辑应用的障碍及潜在的解决思路

生物设计研究(英文) Pub Date : 2022-12-15 eCollection Date: 2022-01-01 DOI: 10.34133/bdr.0001

Tien Van Vu, Ngan Thi Nguyen, Jihae Kim, Swati Das, Jinsu Lee, Jae-Yean Kim

{"title":"The Obstacles and Potential Solution Clues of Prime Editing Applications in Tomato.","authors":"Tien Van Vu, Ngan Thi Nguyen, Jihae Kim, Swati Das, Jinsu Lee, Jae-Yean Kim","doi":"10.34133/bdr.0001","DOIUrl":"10.34133/bdr.0001","url":null,"abstract":"Precision genome editing is highly desired for crop improvement. The recently emerged CRISPR/Cas technology offers great potential applications in precision plant genome engineering. A prime editing (PE) approach combining a reverse transcriptase (RT) with a Cas9 nickase and a \"priming\" extended guide RNA (gRNA) has shown a high frequency for precise genome modification in mammalian cells and several plant species. Nevertheless, the applications of the PE approach in dicot plants are still limited and inefficient. We designed and tested prime editors for precision editing of a synthetic sequence in a transient assay and for desirable alleles of 10 loci in tomato by stable transformation. Our data obtained by targeted deep sequencing also revealed only low PE efficiencies in both the tobacco and tomato systems. Further assessment of the activities of the PE components uncovered that the fusion of RT to Cas9 and the structure of PE gRNAs (pegRNAs) negatively affected the cleaving activity of the Cas9 nuclease. The self-complementarity between the primer binding sequences (PBSs) and spacer sequence might pose risks to the activity of the Cas9 complex. However, modifying the pegRNA sequences by shortening or introducing mismatches to the PBSs to reduce their melting temperatures did not enhance the PE efficiency at the MADS-box protein (SlMBP21), alcobaca (SlALC), and acetolactate synthase 1 (SlALS1) loci. Our data show challenges of the PE approach in tomato, indicating that a further improvement of the PE system for successful applications is demanded, such as the use of improved expression systems for enriching active PE complexes.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":" ","pages":"0001"},"PeriodicalIF":0.0,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10593121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42107228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Biological and Molecular Components for Genetically Engineering Biosensors in Plants. 植物基因工程生物传感器的生物和分子成分。

生物设计研究(英文) Pub Date : 2022-11-09 eCollection Date: 2022-01-01 DOI: 10.34133/2022/9863496

Yang Liu, Guoliang Yuan, Md Mahmudul Hassan, Paul E Abraham, Julie C Mitchell, Daniel Jacobson, Gerald A Tuskan, Arjun Khakhar, June Medford, Cheng Zhao, Chang-Jun Liu, Carrie A Eckert, Mitchel J Doktycz, Timothy J Tschaplinski, Xiaohan Yang

{"title":"Biological and Molecular Components for Genetically Engineering Biosensors in Plants.","authors":"Yang Liu, Guoliang Yuan, Md Mahmudul Hassan, Paul E Abraham, Julie C Mitchell, Daniel Jacobson, Gerald A Tuskan, Arjun Khakhar, June Medford, Cheng Zhao, Chang-Jun Liu, Carrie A Eckert, Mitchel J Doktycz, Timothy J Tschaplinski, Xiaohan Yang","doi":"10.34133/2022/9863496","DOIUrl":"10.34133/2022/9863496","url":null,"abstract":"Plants adapt to their changing environments by sensing and responding to physical, biological, and chemical stimuli. Due to their sessile lifestyles, plants experience a vast array of external stimuli and selectively perceive and respond to specific signals. By repurposing the logic circuitry and biological and molecular components used by plants in nature, genetically encoded plant-based biosensors (GEPBs) have been developed by directing signal recognition mechanisms into carefully assembled outcomes that are easily detected. GEPBs allow for in vivo monitoring of biological processes in plants to facilitate basic studies of plant growth and development. GEPBs are also useful for environmental monitoring, plant abiotic and biotic stress management, and accelerating design-build-test-learn cycles of plant bioengineering. With the advent of synthetic biology, biological and molecular components derived from alternate natural organisms (e.g., microbes) and/or de novo parts have been used to build GEPBs. In this review, we summarize the framework for engineering different types of GEPBs. We then highlight representative validated biological components for building plant-based biosensors, along with various applications of plant-based biosensors in basic and applied plant science research. Finally, we discuss challenges and strategies for the identification and design of biological components for plant-based biosensors.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"2022 ","pages":"9863496"},"PeriodicalIF":0.0,"publicationDate":"2022-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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 Prediction and Design of Novel Conopeptides for Biomedical Research and Development. 用于生物医学研究和开发的新型Conopeptides的高通量预测和设计。

生物设计研究(英文) Pub Date : 2022-11-07 eCollection Date: 2022-01-01 DOI: 10.34133/2022/9895270

Bingmiao Gao, Yu Huang, Chao Peng, Bo Lin, Yanling Liao, Chao Bian, Jiaan Yang, Qiong Shi

{"title":"High-Throughput Prediction and Design of Novel Conopeptides for Biomedical Research and Development.","authors":"Bingmiao Gao, Yu Huang, Chao Peng, Bo Lin, Yanling Liao, Chao Bian, Jiaan Yang, Qiong Shi","doi":"10.34133/2022/9895270","DOIUrl":"https://doi.org/10.34133/2022/9895270","url":null,"abstract":"Cone snail venoms have been considered a valuable treasure for international scientists and businessmen, mainly due to their pharmacological applications in development of marine drugs for treatment of various human diseases. To date, around 800 Conus species are recorded, and each of them produces over 1,000 venom peptides (termed as conopeptides or conotoxins). This reflects the high diversity and complexity of cone snails, although most of their venoms are still uncharacterized. Advanced multiomics (such as genomics, transcriptomics, and proteomics) approaches have been recently developed to mine diverse Conus venom samples, with the main aim to predict and identify potentially interesting conopeptides in an efficient way. Some bioinformatics techniques have been applied to predict and design novel conopeptide sequences, related targets, and their binding modes. This review provides an overview of current knowledge on the high diversity of conopeptides and multiomics advances in high-throughput prediction of novel conopeptide sequences, as well as molecular modeling and design of potential drugs based on the predicted or validated interactions between these toxins and their molecular targets.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"2022 ","pages":"9895270"},"PeriodicalIF":0.0,"publicationDate":"2022-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521759/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0