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Past Issue in 2015
Volume: 5, Issue: 7
Biochemistry
Immunoprecipitation of Proteins in Caenorhabditis elegans
Immunoprecipitation (IP) is a biochemical technique to precipitate a protein out of solution using an antigen that can specifically bind to that protein. IP can be performed to isolate and concentrate one particular protein from a sample of thousands of different proteins. IP is also readily performed to pull down interacting proteins of complexes out of solution. This protocol outlines the methods used to IP proteins in whole worm lysates and their preparation for detection on Western blots using denaturing conditions.
Immunology
Intracellular Cytokine Staining (ICS) on Human Lymphocytes or Peripheral Blood Mononuclear Cells (PBMCs)
Production of cytokines plays an important role in the immune response. Cytokines are involved in many different pathways including the induction of many anti-viral proteins by IFN gamma, the induction of T cell proliferation by IL-2 and the inhibition of viral gene expression and replication by TNF alpha. Cytokines are not preformed factors but are rapidly produced and secreted in response to cellular activation. Intracellular cytokine detection by flow cytometry has emerged as the premier technique for studying cytokine production at the single-cell level. It detects the production and accumulation of cytokines within the endoplasmic reticulum after cell stimulation, allowing direct TH1 versus TH2 determination. It can also be used in combination with other flow cytometry protocols for immunophenotyping using cell surface markers or with MHC multimers to detect an antigen specific response, making it an extremely flexible and versatile method. This capability, combined with the high throughput nature of the instrumentation, gives intracellular cytokine staining an enormous advantage over existing single-cell techniques such as ELISPOT, limiting dilution, and T cell cloning. The principle steps of intracellular cytokine staining is as follows:1. Cells are activated for a few hours using either a specific peptide or a non-specific activation cocktail;2. An inhibitor of protein transport (e.g. Brefeldin A) is added to retain the cytokines within the cell;3. Next, EDTA is added to remove adherent cells from the activation vessel;4. After washing, antibodies to cell surface markers can be added to the cells;5. The cells are then fixed in paraformaldehyde and permeabilized;6. The anti-cytokine antibody is added and the cells can be analyzed by flow cytometer.
Microbiology
Membrane Flotation Assay
Many postitive-stranded RNA viruses, such as Hepatitis C virus (HCV), highjack cellular membranes, including the Golgi, ER, mitchondria, lipid droplets, and utilize them for replication of their RNA genome or assembly of new virions. By investigating how viral proteins associate with cellular membranes we will better understand the roles of cellular membranes in the viral life cycle. Our lab has focused specifically on the role of lipid droplets and lipid-rich membranes in the life cycle of HCV. To analyze the role of lipid-rich membranes in HCV RNA replication, we utilized a membrane flotation assay based on an 10-20-30% iodixanol density gradient developed by Yeaman et al. (2001). This gradient results in a linear increase in density over almost the entire length of the gradient, and membrane particles are separated in the gradient based on their buoyant characteristics. To preserve membranes in the lysate, cells are broken mechanically in a buffer lacking detergent. The cell lysate is loaded on the bottom of the gradient, overlaid with the gradient, and membranes float up as the iodixanol gradient self-generates. The lipid content of membranes and the concentration of associated proteins will determine the separation of different membranes within the gradient. After centrifugation, fractions can be sampled from the top of the gradient and analyzed using standard SDS-PAGE and western blot analysis for proteins of interest.
Purification of 70S Ribosomes from Bacillus subtilis
The eubacterial ribosome (70S) is a macromolecular complex that is composed of a small (30S) subunit and a large (50S) subunit. The small subunit comprises the 16S ribosomal RNA (rRNA) and more than 20 ribosomal proteins (r-proteins), whereas the large subunit comprises the 23S and 5S rRNAs and more than 30 r-proteins. Bacillus subtilis (B. subtilis) has 57 r-ribosomal protein genes and three rRNAs (16S, 23S and 5S rRNAs). Among them, we identified 21 r-proteins of the small subunit and 31 r-proteins of the large subunit in B. subtilis (Nanamiya et al., 2004). The functions and roles of individual components of the ribosome have not yet been completely clarified. Herein we describe in detail an ultracentrifugation-based protocol for the preparation of 70S ribosomes from exponentially growing cells of B. subtilis.
Cyst Detection in Toxoplasma gondii Infected Mice and Rats Brain
Toxoplasmosis caused by the intracellular parasite Toxoplasma gondii, is characterized by a life-long chronic infection. The parasite is an efficient neurotropic infectious agent that establishes its “safe” life by forming intracellular cysts in chronically infected animals and humans. This protocol describes the specific recipes and method to stain brain cysts from infected mice and rats for further quantification using epifluorescence microscopy. This method provides the possibility to scan the entire brain and thus to numerate all cysts.
Lectin Binding Analysis of Streptococcus mutans Glycoproteins
Bacterial glycoproteins are of increasing interest due to their abundance in nature and importance in health and infectious diseases. However, only a very small fraction of bacterial glycoproteins have been characterized and its post-translational modification machinery identified. While analysis of glycoproteins can be achieved through various techniques, this is often limited by the specific characteristics of individual proteins such as type and level of glycosylation. Lectins are sugar-binding proteins that recognize specific glycoconjugates in a manner similar to antigen-antibody interactions. Here, we describe a simple method for the detection of glycoproteins using lectin-based Western blot analysis, which can be applied to different organisms and coupled with various other strategies for complementary analysis.
Neuroscience
Nictation Assays for Caenorhabditis and Other Nematodes
Nictation is a dauer-specific standing and waving behavior of the nematodes including Caenorhabditis species. Nictation enhances the capability of free-living nematodes to hitchhike to other animals as well as parasitic nematodes to infect their hosts. However, lack of an assay for this behavior has made it difficult to elucidate its underlying regulatory mechanisms and related genetic pathways. We have developed nictation assays that enable the quantification of the nictation behavior of individuals and groups of worms. Gauze assay is less quantitative but is an easier way to observe nictation behavior in plates with plenty of dauers. The micro-dirt chip made from PDMS mold is a more sophisticated method to quantify the nictation behavior. Nictation can be quantified on a micro-dirt chip either by measuring the average nictating time of individual dauers or by the fraction of nictating worms in a given dauer population.
Plant Science
Leaf Disc Stress Tolerance Assay for Tobacco
Stress tolerance is a multigenic trait that depends on the coordinated action of several genes. Various physiological parameters, such as plant height and weight, total yield, chlorophyll content, photosynthesis rate, level of reactive oxygen species (ROS) and anti-oxidant activity could be correlated directly with the level of stress tolerance potential of any particular genotype. To evaluate the stress tolerance potential of a plant, leaf disc stress tolerance assay is a very rapid and widely acceptable experiment with minimum instrumentation facilities.
TUNEL Assay in Kiwifruit Stigmatic Arms
Terminal deoxynucleotidyl transferase-mediated dUTP nick end labelling (TUNEL) is a method for detecting DNA fragmentation by labelling the 3' terminal end of nucleic acids. This method can be used both in animal and plant tissues. In animal tissues, the use of Proteinase K is sufficient for permeabilizing the cells and to obtain optimal labelling, but in plant tissues, the presence of the cell wall, does not allow proper labelling. For this reason, we carried out several modifications to the original TUNEL protocol (ApoAlert® DNA Fragmentation Assay Kit, Clontech) to obtain an optimal labelling. These modifications were additional treatments with cellulase, Triton X-100 and Proteinase K. Also, we describe the optimization of the positive controls by adjusting the units of DNase used. The PI concentration for counterstaining has been also specifically adjusted to avoid excessive background noise and hence to correctly observe both labeled and unlabelled nuclei. This work also describes an additional protocol to collect, store and include samples (specifically stigmatic arms) in such a way that they do not interfere with the TUNEL labelling.
Stress Tolerance Assay at the Seed Germination Stage for Tobacco
Stress tolerance of plants is a complex phenomenon that depends on the inter-related action of several morphological, physiological and biochemical parameters. Although stress affects normal physiological growth of a plant irrespective of its developmental stage, seed germination and seed setting are considered to be the most sensitive two. Therefore, to evaluate the stress tolerance potential of a particular plant species or variety, rate of seed germination in presence of stress is an important agronomic trait. This will provide a clear indication about the stress tolerance potential with minimum instrumentation facilities. The method is very simple, effective and highly reproducible that would provide quick and reliable results to the researchers.
Arabidopsis thaliana Root Hair Cell Cytoplasmic pH (pHc) Imaging
For monitoring the cellular pH in plants, engineered green fluorescent protein (GFP) has been used to indicate cellular pH. Pt-GFP is a pH-reporter protein which has been used ratiometrically in the double excitation mode, according to the fluorescence properties described for Pt-GFP (Schulte et al., 2006), and depending on our previous experiments, we present here a little and efficient protocol for monitoring the cytosolic pH value. In this protocol, root hair cellular pH was monitored in the PtGFP reporter lines. Cellular pH can be obtained according to the calibration curve which was performed in situ by using a series pH buffer.
Gravitropic Analysis of Tomato Seedlings using Time Lapse Video Imaging
Plants use gravity as a guide for growth and development. Gravitropism, a gravity-directed growth process, directs upward shoot movement for efficient photosynthesis and gaseous exchange. In addition, it also directs downward growth of roots in soil, for assimilation of water and nutrients required for growth and development. Using time lapse video imaging this process can be efficiently studied in a real time scale. The analysis of the response under different conditions can help to unravel the mechanisms regulating gravitropism.
Microscopic Observation, Three-dimensional Reconstruction, and Volume Measurements of Sperm Nuclei
Karyogamy, a migration of the sperm nucleus toward the egg nucleus and their subsequent nuclear fusion, is an important biological event for initiating zygote formation toward early embryogenesis in angiosperms. However, how the male nucleus approaches and fuses with the female nucleus still remains unclear. Recently, time-lapse measurement of nuclear volume during karyogamic events revealed that the sperm nucleus enlarges during contact with the egg nucleus via possible one-directional migration of egg chromatin into sperm nucleus (Ohnishi et al., 2014). Here, we describe the protocol for microscopic observation, three-dimensional reconstruction, and volume measurements of sperm nuclei in rice zygotes/fused gametes, which are produced by an in vitro fertilization system (Uchiumi et al., 2006; Uchiumi et al., 2007). The present protocol will be applied for monitoring nuclear dynamics in cells during cell division, differentiation, de-differentiation and polarity formation as well as karyogamy progression.