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Volume:9 Issue: 12 | Bio-protocol
Past Issue in 2019
Volume: 9, Issue: 12
Cancer Biology
Capillary Nano-immunoassay for Quantification of Proteins from CD138-purified Myeloma Cells
Protein analysis in bone marrow samples from patients with multiple myeloma (MM) has been limited by the low concentration of proteins obtained after CD138+ cell selection. A novel approach based on capillary nano-immunoassay could make it possible to quantify dozens of proteins from each CD138+ purified MM sample in an automated manner. Up to now, the knowledge of protein level in those cells was limited because a relatively small quantity of sample is available after the diagnostic procedure. Moreover, the sample often is required for nucleic acids analysis. We have developed the procedure for obtaining proteins from bone marrow samples preserved in RLT+ buffer, and we have successfully applied this approach for the quantification of proteins in the setting of patients with MM. Proteins are extracted from RLT+ buffer, the content is quantified by total protein assay with WES machine and finally, the particular protein expression level is evaluated using specific antibodies by capillary nano-immunoassay with WES machine. The present protocol enables us to quantify many proteins from a limited amount of sample, without losing the opportunity to obtain nucleic acids at the same time. Proteins are quantified automatically in an assay with a low probability of human errors, which makes it a useful tool for biomarkers development.
Fluorescence HPLC Analysis of the in-vivo Activity of Glucosylceramide Synthase
Almost all functions of cells or organs rely on the activities of cellular enzymes. Indeed, the in-vivo activities that directly represent the cellular effects of enzymes in live organs are critical importance to appreciate the roles enzymes play in modulating physiological or pathological processes, although assessments of such in-vivo enzyme activity are more difficult than typical test-tube assays. Recently, we, for the first time, developed a direct and easy-handling method for HPLC analyzing the in-vivo activity of glucosylceramide synthase (GCS). GCS that converts ceramide into glucosylceramide is a limiting-enzyme in the syntheses of glycosphingolipids and is one cause of cancer drug resistance. In our method developed, rubusoside nanomicelles delivers fluorescence N-[6-[(7-nitro-2,1,3-benzoxadiazol-4-yl)amino]hexanoyl]-D-erythro-sphingosine (NBD C6-ceramide) into mice, tissues uptake the cell-permeable substrate, and GCS converts it into NBD C6-glucosylceramide in all organs simultaneously. Further, HPLC analyzes the extracted NBD C6-glucosylceramide to assess alterations of the in-vivo GCS activities in tissues. This method can be broadly used to assess the in-vivo GCS activities in any kind of animal models to appreciate either the role GCS plays in diseases or the therapeutic efficacies of GCS inhibitors.
Cell Biology
Tandem Affinity Purification of SBP-CBP-tagged Type Three Secretion System Effectors
Identification of protein-protein interactions of bacterial effectors and cellular targets during infection is at the core to understand how bacteria manipulate the infected host to overcome the immune response. Potential interacting proteins might be identified by genetic methods, i.e., two hybrid screens and could be verified by co-immunoprecipitation. The tandem affinity purification (TAP) method allows an unbiased screen of potential interaction partners of bacterial effectors in a physiological approach: target cells can be infected with a bacterial strain harboring the TAP-tagged bacterial effector protein which is translocated in the host similar as under physiological infection conditions. No transfection and overexpression of the bacterial protein in the eukaryotic host are needed. Therefore, also host target cells not easy to transfect can be analyzed by this method. Moreover, the two consecutive affinity tags Calmodulin-Binding-Peptide (CBP) and Streptavidin-Binding-Peptide (SBP) fused to the translocated bacterial protein allow an outstanding clear purification of protein complexes formed between the bacterial protein of interest and host cell proteins with less occurrence of contaminants. Mass spectrometry allows an unbiased identification of interacting eukaryotic proteins.
Visualizing Filamentous Actin in Chlamydomonas reinhardtii
This protocol aims to visualize the filamentous actin network in Chlamydomonas reinhardtii. We improved fixed-cell labeling conditions using the F-actin probe, phalloidin. We created a Chlamydomonas-optimized protocol by halving the phalloidin incubation time, electing for optimal fixation conditions, and selecting for a healthy cell population. This phalloidin protocol is quick, effective, and is the only labeling method to date that allows for reliable actin filament detection in fixed vegetative Chlamydomonas cells. This method reveals previously unidentified actin structures in Chlamydomonas and novel insights into cytoskeletal dynamics.
Developmental Biology
Determining Oxidative Damage by Lipid Peroxidation Assay in Rat Serum
It has been well-established that malondialdehyde (MDA), which is generated during the process of lipid peroxidation, is a commonly known biomarker for oxidative stress. Therefore, the serum levels of MDA are detected by using the lipid peroxidation assay with commercially available kit to determine the induction of oxidative stress in rat models.
Environmental science
Detachment Procedure of Bacteria from Atmospheric Particles for Flow-cytometry Counting
The protocol separates bacteria from atmospheric particles, obtaining with greater precision their abundance in the atmospheric deposition. This procedure is similar to the one used to separate bacteria in streambed sediments. The detachment procedure consists of a chemical treatment with sodium pyrophosphate and Tween 20 and a physical treatment with agitation and ultrasonic bath to disperse the bacteria in the liquid sample. We recover the total (free and attached) bacteria by generating a density gradient with Nycodenz by centrifugation. The techniques prior to this procedure do not include the microorganisms that are attached to the aerosol particles and, therefore, considerably underestimate the total load and deposition of airborne microorganisms.
Microbiology
Production and Purification of Dengue Virus-like Particles from COS-1 Cells
Non-infectious virus-like particles (VLPs) containing dengue virus (DENV) pre-membrane (prM) and envelope (E) proteins have been demonstrated to be highly immunogenic and can be used as a potential vaccine candidate as well as a tool for serodiagnostic assays. Successful application of VLPs requires abundant, and high-purity production methods. Here, we describe a robust protocol for producing DENV VLPs from transiently-transformed or stable COS-1 cells and further provide an easily adaptable antigen purification method by sucrose gradient centrifugation.
Analysis of Functional Virus-generated PAMP RNAs Using IFNα/β ELISA Assay
Virus-generated PAMP RNAs are key factors that activate host immune response. The PAMP RNAs are therefore usually closely related with viral disease pathogenesis. Quantitative real time PCR is a conventional method to assess RNA. However, it cannot be used for detecting short dsRNAs generated by viral replicase. This protocol was established to analyze the PAMP RNAs produced by viruses which are able to induce host immune response. Classical viral PAMP RNAs and non-classical viral PAMP RNAs are analyzed separately. Briefly, to access total viral PAMP RNAs, total RNA was extracted from the virus infected cells and then transfected into Cop5 cells. Whereas, to assess non-classical viral PAMP RNAs, the constructs expressing viral replicase are transfected into Cop5 cells. The amount of IFNα/β produced by Cop5 cells, determined by ELISA, is correlated with the total and non-classical viral PAMP RNAs. Since this method is based on type I IFN response, it is therefore suitable for measuring the functional virus-generated PAMP RNAs and also for assessing the efficiency of these PAMP RNAs.
Imaging Gene Expression Dynamics in Pseudomonas fluorescens In5 during Interactions with the Fungus Fusarium graminearum PH-1
Genomics, transcriptomics and metabolomics are powerful technologies for studying microbial interactions. The main drawback of these methods is the requirement for destructive sampling. We have established an alternative but complementary technique based on a microplate system combined with promoter fusions for visualizing gene expression in space and time. Here we provide a protocol for measuring spatial and temporal gene expression of a bacterial reporter strain interacting with a fungus on a solid surface.
Probing Conformational States of a Target Protein in Escherichia coli Cells by in vivo Cysteine Cross-linking Coupled with Proteolytic Gel Analysis
Transporters are dynamic membrane proteins that are essential to the physiology of cells. To function, transporters must cycle between various conformational states, so to understand their mechanistic details, it is critical to characterize how their structure changes during the transport cycle. One approach to studying the dynamics of transporters takes advantage of the chemistry of cysteine by using sulfhydryl-reactive, bi-functional cross-linkers to probe changes in the distance between two specific residues that have been substituted to cysteine. This approach is mostly used to study transporters in vitro, not in their natural cellular environment. Here we describe a protocol based on structure-guided cysteine cross-linking and proteolysis-coupled gel analysis to probe conformational changes of a target transporter in live Escherichia coli cells. Although cross-linking approaches have been used to probe the proximity between transmembrane segments in membrane proteins in vivo, to our knowledge this protocol is the first to be used to interrogate transporter dynamics in cells. The use of this protocol is optimal for proteins with known or modeled structures to guide the replacement of specific residues with cysteines and the selection of cross-linking agents with various spacer arm lengths. This protocol allows for discriminating easily cross-linked and uncross-linked species and does not require the often difficult or unavailable reconstitution of transport activity in an in vitro system. In addition, this protocol could be used to probe the conformation of transporters in cells treated with transport inhibitors in order to better understand their mechanism of action, and potentially dynamic interactions between domains in proteins that are not transporters.
Molecular Biology
Immunoprecipitation and Sequencing of Acetylated RNA
Generation of the epitranscriptome through chemical modifications of protein-coding messenger RNAs (mRNAs) has emerged as a new mechanism of post-transcriptional gene regulation. While most mRNA modifications are methylation events, a single acetylated ribonucleoside has been described in eukaryotes, occurring at the N4-position of cytidine (N4-acetylcytidine or ac4C). Using a combination of antibody-based enrichment of acetylated regions and deep sequencing, we recently reported ac4C as a novel mRNA modification that is catalyzed by the N-acetyltransferase enzyme NAT10. In this protocol, we describe in detail the procedures to identify acetylated mRNA regions transcriptome-wide using acetylated RNA immunoprecipitation and sequencing (acRIP-seq).
Neuroscience
Measurement of Sleep and Arousal in Drosophila
Sleep is a conserved neurobehavioral state observed in animals with sufficiently complex nervous systems and is critical for survival. While the exact function of sleep remains unknown, the lack of sleep can have a range of physiological and behavioral effects. Studies in invertebrates and vertebrates have identified conserved neural mechanisms and cellular pathways in control of sleep, wakefulness and arousal. Methodologies to measure sleep have ranged from EEG recordings in humans and rodents to in-depth analysis of locomotor patterns in flies, fish and worms. Here we focus on sleep measurements using activity monitoring in the highly versatile experimental model system, Drosophila melanogaster, which is amenable to a number of genetic, physiological and behavioral manipulations. Further, we also describe methods used to manipulate sleep and wakefulness to understand the neural regulation of sleep and how organisms balance sleep, wakefulness and behavioral arousal. Sleep as a behavioral state is regulated by a number of factors including food, environmental conditions, and genetic background. The methodologies described here provide, a high-throughput approach to study neural regulation of sleep and factors that affect this complex behavior.
A High-throughput qPCR-based Method to Genotype the SOD1G93A Mouse Model for Relative Copy Number
The most commonly used mouse model in ALS preclinical research expresses multiple copies of the human SOD1 (G93A) transgene. During the course of breeding, successive generations of mice can lose copies of the transgene. Because shorter lifespan of these mice is dependent on transgene copy number, it is essential to ensure that no low-copy, and therefore longer-lived, mice are included in preclinical studies. Existing techniques for SOD1G93A mouse genotyping are broadly based on creating a standard curve using a reference gene and deducing the relative amount of SOD1 by comparison with the standard curve. This type of technique is used in Alexander et al. (2004), Vieira et al. (2017) and Maier et al. (2018). However, it is not described in detail (see Note 1). This paper provides a detailed protocol for determining the relative copy number of the human SOD1 transgene. Briefly, the protocol involves first the extraction of high-quality genomic DNA from mouse ear tissue, creation of a genomic DNA concentration-based standard curve, and qPCR analysis of up to 88 samples at once alongside the standard curve with Gapdh as a reference gene. Analysis involves the normalization of each unknown sample using the standard curve followed by determination of the copy number of the sample relative to the cohort median. This protocol has been optimized to produce high-quality genomic DNA and consistent results, and the relative copy number cutoffs have been optimized and validated empirically by comparison of relative copy number and mouse lifespan.
Rat Model of Empathy for Pain
Empathy for pain is referred to as an evolutionary behavior of social animals and humans associated with the ability to feel, recognize, understand and share the other's distressing (pain, social rejection and catastrophe) states. Impairment of empathy can definitely lead to deficits in social communication and sociability (attachment, bond, reciprocity, altruism and morality) that may be fundamental to some psychiatric disorders such as autism spectrum disorder (ASD), psychopathy, misconduct, antisocial personality disorder and schizophrenia. So far, the underlying mechanisms of empathy are poorly known due to lack of animal models and scarce understanding of its biological basis. Recently, we have successfully identified and validated the behavioral identities of empathy for pain in rats that can be widely used as a rodent model for studying the underlying biological mechanisms of empathy. Priming dyadic social interaction between a naive cagemate observer (CO) and a cagemate demonstrator (CD), rather than a non-cagemate, in pain for 30 min in a testing box can repeatedly and constantly result in empathic responses of the CO toward the familiar CD's distressing condition, displaying as allo-licking at the injury site, allo-grooming at the body and social transfer of pain. The familiarity-based, distress-specific social consolation and subsequent social transfer of pain can be qualitatively and quantitatively rated as experimental biomarkers for empathy for pain. The rodent model of empathy for pain is state-of-the-art and has more advantages than the existing ones used for social neuroscience since it can reflect sensory, emotional and cognitive processes of the brain in running the prosocial and altruistic behaviors in animals who could not report verbally. Here we would like to provide and share the protocol of the model for wide use.
Live-cell Migration Assays to Study Motility of Neural and Glial (Oligodendrocyte) Progenitor Cells
Cell motility has been extensively studied in in vitro models using fibroblasts and keratocytes, but the cell type-specific mechanisms underlying migration of lineage- or disease-specific cells, such as neural and glial progenitor cells, remain an active field for investigation. The migrating neural and glial progenitor cells contribute to the development, tissue repair and tumor invasion in the central nervous system (CNS). Cell migration is a highly dynamic process which relies on membranous protrusions to assemble, extend, disassemble and retract. In the CNS, the motility of neural and glial progenitor cells is affected by various cell-autonomous and non-cell-autonomous mechanisms such as signaling molecules, actin and microtubule interactions, and environmental cues. Here, we described a live-cell migration assay for use in the assessment of neural and glial progenitor cell migration. We first will demonstrate the procedures for isolating and culturing neural and glial progenitor cells. Next, we will demonstrate the acquisition of time-lapse images using phase contrast microscopy, the methods for quantification and the analyses of various motility parameters including speed, velocity, straightness and leading-edge dynamics. This method allows researchers to dissect the mechanisms of cell motility in response to different environmental cues, such as chemoattractive and repulsive signals, matrix adhesiveness and stiffness. This assay also allows researchers to study migration of pharmacologically and genetically manipulated cells.
Optical Stimulation and Electrophysiological Analysis of Regenerating Peripheral Axons
Although axons in the peripheral nervous system can regenerate, functional recovery after nerve injuries is poor. Activity-based therapies, such as exercise and electrical stimulation, enhance the regeneration of cut peripheral axons. Despite their effectiveness, clinical application of these experimental techniques has been limited. At least part of the basis for this translational barrier has been a lack of information as to the precise mechanism of activity-based therapies on peripheral axon regeneration. To evaluate the requirements for neuron-type specific activation to promote regeneration using these therapies, in the current protocol, we employed optogenetics. Utilizing the advantages of transgenic mouse lines we targeted opsin expression to different neuron types. Using fiber optics we activated those neurons with high temporal specificity as a model of activity-based intervention after nerve injury and to measure functional recovery achieved after such a treatment.
Neurostore: A Novel Cryopreserving Medium for Primary Neurons
Primary neuronal culture from rodents is a key tool in neurobiology. However, the preparation of primary cultures requires precise planning, starting from animal mating. Furthermore, each preparation generates a high amount of cells that eventually go wasted. The possibility to cryopreserve primary neural cells represents a resource for in vitro studies and significantly reduces the sacrifice of animals. Here we describe that Neurostore buffer supports the cryopreservation of primary neurons.