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Purification and Cryo-Electron Microscopy Analysis of Bacterial Appendages. 细菌附属物的纯化和冷冻电镜分析。
IF 1
Bio-protocol Pub Date : 2024-07-20 DOI: 10.21769/BioProtoc.5032
Juan C Sanchez, Joseph K Baumgardt, Elizabeth R Wright
{"title":"Purification and Cryo-Electron Microscopy Analysis of Bacterial Appendages.","authors":"Juan C Sanchez, Joseph K Baumgardt, Elizabeth R Wright","doi":"10.21769/BioProtoc.5032","DOIUrl":"10.21769/BioProtoc.5032","url":null,"abstract":"<p><p>A number of extracellular helical protein polymers are crucial for supporting bacterial motility. The bacterial flagellum is a polymeric appendage used to support cellular motility. Historically, structural studies of flagellar and other filaments were limited to those present as or locked into straightened states. Here, we present a robust workflow that produces biologically relevant high-resolution cryo-electron microscopy (cryo-EM) structures of bacterial flagellar filaments. We highlight how a simple purification method, centered around several centrifugation steps, exploits the process of filament ejection in <i>Caulobacter crescentus</i> and results in isolated filaments amenable to transmission electron microscopy (TEM) studies. The quality of the sample is validated by SDS-PAGE and negative stain TEM analysis before a sample is vitrified for cryogenic electron microscopy (cryo-EM) data collection. We provide a detailed protocol for reconstructing either straight or curved flagellar filaments by cryo-EM helical reconstruction methods, followed by an overview of model building and validation. In our hands, this workflow resulted in several flagellar structures below 3 Å resolution, with one data set reaching a global resolution of 2.1 Å. The application of this workflow supports structure-function studies to better understand the molecular interactions that regulate filament architecture in biologically relevant states. Future work will not only examine interactions that regulate bacterial flagellar and other filament organization but also provide a foundation for developing new helical biopolymers for biotech applications. Key features • Rapid high-quality purification of bacterial flagella via simple bacterial culturing, centrifugation, and resuspension methods. • High-throughput cryo-EM data collection of filamentous objects. • Use of cryoSPARC implementations of helical reconstruction algorithms to generate high-resolution 3D structures of bacterial flagella or other helical polymers.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11292135/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141891270","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
Well Plate-Based Localized Electroporation Workflow for Rapid Optimization of Intracellular Delivery. 基于井板的局部电穿孔工作流程,用于快速优化细胞内给药。
IF 1
Bio-protocol Pub Date : 2024-07-20 DOI: 10.21769/BioProtoc.5037
Cesar A Patino, Sevketcan Sarikaya, Prithvijit Mukherjee, Nibir Pathak, Horacio D Espinosa
{"title":"Well Plate-Based Localized Electroporation Workflow for Rapid Optimization of Intracellular Delivery.","authors":"Cesar A Patino, Sevketcan Sarikaya, Prithvijit Mukherjee, Nibir Pathak, Horacio D Espinosa","doi":"10.21769/BioProtoc.5037","DOIUrl":"10.21769/BioProtoc.5037","url":null,"abstract":"<p><p>Efficient and nontoxic delivery of foreign cargo into cells is a critical step in many biological studies and cell engineering workflows with applications in areas such as biomanufacturing and cell-based therapeutics. However, effective molecular delivery into cells involves optimizing several experimental parameters. In the case of electroporation-based intracellular delivery, there is a need to optimize parameters like pulse voltage, duration, buffer type, and cargo concentration for each unique application. Here, we present the protocol for fabricating and utilizing a high-throughput multi-well localized electroporation device (LEPD) assisted by deep learning-based image analysis to enable rapid optimization of experimental parameters for efficient and nontoxic molecular delivery into cells. The LEPD and the optimization workflow presented herein are relevant to both adherent and suspended cell types and different molecular cargo (DNA, RNA, and proteins). The workflow enables multiplexed combinatorial experiments and can be adapted to cell engineering applications requiring in vitro delivery. Key features • A high-throughput multi-well localized electroporation device (LEPD) that can be optimized for both adherent and suspended cell types. • Allows for multiplexed experiments combined with tailored pulse voltage, duration, buffer type, and cargo concentration. • Compatible with various molecular cargoes, including DNA, RNA, and proteins, enhancing its versatility for cell engineering applications. • Integration with deep learning-based image analysis enables rapid optimization of experimental parameters.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11291937/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141891273","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
Analysis and Quantification of the Mitochondrial-ER Lipidome. 线粒体-ER 脂质体的分析和定量。
IF 1
Bio-protocol Pub Date : 2024-07-05 DOI: 10.21769/BioProtoc.5028
Alexis R Diaz-Vegas, Anthony S Don, James G Burchfield
{"title":"Analysis and Quantification of the Mitochondrial-ER Lipidome.","authors":"Alexis R Diaz-Vegas, Anthony S Don, James G Burchfield","doi":"10.21769/BioProtoc.5028","DOIUrl":"10.21769/BioProtoc.5028","url":null,"abstract":"<p><p>Mitochondria are vital organelles essential for cellular functions, but their lipid composition and response to stressors are not fully understood. Recent advancements in lipidomics reveal insights into lipid functions, especially their roles in metabolic perturbations and diseases. Previous methods have focused on the protein composition of mitochondria and mitochondrial-associated membranes. The advantage of our technique is that it combines organelle isolation with targeted lipidomics, offering new insights into the composition and dynamics of these organelles in pathological conditions. We developed a mitochondria isolation protocol for L6 myotubes, enabling lipidomics analysis of specific organelles without interference from other cellular compartments. This approach offers a unique opportunity to dissect lipid dynamics within mitochondria and their associated ER compartments under cellular stress. Key features • Analysis and quantification of lipids in mitochondria-ER fraction through liquid chromatography-tandem mass spectrometry-based lipidomics (LC-MS/MS lipidomics). • LC-MS/MS lipidomics provide precise and unbiased information on the lipid composition in in vitro systems. • LC-MS/MS lipidomics facilitates the identification of lipid signatures in mammalian cells.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11237982/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141618020","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
Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis. 拟南芥多基因高效编辑的多功能克隆策略
IF 1
Bio-protocol Pub Date : 2024-07-05 DOI: 10.21769/BioProtoc.5029
Ziqiang P Li, Jennifer Huard, Emmanuelle M Bayer, Valérie Wattelet-Boyer
{"title":"Versatile Cloning Strategy for Efficient Multigene Editing in <i>Arabidopsis</i>.","authors":"Ziqiang P Li, Jennifer Huard, Emmanuelle M Bayer, Valérie Wattelet-Boyer","doi":"10.21769/BioProtoc.5029","DOIUrl":"10.21769/BioProtoc.5029","url":null,"abstract":"<p><p>CRISPR-Cas9 technology has become an essential tool for plant genome editing. Recent advancements have significantly improved the ability to target multiple genes simultaneously within the same genetic background through various strategies. Additionally, there has been significant progress in developing methods for inducible or tissue-specific editing. These advancements offer numerous possibilities for tailored genome modifications. Building upon existing research, we have developed an optimized and modular strategy allowing the targeting of several genes simultaneously in combination with the synchronized expression of the Cas9 endonuclease in the egg cell. This system allows significant editing efficiency while avoiding mosaicism. In addition, the versatile system we propose allows adaptation to inducible and/or tissue-specific edition according to the promoter chosen to drive the expression of the Cas9 gene. Here, we describe a step-by-step protocol for generating the binary vector necessary for establishing <i>Arabidopsis</i> edited lines using a versatile cloning strategy that combines Gateway<sup>®</sup> and Golden Gate technologies. We describe a versatile system that allows the cloning of as many guides as needed to target DNA, which can be multiplexed into a polycistronic gene and combined in the same construct with sequences for the expression of the Cas9 endonuclease. The expression of Cas9 is controlled by selecting from among a collection of promoters, including constitutive, inducible, ubiquitous, or tissue-specific promoters. Only one vector containing the polycistronic gene (tRNA-sgRNA) needs to be constructed. For that, sgRNA (composed of protospacers chosen to target the gene of interest and sgRNA scaffold) is cloned in tandem with the pre-tRNA sequence. Then, a single recombination reaction is required to assemble the promoter, the zCas9 coding sequence, and the tRNA-gRNA polycistronic gene. Each element is cloned in an entry vector and finally assembled according to the Multisite Gateway<sup>®</sup> Technology. Here, we detail the process to express zCas9 under the control of egg cell promoter fused to enhancer sequence (EC1.2en-EC1.1p) and to simultaneously target two multiple C2 domains and transmembrane region protein genes (<i>MCTP3</i> and <i>MCTP4</i>, respectively at3g57880 and at1g51570), using one or two sgRNA per gene. Key features • A simple method for <i>Arabidopsis</i> edited lines establishment using CRISPR-Cas9 technology • Versatile cloning strategy combining various technologies for convenient cloning (Gateway<sup>®</sup>, Golden Gate) • Multigene targeting with high efficiency.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11237983/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617808","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
A Protocol for Preparing Mucoadhesive Emulsion Microgels and Assessing Their Mucoadhesion Properties In Vitro. 制备黏附性乳液微凝胶并评估其体外黏附特性的方案
IF 1
Bio-protocol Pub Date : 2024-07-05 DOI: 10.21769/BioProtoc.5027
Mariia S Saveleva, Mikhail E Lobanov, Oksana A Mayorova
{"title":"A Protocol for Preparing Mucoadhesive Emulsion Microgels and Assessing Their Mucoadhesion Properties In Vitro.","authors":"Mariia S Saveleva, Mikhail E Lobanov, Oksana A Mayorova","doi":"10.21769/BioProtoc.5027","DOIUrl":"10.21769/BioProtoc.5027","url":null,"abstract":"<p><p>Intravesical instillation is an efficient therapeutic technique based on targeted administration of a drug directly into the lesion for the treatment of bladder diseases. This is an alternative to traditional systemic administration of drugs. However, this technique requires repeated procedures, which can lead to even greater inflammation and infection of the urethra. To date, novel systems that allow prolonged drug retention in the bladder cavity are actively being developed. We recently reported a targeted drug delivery system based on the mucoadhesive emulsion microgels consisting of the natural component whey protein isolate. Such micron-sized carriers possess high loading capacity, a prolonged drug release profile, and efficient mucoadhesive properties to the bladder urothelium. As a continuation of this work, we present a protocol for the synthesis of mucoadhesive emulsion microgels. Detailed procedures for preparing precursor solutions as well as studying the physico-chemical parameters of microgels (including loading capacity and drug release rate) and the mucoadhesive properties using the model of porcine bladder urothelium are discussed. Precautionary measures and nuances that are worth paying attention to during each experimental stage are given as well. Key features • The protocol for the synthesis of mucoadhesive emulsion microgels based on whey protein isolate is presented. The experimental conditions of emulsion microgels synthesis are discussed. • Methods for studying the physico-chemical properties of mucoadhesive emulsion microgels (size of emulsion microgels particles, loading capacity, release kinetics) are described. • The method for assessing mucoadhesive properties of emulsion microgels is demonstrated using the porcine bladder tissue model ex vivo.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11237984/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617745","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
Quantification of Proliferating and Mitotically Active Retinal Cells in Mice by Flow Cytometry. 通过流式细胞术量化小鼠视网膜细胞的增殖和有丝分裂活性。
IF 1
Bio-protocol Pub Date : 2024-07-05 DOI: 10.21769/BioProtoc.5024
Hope K Vanzo-Sparks, Sarah E Webster, Mark K Webster, Cindy L Linn
{"title":"Quantification of Proliferating and Mitotically Active Retinal Cells in Mice by Flow Cytometry.","authors":"Hope K Vanzo-Sparks, Sarah E Webster, Mark K Webster, Cindy L Linn","doi":"10.21769/BioProtoc.5024","DOIUrl":"10.21769/BioProtoc.5024","url":null,"abstract":"<p><p>Adult mammals lack the ability to regenerate retinal neurons after injury. However, in previous studies from this lab, topical application of the selective alpha7 nicotinic acetylcholine receptor (nAChR) agonist, PNU-282987, has been associated with an increase in the number of retinal neurons in adult murine models both in the presence and absence of injury to the retina. Additionally, studies assaying mitotic markers have shown a substantial increase in the amount of mitotically active and proliferating cells with the topical application of the alpha7 nAChR agonist. However, these previous studies were performed using fluorescent immunolabeling and subsequent confocal microscopy, thus limiting the number of antibodies that can be multiplexed. As a result, we have developed a flow cytometry method that allows for the multiplexing and analysis of multiple external and internal markers in dissociated retinal cells. In this paper, a step-by-step protocol is described for the labeling of multiple retinal cell types such as retinal ganglion cells, rod photoreceptors, and Müller glia, concurrently with Müller glia-derived progenitor cells that arise after treatment with PNU-282987. Key features • Neurogenesis in the adult mammalian retina. • Flow cytometry of retinal cells. • PNU-282987-induced mitotic activity in the retina. • Dissociation of the retina for flow cytometry analysis. Graphical overview <b>Schematic demonstrating the protocol for preparation of retinal cells for flow cytometry analysis.</b> (A) Adult mice (3-6 months) are subjected to topical PBS eyedrop treatment containing DMSO (control groups) or PNU-282987 (experimental groups). Both eyedrop treatments contain 1 mg/mL of BrdU to label proliferating cells. After treatment, mice are euthanized, and retinae are harvested for dissociation using papain. (B) Dissociated retina cells are fixed and permeabilized before aliquots are taken for cell counts on a hemocytometer. After determining the number of cells present, conjugated antibodies and unconjugated primary antibodies are added at the appropriate dilutions. Fluorescent secondary antibodies are added for markers that are unconjugated. Cells are then subjected to flow cytometric analysis using a BD LSRFortessa.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11247376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141621977","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
Imaging Assays to Detect DNA Damage in Trypanosome Parasites Using γH2A. 利用 γH2A 检测锥虫寄生虫 DNA 损伤的成像测定。
IF 1
Bio-protocol Pub Date : 2024-07-05 DOI: 10.21769/BioProtoc.5026
Rajiv S Jumani, Bryanna Thomas, Srinivasa P S Rao
{"title":"Imaging Assays to Detect DNA Damage in Trypanosome Parasites Using γH2A.","authors":"Rajiv S Jumani, Bryanna Thomas, Srinivasa P S Rao","doi":"10.21769/BioProtoc.5026","DOIUrl":"10.21769/BioProtoc.5026","url":null,"abstract":"<p><p>Diseases caused by trypanosomatid parasites remain a significant unmet medical need for millions of people globally. Trypanosomatid parasites such as <i>Trypanosoma cruzi</i> and subspecies of <i>Trypanosoma brucei</i> cause Chagas disease and human African trypanosomiasis (HAT), respectively. Although efforts to find novel treatments have been successful for HAT, Chagas disease is still treated with decades-old therapies that suffer from long treatment durations and severe safety concerns. We recently described the identification and characterization of the cyanotriazole compound class that kills trypanosomes, in vitro and in vivo, by selective inhibition of the trypanosome nuclear topoisomerase II enzyme. To evaluate whether inhibition of the topoisomerase II enzyme led to parasite death due to lethal double-strand DNA breaks, we developed assays for detecting DNA damage in both intracellular amastigotes of <i>T. cruzi</i> and bloodstream-form <i>T. brucei</i> by using the canonical DNA damage marker γH2A. Herein, this article describes the protocols for detecting DNA damage using an immunofluorescence assessment of γH2A by microscopy in trypanosome parasites. Key features • Immunofluorescence-based assay to detect the γH2A response in <i>T. brucei</i> and <i>T. cruzi</i> parasites. • Robust DNA damage pathway-based cellular assays to evaluate topoisomerase II poisons' ability to cause DNA damage. • A 384-well plate-based <i>T. cruzi</i> protocol allows high-resolution and high-throughput evaluation of compounds that cause DNA damage by measuring γH2A in intracellular parasites. • This assay could be modifiable for evaluation of DNA damage responses in various intracellular and extracellular eukaryotic pathogens.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11237981/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617747","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
Quantification of Autophagosomes in Human Fibroblasts Using Cyto-ID® Staining and Cytation Imaging. 利用 Cyto-ID® 染色和细胞成像技术量化人类成纤维细胞中的自噬体
IF 1
Bio-protocol Pub Date : 2024-07-05 DOI: 10.21769/BioProtoc.5025
Barbara Hochecker, Katja C Matt, Alica L Meßmer, Melanie M Scherer, Jörg Bergemann
{"title":"Quantification of Autophagosomes in Human Fibroblasts Using Cyto-ID<sup>®</sup> Staining and Cytation Imaging.","authors":"Barbara Hochecker, Katja C Matt, Alica L Meßmer, Melanie M Scherer, Jörg Bergemann","doi":"10.21769/BioProtoc.5025","DOIUrl":"10.21769/BioProtoc.5025","url":null,"abstract":"<p><p><sup>As an essential process for the maintenance of cellular homeostasis and function, autophagy is responsible for the lysosome-mediated degradation of damaged proteins and organelles; therefore, dysregulation of autophagy in humans can lead to a variety of diseases. The link between impaired autophagy and disease highlights the need to investigate possible interventions to address dysregulations. One possible intervention is hyperthermia, which is described in this protocol. To investigate these interventions, a method for absolute quantification of</sup> autophagosomal compartments is required that allows comparison of autophagosomal activity under different conditions. Existing methods such as western blotting and immunohistochemistry for analysing the location and relative abundance of intracellular proteins associated with autophagy, or transmission electron microscopy (TEM), which are either very time-consuming, expensive, or both, are less suitable for this purpose. The method described in this protocol allows the absolute quantification of autophagosomes per cell in human fibroblasts using the CYTO-ID® Autophagy Detection Kit after heat therapy compared to a control. The Cyto-ID® assay is based on the use of a specific dye that selectively stains autophagic compartments, combined with an additional Hoechst 33342 dye for nuclear staining. The subsequent recognition of these stained compartments by the Cytation Imager enables the software to determine the number of autophagosomes per nucleus in living cells. Additionally, this absolute quantification uses an image-based method, and the protocol is easy to use and not time-consuming. Furthermore, the method is not only suitable for heat therapy but can also be adapted to any other desired therapy or substance. Key features • Absolute quantification of autophagic compartments in living cells. • Optimised protocol for the determination of autophagy in primary human skin fibroblasts. • Allows the testing of active substances and treatments concerning autophagy. • Imaging-based method for the determination of autophagy.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11247374/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141621976","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
Phylogenomics of Plant NLR Immune Receptors to Identify Functionally Conserved Sequence Motifs. 通过植物 NLR 免疫受体系统发生组学鉴定功能保守的序列基元。
IF 1
Bio-protocol Pub Date : 2024-07-05 DOI: 10.21769/BioProtoc.5023
Toshiyuki Sakai, AmirAli Toghani, Hiroaki Adachi
{"title":"Phylogenomics of Plant NLR Immune Receptors to Identify Functionally Conserved Sequence Motifs.","authors":"Toshiyuki Sakai, AmirAli Toghani, Hiroaki Adachi","doi":"10.21769/BioProtoc.5023","DOIUrl":"10.21769/BioProtoc.5023","url":null,"abstract":"<p><p>In recent years, the increase in genome sequencing across diverse plant species has provided a significant advantage for phylogenomics studies, allowing the analysis of one of the most diverse gene families in plants: nucleotide-binding leucine-rich repeat receptors (NLRs). However, due to the sequence diversity of the NLR gene family, identifying key molecular features and functionally conserved sequence patterns is challenging through multiple sequence alignment. Here, we present a step-by-step protocol for a computational pipeline designed to identify evolutionarily conserved motifs in plant NLR proteins. In this protocol, we use a large-scale NLR dataset, including 1,862 NLR genes annotated from monocot and dicot species, to predict conserved sequence motifs, such as the MADA and EDVID motifs, within the coiled-coil (CC)-NLR subfamily. Our pipeline can be applied to identify molecular signatures that have remained conserved in the gene family over evolutionary time across plant species. Key features • Phylogenomics analysis of plant NLR immune receptor family. • Identification of functionally conserved sequence patterns among plant NLRs.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11237980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617748","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
Bilateral Common Carotid Artery Stenosis in Mice: A Model of Chronic Cerebral Hypoperfusion-Induced Vascular Cognitive Impairment. 小鼠双侧颈总动脉狭窄:慢性脑灌注不足诱发血管性认知障碍的模型
IF 1
Bio-protocol Pub Date : 2024-07-05 DOI: 10.21769/BioProtoc.5022
Masashi Kakae, Ayaka Kawashita, Haruya Onogi, Takayuki Nakagawa, Hisashi Shirakawa
{"title":"Bilateral Common Carotid Artery Stenosis in Mice: A Model of Chronic Cerebral Hypoperfusion-Induced Vascular Cognitive Impairment.","authors":"Masashi Kakae, Ayaka Kawashita, Haruya Onogi, Takayuki Nakagawa, Hisashi Shirakawa","doi":"10.21769/BioProtoc.5022","DOIUrl":"10.21769/BioProtoc.5022","url":null,"abstract":"<p><p>Vascular cognitive impairment (VCI) is a syndrome defined as cognitive decline caused by vascular disease and is associated with various types of dementia. Chronic cerebral hypoperfusion (CCH) is one of the major contributors to VCI. Among the various rodent models used to study CCH-induced VCI, we have found the mouse bilateral common carotid artery stenosis (BCAS) model to be highly suitable. Here, we introduce the BCAS model of C57BL/6J mice generated using microcoils with an internal diameter of 0.18 mm. To produce the mouse BCAS model, the bilateral common carotid arteries are isolated from the adhering tissues and vagus nerves and twined around the microcoils. This model shows cognitive impairment and white matter lesions preceding neuronal dysfunction around postoperative day 28, which is similar to the human clinical picture. Overall, the mouse BCAS model will continue to be useful in studying CCH-induced VCI. Key features • This mouse BCAS model requires approximately 4 weeks to show phenotypes such as cognitive impairment and white matter injury.</p>","PeriodicalId":93907,"journal":{"name":"Bio-protocol","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11238111/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617746","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
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