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Past Issue in 2013
Volume: 3, Issue: 23
Cancer Biology
Longitudinal Bioluminescent Quantification of Three Dimensional Cell Growth
The use of three-dimensional (3D) cell culture systems is widely accepted as representing a more physiologically relevant means to propagate mammary epithelial and breast cancer cells. However, 3D cultures systems are plagued by several experimental and technical limitations as compared to their traditional 2D counterparts. For instance, quantifying the growth of mammary epithelial or breast cancer organoids longitudinally is particularly troublesome using standard [3H]thymidine or MTT assay systems, or using computer-assisted area calculations. Likewise, the nature of the multicellular aggregates and organoids formed by breast cancer cells under 3D conditions precludes efficient recovery of the cells from 3D matrices, an event that is time consuming and leads to spurious results. The assay described here utilizes stable expression of firefly luciferase as means to quantify the longitudinal outgrowth of cells propagated within a 3D matrices. The major advantages of this technique include its high-throughput nature and ability to longitudinally track single wells over a defined period of time, thereby decreasing the costs associated with assay performance. Finally, this technique can be readily combined with drug treatments and/or genetic manipulations to assay their effects on the growth of 3D organoids.
Cell Biology
Mitochondrial Transmembrane Potential (ψm) Assay Using TMRM
During cellular respiration, nutrients are oxidized to generate energy through a mechanism called oxidative phosphorylation, which occurs in the mitochondria. During oxidative phosphorylation, the gradual degradation of molecules through the TCA cycle releases electrons from the covalent bonds that are broken. These electrons are captured by NAD+ through its reduction into NADH. Finally, NADH transports the electrons to the complexes of the electron chain in the internal membrane of mitochondria. These complexes use the energy released by the electrons to pump protons into the intermembrane space, generating an electrochemical gradient across the internal membrane of mitochondria, which provides energy for the ATP-synthase complex, ultimately producing adenosine triphosphate (ATP). We assessed the mitochondrial membrane potential (ψm) using tetramethylrhodamine methyl ester (TMRM), a cell-permeant, cationic, red fluorescent dye. To measure specifically the mitochondrial membrane potential (ψm) we quantified the fluorescence intensity before and after applying FCCP, a mitochondrial electron chain uncoupler. The difference of intensity before and after applying FCCP corresponds specifically to the mitochondrial membrane potential. We analyzed mitochondrial membrane potential (ψm) by cytofluorimetry. The ratio between the total level of signal and the signal generated after uncoupling provided a normalized value for the difference in cell size. Furthermore, to normalize for the different size of cells that we were analyzing we have analyzed TMRM in live imaging using IN Cell Analyzer, so that the level of mitochondrial membrane potential could be detected per unit of mitochondrial membrane area measured. Thus, our protocol can also be used to compare the mitochondrial membrane potential of cells that are different in size.
ATP and Lactate Quantification
Cells use glucose to generate energy by two different metabolic processes: lactic fermentation and aerobic respiration. In the first common series of reactions, glucose is converted into pyruvate. In anaerobic conditions, pyruvate is transformed into lactate, this process yields to 2 ATP molecules per glucose molecule. In the presence of oxygen, pyruvate is imported into mitochondria where it is used in the Krebs (or TCA) cycle and oxydative phosphorylation. The global process of oxydative phosphorylation yields to 32 ATP per glucose molecule. For reasons not fully understood, in some pathological cases like cancer, cells use anaerobic glycolysis even in the presence of oxygen, in which case the process is called aerobic glycolysis (or Warburg effect). This results in an increased uptake of glucose and lactate production. Measure of intracellular ATP content and lactate concentrations can provide a readout of aerobic glycolyis.
Isolation of CD34+ Cells from Human Fetal Liver and Cord Blood
CD34 is a glycosylated cell surface protein and represents a well-known marker for primitive progenitor cells in various organs, especially cord blood, bone marrow and fetal liver. CD34+ progenitor cells are suitable for a series of studies, e.g. cell differentiation, transplantation as well as construction of humanized mouse models. Here, we describe a method to isolate CD34+ cells from the human cord blood and fetal liver.
Developmental Biology
Acquisition of Leftward Flow in Xenopus laevis
In Xenopus, the left-right axis is established following an extracellular vectorial leftward flow driven by monocilia at the gastrocoel roof plate (GRP) during late gastrulation / neurulation (Schweickert et al., 2007). As the GRP lies inside the developing archenteron, imaging of flow is challenging. Here we present the detailed procedure to visualize leftward flow in Xenopus laevis embryos.
Immunology
Determination of the Intracellular Calcium Concentration in Peritoneal Macrophages Using Microfluorimetry
Calcium is one of the most important intracellular messengers in biological systems. Ca2+ microfluorimetry is a valuable tool to assess information about mechanisms involved in the regulation of intracellular Ca2+ levels in research on cells and in living tissues. In essence, the use of a dye that fluoresces in the presence of a target substance allows the detection of changes in the concentration of this molecule by determining the changes in the fluorescence of the probe (increases or decreases, depending on the nature of the dye used; for a review see Tsien et al. 1985). In this regard, there have been developed two different methodologies to assess intracellular Ca2+ measurements. On the one hand, ratiometric methods are based on the use of a ratio between two fluorescence intensities linked to the physicochemical properties of the probe. This allows correction of artifacts due to bleaching, changes in focus, variations in laser intensity, etc. but makes measurements and data processing more complicated since they require more expensive equipment with the possibility to change the wavelength emission/detection in a rapid way. Some ratiometric Ca2+ indicators are Fura-2 and Indo-1. On the other hand, on binding to Ca2+, indicators used for non-ratiometric measurements show a shift in their fluorescence intensity (the free indicator has usually a very weak fluorescence). Therefore, although an increase in fluorescence signal can be related directly to an increase in Ca2+ concentration, the fluorescence intensity depends on many factors such as acquisition conditions, probe concentration, optical path length, balance between the affinity constants of proteins binding Ca2+, among others. However, the fluxes of Ca2+ are of such a magnitude that these interferences are minor contributors to biases in the measurements. There are many non-ratiometric calcium indicators, some of which are Fluo-3, Fluo-4 and Calcium-Green-3. Consequently, the most suitable Ca2+-probe for each experiment will depend on the range of Ca2+ concentration that has to be evaluated, instrumentation, loading requirements, etc. In the present report we describe the protocol employed to quantify intracellular Ca2+ changes in peritoneal macrophages using Fura-2 as a fluorimetric probe and a microfluorimetric protocol that allows quantification of responding cells to a given stimulus, localization of the main intracellular domains sensing Ca2+ changes and a time-resolved analysis of the Fura-2 fluorescence that reflects the intracellular dynamics of Ca2+ in these cells (Través et al., 2013).
Escherichia coli Outer Membrane Vesicle Immunization Protocol and Induction of Bacterial Sepsis
Outer membrane vesicles (OMVs) are spherical bilayered phospholipids of 20-200 nm in size produced from all Gram-negative bacteria and Gram-positive bacteria investigated to date. OMVs, which resemble the outer membrane and periplasm in composition, are proinflammatory and immunogenic facsimiles, and therefore could activate both innate and adaptive immunity. Here, we describe the OMVs immunization protocol and bacteria challenge protocol to induce bacterial sepsis in mice.
Purification of Human Monocytes and Lymphocyte Populations by Counter Current Elutriation – A Short Protocol
Investigations of the activation processes involved in human monocytes and monocyte-derived macrophages and dendritic cells often required large numbers of cells that have not been possibly altered or activated by adherence to surfaces, by binding of antibodies to surface antigens during positive selection, or by release of activators by platelets or other non myeloid cells during isolation or co-culture. Human peripheral blood monocytes as well as lymphocytes from the same blood donor can be isolated by counterflow elutriation using a modification of the technique of Lionetti et al. (1980) as described previously (Bobak et al., 1986). From a unit of blood drawn into anticoagulant, 60-120 million monocytes can be obtained. These cells are not activated and have been shown to be appropriately capable of differential activation in multiple studies.
Chitinase Assay from Cultured Bone Marrow Derived Macrophages
Chitinases are chitin-degrading enzymes. Chitinases play essential roles in combating chitin-containing pathogens as well as established roles in asthmatic inflammation. This assay is designed to detect chitinase activity in macrophage cell lysates. The chitin substrate is labeled with 4-methylumbelliferone. Hydrolysis of chitin releases 4-methylumbelliferone, and is measured fluorometrically to determine chitinase activity.
Microbiology
Preparation of Outer Membrane Vesicle from Escherichia coli
Outer membrane vesicles (OMVs) are spherical bilayered phospholipids of 20-200 nm in size produced from all Gram-negative bacteria and Gram-positive bacteria investigated to date. Previous biochemical and proteomic studies have revealed that the Gram-negative bacteria-derived OMVs are composed of various components like outer membrane proteins, lipopolysaccharides, outer membrane lipids, periplasmic proteins, DNA, and RNA. Here, in this protocol, we describe the method to isolate the OMVs from the culture supernatant of Escherichia coli (E. coli).
Adherent-invasive Escherichia coli Biofilm Formation Assays
Patients with Crohn’s disease are abnormally colonized by adherent-invasive Escherichia coli (AIEC) bacteria (Chassaing and Darfeuille-Michaud, 2011). These bacteria are able to adhere to and invade intestinal epithelial cells (IEC), to replicate within macrophages, and were recently described to be able to form biofilms (Martinez-Medina et al., 2009; Chassaing and Darfeuille-Michaud, 2013). The reference strain of adherent-invasive E. coli is the strain LF82, associated with ileal Crohn’s disease (Darfeuille-Michaud et al., 1998).This protocol described basic steps of a biofilm formation assay on I) non-cell-treated polystyrene microtiter plates and on II) paraformaldehyde-fixed I-407 IEC monolayers.
Burkholderia glumae Competent Cells Preparation and Transformation
Bukholderia glumae is a gram-negative bacterium which causes grain rot, seedling rot and panicle blight in rice and bacterial wilt in many field crops. This bacterium has been reported from major rice growing regions around the world and is now considered as an emerging major pathogen of rice (Tsushima et al., 1996; Jeong et al., 2003; Kim et al., 2010; Ham et al., 2011). Here we describe two methods for competent cells preparation and transformation of B. glumae. Using these methods, we have applied effector detector system (Sohn et al., 2007) to B. glumae (Sharma et al., 2013).
Neuroscience
Preparation of Primary Neurons from Rat Median Preoptic Nucleus (MnPO)
Studying cell physiology is really important to understand their function and to determine action mechanisms taking place in these cells. Using brain slices can be sometime difficult to directly access to cells like neurons. Even if it more steps are needed to get cultured cells, this type of preparation allow a better access to neurons and provide a good way to study their basal properties. Here we describe a protocol of a short term primary neurons culture from MnPO, allowing to kept neurons in good condition to perform electrophysiological recordings.
Autoradiographic 3H-Gaboxadol Receptor Binding Protocol
Gaboxadol (4,5,6,7-tetrahydroisoxazolo[5,4-c]pyridin-3-ol, THIP), a GABAA receptor δ-subunit specific agonist, when present at low (μM) concentrations, preferentially binds and activates extrasynaptic (non-γ2, δ-subunit-containing) GABAARs (Storustovu and Ebert, 2006; Richardson et al., 2011, 2013). In this prototype saturation binding experiment, a series of concentrations of [3H]gaboxadol (5, 10, 25, 50, 75, 100, 250 and 400 nM) will be used. GABA at 200 μM will be added into binding mixtures as a cold displacer for [3H]gaboxadol. Slide mailers are used and each requires 7 ml binding mixture. Pre-, post-washing and binding buffer is 50 mM Tris-Citrate (pH 7.1). The detailed procedure is outlined below.
Plant Science
Measurement of Potassium Content in Arabidopsis
Potassium is an essential element in plant growth and has an important role in regulating cell water potential and turgor in osmotic regulation. Potassium content in plants is high compared to trace elements, however, it is difficult to measure a relatively small change of potassium content in the large total. Here, we describe a procedure for measuring potassium in Arabidopsis that is easy to handle in preparative scale and avoids contamination.
Stem Cell
Serial Transfer of Human Hematopoietic and Hepatic Stem/progenitor Cells
A range of assays have been developed to determine the stemness or stem cell activity of human stem cells. The key assays of stem cells are functional: they must show self-renewal and the ability to generate the appropriate tissue. The best assays available to study this property in putative human stem cells involve xeno-transplantation into immune-deficient mice. Demonstration of both long-term (2-3 months) multi-lineage reconstitution of human blood or liver in a murine host and the ability of the putative stem cells to mediate reconstitution of a secondary host upon re-isolation from the primary mouse are generally accepted as the gold standard for demonstrating the presence of human hematopoietic and hepatic stem cells. Here, we describe a method of reconstituting NOD-scid IL-2Rγ-/-(NSG) mice with CD34+ stem cells from human fetal liver and repurification of CD34+ cells for serial transplantation.