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Past Issue in 2014
Volume: 4, Issue: 15
Biochemistry
Quantitative Analysis of Cellular Diacylglycerol Content
Diacylglycerol (DAG) is a bioactive lipid with diverse biological roles. DAG transiently accumulates in a membrane upon receipt of an appropriate stimulus that activates phospholipase C to cleave phospholipids. The resulting hydrolysis product DAG binds to proteins such as protein kinase C to initiate a variety of downstream cellular processes. DAG kinases attenuate such responses by converting DAG to phosphatidic acid.This protocol describes an assay designed to quantify cellular DAG levels. The assay exploits the enzymatic conversion of DAG (sn-1,2-diacylglycerol) to phosphatidic acid (1,2-diacyl- sn-glycerol-3-phosphate) in conjunction with the incorporation of a radiolabeled phosphate group by DAG kinase (Figure 1). This assay was described in (Strijbis et al., 2013).
Immunology
Generation and Maturation of Human Monocyte-derived DCs
Dendritic cells (DC) are antigen-presenting cells, which play a critical role in the regulation of the adaptive immune response. They act as a bridge between the innate and the adaptive immune systems. An approach to study their function and potentiality is to generate DC-like cells by culturing CD14+ monocyte-enriched peripheral blood mononuclear cells (PBMC). In the presence of GM-CSF and IL-4, these cultures give rise to large numbers of DC-like cells. Generating human-DC from PBMC is a useful tool to study biological functions of human DC.
Microbiology
Purification of Herpesvirus Virions and Capsids
This protocol was designed for large-scale purification of herpesvirus particles by cell culture. Virions and capsids are isolated from extracellular culture media and cell nuclei, respectively. Purity and concentration of the purified samples are usually sufficient for structural studies with cryo electron microscopy and cryo electron tomography. The protocol should also be generally suitable for purifying herpesvirus virions and capsids for other types of studies.
Fluorometric Estimation of Viral Thermal Stability
Differential Scanning Fluorimetry (DSF) is a rapid, economical, and a straightforward technique for estimating the thermal stability of proteins. The principle involves the binding of a fluorescent dye to thermally exposed hydrophobic pockets of a protein. The dyes used in this technique are highly fluorescent in a non-polar environment and are quenched when exposed to aqueous solution. The change in fluorescence can be used to follow unfolding of proteins induced by temperature, pH, or chaotropic agents. The method is well characterized for monomeric proteins. Here, we extend the application to supramolecular protein and nucleo-protein complexes using virus particles as an example. SYPRO-orange™ dye is the dye of choice because it is matched for use with q-PCR instruments and the fluorescence response is stable across a wide range of pH and temperatures. Advantages of this technique over standard biophysical methods include the ability for high-throughput screening of biological and technical replicates and the high sensitivity.
Infectious Virus Yield Assay for Hepatitis E Virus
Hepatitis E virus (HEV) is one of the main causes of acute hepatitis worldwide. Infections are particularly severe in pregnant women and chronic hepatitis E is known to occur in immunocompromised patients. Current therapy (ribavirin or pegylated alpha interferon) has severe side effects and cannot be employed in all patients. In order to evaluate potential new inhibitors of HEV replication, a virus yield assay can be employed in which the amount of viral RNA progeny released into the culture medium is quantified by reverse-transcription quantitative PCR (RT-qPCR) (Debing et al., 2014).
Quantification of Flavin Production by Bacteria
This protocol provides a simple and fast method of quantification for intracellular flavin content, and for flavin secretion by bacteria. Intracellular flavins are extracted from bacterial pellets, and secreted flavins are examined in the cell growth medium. Flavins are separated and measured using HPLC with fluorescence detection, and quantified based on a comparison to standards.
Luminescence-based Antiviral Assay for Hepatitis E Virus
Hepatitis E virus (HEV) is one of the main causes of acute hepatitis worldwide. Infections are particularly severe in pregnant women and chronic hepatitis E is known to occur in immunocompromised patients. Current therapy (ribavirin or pegylated alpha interferon) has severe side effects and cannot be employed in all patients. In order to evaluate potential new inhibitors of HEV replication, a luminescence-based replicon assay is particularly useful since it offers a rapid read-out and does not pose any biosafety risks (Debing et al., 2014).
Assay for GTP Cyclohydrolase II Activity in Bacterial Extracts
Riboflavin is the precursor of flavin nucleotides FMN and FAD, they play significant roles in all organisms. GTP is the initial precursor on riboflavin biosynthesis pathway and GTP cyclohydrolase II catalyzes the first step of this pathway. It converts GTP to 2,5-diamino-6-ribosylamino-4 (3H) -pyrimidinone 5'-phosphate. This protocol provides a reliable and fast method to assay GTP cyclohydrolase II activity from crude bacterial extracts. The product of the reaction catalyzed by GTP cyclohydrolase II, 2,5-diamino-6-ribosylamino-4 (3H) -pyrimidinone 5'-phosphate, is converted to its fluorescent derivative 6,7-dimethylpterin, which is then separated on a XTerra MS C18 column and detected using fluorescence HPLC system.
Plant Science
DNA Fragmentation Analysis
DNA fragmentation with length corresponding to multiple integer of approximately 180 base pairs is a distinct feature of apoptosis in animals and programmed cell death in plants. This feature can simply be detected by DNA gel electrophoresis followed by ethidium bromide staining, although in some cases it is difficult to distinguish the DNA laddering. We herein describe a protocol to detect a programmed cell death-associated DNA laddering of plant tissues. After agarose-gel electrophoresis of genomic DNA, Southern hybridization using DIG-labeled genomic DNA probe is performed, that improves detection of DNA laddering.
Floral Dip Transformation in Lepidium campestre
Floral dip is a very common technique to stably transform Arabidopsis thaliana (Clough and Bent, 1998; Martinez-Trujillo et al., 2004; Zhang et al., 2006) and has also been adapted to some other plant species (Curtis and Nam, 2001; Tague, 2001; Bartholmes et al., 2008). Here, we describe this method optimized for transformation of the Brassicaceae plant Lepidium campestre (L. campestre).
Isolation of Tomato Fruit Chromoplasts and Determination of ATP Levels
It has recently been reported that tomato fruit chromoplasts can synthesize ATP de novo using an ATP synthase complex harboring an atypical γ-subunit which is also present in a variety of plant species. However many aspects related with the biochemical processes underlying this process remain largely unknown. Here we describe detailed protocols for the isolation of tomato fruit chromoplasts and the determination of ATP levels (end-point measurements) and ATP synthesis rates (kinetic measurements) in these organelles using bioluminescent luciferin/luciferase based assays.
Quantifying Fruit Dehiscence Using the Random Impact Test (RIT)
Fruit dehiscence is an important evolutionary and agronomic trait. For quantifying and comparing the exact fruit dehiscence capability between individual plants, the random impact test has been described (Morgan et al., 1998; Bruce et al., 2002; Arnaud et al., 2010). Here, we describe the random impact test optimized to measure dehiscence capability in the Brassicaceae plant Lepidium campestre (L. campestre). However, with slight alterations regarding agitation force, agitation time, and drying conditions, the test should be applicable to a wide range of plant species with dehiscent fruits.