Bio-protocol最新文献

{"title":"Optogenetic Induction of Pyroptosis, Necroptosis, and Apoptosis in Mammalian Cell Lines.","authors":"Kateryna Shkarina,&nbsp;Petr Broz","doi":"10.21769/BioProtoc.4762","DOIUrl":"https://doi.org/10.21769/BioProtoc.4762","url":null,"abstract":"<p><p>Regulated cell death plays a key role in immunity, development, and homeostasis, but is also associated with a number of pathologies such as autoinflammatory and neurodegenerative diseases and cancer. However, despite the extensive mechanistic research of different cell death modalities, the direct comparison of different forms of cell death and their consequences on the cellular and tissue level remain poorly characterized. Comparative studies are hindered by the mechanistic and kinetic differences between cell death modalities, as well as the inability to selectively induce different cell death programs in an individual cell within cell populations or tissues. In this method, we present a protocol for rapid and specific optogenetic activation of three major types of programmed cell death: apoptosis, necroptosis, and pyroptosis, using light-induced forced oligomerization of their major effector proteins (caspases or kinases).</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 14","pages":"e4762"},"PeriodicalIF":0.0,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10366993/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10241468","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":"HDR-based CRISPR/Cas9-mediated Knockout of PD-L1 in C57BL/6 Mice.","authors":"Laura V Heeb,&nbsp;Betül Taskoparan,&nbsp;Antonios Katsoulas,&nbsp;Michal Beffinger,&nbsp;Pierre-Alain Clavien,&nbsp;Sebastian Kobold,&nbsp;Anurag Gupta,&nbsp;Johannes Vom Berg","doi":"10.21769/BioProtoc.4724","DOIUrl":"https://doi.org/10.21769/BioProtoc.4724","url":null,"abstract":"<p><p>The immune-inhibitory molecule programmed cell death ligand 1 (PD-L1) has been shown to play a role in pathologies such as autoimmunity, infections, and cancer. The expression of PD-L1 not only on cancer cells but also on non-transformed host cells is known to be associated with cancer progression. Generation of PD-L1 deficiency in the murine system enables us to specifically study the role of PD-L1 in physiological processes and diseases. One of the most versatile and easy to use site-specific gene editing tools is the CRISPR/Cas9 system, which is based on an RNA-guided nuclease system. Similar to its predecessors, the Zinc finger nucleases or transcription activator-like effector nucleases (TALENs), CRISPR/Cas9 catalyzes double-strand DNA breaks, which can result in frameshift mutations due to random nucleotide insertions or deletions via non-homologous end joining (NHEJ). Furthermore, although less frequently, CRISPR/Cas9 can lead to insertion of defined sequences due to homology-directed repair (HDR) in the presence of a suitable template. Here, we describe a protocol for the knockout of PD-L1 in the murine C57BL/6 background using CRISPR/Cas9. Targeting of exon 3 coupled with the insertion of a HindIII restriction site leads to a premature stop codon and a loss-of-function phenotype. We describe the targeting strategy as well as founder screening, genotyping, and phenotyping. In comparison to NHEJ-based strategy, the presented approach results in a defined stop codon with comparable efficiency and timelines as NHEJ, generates convenient founder screening and genotyping options, and can be swiftly adapted to other targets.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 14","pages":"e4724"},"PeriodicalIF":0.0,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10366997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9937128","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":"Production and Purification of Cell Culture-generated Hepatitis B Virus by Transient Transfection and Density Gradient.","authors":"Asako Murayama,&nbsp;Hirofumi Akari,&nbsp;Takanobu Kato","doi":"10.21769/BioProtoc.4779","DOIUrl":"https://doi.org/10.21769/BioProtoc.4779","url":null,"abstract":"<p><p>An efficient cell culture system for hepatitis B virus (HBV) is indispensable for research on viral characteristics and antiviral agents. Currently, for HBV infection assays in cell culture, HBV genome-integrated cell line-derived viruses are commonly used. However, these viruses are not suitable for the evaluation of polymorphism-dependent viral characteristics or resistant mutations against anti-viral agents. To detect the infection of cell culture-generated HBV (HBVcc) by the transient transfection of the HBV molecular clone, a large amount of purified viruses is needed, because such viruses exhibit limited infection efficiencies in cell culture. Here, we describe how to generate and purify HBVcc by the transient transfection of HBV molecular clones. This system provides a powerful tool for studying the infection and propagation of HBV and for developing anti-viral agents against HBV.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 14","pages":"e4779"},"PeriodicalIF":0.0,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/2d/24/BioProtoc-13-14-4779.PMC10366991.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10241475","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":"Relative Membrane Potential Measurements Using DISBAC₂(3) Fluorescence in <i>Arabidopsis thaliana</i> Primary Roots.","authors":"Shiv Mani Dubey,&nbsp;Matyáš Fendrych,&nbsp;Nelson Bc Serre","doi":"10.21769/BioProtoc.4778","DOIUrl":"https://doi.org/10.21769/BioProtoc.4778","url":null,"abstract":"<p><p>In vivo microscopy of plants with high-frequency imaging allows observation and characterization of the dynamic responses of plants to stimuli. It provides access to responses that could not be observed by imaging at a given time point. Such methods are particularly suitable for the observation of fast cellular events such as membrane potential changes. Classical measurement of membrane potential by probe impaling gives quantitative and precise measurements. However, it is invasive, requires specialized equipment, and only allows measurement of one cell at a time. To circumvent some of these limitations, we developed a method to relatively quantify membrane potential variations in <i>Arabidopsis thaliana</i> roots using the fluorescence of the voltage reporter DISBAC₂(3). In this protocol, we describe how to prepare experiments for agar media and microfluidics, and we detail the image analysis. We take an example of the rapid plasma membrane depolarization induced by the phytohormone auxin to illustrate the method. Relative membrane potential measurements using DISBAC₂(3) fluorescence increase the spatio-temporal resolution of the measurements and are non-invasive and suitable for live imaging of growing roots. Studying membrane potential with a more flexible method allows to efficiently combine mature electrophysiology literature and new molecular knowledge to achieve a better understanding of plant behaviors. Key features Non-invasive method to relatively quantify membrane potential in plant roots. Method suitable for imaging seedlings root in agar or liquid medium. Straightforward quantification.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 14","pages":"e4778"},"PeriodicalIF":0.0,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/2c/54/BioProtoc-13-14-4778.PMC10367083.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9937130","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":"Three-color dSTORM Imaging and Analysis of Recombination Foci in Mouse Spread Meiotic Nuclei.","authors":"Lieke Koornneef,&nbsp;Maarten W Paul,&nbsp;Adriaan B Houtsmuller,&nbsp;Willy M Baarends,&nbsp;Johan A Slotman","doi":"10.21769/BioProtoc.4780","DOIUrl":"https://doi.org/10.21769/BioProtoc.4780","url":null,"abstract":"<p><p>During the first meiotic prophase in mouse, repair of SPO11-induced DNA double-strand breaks (DSBs), facilitating homologous chromosome synapsis, is essential to successfully complete the first meiotic cell division. Recombinases RAD51 and DMC1 play an important role in homology search, but their mechanistic contribution to this process is not fully understood. Super-resolution, single-molecule imaging of RAD51 and DMC1 provides detailed information on recombinase accumulation on DSBs during meiotic prophase. Here, we present a detailed protocol of recombination foci analysis of three-color direct stochastic optical reconstruction microscopy (dSTORM) imaging of SYCP3, RAD51, and DMC1, fluorescently labeled by antibody staining in mouse spermatocytes. This protocol consists of sample preparation, data acquisition, pre-processing, and data analysis. The sample preparation procedure includes an updated version of the nuclear spreading of mouse testicular cells, followed by immunocytochemistry and the preparation steps for dSTORM imaging. Data acquisition consists of three-color dSTORM imaging, which is extensively described. The pre-processing that converts fluorescent signals to localization data also includes channel alignment and image reconstruction, after which regions of interest (ROIs) are identified based on RAD51 and/or DMC1 localization patterns. The data analysis steps then require processing of the fluorescent signal localization within these ROIs into discrete nanofoci, which can be further analyzed. This multistep approach enables the systematic investigation of spatial distributions of proteins associated with individual DSB sites and can be easily adapted for analyses of other foci-forming proteins. All computational scripts and software are freely accessible, making them available to a broad audience. Key features Preparation of spread nuclei, resulting in a flattened preparation with easy antibody-accessible chromatin-associated proteins on dSTORM-compatible coverslips. dSTORM analysis of immunofluorescent repair foci in meiotic prophase nuclei. Detailed descriptions of data acquisition, (pre-)processing, and nanofoci feature analysis applicable to all proteins that assemble in immunodetection as discrete foci. Graphical overview.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 14","pages":"e4780"},"PeriodicalIF":0.0,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/15/8e/BioProtoc-13-14-4780.PMC10367009.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10258889","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":"Recoil Measurements in <i>Drosophila</i> Embryos: from Mounting to Image Analysis.","authors":"Luis Eduardo Sánchez-Cisneros,&nbsp;Sourabh Bhide,&nbsp;Luis Daniel Ríos-Barrera","doi":"10.21769/BioProtoc.4806","DOIUrl":"https://doi.org/10.21769/BioProtoc.4806","url":null,"abstract":"<p><p>Tension and force propagation play a central role in tissue morphogenesis, as they enable sub- and supra-cellular shape changes required for the generation of new structures. Force is often generated by the cytoskeleton, which forms complex meshworks that reach cell-cell or cell-extracellular matrix junctions to induce cellular rearrangements. These mechanical properties can be measured through laser microdissection, which concentrates energy in the tissue of interest, disrupting its cytoskeleton. If the tissue is undergoing tension, this cut will induce a recoil in the surrounding regions of the cut. This protocol describes how one can perform laser microdissection experiments and subsequently measure the recoil speed of the sample of interest. While we explain how to carry out these experiments in <i>Drosophila embryos</i>, the recoil calibration and downstream analyses can be applied to other types of preparations. Key features Allows measuring tension in live <i>Drosophila</i> embryos with a relatively simple approach. Describes a quick way to mount a high number of embryos. Includes a segmentation-free recoil quantification that reduces bias and speeds up analysis. Graphical overview.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 14","pages":"e4806"},"PeriodicalIF":0.0,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10366990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10258893","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":"Characterization of Microtubule Lattice Heterogeneity by Segmented Subtomogram Averaging.","authors":"Clément Bousquet,&nbsp;John M Heumann,&nbsp;Denis Chrétien,&nbsp;Charlotte Guyomar","doi":"10.21769/BioProtoc.4723","DOIUrl":"https://doi.org/10.21769/BioProtoc.4723","url":null,"abstract":"<p><p>Microtubule structure is commonly investigated using single-particle analysis (SPA) or subtomogram averaging (STA), whose main objectives are to gather high-resolution information on the αβ-tubulin heterodimer and on its interactions with neighboring molecules within the microtubule lattice. The maps derived from SPA approaches usually delineate a continuous organization of the αβ-tubulin heterodimer that alternate regularly head-to-tail along protofilaments, and that share homotypic lateral interactions between monomers (α-α, β-β), except at one unique region called the seam, made of heterotypic ones (α-β, β-α). However, this textbook description of the microtubule lattice has been challenged over the years by several studies that revealed the presence of multi-seams in microtubules assembled in vitro from purified tubulin. To analyze in deeper detail their intrinsic structural heterogeneity, we have developed a segmented subtomogram averaging (SSTA) strategy on microtubules decorated with kinesin motor-domains that bind every αβ-tubulin heterodimer. Individual protofilaments and microtubule centers are modeled, and sub-volumes are extracted at every kinesin motor domain position to obtain full subtomogram averages of the microtubules. The model is divided into shorter segments, and subtomogram averages of each segment are calculated using the main parameters of the full-length microtubule settings as a template. This approach reveals changes in the number and location of seams within individual microtubules assembled in vitro from purified tubulin and in <i>Xenopus</i> egg cytoplasmic extracts. Key features This protocol builds upon the method developed by J.M. Heumann to perform subtomogram averages of microtubules and extends it to divide them into shorter segments. Microtubules are decorated with kinesin motor-domains to determine the underlying organization of its constituent αβ-tubulin heterodimers. The SSTA approach allows analysis of the structural heterogeneity of individual microtubules and reveals multi-seams and changes in their number and location within their shaft. Graphical overview.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 14","pages":"e4723"},"PeriodicalIF":0.0,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/56/2f/BioProtoc-13-14-4723.PMC10366996.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9882806","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 situ Quantification of Cytosine Modification Levels in Heterochromatic Domains of Cultured Mammalian Cells.","authors":"Maria Arroyo,&nbsp;Cristina M Cardoso,&nbsp;Florian D Hastert","doi":"10.21769/BioProtoc.4716","DOIUrl":"https://doi.org/10.21769/BioProtoc.4716","url":null,"abstract":"<p><p>Epigenetic modifications of DNA, and especially cytosine, play a crucial role in regulating basic cellular processes and thereby the overall cellular metabolism. Their levels change during organismic and cellular development, but especially also in pathogenic aberrations such as cancer. Levels of respective modifications are often addressed in bulk by specialized mass spectrometry techniques or by employing dedicated ChIP-seq protocols, with the latter giving information about the sequence context of the modification. However, to address modification levels on a single cell basis, high- or low-content microscopy techniques remain the preferred methodology. The protocol presented here describes a straightforward method to detect and quantify different DNA modifications in human cell lines, which can also be adapted to other cultured mammalian cell types. To this end, cells are immunostained against two different cytosine modifications in combination with DNA counterstaining. Image acquisition takes place on a confocal microscopy system. A semi-automated analysis pipeline helps to gather data in a fast and reliable fashion. The protocol is comparatively simple, fast, and cost effective. By employing methodologies that are often well established in most molecular biology laboratories, many researchers are able to apply the described protocol straight away in-house.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 14","pages":"e4716"},"PeriodicalIF":0.0,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/9a/2f/BioProtoc-13-14-4716.PMC10366683.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9883069","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":"Biophysical Analysis of Mechanical Signals in Immotile Cilia of Mouse Embryonic Nodes Using Advanced Microscopic Techniques.","authors":"Takanobu A Katoh,&nbsp;Toshihiro Omori,&nbsp;Takuji Ishikawa,&nbsp;Yasushi Okada,&nbsp;Hiroshi Hamada","doi":"10.21769/BioProtoc.4715","DOIUrl":"https://doi.org/10.21769/BioProtoc.4715","url":null,"abstract":"<p><p>Immotile cilia of crown cells at the node of mouse embryos are required for sensing leftward fluid flow that gives rise to the breaking of left-right (L-R) symmetry. The flow-sensing mechanism has long remained elusive, mainly because of difficulties inherent in manipulating and precisely analyzing the cilium. Recent progress in optical microscopy and biophysical analysis has allowed us to study the mechanical signals involving primary cilia. In this study, we used high-resolution imaging with mechanical modeling to assess the membrane tension in a single cilium. Optical tweezers, a technique used to trap sub-micron-sized particles with a highly focused laser beam, allowed us to manipulate individual cilia. Super-resolution microscopy allowed us to discern the precise localization of ciliary proteins. Using this protocol, we provide a method for applying these techniques to cilia in mouse embryonic nodes. This method is widely applicable to the determination of mechanical signals in other cilia.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 14","pages":"e4715"},"PeriodicalIF":0.0,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f6/48/BioProtoc-13-14-4715.PMC10366680.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10258896","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":"Simplifying Barley Leaf Rust Research: An Easy and Reproducible Infection Protocol for <i>Puccinia hordei</i> on a Small Laboratory Scale.","authors":"Caroline I Skoppek,&nbsp;Jana Streubel","doi":"10.21769/BioProtoc.4721","DOIUrl":"https://doi.org/10.21769/BioProtoc.4721","url":null,"abstract":"<p><p>Barley (<i>Hordeum vulgare</i>) is one of the most important agricultural crops in the world, but pathogen infections regularly limit its annual yield. A major threat is the infection with the biotrophic leaf rust fungus, <i>Puccinia hordei</i>. Rust fungi have a complex life cycle, and existing resistances can be easily overcome. To address this problem, it is crucial to develop barley varieties with improved and durable resistance mechanisms. An essential step towards this goal is a simple and reproducible infection protocol to evaluate potential resistance phenotypes in the lab. However, available protocols sometimes lack detailed procedure or equipment information, use spore application methods that are not suitable for uniform spore dispersion, or require special mineral oils or engineered fluids. In addition, they are often optimized for pathogen-dedicated greenhouses or phytochambers, which may not be available to every research institute. Here, we describe an easy and user-friendly procedure to infect barley with <i>Puccinia hordei</i> on a small laboratory scale. This procedure utilizes inexpensive and simple tools to evenly split and apply spores to barley leaves. The treated plants are incubated in affordable and small phytocabinets. Our protocol enables a quick and reproducible infection of barley with leaf rust, a method that can easily be transferred to other rust fungi, including stripe rust, or to other plant species. Key features Step-by-step infection protocol established for barley cv. Golden Promise, the gold standard genotype for genetic transformation Plant age-independent protocol Precise spore application by using inexpensive pipe cleaners for uniform symptom formation and increased reproducibility No specialized equipment needed Includes simple spore harvesting method Protocol is applicable to other biotrophic pathogens (stripe rust or powdery mildew) and other plants (e.g., wheat) Protocol is also applicable for a detached leaf assay Graphical overview.</p>","PeriodicalId":8938,"journal":{"name":"Bio-protocol","volume":"13 14","pages":"e4721"},"PeriodicalIF":0.0,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/27/42/BioProtoc-13-14-4721.PMC10366994.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10241472","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}