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Past Issue in 2016
Volume: 6, Issue: 1
Cancer Biology
PhagoKinetic Track Assay: Imaging and Analysis of Single Cell Migration
Cell migration is a highly complex and dynamic biological process, essential in several physiological phenomena and pathologies including cancer dissemination and metastasis formation. Thus understanding single cell migration is highly relevant and requires a suitable image-based assay. Depending on the speed of the moving cells, one may require fast time-lapse microscopy, which is not always suitable for high-throughput screening. To overcome this, a quantitative and fixed single cell migration assay was developed based on the PhagoKinetic Tracks (PKT) procedure. Briefly, cells are seeded on top of a monolayer of carboxylated latex beads, and as cells migrate, they phagocytose these beads and leave behind a migratory track. These bead-free migratory tracks can be visualized using a standard bright field microscope and analysed for a multiparametric quantitative assessment of single cell migration (Naffar-Abu-Amara et al., 2008).Here we describe a detailed and optimized protocol of the PKT assay, adaptable for both RNAi and drug screening (van Roosmalen et al., 2015). This protocol allows the user to study migratory behaviour at the single cell level, without fast and live-imaging microscopy.
Preparation of Recombinant Galectin-3 for Cancer Studies
Galectin-3 is a member of a class of proteins termed Galectins, characterized by their ability to bind glycans containing β-galactose (Cummings and Liu, 2009). Galectin-3 binds preferentially to proteoglycans terminating with N-acetyllactosamine (LacNAc) chains (i.e., tandem repeats of galactose) (Newlaczyl and Yu, 2011). Galectin-3 is unique among the galectins in its chimeric structure. It shares a conserved carbohydrate recognition domain (CRD) with the other galectins, but has a long amino-terminal tail that is thought to be involved in protein aggregation. It can also form homodimers through its CRD (Cummings and Liu, 2009). Galectin-3 has been found to have diverse functions in tumorigenesis including: signaling, apoptosis inhibition, immune suppression, cell growth, and metastasis among others. Galectin-3 is frequently upregulated in cancers (Nangia-Makker et al., 2008). Its function largely depends on its expression and localization properties (Newlaczyl and Yu, 2011). Because of its many roles in cancer-associated processes, establishing a method for Galectin-3 production is valuable for further study of its functions in cancer. Here, we describe how Galectin-3 purification was achieved by cloning of the human Galectin-3 gene into pGEX-2T vector containing the gene for glutathione-S-transferase (GST) upstream of its cloning site. The Galectin-3 gene was cloned into this vector via restriction digests of both the plasmid and the Galectin-3 gene by restriction enzymes BamHI and EcoRI, followed by ligation of the two fragments. The resulting plasmid was then used to transform BL21, an Escherichia coli (E. coli) strain specialized for protein expression. Finally, we discuss how the GST fusion protein was isolated and the recombinant Galectin-3 protein was further purified from the GST.
Measurement of 2-methylthio Modifications in Mitochondrial Transfer RNAs by Reverse-transcription Quantitative PCR
2-Methylthio-N6-isopentenyladenosine (ms2i6A) is an evolutionally conserved posttranscriptional modification found at position 37 of four mammalian mitochondrial tRNAs, mt-tRNASer(UCN), mt-tRNATrp, mt-tRNAPhe and mt-tRNATyr. The ms2 modification in ms2i6A strengthens codon-anticodon interaction and contributes to accurate and efficient decoding. Deficiency of ms2 modifications impairs mitochondrial protein synthesis, which ultimately leads to the development of myopathy in mice and patients having mitochondrial diseases. Therefore, the level of ms2 could be utilized as an indicator that reflects the status of mitochondrial protein synthesis. Here, we describe a simple and fast quantitative PCR-based method to measure the ms2 level in total RNA sample.
Immunology
Protocol-In vitro T Cell Proliferation and Treg Suppression Assay with Celltrace Violet
Measurement of the incorporation of radionuclides such as 3H-thymidine is a classical immunological technique for assaying T cell proliferation. However, such an approach has drawbacks beyond the inconvenience of working with radioactive materials, such as the inability of bulk radionuclide incorporation measurements to accurately quantitate T cell divisions, and an inability to combine proliferation analyses with simultaneous evaluation of the expression of cellular markers in divided cells. By labeling T cells with reactive dyes such as CFSE, Celltrace Violet, and others that are partitioned equally between daughter cells at each cell division, one can relatively easily track generations of proliferated cells and their expression of various molecules by flow cytometry. FoxP3+ regulatory T cells (Treg) are critical mediators of immune tolerance and evaluation of their functionality is an important step in characterizing many immune models (Rudensky, 2011). Classically CD4+ Treg and conventional or “responder” T cells have been isolated based on their surface expression of CD25 (Treg: CD4+CD25+, Tresp: CD4+CD25-). However, we and others have noted that populations of CD4+CD25- cells express the FoxP3 transcription factor and have suppressive function. Therefore we have utilized the transgenic FoxP3-EGFP mouse to facilitate live purification of suppressor and responder populations based on EGFP (and thus FoxP3) expression. Here we present our adapted protocol for assaying regulatory T cell suppression of Celltrace Violet-labeled responder T cells.
Neuroscience
Fluoro-Jade B Staining for Neuronal Cell Death
Fluoro-Jade is a fluorescent derivative used for histological staining of degenerating neurons. This technique is simple and sensitive enough to label distal dendrites, axons, axon terminals as well as neuronal bodies. Fluoro-Jade has excitation and emission peak of 480 and 525 nanometer respectively. It can be visualized using a fluorescein/FITC filter. Some reports have demonstrated that Fluoro-Jade can also be useful to detect glial cell death (Anderson et al., 2013; Damjanac et al., 2007).
Isolation and Purification of Murine Microglial Cells for Flow Cytometry
The detailed protocol is used to isolate different cell types from murine brain as glial cells, including microglia, using an enzymatic digestion that minimizes cellular mortality. A Percoll gradient (30% to 80%) separation allows a maximal recovery of isolated murine microglial cells prior to flow cytometry analysis.
Neurite Outgrowth Assay
Neurite outgrowth in culture provides an easy way to determine the effects of a particular substrate or exogenous factor on neuron behavior. Dissociated neurons can be plated on a variety of substrates and the length of the longest neurite outgrowth can be compared. Here, we describe how to isolate and dissociate dorsal root ganglion (DRG) neurons, culture them on coverslips, and measure longest neurite outgrowth.
Plant Science
Saccharification Protocol for Small-scale Lignocellulosic Biomass Samples to Test Processing of Cellulose into Glucose
Second generation biofuels are derived from inedible lignocellulosic biomass of food and non-food crops. Lignocellulosic biomass is mainly composed of cell walls that contain a large proportion of cellulosic and hemicellulosic polysaccharides. An interesting route to generate biofuels and bio-based materials is via enzymatic hydrolysis of cell wall polysaccharides into fermentable sugars, a process called saccharification. The released sugars can then be fermented to fuels, e.g., by use of yeast. To test the saccharification efficiency of lignocellulosic biomass on a lab-scale, a manual saccharification protocol was established that uses only small amounts of biomass and a low concentration of enzyme. This protocol can be used for different plant species like Arabidopsis thaliana, tobacco, maize and poplar. The low enzyme concentrations make it possible to detect subtle improvements in saccharification yield and to analyze the speed of hydrolysis. Although a specific acid and alkali pretreatment were included, the saccharification step can be preceded by any other pretreatment. Because no advanced equipment is necessary, this protocol can be carried out in many laboratories to analyze saccharification yield. The protocol was initially described in Van Acker et al. (2013).
Measurement of Uptake and Root-to-Shoot Distribution of Sulfate in Arabidopsis Seedlings
Sulfur is an essential macronutrient required for growth and development of plants. Plants take up sulfate from the soil environment through the function of plasma membrane-bound sulfate transporters expressed at the root surface cell layers. Plants then utilize the incorporated sulfate as the main sulfur source to synthesize sulfur-containing compounds such as cysteine and methionine. Measurement of root sulfate uptake capacity is essential for analyzing mutants showing altered levels of sulfate transporters and/or sulfur metabolic enzymes as a result of genetic modification or due to the effect of intrinsic or environmental factors modulating their gene expression. The method described in this protocol allows quantitative investigation of sulfate uptake rates and root-to-shoot sulfate distribution in Arabidopsis seedlings using [35S] sulfate as a radioactive tracer. The method is designed for parallel comparisons of multiple Arabidopsis accessions, mutants or transgenic lines at the seedling stage.
Super-resolution Imaging of Live BY2 Cells Using 3D-structured Illumination Microscopy
Light microscopy is the standard tool for studying sub-cellular structures however, owing to the diffractive properties of light, resolution is limited to 200 nm. Super-resolution microscopy methods circumvent this limit, offering greater resolution, particularly when studying fluorescently labeled sub-cellular structures. Super-resolution methods such as 3D-SIM (Structured Illumination Microscopy) fill a useful niche between confocal and electron microscopy. We have previously had success using fixed plant tissue samples with 3D-SIM (Bell and Oparka, 2014). However, sensitive structures can be altered by fixation and embedding procedures, so we developed a method for imaging live cells. In this protocol we used 3D-SIM to image the ER and Hechtian Strands in live, plasmolysed BY2 cells.
Quantification of Low Molecular Weight Thiols in Arabidopsis
Low-molecular-weight (LMW) thiols are a class of highly reactive compounds due to their thiol moiety. They play important roles in the maintenance of cellular redox homeostasis, detoxification, and development. Monobromobimane (mBBr) is weakly fluorescent but selectively reacts with thiols to yield highly fluorescent thioethers (mBSR) products, which is especially useful for the quantification of LMW thiols. The stable mBSR products can be separated by high-performance liquid chromatography (HPLC) equipped with a fluorescent detector. The main cellular LMW thiols are L-cysteine, gamma-glutamylcysteine, and glutathione (GSH). The following protocol describes the extraction and quantification of L-cysteine, gamma-glutamylcysteine, and glutathione from Arabidopsis tissues as reported (Xiang and Oliver, 1998; Zhao et al., 2014; Wang et al., 2015) with minor revision. Modifications may be required if the HPLC system or the C18 column is different.