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Past Issue in 2016
Volume: 6, Issue: 13
Biochemistry
An Improved and Simplified Radial Gel Diffusion Assay for the Detection of Xylanase Activity
Xylanase (E.C. 3.2.1.8) degrades β-1, 4 xylan by cleaving β-1, 4 glycosidic linkages randomly, resulting in the generation of xylose and xylo-oligosaccharides. Xylanases are produced by organisms including fungi, bacteria, yeast, marine algae, protozoans, snails, crustaceans and insects. Xylanases present considerable industrial interest for their use in paper manufacturing, improvement of animal feed digestibility, and clarification of fruit juices. In addition, this enzyme is the component of cell wall-degrading enzymes (CWDEs) during plant–pathogen interaction. Thus, considering their various applications in plant defence and also in industry, the characterization of xylanase activity becomes an important aspect. Conventionally, xylanase activity is determined by radial gel diffusion assay using Congo red staining (Emami and Hack, 2001) and by DNSA assay which is a colorimetric method for xylanase activity (McLauchlan et al., 1999; Kutasi et al., 2001). Comparatively, radial gel diffusion assay using Congo red staining is a qualitative assay whereas DNSA method is a quantitative assay. Moreover, Congo red is a chemical considered as hazardous category 1B (Carcinogenicity) and category 12 (Reproductive toxicity) by the 2012 OSHA Hazard Communication Standard (29 CFR 1910.1200). In the present study, the proposed method enables qualitative detection of xylanase activity using ethanol precipitation in the radial gel diffusion assay which is safer and simpler. The ethanol precipitation in agar plate has been adapted from the method for detecting xylanase activity in polyacrylamide gels (Royer and Nakas, 1990).
Cancer Biology
High Fat Diet-induced Breast Cancer Model in Rat
Obesity has been linked to breast cancer progression but the underlying mechanisms remain obscure. Being overweight or obese for a woman at the time she is diagnosed with breast cancer is linked to a high risk of recurrence regardless of treatment factors. In rodents, high body weight is also associated with increased incidence of spontaneous and chemically induced tumors. To study the complex interaction between the mammary epithelia and the microenvironment, with a focus on the mechanism underlying the role obesity plays in the regulation of the cancer stem cell traits and the development of mammary cancer in vivo, we have established a diet-induced obesity (DIO) rat model of breast cancer (Chang et al., 2015).
Cell Biology
Isolation and Primary Culture of Adult Mouse Cardiac Fibroblasts
Fibroblasts are often used as a feeder layer for progenitor or stem cells in co-culture systems. In the heart fibroblasts are important for cardiac development, homeostasis, and remodelling. They provide cardiomyocytes and progenitor cells not only with nutrition but also secrete extracellular matrix that forms the microenvironment that ensures cell survival and function. Although different kinds of mouse fibroblasts have been used in co-cultures (embryonic, skin and cardiac fibroblasts) adult mouse cardiac fibroblasts (AMCFs) create the closest microenvironment to the adult murine heart for culturing adult mouse cardiac progenitor cells. This protocol describes the isolation of cardiac fibroblasts from adult mouse hearts as well as their maintenance in culture.
T Cell Transfer Model of Colitis
Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC) is mainly caused by disordered immune regulation and dysregulated intestinal microbiota. Here we present the T cell transfer model which has extensively used in many studies to identify the regulatory T cell function in gut inflammation. Naïve T cells only or together with Treg cells isolated from different donors were transferred into immunodeficient Rag1-/- mice and the disease progression was assessed by the loss of body weight and the scoring analysis. This model provides a reliable work system for the study of gut inflammation.
Subchromoplast Fractionation Protocol for Different Solanaceae Fruit Species
Macromolecules, proteins, lipids, and other small molecules, such as carotenoids can be studied within different tissues and organelles using an array of in vitro and in vivo methodologies. In the case of tomato and other fleshy fruit the predominant organelle in ripe fruit is the chromoplast. The characteristic feature of this organelle is the presence of pigments, carotenoids at high levels. In order to fully understand the underlying biological mechanisms that operate within the chromoplast, it is necessary to perform studies at the subchromoplast level. This protocol allows the separation of plastoglobules (lipoprotein particles, which are coupled to thylakoid membranes in the chloroplasts) and membranes (thylakoid, envelope-like) of chromoplasts through a sucrose gradient. The subchromoplast compartments can then be analysed independently. Comparisons between mutant/transgenic genotypes and their backgrounds can be performed accurately with simultaneous processing during the same fractionation run. The procedure was initially developed for ripening tomato fruit but translation to sweet and hot pepper has been shown.
Developmental Biology
Aorta Ring Assay
Angiogenesis is the nature and pathological process of blood vessel growth from pre-existing vascular buds. It plays an important role in cancer and cardiovascular disease. The aorta ring assay is an approach to study angiogenesis. In this experiment, we used the aorta of rat as the study material, cleaned the surrounding tissue of aorta and cut it into 1 mm long rings. Next, the rings were cultured in growth factor-reduced matrigel polymerized at 37 °C. Angiogenesis was assessed at 7 days by using an inverted microscope platform.
Immunology
Mouse Embryonic Fibroblast Cell Culture and Stimulation
Culture of mouse embryonic fibroblast (MEF) cells represents a powerful system to test gene function due to their easy accessibility, rapid growth rates, and the possibility of a large number of experiments. Fibroblasts are a group of heterogeneous resident cells of mesenchymal origin that have various locations, diverse appearances and distinctive activities. Because of their ubiquitous distribution as tissue cells, these cells are poised to respond to factors released by newly activated innate immune cells, thus becoming a useful tool to study inflammation and immunity. Here, we describe procedures for mouse embryonic fibroblast cell isolation, primary culture, and stimulation. Specifically, we have optimized a step of serum starvation prior to stimulation. This step is necessary to maintain the quiescent status of these cells before they are exposed to pro-inflammatory stimuli for optimal responses. As shown in our previous studies, these mouse fibroblasts do not express Tnf, Csf2 or Il2 mRNAs at levels readily detectable by routine northern blotting techniques (Lai WS et al., 2006).
Measurement of mRNA Decay in Mouse Embryonic Fibroblasts
mRNA stability control is a critical step in the post-transcriptional regulation of gene expression. Actinomycin D, an antibiotic initially used as an anti-cancer drug, has turned out to be a convenient tool for studying the turnover rates of transcripts in cells, due to its inhibition of mRNA synthesis. Here, we describe a protocol for the measurement of mRNA decay after adding actinomycin D into the medium of stable fibroblast cell lines derived from wild-type and tristetraprolin (TTP)-deficient mouse embryonic fibroblast (MEF) cultures, as well as a protocol for determining the relative transcript abundance using semi-quantitative real-time RT-PCR. Northern blotting or NanoString n-Counter are alternative methods to measure mRNA abundance, which is quantified using a phosphorimager in the former case. This protocol is suitable for studying primary cultured cells and stable cell lines derived from transgenic mice and their respective controls, and provides for direct comparisons of mRNA decay rates in otherwise identical cells with and without the gene of interest.
Molecular Biology
Estimation of the Chromosomal Copy Number in Synechococcus elongatus PCC 7942
Cyanobacteria are prokaryotic organisms that perform oxygenic photosynthesis. Freshwater cyanobacteria, such as Synechococcus elongatus PCC 7942 and Synechocystis sp. PCC 6803, are model organisms for the study of photosynthesis, gene regulation, and biotechnological applications because they are easy to manipulate genetically. However, while studying these cyanobacteria, care has to be taken with respect to genetic heterogeneity in the establishment of gene disruptants, because these cyanobacteria contain multiple chromosomal copies per cell. Here, we describe a method for the estimation of chromosomal copy number in Synechococcus 7942. Using this method, we have recently observed that the chromosomal copy number of Synechococcus 7942 significantly changes during its growth phases. This technique is available for studying polyploidy not only in cyanobacteria, but also in other polyploid organisms.
Neuroscience
Locomotion Activity Measurement in an Open Field for Mice
The Open Field (OF) paradigm is one of the most known primary behavioral tests to evaluate locomotion and exploration. Altered OF behaviour is relatively simple to observe, but understanding and explaining the reasons for the observed changes is a complex task. Generally, there are two factors, which determine the behavior in this paradigm; one, a positive exploratory drive originating from the nature of rodents to explore new environments (for food and shelter); and two, the animal nature of avoiding open and brightly lit spaces (exposure to predators).OF measures locomotor activity, exploratory drive, neophobia and certain aspects of anxiety in rodents at the same time. Furthermore, one can differ between horizontal and vertical activities (number of rearings) in the OF. After all, an altered OF behavior might come from the alterations of all of the above mentioned measures. For the proper interpretation of experimental results one has to be careful.With the aid of the present protocol we investigated the effect of systemic L-kynurenine sulphate on open field behavior of adult male C57Bl/6j mice (Varga et al., 2015).
Denervation of Mouse Lower Hind Limb by Sciatic and Femoral Nerve Transection
The requirement and influence of the peripheral nervous system on tissue replacement in mammalian appendages remain largely undefined. Reports from salamander models of appendage regeneration (Singer, 1952; Singer, 1947; Kumar et al., 2007), and of human clinical skin and nail problems associated with spinal cord injury patients (Stover et al., 1994) suggest that appendage regeneration may have an important nerve component. To explore this question, we have generated hind limb tissues devoid of nerve supply. This protocol, combined with multi-color ‘Rainbow’ reporter mouse lines permits single cell clonal analysis and genetic lineage tracing studies in the absence of nerve supply (Rinkevich et al., 2014), exposing nerve requirements on cellular replacement and differentiation during tissue growth, maintenance, and regeneration.
Plant Science
Indirect Immunofluorescence Assay in Chlamydomonas reinhardtii
Determining the protein localization is essential to elucidate its in vivo function. Fluorescence-tagged proteins are widely used for it, but it is sometimes difficult to express tagged proteins in Chlamydomonas. Alternatively, indirect immunofluorescence assay is also one of the widely used methods and many reports determining the localization of Chlamydomonas proteins using this method are published. Here, we introduce a protocol of indirect immunofluorescence assay adapted from our papers reporting LCIB (CO2-recycling factor in the vicinity of pyrenoid; Yamano et al., 2010), LCI1 (plasma membrane-localized inorganic carbon transporter; Ohnishi et al., 2010), HLA3 (plasma membrane-localized ABC-type bicarbonate transporter; Yamano et al., 2015), and LCIA (chloroplast envelope anion channel; Yamano et al., 2015) in Chlamydomonas reinhardtii. The protocol described here could be useful for observing the protein of interest in other algae cells.
Chromosome Dosage Analysis in Plants Using Whole Genome Sequencing
Relative chromosome dosage, i.e., increases or decreases in the number of copies of specific chromosome regions in one sample versus another, can be determined using aligned read-counts from Illumina sequencing (Henry et al., 2010). The following protocol was used to identify the different classes of aneuploids that result from uniparental genome elimination in Arabidopsis thaliana, including chromosomes that have undergone chromothripsis (Tan et al., 2015). Uniparental genome elimination results in the production of haploid progeny from crosses to specific strains called “haploid inducers” (Ravi et al., 2014). On the other hand, chromothripsis, which was first discovered in cancer genomes, is a phenomenon that results in clustered, highly rearranged chromosomes. In plants, chromothripsis has been observed as a result of genome elimination (Tan et al., 2015). Detecting variation in chromosome dosage has multiple applications beside those linked to genome elimination. For example, a dosage variant population of poplar hybrids was created by gamma-irradiation of pollen grains. Hundreds of dosage lesions, insertions and deletions, were identified using this technique and provide a way to associate loci with the phenotypic consequences observed in this population (Henry et al., 2015).This method has been successfully used to detect changes in chromosome dosage in many different species, including Arabidopsis thaliana (Tan et al., 2015), Arabidopsis suecica (Ravi et al., 2014), rice (Henry et al., 2010) and poplar (Henry et al., 2015). It is important to note that dosage plots always indicate dosage variation relative to the control sample used (Note 1). Therefore, this approach is not suitable to detect ploidy variants (diploid vs triploid, for example). Similarly, this technique does not allow the detection of balanced chromosomal rearrangements such as reciprocal translocations.
Identification of Natural Hybrids by SSR Markers in Mussaenda
Detection of natural hybrids is of great significance for plant taxonomy, reproductive biology, and population genetic studies. Compared with methods depending on morphological characters, molecular markers provide reliable and much more accurate results. This protocol describes approaches employing microsatellite (SSR) markers to identify inter-specific hybrids in Mussaenda (Rubiaceae).
Stem Cell
Retinal Differentiation of Mouse Embryonic Stem Cells
Groundbreaking studies from Dr. Yoshiki Sasai’s laboratory have recently introduced novel methods to differentiate mouse and human Embryonic Stem Cells (mESCs and hESCs) into organ-like 3D structures aimed to recapitulate developmental organogenesis programs (Eiraku et al., 2011; Eiraku and Sasai, 2012; Nakano et al., 2012; Kamiya et al., 2011). We took advantage of this method to optimize a 3D protocol to efficiently generate retinal progenitor cells and subsequently retinal neurons in vitro. This culture system provides an invaluable platform both to study early developmental processes and to obtain retinal neurons for transplantation approaches. The protocol described here has been successfully applied to several mouse ESC (including the R1, WD44 and G4 cell lines) and mouse induced-Pluripotent Stem Cell (iPSCs) lines.