MLGA--a rapid and cost-efficient assay for gene copy-number analysis

Structural variation is an important cause of genetic variation. Whole genome analysis techniques can efficiently identify copy-number variable regions but there is a need for targeted methods, to verify and accurately size variable regions, and to diagnose large sample cohorts. We have developed a technique based on multiplex amplification of size-coded selectively circularized genomic fragments, which is robust, cheaper and more rapid than current multiplex targeted copy-number assays.     

Agrobacterium-mediated transient expression in citrus leaves: a rapid tool for gene expression and functional gene assay

In this study, we present a method for transient expression of the type III effector AvrGf1 from Xanthomonas citri subsp. citri strain A^w in grapefruit leaves (Citrus paradisi) via Agrobacterium tumefaciens. The coding sequence of avrGf1 was placed under the control of the constitutive CaMV 35S promoter in the binary vectors pGWB2 and pGWB5. Infiltration of grapefruit leaves with A. tumefaciens carrying these constructs triggered a hypersensitive response (HR) in grapefruit 4 days after inoculation. When transiently expressed in grapefruit leaves, two mutants, AvrGf1ΔN116 and AvrGf1ΔC83, failed to induce an HR. Moreover, using bioinformatics tools, a chloroplast transit signal was predicted at the N terminus of AvrGf1. We demonstrated chloroplast localization by using an AvrGf1::GFP fusion protein, where confocal images revealed that GFP fluorescence was accumulating in the stomatal cells that are abundant in chloroplasts. Transient expression in citrus has the potential for aiding in the development of new disease defense strategies in citrus.     

Array rank order regression analysis for the detection of gene copy-number changes in human cancer

cDNA microarray technology has been applied to the detection of DNA copy-number changes in malignant tumors. Test and control genomic DNA samples are differentially labeled and cohybridized to a spotted cDNA microarray. The ratio of test to control fluorescence intensities for each spot reflects relative gene copy number. The low signal-to-noise ratios of this assay and the variable levels of gene amplification and deletion among tumors hamper the detection of deviations from the diploid complement. We describe a regression-based statistical method to test for altered copy number on each gene and apply the technique to copy-number profiles in 10 thyroid tumors. We show that a novel transformation of fluorescence ratios into array rank order efficiently normalizes the heterogeneity among copy-number profiles and improves the reproducibility of the results. Array rank order regression analysis enhances the detection of consistent changes in gene copy number in solid tumors by cDNA microarray-based comparative genome hybridization.     

The neutral coalescent process for recent gene duplications and copy-number variants

I describe a method for simulating samples from gene families of size two under a neutral coalescent process, for the case where the duplicate gene either has fixed recently in the population or is still segregating. When a duplicate locus has recently fixed by genetic drift, diversity in the new gene is expected to be reduced, and an excess of rare alleles is expected, relative to the predictions of the standard coalescent model. The expected patterns of polymorphism in segregating duplicates ("copy-number variants") depend both on the frequency of the duplicate in the sample and on the rate of crossing over between the two loci. When the crossover rate between the ancestral gene and the copy-number variant is low, the expected pattern of variability in the ancestral gene will be similar to the predictions of models of either balancing or positive selection, if the frequency of the duplicate in the sample is intermediate or high, respectively. Simulations are used to investigate the effect of crossing over between loci, and gene conversion between the duplicate loci, on levels of variability and the site-frequency spectrum.     

Standardization of a sensitive and rapid assay for lymphotoxin.

Actinomycin-treated mouse L cells and human HeLa cells are sensitive indicators of lymphotoxin activity in supernatant fluids of mitogen-stimulated lymphocytes. Without actinomycin, various strains of these cells are 10–200 times less sensitive. The concentration of actinomycin used amplifies the toxic effect of LT but is not itself cytotoxic. Actinomycin-treated indicator cells permit detection of LT activity where toxicity is not often found, as in supernatants of mixed lymphocyte cultures and of cell-mediated cytotoxicity reactions. This assay makes available to any investigator a sensitive indicator of LT activity.     

Ultrasonication as a rapid and high yield DNA extraction method for bacterial gene quantification by NanoGene assay

We demonstrated ultrasonication as a rapid and high yield DNA extraction method suitable for bacterial gene quantification by NanoGene assay. The NanoGene assay utilizes DNA hybridization in solution and a combination of magnetic beads and quantum dot nanoparticles. Unlike the existing gene quantification assays, the NanoGene method is capable of quantifying genes in the presence of environmental inhibitors and cell materials. The performance of the ultrasonication was compared with heating and freeze-thaw. They first were evaluated for their cell lysis capability in humic acids laden sand samples, via EtBr assay. Using autoclaved samples as a bench mark, their cell lysis capability were 106 ± 3, 68 ± 5, and 48 ± 15%, respectively. Morphological changes of cells for each method were also observed by FE-SEM. More importantly, ultrasonication performed significantly better (more than 3× fluorescence signal) than commercial DNA extraction methods during bacterial gene quantification in humic acids laden sand samples.     

Genomic rearrangements and gene copy-number alterations as a cause of nervous system disorders

Genomic disorders are a group of human genetic diseases caused by genomic rearrangements resulting in copy-number variation (CNV) affecting a dosage-sensitive gene or genes critical for normal development or maintenance. These disorders represent a wide range of clinically distinct entities but include many diseases affecting nervous system function. Herein, we review selected neurodevelopmental, neurodegenerative, and psychiatric disorders either known or suggested to be caused by genomic rearrangement and CNV. Further, we emphasize the cause-and-effect relationship between gene CNV and complex disease traits. We also discuss the prevalence and heritability of CNV, the correlation between CNV and higher-order genome architecture, and the heritability of personality, behavioral, and psychiatric traits. We speculate that CNV could underlie a significant proportion of normal human variation including differences in cognitive, behavioral, and psychological features.     

A reverse-hybridization assay for the rapid and simultaneous detection of nine HFE gene mutations

Hereditary hemochromatosis (HH) is a very common autosomal recessive disorder of iron metabolism and frequently associated with mutations in the HFE gene. Molecular genetic testing for HFE mutations is considered valuable for carrier identification, as well as for early diagnosis of the disease, allowing simple treatment by phlebotomy and normal survival of patients. We have developed a reverse-hybridization assay for the routine diagnosis of eight previously described and one novel (E168Q) HFE point mutations. The test is based on multiplex DNA amplification and ready-to-use membrane teststrips, which contain oligonucleotide probes for each wild-type and mutated allele immobilized as an array of parallel lines. The procedure is rapid and accessible to automation on commercially available equipment, and by adding new probes the teststrip can easily be adapted to cover an increasing number of mutations.     

A rapid and sensitive assay for arginase

An assay for arginase is described that uses l-[guanido-¹⁴C]arginine as substrate. Unhydrolyzed arginine is removed in a batch procedure with sulfonate resin and the [¹⁴C]urea product is determined quantitatively in the resin supernatant. The assay requires 5 min and is performed in one tube. The sensitivity is approximately 0.1 munits of arginase. Arginase activities in fetal calf serum and in murine macrophage extract have been determined and the bovine liver enzyme has been used as a reference.     

A rapid filtration assay for cAMP

The receptor-binding assay for cAMP was improved by using polyethylenimine-treated glass filters. A polyethylenimine-treated glass filter has high protein binding capacity. This high capacity allows an increase in the amount of protein per assay tube and the use of a crude preparation, such as a beef heart extract, as specific binding protein instead of a purified protein, which has been used in the classical filtration assays involving cellulose ester filters. Since the time required for the separation of the protein-cAMP complex and the free nucleotide can be shortened by the use of polyethylenimine-treated filters, the dissociation of the bound ligand during the separation procedure, which is a serious problem with other modified assay methods involving charcoal adsorption, is minimized. Filtration through polyethylenimine-treated glass filters also gives low blanks and prevents the loss of protein or ligand due to breakage of the filters, which is often observed with fragile cellulose ester membranes. In consequence, this simple and rapid filtration assay allows more accurate and reproducible determinations.     

A rapid assay for ribokinase.

A rapid method capable of detecting low levels of ribokinase is given. [γ-³²P]ATP is converted to ribose 5-[³²P]phosphate which is not absorbable onto charcoal. The assay is linear in enzyme concentration to a lower limit of at least 4 × 10^?2 mg of enzyme/ml.     

A rapid assay for lipoprotein lipase

A rapid assay for lipoprotein lipase activity employing a (14)C-labeled substrate is described. The method is very sensitive and suitable for routine use.     

A rapid spectrophotometric assay for catechol-O-methyltransferase

A new assay technique for catechol-O-methyltransferase is described. 3,4-Dihydroxyacetophenone is used as the substrate for the assay and the products, 3-hydroxy-4-methoxyacetophenone and 4-hydroxy-3-methoxyacetophenone are detected spectrophotometrically at 344 nm in borate buffer, pH 10.0. This spectrophotometric procedure is simple, rapid, and inexpensive while retaining reasonably high sensitivity and precision.     

A rapid and inexpensive labeling method for microarray gene expression analysis

Background  

Global gene expression profiling by DNA microarrays is an invaluable tool in biological research. However, existing labeling methods are time consuming and costly and therefore often limit the scale of microarray experiments and sample throughput. Here we introduce a new, fast, inexpensive method for direct random-primed fluorescent labeling of eukaryotic cDNA for gene expression analysis and compare the results obtained on the NimbleGen microarray platform with two other widely-used labeling methods, namely the NimbleGen-recommended double-stranded cDNA protocol and the indirect (aminoallyl) method.     

Relationship between gene expression and observed intensities in DNA microarrays—a modeling study

A theoretical study of the physical properties which determine the variation in signal strength from probe to probe on a microarray is presented. A model which incorporates probe-target hybridization, as well as the subsequent dissociation which occurs during stringent washing of the microarray, is introduced and shown to reasonably describe publicly available spike-in experiments carried out at Affymetrix. In particular, this model suggests that probe-target dissociation during the stringent wash plays a critical role in determining the observed hybridization intensities. In addition, it is demonstrated that non-specific hybridization introduces uncertainties which significantly limit the ability of any model to accurately quantify absolute gene expression levels while, in contrast, target folding appears to have little effect on these results. Finally, for data from target spike-in experiments, our model is shown to compare favorably with an existing statistical model in determining target concentration levels.