A PCR-based method for detection and quantification of small RNAs

Recent cloning efforts have identified hundreds of thousands of small RNAs including micro RNAs (miRNAs), Piwi-interacting RNAs (piRNAs), and small nucleolar RNAs (snoRNAs). These non-coding small RNAs need to be further validated and characterized by detecting and quantifying their expression in different tissues and during different developmental courses. A simple, accurate, and sensitive method for small RNA expression profiling is in high demand. Here, we report such a PCR-based method.     

A simple and novel method for recovering adenovirus 41 in small volumes of source water

Aim: A new procedure was developed to recover adenovirus 41 in small volumes (1 l) of water samples based on adsorption, elution and evaporation. Methods and Results: One litre of source water seeded with adenovirus 41 was adjusted to pH 3·5 and filtered using a large pore size (8·0 μm) negatively charged membrane filter (SCWP, 47 mm diameter, made of mixed‐cellulose esters). Then, the filter was eluted using 4 ml of 1·5% beef extract plus 0·75% glycerol (pH 9·0). The eluate was reconcentrated to 0·1 ml or less volumes through evaporation assisted with air flow and heating at 55°C. Recovery of adenovirus 41 reached 55% under tested conditions and reduced filtration time by 85% in contrast to the widely used small pore size filter (0·45 μm pore size, 47 mm diameter). Reconcentration by evaporation achieved approx. 86·8% recovery from source water in approx. 1 h at no cost. Conclusion: The virus concentration method developed in this study is simple and cost‐effective and can be used to efficiently recover adenovirus 41 from turbid water samples. Significance and Impact of the Study: The procedure developed can be applied to detect adenovirus 41 in source water within hours of sampling. In addition, this is the first application of evaporation to concentrate viruses in water samples.     

A simple method for hyaluronic acid quantification in culture broth

The carbazole assay has been used for determination of the percentage of hyaluronic acid in biological fluids. However, it is difficult to measure the concentration of hyaluronic acid in culture broth because glucose and polysaccharides remaining after cultures can react with sulfuric acid and carbazole. The glucose and polysaccharide remnants must be completely removed in order to get the correct value for hyaluronic acid. The turbidity assay, another method for estimating the concentration of hyaluronic acid, is based on the formation of insoluble complexes between hyaluronic acid and cetyltrimethylammonium bromide. This method is very easy and fast compared with the carbazole assay. Because concentrations of hyaluronic acid measured by the turbidity assay were ranged around 100% of those measured by the carbazole assay, the content of hyaluronic acid in culture broth can be determined by the turbidity assay. The turbidity method also has the advantage of being safer than the carbazole assay.     

A novel method for characterisation and quantification of plant root exudates

A microcosm unit is described which readily allows manipulation of experimental conditions to enable the subsequent impact on root exudation release to be monitored with time. Festuca ovina and Plantago lanceolata seedlings were grown in this microcosm unit over a 34 day experimental period under conditions of high (3.75 mol m^–3 N) or low (1.25 mol m^–3 N) nitrate-nitrogen treatment. At the end of the experimental period the seedlings in the microcosms were labelled with [¹⁴C]-CO₂ and the fate of the label within the plant and its release by the roots monitored. Total organic carbon (TOC) content of the collected exudate material was measured throughout the experimental period as well as during the ¹⁴C-chase period and comparison of plant C budgets using these two measurements is discussed. Nitrogen treatment as found to have a greater effect on exudate release by F. ovina than by P. lanceolata seedlings as indicated by both the total organic carbon and ¹⁴C results. The use and applications of the microcosm unit are discussed.     

A novel and simple method for construction of recombinant adenoviruses

Recombinant adenoviruses have been widely used for various applications, including protein expression and gene therapy. We herein report a new and simple cloning approach to an efficient and robust construction of recombinant adenoviral genomes based on the mating-assisted genetically integrated cloning (MAGIC) strategy. The production of recombinant adenovirus serotype 5-based vectors was greatly facilitated by the use of the MAGIC procedure and the development of the Adeasy™ adenoviral vector system. The recombinant adenoviral plasmid can be generated by a direct and seamless substitution, which replaces the stuff fragment in a full-length adenoviral genome with the gene of interest in a small plasmid in Escherichia coli. Recombinant adenoviral plasmids can be rapidly constructed in vivo by using the new method, without manipulations of the large adenoviral genome. In contrast to other traditional systems, it reduces the need for multiple in vitro manipulations, such as endonuclease cleavage, ligation and transformation, thus achieving a higher efficiency with negligible background. This strategy has been proven to be suitable for constructing an adenoviral cDNA expression library. In summary, the new method is highly efficient, technically less demanding and less labor-intensive for constructing recombinant adenoviruses, which will be beneficial for functional genomic and proteomic researches in mammalian cells.     

A novel and simple method for endotracheal intubation of mice

Endotracheal intubation in mice is necessary for experiments involving intratracheal instillation of various substances, repeated pulmonary function assessments and mechanical ventilation. Previously described methods for endotracheal intubation in mice require the use of injection anaesthesia to immobilize the animal during the intubation procedure or the use of a volatile anaesthetic prior to intubation for immobilization. With these methods, the control of anaesthetic depth during the intubation procedure is absent. We describe a method for simple and rapid intratracheal intubation in mice for mechanical ventilation, using a self-built plastic support to facilitate the intubation procedure. General anaesthesia is maintained by means of inhalation through a non-rebreathing circuit connected to the plastic support. This set-up gives the operator control of anaesthetic depth and sufficient time to perform the intubation procedure. A purpose-made laryngoscopic blade is used to facilitate the intubation tube entering the trachea. The blade of the purpose-made laryngoscope is constructed as a retraction guide and is curved for easy handling. Under direct vision, the epiglottis is gently lifted by the laryngoscopic blade while the intubation tube is pushed into the trachea. Following this novel intubation technique, we were able to mechanically ventilate mice for at least 2 h without severely disturbing blood gases. Histological evaluation of the lungs and microscopic evaluation of the trachea and larynx showed no signs of trauma related to the intubation technique or mechanical ventilation.     

A novel, simple and rapid method for the isolation of mitochondria which exhibit respiratory control, from rat small intestinal mucosa

A method is described for the isolation of functional mitochondria from rat intestinal mucosa. Its novel feature is the removal of mucus from the initial homogenate by treatment with DEAE-cellulose. The preparations exhibited acceptable ADP:O ratios, high State-3 respiration rates, and respiratory control ratios in excess of 3 when succinate, beta-hydroxybutyrate, glutamate/malate and glutamine were test substrates.     

A simple method for the preparation of small unilamellar vesicles

A simple and quick method for the preparation of small unilamellar vesicles (SUV) was developed. SUV are spontaneously formed by swelling of the specially prepared phospholipid film in water/buffer. Normally, large multilamellar vesicles (MLV) are formed when a phospholipid film is dissolved in water. To prevent the formation of multilamellar structures we used the slightly charged phospholipids which exhibit infinite swelling while the formation of large structures was prevented by the deposition of the phospholipid film on the support with small surfaces. These two requirements were met by mixing a small amount of ionic detergent into phospholipid which was deposited on microcrystals. The size and size distribution of the produced vesicles depend on the size and homogeneity of the microcrystals. When 1.5 wt% of cetyltetramethylammonium bromide (CTAB) in egg yolk phosphatidylcholine was deposited on zeolite X microcrystals with crystallite sizes of approx. 0.4 μm a homogeneous population of vesicles with average diameter 21.5 nm was obtained.     

A simple and sensitive enzymatic method for cholesterol quantification in macrophages and foam cells

A precise and sensitive method for measuring cellular free and esterified cholesterol is required in order to perform studies of macrophage cholesterol loading, metabolism, storage, and efflux. Until now, the use of an enzymatic cholesterol assay, commonly used for aqueous phase plasma cholesterol assays, has not been optimized for use with solid phase samples such as cells, due to inefficient solubilization of total cholesterol in enzyme compatible solvents. We present an efficient solubilization protocol compatible with an enzymatic cholesterol assay that does not require chemical saponification or chromatographic separation. Another issue with enzyme compatible solvents is the presence of endogenous peroxides that interfere with the enzymatic cholesterol assay. We overcame this obstacle by pretreatment of the reaction solution with the enzyme catalase, which consumed endogenous peroxides resulting in reduced background and increased sensitivity in our method. Finally, we demonstrated that this method for cholesterol quantification in macrophages yields results that are comparable to those measured by stable isotope dilution gas chromatography with mass spectrometry detection. In conclusion, we describe a sensitive, simple, and high-throughput enzymatic method to quantify cholesterol in complex matrices such as cells.     

A simple method for high-throughput quantification of genome-wide DNA methylation by fluorescence polarization

To rapidly determine DNA methylation levels from a large number of biological or clinical samples, we have developed an accurate and sensitive method for high-throughput quantification of global methylation of 5′-Cm⁵CGG-3′ sites in the genome, visualized by fluorescence polarization (FP) based measurement of DNA methylation (FPDM). In FPDM, the methyl-sensitive HpaII and methyl-insensitive MspI restriction enzymes were employed to achieve DNA cleavage, followed by incorporation of fluorescent dCMP into the enzyme-cleavage products through polymerase chain extension, yielding an FP-ratio between the HpaII- and MspI-restricted preparations as a measure of methylation. FPDM provided stable estimates of methylation level of submicrograms of lambda or human DNA, and of a 255-bp DNA segment containing a single HpaII/MspI restriction site in accord with, and more accurate than, determination by gel electrophoresis. FPDM was also applied to measure dose-dependent DNA hypomethylation in human embryonic kidney 293T cells treated with the DNA-methyltransferase inhibitor 5-aza-dC.     

A novel truncated form of apolipoprotein A-I transported by dense LDL is increased in diabetic patients

Diabetic (DM) patients have exacerbated atherosclerosis and high CVD burden. Changes in lipid metabolism, lipoprotein structure, and dysfunctional HDL are characteristics of diabetes. Our aim was to investigate whether serum ApoA-I, the main protein in HDL, was biochemically modified in DM patients. By using proteomic technologies, we have identified a 26 kDa ApoA-I form in serum. MS analysis revealed this 26 kDa form as a novel truncated variant lacking amino acids 1-38, ApoA-IΔ(1-38). DM patients show a 2-fold increase in ApoA-IΔ(1-38) over nondiabetic individuals. ApoA-IΔ(1-38) is found in LDL, but not in VLDL or HDL, with an increase in LDL3 and LDL4 subfractions. To identify candidate mechanisms of ApoA-I truncation, we investigated potentially involved enzymes by in silico data mining, and tested the most probable molecule in an established animal model of diabetes. We have found increased hepatic cathepsin D activity as one of the potential proteases involved in ApoA-I truncation. Cathepsin D-cleaved ApoA-I exhibited increased LDL binding affinity and decreased antioxidant activity against LDL oxidation. In conclusion, we show for the first time: a) presence of a novel truncated ApoA-I form, ApoA-IΔ(1-38), in human serum; b) ApoA-IΔ(1-38) is transported by LDL; c) ApoA-IΔ(1-38) is increased in dense LDL fractions of DM patients; and d) cathepsin D-ApoA-I truncation may lead to ApoA-IΔ(1-38) binding to LDLs, increasing their susceptibility to oxidation and contributing to the high cardiovascular risk of DM patients.     

Phospholipase A2 and small, dense low-density lipoprotein

High levels of small, dense LDL in plasma are associated with increased risk for cardiovascular disease. There are some biochemical characteristics that may render small, dense LDL particles more atherogenic than larger, buoyant LDL particles. First, small, dense LDL particles contain less phospholipids and unesterified cholesterol in their surface monolayer than do large, buoyant LDL particles. This difference in lipid content appears to induce changes in the conformation of apolipoprotein B-100, leading to more exposure of proteoglycan-binding regions. This may be one reason for the high-affinity binding of small, dense LDL to arterial proteoglycans. Reduction of the phospholipid content in the surface monolayer LDL by treatment with secretory phospholipase A2 (sPLA2) forms small, dense LDL with an enhanced tendency to interact with proteoglycans. Circulating levels of sPLA2-IIA appears to be an independent risk factor for coronary artery disease and a predictor of cardiovascular events. In addition, in-vivo studies support the hypothesis that sPLA2 proteins contribute to atherogenesis and its clinical consequences. These data suggest that modification of LDL by sPLA2 in the arterial tissue or in plasma may be a mechanism for the generation of atherogenic lipoprotein particles in vivo, with a high tendency to be entrapped in the arterial extracellular matrix.     

A simple and accurate method for quantification of magnetosomes in magnetotactic bacteria by common spectrophotometer

A simple apparatus for measuring the magnetism of magnetotactic bacteria was developed with a common laboratory spectrophotometer, which was based on measuring the change in light scattering resulting from cell alignment in a magnetic field. A multiple coils were built around the cuvette holder of the spectrophotometer to compensate geomagnetic field and to generate two mutually perpendicular magnetic fields. In addition, we defined a novel magnetism parameter, R_mag, by modifying the definition of C_mag to a normalized parameter with the culture absorbance obtained without application of magnetic field. The number of magnetosomes in each cell was determined by transmission electron microscopy to assess the relationship between the two magnetism parameters and the distribution of magnetosomes in the cells. We found that both R_mag and C_mag were linearly correlated rather with the percentage of magnetosome-containing bacteria than with the average magnetosome numbers, and R_mag exhibited a better linearity than C_mag with respect to the percentage of magnetosome-containing bacteria.     

A simple and accurate method for quantification of magnetosomes in magnetotactic bacteria by common spectrophotometer

A simple apparatus for measuring the magnetism of magnetotactic bacteria was developed with a common laboratory spectrophotometer, which was based on measuring the change in light scattering resulting from cell alignment in a magnetic field. A multiple coils were built around the cuvette holder of the spectrophotometer to compensate geomagnetic field and to generate two mutually perpendicular magnetic fields. In addition, we defined a novel magnetism parameter, R(mag), by modifying the definition of C(mag) to a normalized parameter with the culture absorbance obtained without application of magnetic field. The number of magnetosomes in each cell was determined by transmission electron microscopy to assess the relationship between the two magnetism parameters and the distribution of magnetosomes in the cells. We found that both R(mag) and C(mag) were linearly correlated rather with the percentage of magnetosome-containing bacteria than with the average magnetosome numbers, and R(mag) exhibited a better linearity than C(mag) with respect to the percentage of magnetosome-containing bacteria.     

A simple HPLC-UV method for the simultaneous quantification of gefitinib and erlotinib in human plasma

Gefitinib and erlotinib are two oral tyrosine kinase inhibitors (TKI) approved for the treatment of advanced non-small cell lung cancer (NSCLC). Published methods for simultaneous analysis of erlotinib and gefitinib in plasma are exclusively based on mass spectrometry. The purpose of this study was to develop a simple and sensitive HPLC-UV method to simultaneously quantify these two TKI in plasma. Following liquid-liquid extraction, gefitinib, erlotinib and sorafenib (internal standard), were separated with gradient elution (on a C8+ Satisfaction(?) using a mobile phase of acetonitrile/20mM ammonium acetate pH 4.5). Samples were eluted at a flow rate of 0.4 ml/min throughout the 15-min run. Dual UV wavelength mode was used, with gefitinib and erlotinib monitored at 331 nm, and sorafenib at 249 nm. The calibration was linear in the range 20-1000 ng/ml and 80-4000 ng/ml for gefitinib and erlotinib, respectively. Inter- and intra-day imprecision were less than 7.2% and 7.6% for gefitinib and erlotinib, respectively. This analytical method was successfully applied to assess the steady state plasma exposure to these TKI in NSCLC patients. This simple, sensitive, accurate and cost-effective method can be used in routine clinical practice to monitor gefitinib or erlotinib concentrations in plasma from NSCLC patients.