Virus detection and identification using random multiplex (RT)-PCR with 3'-locked random primers

<p>Abstract</p> <p>Background</p> <p>PCR-based detection and identification of viruses assumes a known, relatively stable genome. Unfortunately, high mutation rates may lead to extensive changes in viral nucleic acid sequences making dedicated PCR primer use problematic. Furthermore, in bioterrorism, viral consensus sequences can be genetically modified as a countermeasure to RT-PCR and DNA chip detection. Accordingly, there is a great need for the development of rapid and universal virus detection and identification technologies.</p> <p>Results</p> <p>We report herein that viral genomic DNA or RNA can be separated from host nucleic acids in plasma by filtration and nuclease digestion, and randomly amplified in a single PCR using a mixture of primers designed to be resistant to primer-dimer amplification (5'-VVVVVVVVAA-3', V = A, G or C; 3⁸or 6561 primers). We have termed this novel PCR method Random Multiplex (RT)-PCR since hundreds of overlapping PCR amplifications occur simultaneously. Using this method, we have successfullydetected and partially sequenced 3 separate viruses in human plasma without using virus-specific reagents (<it>i.e., </it>Adenovirus Type 17, Coxsackievirus A7, and Respiratory Syncytial Virus B). The method is sensitive to ~1000 genome equivalents/ml and may represent the fastest means of detection of unknown viruses.</p> <p>Conclusion</p> <p>These studies suggest that the further development of random multiplex (RT)-PCR may lead to a diagnostic assay that can universally detect viruses in donated blood products as well as in patients suffering with idiopathic disease states of possible viral etiology.</p

Preliminary Feeding Assessments for Asiatic Garden Beetle, Maladera formosae (Coleoptera: Scarabaeidae), Grubs and Adults

The Asiatic garden beetle, Maladera formosae (Brenske) (syn. M. castanea [Arrow]), is an annual white grub species that was unintentionally introduced from east Asia to North America in 1921 in New Jersey, and has since spread to at least 25 states and two Canadian provinces. Grub populations in the Great Lakes region have recently emerged as significant early-season pests of field crops, particularly field corn, grown in sandy soils. Asiatic garden beetle has also recently become established in other regions including Alabama. Prior research on this species was conducted mainly in the 1930s in horticultural and turfgrass systems of New York and New Jersey. In this study, we document Asiatic garden beetle preference and performance on previously un-investigated food resources, in populations from Ohio and Alabama. The objectives of these experiments were to a) understand if grubs show preference to potential diet choices present in a typical Ohio corn-soybean rotation, and gained mass when provided a single diet, and b) to conduct a preliminary assessment on the development, survival, and fecundity of field-collected beetles on different diets present in suburban Alabama. In general, grubs were more likely to be found at corn and marestail and they significantly increased in body mass when subjected to those diets. However, they were also able to survive and gain mass when provided soybean, crop residues or bare soil. Adults consumed more rose flower petals than floral tissue of white clover and Queen Anne’s lace. In no-choice trials, only females that were fed a diet of rose petals laid eggs, and diet consumption rates were similar among males and females. These findings provide insight into the feeding behaviors of Asiatic garden beetle grubs and adults collected from novel environments

Phase II trial of the regulatory T cell-depleting agent, denileukin diftitox, in patients with unresectable stage IV melanoma

<p>Abstract</p> <p>Background</p> <p>We previously found that administration of an interleukin 2/diphtheria toxin conjugate (DAB/IL2; Denileukin Diftitox; ONTAK) to stage IV melanoma patients depleted CD4⁺CD25^HIFoxp3⁺regulatory T cells and expanded melanoma-specific CD8⁺T cells. The goal of this study was to assess the clinical efficacy of DAB/IL2 in an expanded cohort of stage IV melanoma patients.</p> <p>Methods</p> <p>In a single-center, phase II trial, DAB/IL2 (12 μg/kg; 4 daily doses; 21 day cycles) was administered to 60 unresectable stage IV melanoma patients and response rates were assessed using a combination of 2-[¹⁸F]-fluoro-2-deoxy-glucose (FDG)-positron emission tomography (PET) and computed tomography (CT) imaging.</p> <p>Results</p> <p>After DAB/IL2 administration, 16.7% of the 60 patients had partial responses, 5% stable disease and 15% mixed responses. Importantly, 45.5% of the chemo/immuno-naïve sub-population (11/60 patients) experienced partial responses. One year survival was markedly higher in partial responders (80 ± 11.9%) relative to patients with progressive disease (23.7 ± 6.5%; <it>p </it>value < 0.001) and 40 ± 6.2% of the total DAB/IL2-treated population were alive at 1 year.</p> <p>Conclusions</p> <p>These data support the development of multi-center, randomized trials of DAB/IL2 as a monotherapy and in combination with other immunotherapeutic agents for the treatment of stage IV melanoma.</p> <p>Trial registration</p> <p><a href="http://www.clinicaltrials.gov/ct2/show/NCT00299689">NCT00299689</a></p

Analysis of micromixers and biocidal coatings on water-treatment membranes to minimize biofouling.

Biofouling, the unwanted growth of biofilms on a surface, of water-treatment membranes negatively impacts in desalination and water treatment. With biofouling there is a decrease in permeate production, degradation of permeate water quality, and an increase in energy expenditure due to increased cross-flow pressure needed. To date, a universal successful and cost-effect method for controlling biofouling has not been implemented. The overall goal of the work described in this report was to use high-performance computing to direct polymer, material, and biological research to create the next generation of water-treatment membranes. Both physical (micromixers - UV-curable epoxy traces printed on the surface of a water-treatment membrane that promote chaotic mixing) and chemical (quaternary ammonium groups) modifications of the membranes for the purpose of increasing resistance to biofouling were evaluated. Creation of low-cost, efficient water-treatment membranes helps assure the availability of fresh water for human use, a growing need in both the U. S. and the world

Depletion of Ascorbic Acid Restricts Angiogenesis and Retards Tumor Growth in a Mouse Model

Angiogenesis requires the deposition of type IV collagen by endothelial cells into the basement membrane of new blood vessels. Stabilization of type IV collagen triple helix depends on the hydroxylation of proline, which is catalyzed by the iron-containing enzyme prolyl hydroxylase. This enzyme, in turn, requires ascorbic acid to maintain the enzyme-bound iron in its reduced state. We hypothesized that dietary ascorbic acid might be required for tumor angiogenesis and, therefore, tumor growth. Here, we show that, not surprisingly, ascorbic acid is necessary for the synthesis of collagen type IV by human endothelial cells and for their effective migration and tube formation on a basement membrane matrix. Furthermore, ascorbic acid depletion in mice incapable of synthesizing ascorbic acid (Gulo(-/-)) dramatically restricts the in vivo growth of implanted Lewis lung carcinoma tumors. Histopathological analyses of these tumors reveal poorly formed blood vessels, extensive hemorrhagic foci, and decreased collagen and von Willebrand factor expression. Our data indicate that ascorbic acid plays an essential role in tumor angiogenesis and growth, and that restriction of ascorbic acid or pharmacological inhibition of prolyl hydroxylase may prove to be novel therapeutic approaches to the treatment of cancer

Selective inhibition of choline kinase simultaneously attenuates MAPK and PI3K/AKT signaling

Choline is an essential anabolic substrate for the synthesis of phospholipids. Choline kinase phosphorylates choline to phosphocholine that serves as a precursor for the production of phosphatidylcholine, the major phospholipid constituent of membranes and substrate for the synthesis of lipid signaling molecules. Nuclear magnetic resonance (NMR)-based metabolomic studies of human tumors have identified a marked increase in the intracellular concentration of phosphocholine relative to normal tissues. We postulated that the observed intracellular pooling of phosphocholine may be required to sustain the production of the pleiotropic lipid second messenger, phosphatidic acid. Phosphatidic acid is generated from the cleavage of phosphatidylcholine by phospholipase D2 and is a key activator of the mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3-kinase (PI3K)/AKT survival signaling pathways. In this study we show that the steady-state concentration of phosphocholine is increased by the ectopic expression of oncogenic H-Ras(V12) in immortalized human bronchial epithelial cells. We then find that small interfering RNA (siRNA) silencing of choline kinase expression in transformed HeLa cells completely abrogates the high concentration of phosphocholine, which in turn decreases phosphatidylcholine, phosphatidic acid and signaling through the MAPK and PI3K/AKT pathways. This simultaneous reduction in survival signaling markedly decreases the anchorage-independent survival of HeLa cells in soft agar and in athymic mice. Last, we confirm the relative importance of phosphatidic acid for this pro-survival effect as phosphatidic acid supplementation fully restores MAPK signaling and partially rescues HeLa cells from choline kinase inhibition. Taken together, these data indicate that the pooling of phosphocholine in cancer cells may be required to provide a ready supply of phosphatidic acid necessary for the feed-forward amplification of cancer survival signaling pathways.James Graham Brown Cancer CenterUnited States Department of Health & Human Services National Institutes of Health (NIH) - USA (1 R01 CA11642801)Kentucky Lung Cancer Research Progra