Simple and Portable Magnetic Immunoassay for Rapid Detection and Sensitive Quantification of Plant Viruses

Plant pathogens cause major economic losses in the agricultural industry because late detection delays the implementation of measures that can prevent their dissemination. Sensitive and robust procedures for the rapid detection of plant pathogens are therefore required to reduce yield losses and the use of expensive, environmentally damaging chemicals. Here we describe a simple and portable system for the rapid detection of viral pathogens in infected plants based on immunofiltration, subsequent magnetic detection, and the quantification of magnetically labeled virus particles. Grapevine fanleaf virus (GFLV) was chosen as a model pathogen. Monoclonal antibodies recognizing the GFLV capsid protein were immobilized onto immunofiltration columns, and the same antibodies were linked to magnetic nanoparticles. GFLV was quantified by immunofiltration with magnetic labeling in a double-antibody sandwich configuration. A magnetic frequency mixing technique, in which a two-frequency magnetic excitation field was used to induce a sum frequency signal in the resonant detection coil, corresponding to the virus concentration within the immunofiltration column, was used for high-sensitivity quantification. We were able to measure GFLV concentrations in the range of 6 ng/ml to 20 μg/ml in less than 30 min. The magnetic immunoassay could also be adapted to detect other plant viruses, including Potato virus X and Tobacco mosaic virus, with detection limits of 2 to 60 ng/ml.     

Extraction and Quantification of Solutes in Solidified Agar Culture Media

A method is described for determining the concentration of certain solutes in solidified culture media. The method is based upon the finding that under specified conditions the concentration of solute in an agar gel (C_g) is related to the concentration of solute in a centrifugally extracted gel supernatant (C_s) by the ratio, C_g/C_s, which is characteristic for each solute. The method avoids direct assays of the gels and instead involves assaying the supernatants from inoculated and uninoculated (control) gels with conventional liquid assay techniques and then calculating solute concentrations in the inoculated gels by use of the C_g/C_s ratios determined from the controls. Uninoculated agar gels containing known concentrations of various solutes and similar gels inoculated with Neurospora crassa or Escherichia coli were centrifuged at various times, and the supernatants were assayed for solute concentrations. The solute concentrations in the supernatants from the inoculated gels multiplied by the C_g/C_s ratios for those solutes determined at the same times for the uninoculated controls gave calculated solute concentrations in the inoculated gels. The differences between these calculated solute concentrations and those initially present in the inoculated gels indicated the amounts of solutes utilized from the gels by the microorganisms at various incubation times.     

A Simple Sensitive Method for Determining Staphylococcal Thermonuclease in Cheese

A simple quantitative method is described for the determination of staphylococcal thermostable nuclease in cheese. The method does not require concentration or purification of the nuclease prior to determination because of the increased sensitivity of the assay (0.5 ng/ml). Assay results of cheddar cheese made from pasteurized milk inoculated with enterotoxin-A producing Staphylococcus aureus strains demonstrated the sensitivity and reliability of the method for indicating the presence of Staph. aureus at concentrations of ≥ 1.4 × 10⁶/g of cheese.     

A Simple and Sensitive Method for Measuring Tumor-Specific T Cell Cytotoxicity

A simple and sensitive method to quantitatively measure the cytolytic effect of tumor-specific T killer cells is highly desirable for basic and clinical studies. Chromium (⁵¹Cr) release assay has been the “gold standard” for quantifying cytolytic activities of cytotoxic T lymphocytes (CTLs) against target cells and this method is still being used in many laboratories. However, a major drawback of this method is the use of radioactive materials, which is inconvenient to handle because of environmental safety concerns and expensive due to the short half-life of the isotope. Consequently, several nonradioactive methods have been reported recently. Here we report a new method that we recently developed for quantifying antigen-specific cytolytic activity of CTLs. This method fully exploits the high sensitivity and the relative simplicity of luciferase quantitative assay. We initially expected the released luciferase in the supernatant to be the adequate source for monitoring cell death. However, to our total surprise, incubation of these killer T cells with the tumor cell targets did not result in significant release of luciferase in the culture medium. Instead, we found that the remaining luciferase inside the cells could accurately reflect the overall cell viability.     

A Simple, Fast and Reliable Method for Obtaining Dopamine Histofluorescence from Mesencephalic Cultures

A modified glyoxylic acid technique for obtaining dopamine histofluorescence from cultured mesencephalic cells is described. This method requires only two solutions: one contains glyoxylic acid, sucrose and monobasic potassium phosphate and is used at room temperature, the other is a Hepes buffered solution used at 37 C. Relatively high concentrations of a monoamine oxidase inhibitor and dopamine are added to the cultures to load dopaminergic neurons; the cell bodies and their processes take up and hold dopamine quickly and evenly. The cultures are dipped in a glyoxylic acid solution, dried in air, heated for 5 min and coverslipped with mineral oil. Since the cultures remain in their culture dishes, the entire procedure takes less than 2 hr. The green histofluorescence characteristic of dopamine is seen when the cultures are viewed by standard fluorescence microscopy. Various cell body types and sizes can be distinguished, as well as the complete extent of their processes and varicosities.     

A Simple Purification Method for Chloroperoxidase and Its Use in Organic Media

A simple two-step purification method for chloroperoxidase from Caldariomyces fumago has been developed. After filtration of the mycelium the enzyme was bound to a DEAE Sepharose fast flow column. The enzyme was eluted with a 20–200 mM phosphate buffer, pH=5.8. After gel filtration on a Superose 12 HPLC column pure enzyme was obtained. Instead of gel filtration it was also possible to purify the enzyme by concentration over a membrane filter, 10 K cutoff. Concentration to 8% of the original volume yielded an enzyme preparation with R_z=1.31^b in 77% yield. The enzyme was active in t-butyl alcohol/water mixtures up to 70% t-butyl alcohol. The sulfoxidation of thioanisole proceeded readily (conversion > 99%) and with high enantioselectivity (>99%) in t-butyl alochol/water mixtures.     

A Simple Method for Staining Fungal Substrate Hyphae in Agar Media

Morphogenetic processes often occur in fungal cultures in agar medium. These processes are difficult to study by light microscopy because the hyphae or other structures fail to have sufficient contrast for detailed study and photography. To overcome this difficulty, we developed a method to stain hyphae inside the agar without affecting the medium itself.     

A Simple and Highly Sensitive Method for Magnetic Nanoparticle Quantitation Using H-NMR Spectroscopy

Iron oxide superparamagnetic nanoparticles (SPIONs) have drawn significant attention because of their potential impact on medical diagnosis and therapy. However, the difficulty of achieving reliable and standardized quantification of these nanoparticles has limited the uniform study of nanoparticle systems. Current measurement techniques have limited sensitivity, and are sophisticated and subject to individual instrumental settings. Here, a characterization method using proton nuclear magnetic resonance (¹H-NMR) spectroscopy is presented that can quantify SPIONs regardless of surface modification. In addition to routine quantification of SPIONs during nanoparticle development, the method can also be used with in vitro nanoparticle assays and potentially with tissue samples for biodistribution studies. Specifically, measurement of water relaxivity shifts (R₁ or R₂) of dissolved SPION samples is correlated with nanoparticle concentration. Unmodified and dextran- and poly(ethylene glycol)-coated SPIONs gave linear correlations between SPION concentration and R₁ and R₂ relaxivities over five orders of magnitude, to below 10 ppb iron. Quantification of SPION concentration was also demonstrated in the presence of RAW 264.7 macrophage cells. A linear correlation between the SPION concentration and relaxivities was observed to <10 ng Fe/mL. This method is a rapid and inexpensive approach for quantitation of SPIONs and exhibits a number of advantages over many of the current methods for quantitative SPION analysis.     

Development of a Fast, Reproducible and Effective Method for the Extraction and Quantification of Proteins of Micro-algae

The best method that was developed to extract protein from Chlorella was by sonic disruption of the cells for 3 cycles of 1 min. at 70W on ice in the presence of 1% (w/v) SDS. The best method to quantify the amount of protein in algal extracts is the staining method with the dye bicinchoninic acid. The developed method is reliable for the tested fresh-water micro-alga Chlorella, is also acceptable for the fresh-water micro-alga Chlamydomonas, but is not reliable for the marine micro-algae Dunaliella, Rhodomonas and Synechococcus. The extraction method was the most critical factor factor for determination of proteins in micro-algae and needs to be optimized for each algal species.     

A Sensitive and Simple Method for the Determination of Fatty Acid Hydroperoxides with Horseradish Peroxidase

Glycine, glycylglycine, glycine methyl ester and glycine ethyl ester were found to be effective for the production and release of γ-galactosidase by Escherichia coli. Addition of an appropriate concentration of glycine and glycylglycine to the culture increased total enzyme production 6 to 7-fold and extracellular enzyme production over 240-fold at 24 hr cultivation. The enzyme synthesis was stimulated even at the exponential period of growth, and 93% of enzyme was found in the culture fluid at 24 hr cultivation on addition of 1.2% glycine. A large amount of protein was also accumulated in the culture fluid. A micrograph showed glycine gave swollen and irregular cells, indicating that the cell surface was altered. Various amino acid analogues and some antibiotics had a small or no effect on the production and release of the enzyme as compared with glycine. Polypeptone or brain heart infusion was needed as a nitrogen source for efficient production of the enzyme.     

Methenamine-Silver Staining: a Simple and Sensitive Staining Method for Senile Plaques and Neurofibrillary Tangles

An improved methenamine-silver impregnation method is presented which exhibits sensitivity for amyloid substances comparable to that of anti-β protein immunostaining. In optimally treated sections, this technique stained both β-amyloid deposits and neurofibrillary tangles, which are known to have a β-pleated structure. This simple procedure allows a large number of sections to be stained for routine examination.     

一种简单、快速的苏云金芽胞杆菌基因组DNA提取方法

从培养时间、裂解溶液、抽提和沉淀时间等方面对苏云金芽胞杆菌(Bacillus thuringiensis,Bt)基因组DNA提取技术进行改进.提取8株对蛴螬有杀虫活性的野生Bt菌株的基因组DNA,分析其纯度,并进行PCR分析与酶切分析.试验结果表明,新的提取方法耗时36 min,明显短于旧方法所用时间(97 min);两种方法提取的基因组DNA A260/A280均大于1.8,无明显区别;琼脂糖凝胶电泳结果显示,上样量相同时,新方法提取的基因组DNA浓度是旧方法的5倍以上;新方法提取的基因组DNA能作为模板灵敏地扩增出测试基因,所提取的DNA能被限制性内切酶完全酶切,证明DNA具有很高的纯度.本研究改进的基因组DNA提取方法耗时短、产量高,并能满足PCR扩增、酶切等分子生物学需要.     

High-Throughput,Sensitive Quantification of Repopulating Hematopoietic Stem Cell Clones

Retroviral vector-mediated gene therapy has been successfully used to correct genetic diseases. However, a number of studies have shown a subsequent risk of cancer development or aberrant clonal growths due to vector insertion near or within proto-oncogenes. Recent advances in the sequencing technology enable high-throughput clonality analysis via vector integration site (VIS) sequencing, which is particularly useful for studying complex polyclonal hematopoietic progenitor/stem cell (HPSC) repopulation. However, clonal repopulation analysis using the current methods is typically semiquantitative. Here, we present a novel system and standards for accurate clonality analysis using 454 pyrosequencing. We developed a bidirectional VIS PCR method to improve VIS detection by concurrently analyzing both the 5′ and the 3′ vector-host junctions and optimized the conditions for the quantitative VIS sequencing. The assay was validated by quantifying the relative frequencies of hundreds of repopulating HPSC clones in a nonhuman primate. The reliability and sensitivity of the assay were assessed using clone-specific real-time PCR. The majority of tested clones showed a strong correlation between the two methods. This assay permits high-throughput and sensitive assessment of clonal populations and hence will be useful for a broad range of gene therapy, stem cell, and cancer research applications.Integration of the retroviral DNA provirus into the host genome is an obligatory step in the retroviral life cycle. Because of this unique property, retroviruses have been adapted as vectors (24, 26) and used successfully to correct genetic diseases, such as X-linked severe combined immunodeficiency (SCID), adenosine deaminase (ADA)-deficient SCID, and X-linked adrenoleukodystrophy, by stable genetic modification of hematopoietic progenitor/stem cells (HPSC) (1, 2, 5, 6, 13, 27, 29). However, the risk of insertional mutagenesis from therapeutic vectors has been demonstrated in several cases in which integration events near or within proto-oncogenes triggered leukemia (8, 12, 14, 16, 34). Therefore, it is important to understand the mechanisms for complex hematopoietic repopulation in humans and to study the behaviors of engineered HPSC clones following transplant.Since retrovirus vectors uniquely “mark” individual HPSC by vector integration sites (VIS), clonal repopulation by HPSC can be analyzed by tracking the VIS. Restriction enzyme-based assays are commonly used for the clonal tracking, where genomic DNA is digested with restriction enzymes to generate VIS DNA fragments of different lengths that can be detected by Southern blotting (9, 17, 18, 22) or nucleotide sequencing via linker-mediated PCR (LM-PCR) (32), inverse PCR (INV-PCR) (33), or linear amplification-mediated PCR (LAM-PCR) (30). These approaches have been widely used in biological and clinical research to study composition of the HPSC pool, stem cell engraftment, regulatory decisions of individual stem cells, and genotoxicity of retroviral vectors (17, 22, 23, 25, 29, 31, 35). While mouse HPSC repopulation is typically mono- or oligoclonal (17), the number of HPSC clones repopulating in humans or nonhuman primates is much larger, manifesting several hundreds to thousands of repopulating clones posttransplant (5, 31, 35). Recent advances in sequencing technology have enabled high-throughput and parallel clonality analysis through large-scale VIS sequencing and enumeration of VIS sequences (5, 15, 35, 36). However, these methods can detect only VIS that are proximal to restriction enzyme sites, and additional experimental limitations may exist (10, 15, 36). As a result, current assays can only roughly estimate clonal frequencies, so the current standard is to perform clone-specific real-time PCR for sensitive and accurate quantification. Recently, novel clonal tracking assays that do not require restriction enzyme usage have been described (10, 11). However, these methods involve experimental steps that are technically challenging, and they require further optimization to achieve reliable, high-throughput quantification.Here, we present a novel VIS detection and quantification system based on 454 pyrosequencing and accompanying guidelines for high-throughput quantification of multiple clonal populations. We used a novel bidirectional PCR method to concurrently analyze both the 5′ (left) and the 3′ (right) vector-host junctions in peripheral blood repopulating cells (PBC) in a rhesus macaque transplanted with autologous HPSC transduced with lentivirus vectors (3). The reproducibility and conditions for reliable quantification were tested by two independent experiments conducted on the same PBC collected at four posttransplant time points. The lengths of VIS PCR amplicons, the amount of genomic DNA for analysis, and the intensity of sequencing are important factors influencing the reliability and the sensitivity of the assay. Of 964 unique vector integrants analyzed, the relative quantities of a 398-member subset were determined, demonstrating heterogeneous and dynamic clonal frequency changes over time. Clonal frequencies were further confirmed by clone-specific real-time PCR. We show that this assay detects the majority of VIS that are present in a given clonal population and accurately measures their relative frequencies.     

A Simple, Reliable, and Fast Protocol for Thraustochytrid DNA Extraction

DNA extraction of thraustochytrids, common marine unicellular organisms, is usually accomplished by either the cetyltrimethylammonium bromide (CTAB) or proteinase K protocols. A novel lysis buffer protocol for thraustochytrid total DNA extraction is described. The average isolated total DNA is 20 to 40 kb, and DNA samples are suitable for a variety of uses including 18S–ribosomal DNA polymerase chain reaction, restriction enzyme digestions, and amplified fragment length polymorphism analyses. The new protocol is also faster than the other protocols. Received July 31, 2000; accepted November 2, 2000.     

A Method for the Production of Pre-reduced Anaerobically Sterilized Culture Media

A simplified method for the production of pre-reduced anaerobically sterilized media for the cultivation of strict anaerobes is described.