Current Protocols最新文献

Fungal secondary metabolites (SMs) have captured the interest of natural products researchers in academia and industry for decades. In recent years, the high rediscovery rate of previously characterized metabolites is making it increasingly difficult to uncover novel compounds. Additionally, the vast majority of fungal SMs reside in genetically intractable fungi or are silent under normal laboratory conditions in genetically tractable fungi. The fungal natural products community has broadly overcome these barriers by altering the physical growth conditions of the fungus and heterologous/homologous expression of biosynthetic gene cluster regulators or proteins. The protocols described here summarize vital methodologies needed when researching SM production in fungi. We also summarize the growth conditions, genetic backgrounds, and extraction protocols for every published SM in Aspergillus fumigatus, enabling readers to easily replicate the production of previously characterized SMs. Readers will also be equipped with the tools for developing their own strategy for expressing and extracting SMs from their given fungus or a suitable heterologous model system. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Making glycerol stocks from spore suspensions Alternate Protocol 1: Creating glycerol stocks from non-sporulating filamentous fungi Basic Protocol 2: Activating spore-suspension glycerol stocks Basic Protocol 3: Extracting secondary metabolites from Aspergillus spp grown on solid medium Alternate Protocol 2: Extracting secondary metabolites from Aspergillus spp using ethyl acetate Alternate Protocol 3: High-volume metabolite extraction using ethyl acetate Alternate Protocol 4: Extracting secondary metabolites from Aspergillus spp in liquid medium Support Protocol: Creating an overlay culture Basic Protocol 4: Extracting DNA from filamentous fungi Basic Protocol 5: Creating a DNA construct with double-joint PCR Alternate Protocol 5: Creating a DNA construct with yeast recombineering Basic Protocol 6: Transformation of Aspergillus spp Basic Protocol 7: Co-culturing fungi and bacteria for extraction of secondary metabolites.

Evaluation of the quality of genomic "data products" such as genome assemblies or gene sets is of critical importance in order to recognize possible issues and correct them during the generation of new data. It is equally essential to guide subsequent or comparative analyses with existing data, as the correct interpretation of the results necessarily requires knowledge about the quality level and reliability of the inputs. Using datasets of near universal single-copy orthologs derived from OrthoDB, BUSCO can estimate the completeness and redundancy of genomic data by providing biologically meaningful metrics based on expected gene content. These can complement technical metrics such as contiguity measures (e.g., number of contigs/scaffolds, and N50 values). Here, we describe the use of the BUSCO tool suite to assess different data types that can range from genome assemblies of single isolates and assembled transcriptomes and annotated gene sets to metagenome-assembled genomes where the taxonomic origin of the species is unknown. BUSCO is the only tool capable of assessing all these types of sequences from both eukaryotic and prokaryotic species. The protocols detail the various BUSCO running modes and the novel workflows introduced in versions 4 and 5, including the batch analysis on multiple inputs, the auto-lineage workflow to run assessments without specifying a dataset, and a workflow for the evaluation of (large) eukaryotic genomes. The protocols further cover the BUSCO setup, guidelines to interpret the results, and BUSCO "plugin" workflows for performing common operations in genomics using BUSCO results, such as building phylogenomic trees and visualizing syntenies. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Assessing an input sequence with a BUSCO dataset specified manually Basic Protocol 2: Assessing an input sequence with a dataset automatically selected by BUSCO Basic Protocol 3: Assessing multiple inputs Alternate Protocol: Decreasing analysis runtime when assessing a large number of small genomes with BUSCO auto-lineage workflow and Snakemake Support Protocol 1: BUSCO setup Support Protocol 2: Visualizing BUSCO results Support Protocol 3: Building phylogenomic trees.

This article details the materials and methods required for both active induction and adoptive transfer of experimental autoimmune encephalomyelitis (EAE) in the SJL mouse strain using intact proteins or peptides from the two major myelin proteins: proteolipid protein (PLP) and myelin basic protein (MBP). Additionally, active induction of EAE in the C57BL/6 strain using myelin oligodendrocyte glycoprotein (MOG) peptide is also discussed. Detailed materials and methods required for the purification of both PLP and MBP are described, and a protocol for isolating CNS-infiltrating lymphocytes in EAE mice is included. Modifications of the specified protocols may be necessary for efficient induction of active or adoptive EAE in other mouse strains. © 2021 Wiley Periodicals LLC. Basic Protocol: Active induction of EAE with PLP, MBP, and MOG protein or peptide Alternate Protocol: Adoptive induction of EAE with PLP-, MBP-, or MOG-specific lymphocytes Support Protocol 1: Purification of proteolipid protein Support Protocol 2: Purification of myelin basic protein Support Protocol 3: Isolation of CNS-infiltrating lymphocytes.

The extracellular matrix (ECM) is an architecture that supports the cells in our bodies and regulates various cell functions. The ECM is composed of many proteins and carbohydrates, and these molecules activate various intracellular signaling pathways orchestrated to decide cell fates. Therefore, it is not enough to study the role of single ECM molecules to understand the roles of the ECM in the regulation of cell functions; it is necessary to understand how the ECM, as an assembly of various molecules, regulates cell functions as a whole. For this purpose, in vitro ECM models mimicking native ECM are required. Here, a decellularization technique is presented to reconstitute native ECM in vitro. In this article, methods for preparing decellularized ECM (dECM) are described for use in tumor and stem cell biology. Additionally, a method for confirmation of decellularization and a dECM modification method are described. These dECM types will be useful for comprehensive studies of ECM roles. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparation of in vitro extracellular matrix (ECM) models mimicking native ECM in different malignant tumor tissues Basic Protocol 2: Preparation of in vitro ECM models mimicking native ECM surrounding myoblasts differentiating into myotubes at each myogenic stage Support Protocol 1: Confirmation of myogenic stages by myogenic stages by myogenic gene expression analysis Basic Protocol 3: Confirmation of cell removal Basic Protocol 4: Reduction of chondroitin sulfate chains in cultured cell-derived decellularized ECM Support Protocol 2: Quantification of chondroitin sulfate chain amounts in the decellularized ECM.

Ongoing technological advancements continually increase the demand for energy. Among various types of energy harvesting systems, biologically based systems have been an area of increasing interest for the past couple of decades. Such systems provide clean, safe power solutions, mainly for low- and ultra-low-power applications. The microphotosynthetic power cell (μPSC) is one such system that make use of photosynthetic living cells or organisms to generate power. For strong performance, μPSC technology, because of its interdisciplinary nature, requires optimal engineering of both electrochemical cell design and the culture conditions of the photosynthetic microorganisms. We present here a simple, economical culture method for the photosynthetic microorganism Chlamydomonas reinhardtii suitable for the application of this biologically based power system in any geographical location. This article provides a series of protocols for preparing materials and culture medium designed to facilitate the culture of a suitable C. reinhardtii strain even in a non-biological laboratory. Possible challenges and methods to overcome them are also discussed. Cultured C. reinhardtii perform sufficiently well that they have already been successfully utilized to generate power from a μPSC, generating a peak power of 200 μW from just 2 ml of exponential-phase algal culture in a μPSC with an active electrode surface area of 4.84 cm² . The μPSC thus has potentially broad applications in low- and ultra-low-power devices and sensors. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Algal growth conditions and algal growth chamber fabrication Basic Protocol 2: Preparation of Tris-acetate-phosphate (TAP) nutrient medium Basic Protocol 3: Preparation of suspension algal culture from algal strain Basic Protocol 4: Preparation of stock culture plates (algal strain) from suspension algal culture.

This article describes procedures for two preclinical animal models for genital herpes infection. The guinea pig model shares many features of genital herpes in humans, including a natural route of inoculation, self-limiting primary vulvovaginitis, spontaneous recurrences, symptomatic and subclinical shedding of HSV-2, and latent infection of the associated sensory ganglia (lumbosacral dorsal root ganglia, DRG). Many humoral and cytokine responses to HSV-2 infection in the guinea pig have been characterized; however, due to the limited availability of immunological reagents, assessments of cellular immune responses are lacking. In contrast, the mouse model has been important in assessing cellular immune responses to herpes infection. Both the mouse and guinea pig models have been extremely useful for evaluating preventative and immunotherapeutic approaches for controlling HSV infection and recurrent disease. In this article, we describe procedures for infecting guinea pigs and mice with HSV-2, scoring subsequent genital disease, and measuring replicating virus to confirm infection. We also provide detailed protocols for dissecting and isolating DRG (the site of HSV-2 latency), quantifying HSV-2 genomic copies in DRG, and assessing symptomatic and subclinical shedding of HSV-2 in the vagina. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Primary and recurrent genital herpes infection in the guinea pig model Support Protocol 1: Blood collection via lateral saphenous vein or by cardiac puncture after euthanasia Support Protocol 2: Dissection and isolation of dorsal root ganglia from guinea pigs Support Protocol 3: PCR amplification and quantification of HSV-2 genomic DNA from samples Basic Protocol 2: Primary genital herpes infection in the mouse model Alternate Protocol: Flank infection with HSV-2 in the mouse model Support Protocol 4: Dissection and isolation of mouse dorsal root ganglia.

Microbiome composition studies are increasingly shedding light on animal models of disease. This paper describes a protocol for analyzing the gut microbiome composition prior to and after the induction of mice to experimental autoimmune encephalomyelitis (EAE), the principal animal model of the human neuroinflammatory demyelinating disease multiple sclerosis (MS). We also address and provide data assessing the impact of mice reared in different animal facilities on EAE induction. Furthermore, we discuss potential regulators of the gut-microbiome-brain axis (GMBA) in relation to neuroinflammation and implications on demyelinating disease states. Our results suggest that mice reared in different animal facilities produce different levels of EAE induction. These results highlight the importance of accounting for consistent environmental conditions when inducing EAE and other animal models of disease. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Study of the composition of the gut microbiome in the neuroinflammatory model of experimental autoimmune encephalomyelitis Basic Protocol 2: Experimental procedures for DNA extraction and microbiome analysis.

Mitochondria are the power houses of eukaryotic cells. These organelles contain various oxidoreductase complexes. Electron transfer from different reducing equivalents channeled via these complexes drives proton translocation across the inner mitochondrial membrane, leading to ATP generation. Plant mitochondria contain alternative NAD(P)H dehydrogenases, alternative oxidase, and uncoupling protein, and TCA cycle enzymes are located in their matrix. Apart from ATP production, mitochondria are also involved in synthesis of vitamins and cofactors and participate in fatty acid, nucleotide, photorespiratory, and antioxidant metabolism. Recent emerging evidence suggests that mitochondria play a role in redox signaling and generation of reactive oxygen and nitrogen species. For mitochondrial studies, it is essential to isolate physiologically active mitochondria with good structural integrity. In this article, we explain a detailed procedure for isolation of mitochondria from various heterotrophic tissues, such as germinating chickpea seeds, potato tubers, and cauliflower florets. This procedure requires discontinuous Percoll gradient centrifugation and can give a good yield of mitochondria, in the range of 4 to 8 mg per 50 g tissue with active respiratory capacity. After MitoTracker staining, isolated mitochondria can be visualized by using a confocal microscope. The structure of mitochondria can be monitored by scanning electron microscopy. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Isolation of mitochondria from germinating chickpea seeds, potato tubers, and cauliflower florets Basic Protocol 2: Quantification of mitochondrial protein concentration by Bradford assay Basic Protocol 3: Quantification of mitochondrial respiration using single-channel free-radical analyzer Basic Protocol 4: Staining of mitochondria and confocal imaging Basic Protocol 5: Visualization of isolated mitochondria under scanning electron microscope.

In vivo rodent, whole peripheral nerve models are useful for studying the electrical conduction of sensory and motor fibers under normal physiological conditions as well as for assessing neurological outcomes after the application of physical alterations or pharmacological agents to the nervous system. Significant literature has focused on single-neuron and central nervous system electrophysiology protocol development. However, creation and development of in vivo whole-nerve electrophysiological recording protocols are sparse in the scientific literature. Here, detailed protocols for designing and building an in vivo whole-nerve electrophysiology system are described, including straightforward techniques to create working stimulation and recording electrodes that may be adapted to numerous study designs. Further, we include details for rodent anesthesia, surgical dissection (for the sciatic nerve), compound action potential signal optimization, data acquisition, data analyses, and troubleshooting tips. © 2021 Wiley Periodicals LLC. Basic Protocol 1: In vivo electrophysiology system wiring, hardware, and software setups Support Protocol 1: Design and 3D printing of electrophysiology base electrodes Support Protocol 2: Building needle electrodes Basic Protocol 2: Rodent anesthesia and surgery for nerve exposure Basic Protocol 3: Compound action potential recording and troubleshooting using WinWCP Basic Protocol 4: Compound action potential data analysis using WinWCP.

Campylobacter jejuni is the leading cause of bacterial-derived gastroenteritis worldwide, infecting 96 million individuals annually. During infection, inflammation and tissue pathology occur in the lower gastrointestinal tract, including the recruitment of leukocytes. Neutrophils are the most abundant leukocyte in humans, and recruitment is associated with bacterial infections and the development of various inflammatory disorders, including inflammatory bowel disease. Neutrophils possess three main antibacterial functions: phagocytosis and degradation of microbes, degranulation to release antimicrobial proteins, and extrusion of neutrophil extracellular traps (NETs). Because neutrophils are recruited to the site of C. jejuni infection and they are associated with damaging inflammation in other diseases, it is imperative to understand the immunopathology that occurs during C. jejuni infection and thoroughly study the neutrophil response to the pathogen. Detailed protocols for human and ferret neutrophil isolations, neutrophil gentamicin protection assay, neutrophil activation flow cytometry assay, NET induction and quantification, and neutrophil western blot analysis are included in this article. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Isolation of human and ferret neutrophils Basic Protocol 2: Neutrophil gentamicin protection assay Basic Protocol 3: Neutrophil activation flow cytometry analyses Basic Protocol 4: Neutrophil extracellular trap induction and quantification Basic Protocol 5: Western blot detection of neutrophil-derived antimicrobial proteins.