Bio-protocol最新文献

{"title":"mRNA Delivery Platform Based on Bacterial Outer Membrane Vesicles for Tumor Vaccine.","authors":"Xiaoyu Gao, Yao Li, Guangjun Nie, Xiao Zhao","doi":"10.21769/BioProtoc.4774","DOIUrl":"10.21769/BioProtoc.4774","url":null,"abstract":"<p><p>The rapid display and delivery method for customized tumor mRNA vaccines is limited. Herein, bacteria-derived outer membrane vesicles (OMVs) are employed as an mRNA delivery platform by surface engineering of an RNA-binding protein, L7Ae. OMV-L7Ae can rapidly adsorb boxC/D sequence-labeled mRNA antigens through L7Ae-boxC/D binding and deliver them into HEK-293T and dendritic cells. This platform provides an mRNA delivery technology distinct from lipid nanoparticles (LNPs) for personalized mRNA tumor vaccination and with a <i>Plug-and-Display</i> strategy suitable for rapid preparation of the personalized mRNA tumor vaccine against varied tumor antigens. Key features OMVs are employed as an mRNA delivery platform through L7Ae-boxC/D binding.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 13","pages":"e4774"},"PeriodicalIF":0.0,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10338712/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9879969","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}

{"title":"Human-rabbit Hybrid Translation System to Explore the Function of Modified Ribosomes.","authors":"Eriko Matsuura-Suzuki,&nbsp;Hirotaka Toh,&nbsp;Shintaro Iwasaki","doi":"10.21769/BioProtoc.4714","DOIUrl":"https://doi.org/10.21769/BioProtoc.4714","url":null,"abstract":"<p><p><i>In vitro translation systems</i> are a useful biochemical tool to research translational regulation. Although the preparation of translation-competent cell extracts from mammals has often been a challenge, the commercially available rabbit reticulocyte lysate (RRL) is an exception. However, its valid use, investigating the mechanism of translation machinery such as ribosomes in RRL, presents an analytic hurdle. To overcome this issue, the hybrid translation system, which is based on the supplementation of purified human ribosomes into ribosome-depleted RRL, has been developed. Here, we describe the step-by-step protocol of this system to study translation driven by ribosomes lacking post-translational modifications of the ribosomal protein. Moreover, we combined this approach with a previously developed reporter mRNA to assess the processivity of translation elongation. This protocol could be used to study the potency of heterologous ribosomes.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 13","pages":"e4714"},"PeriodicalIF":0.0,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10339341/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9825894","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}

{"title":"In vitro Selection and in vivo Testing of Riboswitch-inspired Aptamers.","authors":"Michael G Mohsen,&nbsp;Ronald R Breaker","doi":"10.21769/BioProtoc.4775","DOIUrl":"https://doi.org/10.21769/BioProtoc.4775","url":null,"abstract":"<p><p>Engineered aptamers for new compounds are typically produced by using in vitro selection methods. However, aptamers that are developed in vitro might not function as expected when introduced into complex cellular environments. One approach that addresses this concern is the design of initial RNA pools for selection that contain structural scaffolds from naturally occurring riboswitch aptamers. Here, we provide guidance on design and experimental principles for developing riboswitch-inspired aptamers for new ligands. The in vitro selection protocol (based on Capture-SELEX) is generalizable to diverse RNA scaffold types and amenable to multiplexing of ligand candidates. We discuss strategies to avoid propagation of selfish sequences that can easily dominate the selection. We also detail the identification of aptamer candidates using next-generation sequencing and bioinformatics, and subsequent biochemical validation of aptamer candidates. Finally, we describe functional testing of aptamer candidates in bacterial cell culture. Key features Develop riboswitch-inspired aptamers for new ligands using in vitro selection. Ligand candidates can be multiplexed to conserve time and resources. Test aptamer candidates in bacterial cells by grafting the aptamer back onto its expression platform.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 13","pages":"e4775"},"PeriodicalIF":0.0,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10338711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9825898","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}

{"title":"3D Ultrastructural Visualization of Mitosis Fidelity in Human Cells Using Serial Block Face Scanning Electron Microscopy (SBF-SEM).","authors":"Nuria Ferrandiz,&nbsp;Stephen J Royle","doi":"10.21769/BioProtoc.4708","DOIUrl":"https://doi.org/10.21769/BioProtoc.4708","url":null,"abstract":"<p><p>Errors in chromosome segregation during mitosis lead to chromosome instability, resulting in an unbalanced number of chromosomes in the daughter cells. Light microscopy has been used extensively to study chromosome missegregation by visualizing errors of the mitotic spindle. However, less attention has been paid to understanding spindle function in the broader context of intracellular structures and organelles during mitosis. Here, we outline a protocol to visualize chromosomes and endomembranes in mitosis, combining light microscopy and 3D volume electron microscopy, serial block-face scanning electron microscopy (SBF-SEM). SBF-SEM provides high-resolution imaging of large volumes and subcellular structures, followed by image analysis and 3D reconstruction. This protocol allows scientists to visualize the whole subcellular context of the spindle during mitosis.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 13","pages":"e4708"},"PeriodicalIF":0.0,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10336565/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9826325","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}

{"title":"In vivo Electroporation of Skeletal Muscle Fibers in Mice.","authors":"Steven J Foltz,&nbsp;Criss H Hartzell,&nbsp;Hyojung J Choo","doi":"10.21769/BioProtoc.4759","DOIUrl":"10.21769/BioProtoc.4759","url":null,"abstract":"<p><p>In vitro models are essential for investigating the molecular, biochemical, and cell-biological aspects of skeletal muscle. Still, models that utilize cell lines or embryonic cells do not fully recapitulate mature muscle fibers in vivo. Protein function is best studied in mature differentiated tissue, where biological context is maintained, but this is often difficult when reliable detection reagents, such as antibodies, are not commercially available. Exogenous expression of tagged proteins in vivo solves some of these problems, but this approach can be technically challenging because either a mouse must be engineered for each protein of interest or viral vectors are required for adequate levels of expression. While viral vectors can infect target cells following local administration, they carry the risk of genome integration that may interfere with downstream analyses. Plasmids are another accessible expression system, but they require ancillary means of cell penetration; electroporation is a simple physical method for this purpose that requires minimal training or specialized equipment. Here, we describe a method for in vivo plasmid expression in a foot muscle following electroporation.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 13","pages":"e4759"},"PeriodicalIF":0.0,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d9/c4/BioProtoc-13-13-4759.PMC10339231.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10183526","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}

{"title":"Measuring Myeloperoxidase Activity as a Marker of Inflammation in Gut Tissue Samples of Mice and Rat.","authors":"Nikita Hanning,&nbsp;Joris G De Man,&nbsp;Benedicte Y De Winter","doi":"10.21769/BioProtoc.4758","DOIUrl":"https://doi.org/10.21769/BioProtoc.4758","url":null,"abstract":"<p><p>Myeloperoxidase (MPO) is an enzyme contained in lysosomal azurophilic granules of neutrophils. MPO activity has been shown to correlate with the number of neutrophils in histological sections of the gastrointestinal tract and is therefore accepted as a biomarker of neutrophil invasion in the gut. This protocol describes an easy, cost-effective kinetic colorimetric assay to quantify myeloperoxidase activity in intestinal tissue samples. It is explained using tissue collected in mice but can also be used for other laboratory animals. In a first step, tissue specimens are homogenized using a phosphate buffer containing 0.5% hexadecyltrimethylammonium bromide (HTAB), which extracts MPO from neutrophils. The obtained supernatant is added to a reagent solution containing o-dianisidine dihydrochloride, which is a peroxidase substrate. Finally, the change in absorption is measured via spectrophotometry and converted to a standardized unit of enzyme activity. The assay is illustrated and compared to a commercially available enzyme-linked immunoassay (ELISA), demonstrating that MPO activity does not necessarily correlate with MPO protein expression in tissue samples. Key features Optimized for use in mice and rats but can also be used for samples of other species. Measures enzymatic activity instead of mRNA or protein expression. Requires a spectrophotometer. Can be performed in duplo using 10 mg of (dry-blotted) gut tissue or more. Graphical overview.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 13","pages":"e4758"},"PeriodicalIF":0.0,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d4/f9/BioProtoc-13-13-4758.PMC10338346.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10183529","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}

{"title":"Systematic Analysis of Smooth Muscle and Cartilage Ring Formation during Mouse Tracheal Tubulogenesis.","authors":"Haoyu Wu,&nbsp;Ping Wang,&nbsp;Ziying Liu,&nbsp;Chunyan Lu,&nbsp;Wenguang Yin","doi":"10.21769/BioProtoc.4711","DOIUrl":"https://doi.org/10.21769/BioProtoc.4711","url":null,"abstract":"<p><p>The trachea tube is the exclusive route to allow gas exchange between the external environment and the lungs. Recent studies have shown the critical role of mesenchymal cells in tracheal tubulogenesis. Improved methods for studying the dynamics of the tracheal mesenchyme development are needed to investigate the cellular and molecular mechanisms during tracheal tubulogenesis. Here, we describe a detailed protocol for a systematic analysis of tracheal tube development to enable observing tracheal smooth muscle (SM) and cartilage ring formation. We describe immunostaining, confocal and stereomicroscopy imaging, and quantitative methods to study the process of tracheal SM and cartilage ring development, including SM cell alignment, polarization, and changes in cell shape as well as mesenchymal condensation. The technologies and approaches described here not only improve analysis of the patterning of the developing trachea but also help uncover the mechanisms underlying airway disease. This protocol also provides a useful technique to analyze cell organization, polarity, and nuclear shape in other organ systems.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 13","pages":"e4711"},"PeriodicalIF":0.0,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/92/e0/BioProtoc-13-13-4711.PMC10336568.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9823767","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}

{"title":"Autolysin Production from <i>Chlamydomonas reinhardtii</i>.","authors":"Justin Findinier","doi":"10.21769/BioProtoc.4705","DOIUrl":"https://doi.org/10.21769/BioProtoc.4705","url":null,"abstract":"<p><p><i>Chlamydomonas</i> reinhardtii is a model organism for various processes, from photosynthesis to cilia biogenesis, and a great chassis to learn more about biofuel production. This is due to the width of molecular tools available, which have recently expanded with the development of a modular cloning system but, most importantly, with CRISPR/Cas9 editing now being possible. This technique has proven to be more efficient in the absence of a cell wall by using specific mutants or by digesting Chlamydomonas cell wall using the mating-specific metalloprotease autolysin (also called gametolysin). Multiple protocols have been used and shared for autolysin production from Chlamydomonas cells; however, they provide very inconsistent results, which hinders the capacity to routinely perform CRISPR mutagenesis. Here, we propose a simple protocol for autolysin production requiring transfer of cells from plates into a dense liquid suspension, gametogenesis by overnight incubation before mixing of gametes, and enzyme harvesting after 2 h. This protocol has shown to be highly efficient for autolysin production regardless of precise control over cell density at any step. Requiring a minimal amount of labor, it will provide a simple, ready-to-go approach to produce an enzyme critical for the generation of targeted mutants.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 13","pages":"e4705"},"PeriodicalIF":0.0,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d6/ed/BioProtoc-13-13-4705.PMC10336564.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9823771","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}

{"title":"Qualitative and Quantitative Methods to Measure Antibacterial Activity Resulting from Bacterial Competition.","authors":"Boris Taillefer,&nbsp;Marie M Grandjean,&nbsp;Julien Herrou,&nbsp;Donovan Robert,&nbsp;Tâm Mignot,&nbsp;Corinne Sebban-Kreuzer,&nbsp;Eric Cascales","doi":"10.21769/BioProtoc.4706","DOIUrl":"https://doi.org/10.21769/BioProtoc.4706","url":null,"abstract":"<p><p>In the environment, bacteria compete for niche occupancy and resources; they have, therefore, evolved a broad variety of antibacterial weapons to destroy competitors. Current laboratory techniques to evaluate antibacterial activity are usually labor intensive, low throughput, costly, and time consuming. Typical assays rely on the outgrowth of colonies of prey cells on selective solid media after competition. Here, we present fast, inexpensive, and complementary optimized protocols to qualitatively and quantitively measure antibacterial activity. The first method is based on the degradation of a cell-impermeable chromogenic substrate of the β-galactosidase, a cytoplasmic enzyme released during lysis of the attacked reporter strain. The second method relies on the lag time required for the attacked cells to reach a defined optical density after the competition, which is directly dependent on the initial number of surviving cells. Key features First method utilizes the release of β-galactosidase as a proxy for bacterial lysis. Second method is based on the growth timing of surviving cells. Combination of two methods discriminates between cell death and lysis, cell death without lysis, or survival to quasi-lysis. Methods optimized to various bacterial species such as <i>Escherichia coli, Pseudomonas aeruginosa</i>, and <i>Myxococcus xanthus</i>. Graphical overview.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 13","pages":"e4706"},"PeriodicalIF":0.0,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d4/b8/BioProtoc-13-13-4706.PMC10336571.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9826331","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}

{"title":"Large-scale Purification of Type III Toxin-antitoxin Ribonucleoprotein Complex and its Components from <i>Escherichia coli</i> for Biophysical Studies.","authors":"Parthasarathy Manikandan,&nbsp;Kavyashree Nadig,&nbsp;Mahavir Singh","doi":"10.21769/BioProtoc.4763","DOIUrl":"https://doi.org/10.21769/BioProtoc.4763","url":null,"abstract":"<p><p>Toxin-antitoxin (TA) systems are widespread bacterial immune systems that confer protection against various environmental stresses. TA systems have been classified into eight types (I-VIII) based on the nature and mechanism of action of the antitoxin. Type III TA systems consist of a noncoding RNA antitoxin and a protein toxin, forming a ribonucleoprotein (RNP) TA complex that plays crucial roles in phage defence in bacteria. Type III TA systems are present in the human gut microbiome and several pathogenic bacteria and, therefore, could be exploited for a novel antibacterial strategy. Due to the inherent toxicity of the toxin for E. coli, it is challenging to overexpress and purify free toxins from E. coli expression systems. Therefore, protein toxin is typically co-expressed and co-purified with antitoxin RNA as an RNP complex from E. coli for structural and biophysical studies. Here, we have optimized the co-expression and purification method for ToxIN type III TA complexes from E. coli that results in the purification of TA RNP complex and, often, free antitoxin RNA and free active toxin in quantities required for the biophysical and structural studies. This protocol can also be adapted to purify isotopically labelled (e.g., uniformly 15N- or 13C-labelled) free toxin proteins, free antitoxin RNAs, and TA RNPs, which can be studied using multidimensional nuclear magnetic resonance (NMR) spectroscopy methods. Key features Detailed protocol for the large-scale purification of ToxIN type III toxin-antitoxin complexes from <i>E. coli</i>. The optimized protocol results in obtaining milligrams of TA RNP complex, free toxin, and free antitoxin RNA. Commercially available plasmid vectors and chemicals are used to complete the protocol in five days after obtaining the required DNA clones. The purified TA complex, toxin protein, and antitoxin RNA are used for biophysical experiments such as NMR, ITC, and X-ray crystallography.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 13","pages":"e4763"},"PeriodicalIF":0.0,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10338634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9879965","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}