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Past Issue in 2020
Volume: 10, Issue: 6
Biochemistry
Self-organization Assay for Min Proteins of Escherichia coli in Micro-droplets Covered with Lipids
The Min system determines the cell division plane of bacteria. As a cue of spatiotemporal regulation, the Min system uses wave propagation of MinD protein (Min wave). Therefore, the reconstitution of the Min wave in cell-sized closed space will lead to the creation of artificial cells capable of cell division. The Min waves emerge via coupling between the reactions among MinD, MinE, and ATP and the differences in diffusion rate on the cell membrane and in the cytoplasm. Because Min waves appear only under the balanced condition of the reaction-diffusion coupling, special attentions are needed towards several technical points for the reconstitution of Min waves in artificial cells. This protocol describes a technical method for stably generating Min waves in artificial cells.
In vitro Measurement of CMP-Sialic Acid Transporter Activity in Reconstituted Proteoliposomes
Nucleotide-sugar transporters (NSTs) facilitate eukaryotic cellular glycosylation by transporting nucleotide-sugar conjugates into the Golgi lumen and endoplasmic reticulum for use by glycosyltransferases, while also transferring nucleotide monophosphate byproducts to the cytoplasm. Mutations in this family of proteins can cause a number of significant cellular pathologies, and wild type members can act as virulence factors for many parasites and fungi. Here, we describe an in vitro assay to measure the transport activity of the CMP-sialic acid transporter (CST), one of seven NSTs found in mammals. While in vitro transport assays have been previously described for CST, these studies failed to account for the fact that 1) commercially available stocks of CMP-sialic acid (CMP-Sia) are composed of ~10% of the higher-affinity CMP and 2) CMP-Sia is hydrolyzed into CMP and sialic acid in aqueous solutions. Herein we describe a method for treating CMP-Sia with a nonselective phosphatase, Antarctic phosphatase, to convert all free CMP to cytidine. This allows us to accurately measure substrate affinities and transport kinetics for purified CST reconstituted into proteoliposomes.
Cancer Biology
Single-cell qPCR Assay with Massively Parallel Microfluidic System
The single-cell transcriptome is the set of messenger RNA molecules expressed in one cell. It is extremely variable and changes according to external, physical and biochemical conditions. Due to sensitivity shortages, most of genetic studies use bulk samples, providing only the average gene expression. Single-cell technologies have provided a powerful approach to a more detailed understanding of the heterogenic populations and minority cells. However, since it is still a quite novel technique, standardized protocol has to be established. Single-cell qPCR, although partly limited by the number of genes, is relatively simple to analyze. Therefore, its use is accessible without the necessity to recourse to complex bioinformatics analyses. The main steps for single-cell qPCR, as illustrated in this protocol, are composed by single-cell isolation, cell lysate, cDNA reverse-transcription synthesis, amplification for cDNA library generation, and finally, quantitative polymerase chain reaction.
Developmental Biology
Testing Bone Formation Induction by Calvarial Injection Assay in vivo
Bone formation occurs during embryogenesis, skeletal growth and during the process of skeletal renewal throughout life. In the process of bone formation, osteoblasts lay down a collagen-containing matrix, termed osteoid, which is gradually hardened by incorporation of mineral crystals. Although osteoblasts can be induced to differentiate and to deposit mineral in culture, this system does not always provide results that reflect the ability of agents to stimulate bone formation in vivo. This protocol describes a rapid and reliable method for testing local administration of agents on bone formation in vivo. In this method, mice are injected with the agent of question for 5 successive days. Fluorochrome labels are injected prior to, and after agents used for testing, and samples are collected and analysed by undecalcified bone histology and histomorphometry. This provides a robust method for assessing the ability of agents to stimulate bone formation, and if a short-term modification is used, can also be used for testing gene responses in bone to the same stimuli.
Environmental science
Accelerated Snowmelt Protocol to Simulate Climate Change Induced Impacts on Snowpack Dependent Ecosystems
Field studies that simulate the effects of climate change are important for a predictive understanding of ecosystem responses to a changing environment. Among many concerns, regional warming can result in advanced timing of spring snowmelt in snowpack dependent ecosystems, which could lead to longer snow-free periods and drier summer soils. Past studies investigating these impacts of climate change have manipulated snowmelt with a variety of techniques that include manual snowpack alteration with a shovel, infrared radiation, black sand and fabric covers. Within these studies however, sufficient documentation of methods is limited, which can make experimental reproduction difficult. Here, we outline a detailed plot-scale protocol that utilizes a permeable black geotextile fabric deployed on top of an isothermal spring snowpack to induce advanced snowmelt. The method offers a reliable and cost-effective approach to induce snowmelt by passively increasing solar radiation absorption at the snow surface. In addition, control configurations with no snowpack manipulation are paired adjacent to the induced snowmelt plot for experimental comparison. Past and ongoing deployments in Colorado subalpine ecosystems indicate that this approach can accelerate snowmelt by 14-23 days, effectively mimicking snowmelt timing at lower elevations. This protocol can be applied to a variety of studies to understand the hydrological, ecological, and geochemical impacts of regional warming in snowpack dependent ecosystems.
Immunology
Analyzing the Quenchable Iron Pool in Murine Macrophages by Flow Cytometry
Tissue-resident macrophages are pivotal for a tightly-regulated iron metabolism at a cellular and systemic level, since subtle iron alterations increase the susceptibility for microbial infections or drive multiple diseases. However, research on cellular iron homeostasis in macrophages remains challenging due to the limited amount of available methods using radioactive 59Fe isotopes or strong iron chelators, which might be inapplicable in certain experimental settings. This protocol describes the analysis of the quenchable iron pool (QIP) in macrophages by loading these cells with exogenous iron-complexes. Thereby, the cytoplasmic iron pool can be determined, since the iron uptake ability of macrophages inversely correlates with intracellular iron levels. Thus, this assay enables the accurate analysis of even minor alterations in cytoplasmic iron fluxes and is applicable in almost every laboratory environment. In addition, the protocol can also be adopted for other immune cell types in vitro and in vivo.
Characterization of Immunological Niches within Peyer’s Patches by ex vivo Photoactivation and Flow Cytometry Analysis
T follicular helper (Tfh) cells regulate B cell selection for entry into the germinal center (GC) reaction or for differentiation into antibody forming cells. This process takes place at the border between the T and B zones in lymphoid organs and involves physical contacts between T and B cells. During these interactions, T cells endow the B cells with selection signals that promote GC seeding or plasmablast differentiation based on their B cell receptor affinity. In Peyer’s patches (PPs), T cells promote B cell colonization of the subepithelial dome (SED) without effective affinity-based clonal selection. To specifically characterize the T cell population that resides within the SED niche, we performed ex vivo photoactivation of the SED compartment followed by flow cytometry analysis of the labeled cells, as described in this protocol. This technique integrates both spatial and cellular information in studies of immunological niches and can be adapted to various experimental systems.
Method for Measuring Mucociliary Clearance and Cilia-generated Flow in Mice by ex vivo Imaging
Ex vivo biophysical measurements provide valuable insights into understanding both physiological and pathogenic processes. One critical physiological mechanism that is regulated by these biophysical properties is cilia-generated flow that mediates mucociliary clearance, which is known to provide protection against foreign particles and pathogens in the upper airway. To measure ciliary clearance, several techniques have been implemented, including the use of radiolabeled particles and imaging with single-photon emission computerized tomography (SPECT) methods. Although non-invasive, these tests require the use of specialized equipment, limiting widespread use. Here we describe a method of ex vivo imaging of cilia-generated flow, adapted from previously reported methods, to make it more accessible and higher throughput for researchers. We excise trachea from mice quickly after euthanasia, cut it longitudinally and place it in an inhouse made slide. We apply fluorescent particles to measure particle movement under a fluorescent microscope, followed by analysis with ImageJ, allowing calculation of fluid flow generated by cilia under different conditions. This method enables ex vivo measurements in tissue with minimal investment or special equipment, giving opportunity to investigate and discover important biophysical properties associated with ciliary movement of the trachea in physiology and disease.
Microbiology
Purification of Rice Stripe Virus
Although many spherical and rod-shaped plant virus purification protocols are now available, only a few protocols on filamentous plant virus purification have been published. Here, we report a protocol for large-scale purification of Rice stripe virus (RSV) from RSV-infected rice tissues. RSV virions with high infectivity were first precipitated with polyethylene glycol (PEG) followed by pelleting through primary ultracentrifugation, ultracentrifugation in a glycerol cushion and ultracentrifugation in density gradient. The purified RSV virions can not only be viewed as filamentous particles under an electron microscope, but can also be acquired by insect vector through direct injection into insect body or through membrane feeding prior to transmission to rice plants.
Molecular Biology
High-resolution and Deep Phylogenetic Reconstruction of Ancestral States from Large Transcriptomic Data Sets
Phylogenetics is an important area of evolutionary biology that helps to understand the origin and divergence of genes, genomes and species. Building meaningful phylogenetic trees is needed for the accurate reconstruction of the past. To achieve a correct phylogenetic understanding of genes or proteins, reliable and robust methods are needed to construct meaningful trees. With the rapidly increasing availability of genome and transcriptome sequencing data, there is a need for efficient and accurate methodologies for ancestral state reconstruction. Currently available methods are mostly specific for certain gene families, and require substantial adaptation for their application to other gene families. Hence, a generalized framework is essential to utilize large transcriptome resources such as OneKP and MMETSP. Here, we have developed a flexible yet efficient method, based on core strengths such as emphasis on being inclusive in homolog selection, and defining orthologs based on multi-layered inferences. We illustrate how specific steps can be modified to fit the needs of any protein family under consideration. We also demonstrate the success of this protocol by studying and testing the orthologs in various gene families. Taken together, we present a protocol for reconstructing the ancestral states of various domains and proteins across multiple kingdoms of eukaryotes, using thousands of transcriptomes.
Neuroscience
Optic Nerve Crush in Mice to Study Retinal Ganglion Cell Survival and Regeneration
In diseases such as glaucoma, the failure of retinal ganglion cell (RGC) neurons to survive or regenerate their optic nerve axons underlies partial and, in some cases, complete vision loss. Optic nerve crush (ONC) serves as a useful model not only of traumatic optic neuropathy but also of glaucomatous injury, as it similarly induces RGC cell death and degeneration. Intravitreal injection of adeno-associated virus serotype 2 (AAV2) has been shown to specifically and efficiently transduce RGCs in vivo and has thus been proposed as an effective means of gene delivery for the treatment of glaucoma. Indeed, we and others routinely use AAV2 to study the mechanisms that promote neuroprotection and axon regeneration in RGCs following ONC. Herein, we describe a step-by-step protocol to assay RGC survival and regeneration in mice following AAV2-mediated transduction and ONC injury including 1) intravitreal injection of AAV2 viral vectors, 2) optic nerve crush, 3) cholera-toxin B (CTB) labeling of regenerating axons, 4) optic nerve clearing, 5) flat mount retina immunostaining, and 6) quantification of RGC survival and regeneration. In addition to providing all the materials and procedural details necessary to execute this protocol, we highlight its advantages over other similar published approaches and include useful tips to ensure its faithful reproduction in any modern laboratory.
An ex vivo Approach to Assess Mitochondrial ROS by Flow Cytometry in AAV-tagged Astrocytes in Adult Mice
Mitochondrial reactive oxygen species (mROS) are naturally produced signalling molecules extremely relevant for understanding both health- and disease-associated biological processes. The study of mROS in the brain is currently underway to decipher their physiopathological roles and contributions in neurological diseases. Recent advances in this field have highlighted the importance of studying mROS signalling and redox biology at the cellular level. Neurons are especially sensitive to the harmful effects of excess mROS while astrocytic mROS have been shown to play a relevant physiological role in cerebral homeostasis and behaviour. However, given the complexity of the brain, investigating mROS formation in a specific cell-type in adult animals is methodologically challenging. Here we propose an approach to specifically assess mROS abundance in astrocytes that combines i) a targeting strategy based on the use of adeno-associated virus (AAV) vectors expressing the green fluorescent protein (GFP) under an astrocyte (glial fibrillary acidic protein or GFAP) promoter, along with, ii) a robust and widely extended protocol for the measurement of mROS by flow cytometry using commercial probes. The significance of this work is that it allows the selective study of astrocytic mROS abundance by means of easily accessible technology.
Phototactic T-maze Behavioral Assay for Comparing the Functionality of Color-sensitive Photoreceptor Subtypes in the Drosophila Visual System
The Drosophila retina contains light-sensitive photoreceptors (R cells) with distinct spectral sensitivities that allow them to distinguish light by its spectral composition. R7 and R8 photoreceptors are important for color vision, and can be further classified into pale (p) or yellow (y) subtypes depending on the rhodopsin expressed. While both R7y and R7p are sensitive to UV light, R8y and R8p detect light in the green and blue spectrum, respectively. The ability of R7 and R8 photoreceptors to distinguish different spectral sensitivities and the natural preference for Drosophila towards light sources (phototaxis), allow for the development of a phototactic T-maze assay that compares the functionality of different R7 and R8 subtypes. A “UV vs. blue” choice can compare the functionalities of R7p and R8p photoreceptors, while a “UV vs. green” choice can compare the functionalities of R7y and R8y photoreceptors. Additionally, a “blue vs. green” choice could be used to compare R8p and R8y photoreceptors, while a “dark vs. light" choice could be used to determine overall vision functionality. Although electrophysiological recordings and calcium imaging have been used to examine functionality of R7 and R8 photoreceptors, these approaches require expensive equipment and are technically challenging. The phototactic T-maze assay we present here is a robust, straight-forward and an inexpensive method to study genetic and developmental factors that contribute to the individual functionality of R7 and R8 photoreceptors, and is especially useful when performing large-scale genetic screens.
Shared Pheromonal Communication of Specific Fear Between Adult Sprague Dawley Rats
Rats are highly social animals, and mainly communicate with one another in two ways: through ultrasonic vocalizations and pheromones. Most research on pheromones has been dedicated those regarding sexual behavior, but more recently pheromones which signal danger to conspecifics have been identified in rodents. In fact, rats are capable of communicating information regarding a specific fear to a companion with which they share a cage. If a rat is trained to associate a previously neutral odor with a foot shock and then pair housed with another rat, the companion will also display a fear response specific to the trained odor, despite never being shocked itself. This communication relies on pheromones; presenting soiled bedding from a shocked rat to an individually housed naïve rat produces the same fear response in the naïve rat. The current protocol describes how to produce this phenomenon in adult Sprague Dawley rats. It is simple and easily reproduced, requires minimal equipment, and may be completed within one week.
Plant Science
Experiments for in silico evaluation of Optimality of Photosynthetic Nitrogen Distribution and Partitioning in the Canopy: an Example Using Greenhouse Cucumber Plants
Acclimation of leaf traits to fluctuating environments is a key mechanism to maximize fitness. One of the most important strategies in acclimation to changing light is to maintain efficient utilization of nitrogen in the photosynthetic apparatus by continuous modifications of between-leaf distribution along the canopy depth and within-leaf partitioning between photosynthetic functions according to local light availability. Between-leaf nitrogen distribution has been intensively studied over the last three decades, where proportional coordination between nitrogen concentration and light gradient was considered optimal in terms of maximizing canopy photosynthesis, without taking other canopy structural and physiological factors into account. We proposed a mechanistic model of protein turnover dynamics in different photosynthetic functions, which can be parameterized using leaves grown under different levels of constant light. By integrating this dynamic model into a multi-layer canopy model, constructed using data collected from a greenhouse experiment, it allowed us to test in silico the degree of optimality in photosynthetic nitrogen use for maximizing canopy carbon assimilation under given light environments.