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Past Issue in 2014
Volume: 4, Issue: 19
Cancer Biology
Hypoxia Studies with Pimonidazole in vivo
Therapy-induced hypoxia drives changes in the tumor microenvironment that contribute to the poor response to therapy. Hypoxia is capable of driving the expression and/or activation of specific signaling cascades (e.g., c-Met, Axl, CTGF), the recruitment of tumor promoting immune cells, and the induction of cell survival pathways including autophagy (Phan et al., 2013; Hu et al., 2012; Ye et al., 2010). We have recently shown that anti-VEGF therapy-induced hypoxia can result in changes in the extracellular matrix that contribute to the aggressiveness of tumors post therapy (Aguilera et al., 2014). Importantly, therapies that induce hypoxia do not always increase epithelial plasticity and tumor aggressiveness (Ostapoff et al., 2013; Cenik et al., 2013). We have used pimonidazole to evaluate hypoxia in tumors and herein provide a detailed protocol for this useful tool to interrogate the levels of hypoxia in vivo. The utility of the HypoxyprobeTM (pimonidazole hydrochloride) immunohistochemical analysis approach allows for the assessment of hypoxia in different tissues as well as cell types. Pimonidazole is a 2-nitroimidazole that is reductively activated specifically in hypoxic cells and forms stable adducts with thiol groups in proteins, peptides, and amino acids (Cenik et al., 2013; Arnold et al., 2010; Raleigh and Koch, 1990; Raleigh et al., 1998). Furthermore, the amount of pimonidazole that is detected is directly proportional to the level of hypoxia within tumors.
Immunology
Coagulation Assay
Clotting times can be measured by using citrate plasma. The intrinsic pathway of coagulation is measured by the activated partial thromboplastin time (aPTT), the extrinsic pathway of coagulation, monitored by measuring the prothrombin time (PT), and thrombin-induced fibrin-network formation (thrombin clotting time; TCT).
Isolation and in vivo Transfer of Antigen Presenting Cells
Transfer of antigen presenting cells in vivo is a method used by immunologists to examine the potency of antigen presentation by a selected population of cells. This method is most commonly used to analyze presentation of protein antigens to MHC class I or II restricted T cells, but it can also be used for studies of nonconventional antigens such as CD1-presented lipids. In a recent study focusing on CD1d-restricted glycolipid antigen presentation to Natural Killer T cells, we compared antigen presenting properties of splenic B cells, CD8αPos dendritc cells (DCs) and CD8αNeg DCs (Arora et al., 2014). This protocol describes the detailed method used for isolation of these cell populations, and their transfer into recipient mice to analyze their antigen presenting properties.As a percentage of total mononuclear cells, an average spleen contains approximately 1-3% myeloid dendritic cells (DCs). In absolute numbers, this translates to approximately 0.6-1.8 x 106 DCs. To enhance the number of DCs in spleen, mice were injected subcutaneously with cells from a cultured melanoma cell line (B16.Flt3L) which has been engineered to express the fms-related tyrosine kinase 3 ligand (Flt3L) (Mach et al., 2000). This protein is a growth factor homologous to colony stimulating factor-1 and plays a critical role in the differentiation of hematopoietic stem cells. Administration of this protein into mice as a purified protein results in the expansion of both CD8αPos and CD8αNeg DC subsets in multiple organs. Similar expansion is also seen in mice that have been implanted with tumor cells overexpressing this protein (Mach et al., 2000). In our experience, up to 60% of the total mononuclear cells in a spleen from a mouse with a palpable B16.Flt3L tumor can be CD11c positive dendritic cells, thereby giving a total yield of up to 5 x 107 DCs per mouse. A schematic illustrating the cell enrichment protocol is included in Figure 1, and representative data on purity of cell populations obtained with this protocol is shown in Figure 2.
Microbiology
Expression and Purification of the Thermus thermophilus Argonaute Protein
The Argonaute protein of Thermus thermophilus (TtAgo) has recently been studied in detail. For its in vitro characterization, TtAgo was purified after heterologous expression in Escherichia coli (E. coli). As TtAgo expression is toxic, a tightly controlled system was used for protein expression. The expression strain E. coli KRX carries a chromosomal T7 RNA polymerase gene under control of a rhamnose promoter. The ago gene is expressed via an IPTG-inducible T7 promoter. This allows for tightly (double) controlled expression of (toxic) TtAgo. Here, we describe the steps required for controlled expression and purification of this toxic protein.
Construction of Glycine Oxidase Mutant Libraries by Random Mutagenesis, Site Directed Mutagenesis and DNA Shuffling
Glyphosate, a broad spectrum herbicide widely used in agriculture all over the world, inhibits 5-enolpyruvylshikimate-3-phosphate synthase in the shikimate pathway, and glycine oxidase (GO) has been reported to be able to catalyze the oxidative deamination of various amines and cleave the C-N bond in glyphosate (Pedotti et al., 2009). Here, in an effort to improve the catalytic activity of the glycine oxidase that was cloned from a glyphosate-degrading marine strain of Bacillus cereus (BceGO), we used a bacteriophage T7 lysis-based method for high-throughput screening of oxidase activity and engineered the gene encoding BceGO by directed evolution.
Chromogenic Substrate Assay for Determining the Activity of Plasma Kallikrein
The activation of the intrinsic pathway takes place at negatively charged surfaces, such as bacteria, and involves activation of cogulation Factor XII, which then leads to the activation of plasma kallikrein (PK) and coagulation Factor XI. To determine the PK activity on bacterial surfaces, bacteria were pre-incubated with peptides, followed by incubation with plasma, and the effect of peptide was recorded by measuring the PK activity.
Neuroscience
Novel Object Recognition for Studying Memory in Mice
Memory tests are important indexes of the brain functions for rodents behavior assay. Many memory tasks require external forces (e.g. electric shocks) or intrinsic forces (e.g. hunger and thirsty) to trigger the responses. Under those conditions, rodents are under stresses, such as pain, tired, malnutrition or dehydration, which potentially affect the natural neural responses. Novel object recognition is a non-force driving and spontaneous memory test. It is derived from curiosity but easy to be interfered with manipulation factors. In addition to stepwise procedure, the protocol described here emphasizes how to reduce the noise in the novel object recognition.
In utero Electroporation of the Embryonic Mouse Retina
This protocol is useful to manipulate gene expression in the embryonic retina and compare the result with the contralateral non electroporated retina. In addition, the electroporation of a membrane or cytoplasmic tagged GFP allows to determine the effects of gene manipulation on the outgrowth of retinal ganglion cell axons (Garcia-Frigola et al., 2007) or simply to follow axon outgrowth in mutant embryos. DNA can be directed to different quadrants of the retina (ventral or dorsally) by modifying the position of the electrodes (Petros et al., 2009; Sánchez-Arrones et al., 2013). After the procedure, embryos are left developing to the desired stage, including postnatal stages.
Two-choice Digging Task in Mouse for Studying the Cognitive Flexibility
Cognitive flexibility, the higher-order cognition involving reversal learning, has been defined as having the ability to shift one’s previous thoughts or actions to new situations depending on situational demands. Studies of neuropsychiatric disorders such as autism spectrum disorder (ASD) showed that restricted and repetitive patterns of activities are associated with the impairments of cognitive flexibility. Some behavioral tasks including attentional set-shifting task are used to assess cognitive flexibility in mouse models for psychiatric disorders (Birrell and Brown, 2000; Colacicco et al., 2002). Here we present a two-choice digging test, which is simplified and modified from set-shifting task, for using mice to study the reversal learning (Huang et al., 2014).
Plant Science
Carotenoid Extraction and Quantification from Capsicum annuum
Carotenoids are ubiquitous pigments that play key roles in photosynthesis and also accumulate to high levels in fruit and flowers. Specific carotenoids play essential roles in human health as these compounds are precursors for Vitamin A; other specific carotenoids are important sources of macular pigments and all carotenoids are important anti-oxidants. Accurate determination of the composition and concentration of this complex set of natural products is therefore important in many different scientific areas. One of the richest sources of these compounds is the fruit of Capsicum; these red, yellow and orange fruit accumulate multiple carotenes and xanthophylls. This report describes the detailed method for the extraction and quantification of specific carotenes and xanthophylls.
Agrobacterium tumefaciens-mediated Transformation of Walnut (Juglans regia)
Like many woody plant species, walnut (Juglans regia) can be difficult to genetically transform and regenerate. However, somatic embryos have been used successfully for over two decades as a target tissue for transformation and regeneration of transgenic walnut plants. Walnut somatic embryos, initiated originally from developing zygotic embryos or anther tissue, will proliferate numerous secondary embryos from single cells in the epidermal layer. These single cells in intact somatic embryos can be efficiently transformed by Agrobacterium tumefaciens (A. tumefaciens). This gene transfer system is most efficient when Agrobacterium binary vector plasmids contain a scorable maker gene (e.g. uidA) and a selectable marker gene (e.g. nptII). This system should be applicable to any crop that undergoes repetitive embryogenesis from single Agrobacterium-susceptible cells. Here we describe the method of transforming somatic embryos in detail so that this technique can be applied to walnut and other woody plant species.
Endogenous ABA Extraction and Measurement from Arabidopsis Leaves
The endogenous messenger, the phytohormone abscisic acid (ABA) plays a major role in plant’s adaption to drought, salinity, cold and other abiotic stresses. In addition to abiotic stress signaling, ABA is involved also in developmental regulation and in responses to diverse biotic stresses. Dehydration stress results in a strong increase in endogenous ABA levels, which can be perceived by RCAR/PYR1/PYL receptors, initiating the ABA signaling pathway to coordinate the genome-wide gene expression, and plants adaptive physiological responses. ABA biosynthesis triggered by environmental cues as well as developmental signals occurs predominantly in vascular parenchyma cells. The measurement of ABA content in different organ/tissues is required to understandings how ABA is produced and delivered within the plants upon various stress conditions and to elucidate its regulatory role in both physiological and transcriptional responses.Quantitation of ABA can be achieved by two approaches: 1) the use of gas chromatography–tandem mass spectrometry (GC-MS) and 2) the use of immunoassays. Both methods are sensitive to trace amount of ABA down to the low pico-gram (10-12 g/ml FW) range. The GC-MS method needs special facilities, however the antibody based method is relatively simple and can be carried out in laboratory. Here we describe an easy method for ABA extraction from Arabidopsis seedlings, and further determination of ABA levels by competitive ELISA kit.
Localisation and Quantification of Reactive Oxygen Species and Nitric Oxide in Arabidopsis Roots in Response to Fungal Infection
Nitric oxide and reactive oxygen species have emerged as important signalling molecules in plants. The half-lives of NO and ROS are very short therefore rapid and precise measurements are required for the understanding biological roles of these redox active species. Various organelles and compartments generate NO and ROS thus it is important to determine precise location of these free radicals in order to understand their signalling roles. Diaminofluorescen (DAF) and fluorescent 2', 7'-dichlorofluorescein (DCF) dyes are employed to determine NO and ROS localisation. The advantage of this approach is that the dyes diffuse precisely to NO and ROS producing sites and generate fluorescence which can be detected by fluorescence- or confocal laser scanning microscopes. However, this technique has its disadvantages; particularly the specificity of the fluorescence signals needs to be established. Therefore, the use scavenger of NO such as cPTIO and ROS such as ascorbate is required to confirm the specificity of the fluorescence signal and ideally, confirmation of data obtained using other methods due to advantage and disadvantage associated with each method (Gupta and Igamberdiev, 2013). Here we describe a method to detect NO and ROS production from Arabidopsis roots in response to infection by Trichoderma, Fusarium using DAF, gas phase Griess reagent assay and DCF fluorescence methods.
Pea Aphid Survival Assays on Arabidopsis thaliana
Aphids are phloem-feeding insects that successfully colonize specific host plant species. Aphid performance on a given plant is commonly measured by assessing fecundity of an aphid species that is adapted to the host. However, this approach may not reveal roles for plant genes in defense pathways that adapted aphids suppress. The host range of the pea aphid (Acyrthosiphon pisum) is mostly restricted to plants of the legume family, and does not include Arabidopsis (Arabidopsis thaliana). Pea aphids die within a few days of being placed on Arabidopsis plants, and their survival therefore provides a sensitive measure of the status of the host plant defenses. This protocol describes how to measure the survival rate of the pea aphid on the non-host plant Arabidopsis. The protocol consists of two phases: first, obtaining a population of pea aphids of synchronized age; and secondly measuring their survival on Arabidopsis plants.
Analysis of Total Se Content in Rice
Total Se content in rice is normally low and it is difficult to determine it exactly because of Se volatilization and pollution during the digestion process. In this method, rice sample is digested thoroughly and Se volatilization is reduced greatly by designing a specific digestion tube, increasing digestion temperature by three steps, controlling the amount of mixed acid and adjusting the location of digestion tube in the digestion furnace. Se pollution is also reduced greatly by specific cleaning treatments.