Adaptable gene‐specific dye bias correction for two‐channel DNA microarrays

DNA microarray technology is a powerful tool for monitoring gene expression or for finding the location of DNA‐bound proteins. DNA microarrays can suffer from gene‐specific dye bias (GSDB), causing some probes to be affected more by the dye than by the sample. This results in large measurement errors, which vary considerably for different probes and also across different hybridizations. GSDB is not corrected by conventional normalization and has been difficult to address systematically because of its variance. We show that GSDB is influenced by label incorporation efficiency, explaining the variation of GSDB across different hybridizations. A correction method (Gene‐ And Slide‐Specific Correction, GASSCO) is presented, whereby sequence‐specific corrections are modulated by the overall bias of individual hybridizations. GASSCO outperforms earlier methods and works well on a variety of publically available datasets covering a range of platforms, organisms and applications, including ChIP on chip. A sequence‐based model is also presented, which predicts which probes will suffer most from GSDB, useful for microarray probe design and correction of individual hybridizations. Software implementing the method is publicly available.     

High white-tailed deer densities benefit graminoids and contribute to biotic homogenization of forest ground-layer vegetation

Biotic homogenization, with its emphasis on invasions, extinctions, and convergence in taxonomic similarity, provides an important framework for investigating changes in biodiversity across scales. Through their selective foraging, large populations of white-tailed deer are altering population sizes, driving extirpations, and facilitating invasions of plants throughout the eastern United States. I hypothesize that deer can drive biotic homogenization in forest understory communities by shifting species composition to one dominated by grasses, sedges, and ferns (all wind-pollinated plants). I report the effects of 16 years of deer exclusion in a hemlock-northern hardwood stand in N Wisconsin using a block design. Species composition showed greater convergence in control plots than exclosure plots, indicating deer can drive biotic homogenization at the stand level. Total percent cover is nearly 4 times greater in exclosure plots. Percent cover by woody plants, broadleaf herbs, and ferns is 150, 63, and 20 times greater in exclosure plots, respectively, while cover by sedges and grasses is 3.8 and 2.2 times greater in control plots. Cover by species with showy, insect-pollinated flowers is 79 times greater in exclosures. Graminoid-dominated control plots represent a novel state not observed fifty years ago, and could reflect the emergence of a grazing lawn. The increase in graminoids at this study area and throughout the region could under some global change scenarios be an early stage of conversion from forest to savanna or wood pasture.     

Prevalence and Identity of Cryptosporidium spp. in Pig Slurry

Cryptosporidium spp. were detected in 25 of 56 pig slurry samples from 33 Irish farms by PCR and DNA sequencing. The organisms detected included C. suis, Cryptosporidium pig genotype II, and C. muris. We concluded that Cryptosporidium oocysts can persist in treated slurry and potentially contaminate surface water through improper discharge or uncontrolled runoff.     

Effect of sheep urine deposition on the bacterial community structure in an acidic upland grassland soil

The effect of the addition of synthetic sheep urine (SSU) and plant species on the bacterial community composition of upland acidic grasslands was studied using a microcosm approach. Low, medium, and high concentrations of SSU were applied to pots containing plant species typical of both unimproved (Agrostis capillaris) and agriculturally improved (Lolium perenne) grasslands, and harvests were carried out 10 days and 50 days after the addition of SSU. SSU application significantly increased both soil pH (P < 0.005), with pH values ranging from pH 5.4 (zero SSU) to pH 6.4 (high SSU), and microbial activity (P < 0.005), with treatment with medium and high levels of SSU displaying significantly higher microbial activity (triphenylformazan dehydrogenase activity) than treatment of soil with zero or low concentrations of SSU. Microbial biomass, however, was not significantly altered by any of the SSU applications. Plant species alone had no effect on microbial biomass or activity. Bacterial community structure was profiled using bacterial automated ribosomal intergenic spacer analysis. Multidimensional scaling plots indicated that applications of high concentrations of SSU significantly altered the bacterial community composition in the presence of plant species but at different times: 10 days after application of high concentrations of SSU, the bacterial community composition of L. perenne-planted soils differed significantly from those of any other soils, whereas in the case of A. capillaris-planted soils, the bacterial community composition was different 50 days after treatment with high concentrations of SSU. Canonical correspondence analysis also highlighted the importance of interactions between SSU addition, plant species, and time in the bacterial community structure. This study has shown that the response of plants and bacterial communities to sheep urine deposition in grasslands is dependent on both the grass species present and the concentration of SSU applied, which may have important ecological consequences for agricultural grasslands.     

Nourseothricin acetyltransferease: a positive selectable marker for Toxoplasma gondii

Molecular analysis of parasite genomes will require new molecular genetic tools. The nat1 gene of Streptomyces noursei encodes nourseothricin acetyltransferase, conferring resistance to the aminoglycoside antibiotic nourseothricin. Electroporation of nat1 cassettes into RH or Prugniaud strains of Toxoplasma gondii allows for selection of stable nourseothricin-resistant clones.     

Leukotrienes stimulate phosphatidylcholine secretion in cultured type II pneumocytes

We previously reported that arachidonic acid stimulates secretion of phosphatidylcholine in cultures of type II pneumocytes and, based on studies with cyclooxygenase and lipoxygenase inhibitors, suggested that this effect was mediated by lipoxygenase products of arachidonic acid metabolism (Gilfillan, A.M. and Rooney, S.A. (1985) Biochim. Biophys. Acta 833, 336-341). We have now examined the effect of leukotrienes on phosphatidylcholine secretion in type II cells as well as the effect of a leukotriene antagonist, FPL55712, on the stimulatory effect of arachidonic acid. Leukotrienes C4, D4 and E4 stimulated phosphatidylcholine secretion and this effect was dependent on concentration in the range 10(-12)-10(-6) M. Leukotriene E4 was the most stimulatory, followed by D4 and C4. Leukotriene B4 had no effect. Incubation of the cells with 10(-7) M leukotriene E4 for 90 min resulted in a 107% increase in the rate of phosphatidylcholine secretion. Incubation with 10(-6) M leukotrienes D4 and C4 for the same period resulted in 81% and 63% stimulation, respectively. The leukotrienes had no effect on cellular phosphatidylcholine synthesis or on lactate dehydrogenase release. The stimulatory effects of leukotrienes E4 and D4 were abolished by FPL55712. Similarly, the stimulatory effect of 6 X 10(-6) M arachidonic acid on phosphatidylcholine secretion was reduced from 74% to 25% by 10(-5) M FPL55712. Thus, the stimulatory effect of arachidonic acid on surfactant phospholipid secretion in type II cells is mediated at least in part by leukotrienes.     

Impact of Plasmids,Including Those EncodingVirB4/D4 Type IV Secretion Systems,on Salmonella enterica serovar Heidelberg Virulence in Macrophages and Epithelial Cells

Salmonella enterica serovar Heidelberg (S. Heidelberg) can cause foodborne illness in humans following the consumption of contaminated meat and poultry products. Recent studies from our laboratory have demonstrated that certain S. Heidelberg isolated from food-animal sources harbor multiple transmissible plasmids with genes that encode antimicrobial resistance, virulence and a VirB4/D4 type-IV secretion system. This study examines the potential role of these transmissible plasmids in bacterial uptake and survival in intestinal epithelial cells and macrophages, and the molecular basis of host immune system modulation that may be associated with disease progression. A series of transconjugant and transformant strains were developed with different combinations of the plasmids to determine the roles of the individual and combinations of plasmids on virulence. Overall the Salmonella strains containing the VirB/D4 T4SS plasmids entered and survived in epithelial cells and macrophages to a greater degree than those without the plasmid, even though they carried other plasmid types. During entry in macrophages, the VirB/D4 T4SS encoding genes are up-regulated in a time-dependent fashion. When the potential mechanisms for increased virulence were examined using an antibacterial Response PCR Array, the strain containing the T4SS down regulated several host innate immune response genes which likely contributed to the increased uptake and survival within macrophages and epithelial cells.     

A photochemical method to map ethidium bromide binding sites on DNA: application to a bent DNA fragment

It is shown that, when irradiated in the visible, ethidium bromide (EB) engages in direct photochemistry with its DNA binding site. At the photochemical end point, an average of one single-strand break is produced per bound EB molecule in a reaction which also bleaches the dye chromophore. Using high-resolution electrophoresis, we have mapped the distribution of EB photocleavage sites on DNA, at one-base resolution. It is argued that because the photocleavage is stoichiometric, the resulting pattern is similar to, if not identical with, the local distribution of EB binding affinity. When interpreted in the context of the extensive thermodynamic and structural data which are available for EB, a binding distribution of that kind can be used to infer details of DNA structure variation within the underlying helix. As a first application of the method, we have used EB to probe the structure of a 265 bp fragment of DNA, which had been described as being bent as the result of a periodic array of oligo(A) segments [Kitchin et al. (1986) J. Biol. Chem. 261, 11302]. The EB mapping data provide evidence that the oligo(A) elements in this fragment assume a local secondary structure which is different than that assumed by isolated ApA nearest neighbors and that the ends of the oligo(A) elements comprise a junctional domain with EB binding properties which differ from those of the oligo(A) element or of random-sequence DNA.     

Phylogenetic Analysis of Bacillus subtilis Strains Applicable to Natto (Fermented Soybean) Production

Spore-forming Bacillus strains that produce extracellular poly-γ-glutamic acid were screened for their application to natto (fermented soybean food) fermentation. Among the 424 strains, including Bacillus subtilis and B. amyloliquefaciens, which we isolated from rice straw, 59 were capable of fermenting natto. Biotin auxotrophism was tightly linked to natto fermentation. A multilocus nucleotide sequence of six genes (rpoB, purH, gyrA, groEL, polC, and 16S rRNA) was used for phylogenetic analysis, and amplified fragment length polymorphism (AFLP) analysis was also conducted on the natto-fermenting strains. The ability to ferment natto was inferred from the two principal components of the AFLP banding pattern, and natto-fermenting strains formed a tight cluster within the B. subtilis subsp. subtilis group.