Irrigation and its effect on polyphagous shot hole borer attack

Polyphagous shot hole borer (PSHB), Euwallacea whitfordiodendrus (Schedl) (Coleoptera: Curculionidae, Scolytinae), is an ambrosia beetle that has recently invaded southern California, USA. This beetle successfully attacks and reproduces in a multitude of tree species. As direct control methods are limited, we investigated cultural management options, and sought to determine whether irrigation affects the number of attacks host trees experienced. If irrigation plays a role, cultural control methods could be recommended to managers and growers. Three separate experiments were conducted that monitored the number of attacks on trees with different levels of irrigation. Two experiments examined PSHB attacks in established landscape trees where irrigation was either present or absent. A third experiment used young potted box elder with irrigation controlled with timed emitters. In all three experiments, the level of irrigation received by the trees did not affect the number of attacks. The results suggest that changes in irrigation practices do not affect risk from PSHB attack.     

Microarray method to monitor 40 intestinal bacterial species in the study of azo dye reduction

Azo dyes are widely used in dye manufacturing, paper printing, textile industries, and as tattoo pigmentation. Since intestinal and skin bacteria can metabolize certain azo dyes to carcinogenic compounds, many researchers have studied the azoreductases of these bacteria. In this study, we used a microarray method to identify the intestinal bacterial species from cultured fecal samples in Brain Heart Infusion (BHI) broth with or without azo dyes that may be involved in azo dye reduction. The microarray was designed to identify 40 bacterial species that are reported in the literature to be predominant in human feces. Results from this study showed 26-30 species are present in the cultured fecal samples. The representative bacteria were then examined for the azo dye reduction activity.     

PRINTS and its automatic supplement,prePRINTS

The PRINTS database houses a collection of protein fingerprints. These may be used to assign uncharacterised sequences to known families and hence to infer tentative functions. The September 2002 release (version 36.0) includes 1800 fingerprints, encoding approximately 11 000 motifs, covering a range of globular and membrane proteins, modular polypeptides and so on. In addition to its continued steady growth, we report here the development of an automatic supplement, prePRINTS, designed to increase the coverage of the resource and reduce some of the manual burdens inherent in its maintenance. The databases are accessible for interrogation and searching at http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/.     

Residues glutamate 216 and aspartate 301 are key determinants of substrate specificity and product regioselectivity in cytochrome P450 2D6

Cytochrome P450 2D6 (CYP2D6) metabolizes a wide range of therapeutic drugs. CYP2D6 substrates typically contain a basic nitrogen atom, and the active-site residue Asp-301 has been implicated in substrate recognition through electrostatic interactions. Our recent computational models point to a predominantly structural role for Asp-301 in loop positioning (Kirton, S. B., Kemp, C. A., Tomkinson, N. P., St.-Gallay, S., and Sutcliffe, M. J. (2002) Proteins 49, 216-231) and suggest a second acidic residue, Glu-216, as a key determinant in the binding of basic substrates. We have evaluated the role of Glu-216 in substrate recognition, along with Asp-301, by site-directed mutagenesis. Reversal of the Glu-216 charge to Lys or substitution with neutral residues (Gln, Phe, or Leu) greatly decreased the affinity (K(m) values increased 10-100-fold) for the classical basic nitrogen-containing substrates bufuralol and dextromethorphan. Altered binding was also manifested in significant differences in regiospecificity with respect to dextromethorphan, producing enzymes with no preference for N-demethylation versus O-demethylation (E216K and E216F). Neutralization of Asp-301 to Gln and Asn had similarly profound effects on substrate binding and regioselectivity. Intriguingly, removal of the negative charge from either 216 or 301 produced enzymes (E216A, E216K, and D301Q) with elevated levels (50-75-fold) of catalytic activity toward diclofenac, a carboxylate-containing CYP2C9 substrate that lacks a basic nitrogen atom. Activity was increased still further (>1000-fold) upon neutralization of both residues (E216Q/D301Q). The kinetic parameters for diclofenac (K(m) 108 microm, k(cat) 5 min(-1)) along with nifedipine (K(m) 28 microm, k(cat) 2 min(-1)) and tolbutamide (K(m) 315 microm, k(cat) 1 min(-1)), which are not normally substrates for CYP2D6, were within an order of magnitude of those observed with CYP3A4 or CYP2C9. Neutralizing both Glu-216 and Asp-301 thus effectively alters substrate recognition illustrating the central role of the negative charges provided by both residues in defining the specificity of CYP2D6 toward substrates containing a basic nitrogen.     

Impaired functional activity of alveolar macrophages from GM-CSF-deficient mice

We hypothesized that pulmonary granulocyte-macrophage colony-stimulating factor (GM-CSF) is critically involved in determining the functional capabilities of alveolar macrophages (AM) for host defense. To test this hypothesis, cells were collected by lung lavage from GM-CSF mutant mice [GM(-/-)] and C57BL/6 wild-type mice. GM(-/-) mice yielded almost 4-fold more AM than wild-type mice. The percentage of cells positive for the beta(2)-integrins CD11a and CD11c was reduced significantly in GM(-/-) AM compared with wild-type cells, whereas expression of CD11b was similar in the two groups. The phagocytic activity of GM(-/-) AM for FITC-labeled microspheres was impaired significantly compared with that of wild-type AM both in vitro and in vivo (after intratracheal inoculation with FITC-labeled beads). Stimulated secretion of tumor necrosis factor-alpha (TNF-alpha) and leukotrienes by AM from the GM(-/-) mice was greatly reduced compared with wild-type AM, whereas secretion of monocyte chemoattractant protein-1 was increased. Transgenic expression of GM-CSF exclusively in the lungs of GM(-/-) mice resulted in AM with normal or supranormal expression of CD11a and CD11c, phagocytic activity, and TNF-alpha secretion. Thus, in the absence of GM-CSF, AM functional capabilities for host defense were significantly impaired but were restored by lung-specific expression of GM-CSF.     

The effect of host size on the sex ratio of Syngaster lepidus, a parasitoid of Eucalyptus longhorned borers (Phoracantha spp.)

The solitary larval ectoparasitoid, Syngaster lepidus Brullé, parasitizes the cryptic larvae of two wood-boring beetles, Phoracantha recurva Newman and Phoracantha semipunctata F. The objective of this study was to determine how the female parasitoids allocated the sex of progeny when presented with larval hosts of uniform size classes. Host size was directly correlated with age of the Phoracantha larval hosts. Groups of Phoracantha larvae of a single age class (2-, 3-, 4-, or 5-week-old) were exposed to parasitoids, and sex ratios of the resulting parasitoid progeny from each host age class were determined. A significant relationship was observed among the sizes of P. recurva and P. semipunctata hosts and the sex ratio of emerging parasitoids. Parasitized 2-week-old beetle larvae of both Phoracantha spp. produced only male S. lepidus progeny, whereas older larval hosts produced increasing proportions of female parasitoids (up to 80% females from 5-week-old hosts). Two-week-old Phoracantha larvae of both species produced fewer parasitoids than host larvae 3–5-week-old. The size of parasitoid progeny consistently increased with host larval age (size), and female parasitoids were larger than males across all host size classes. Male S. lepidus developed in approximately 25 days from 2-week-old hosts, and 19–21 days in 3–5-week-old hosts. Female S. lepidus developed in 22–25 days, with developmental time increasing with host size.     

Bacterial bioinformatics: pathogenesis and the genome

As the number of completed microbial genome sequences continues to grow, there is a pressing need for the exploitation of this wealth of data through a synergistic interaction between the well-established science of bacteriology and the emergent discipline of bioinformatics. Antibiotic resistance and pathogenicity in virulent bacteria has become an increasing problem, with even the strongest drugs useless against some species, such as multi-drug resistant Enterococcus faecium and Mycobacterium tuberculosis. The global spread of Human Immunodeficiency Virus (HIV) and Acquired Immune Deficiency Syndrome (AIDS) has contributed to the re-emergence of tuberculosis and the threat from new and emergent diseases. To address these problems, bacterial pathogenicity requires redefinition as Koch's postulates become obsolete. This review discusses how the use of bacterial genomic information, and the in silico tools available at present, may aid in determining the definition of a current pathogen. The combination of both fields should provide a rapid and efficient way of assisting in the future development of antimicrobial therapies.     

Arachidonic acid activates mitogen-activated protein (MAP) kinase-activated protein kinase 2 and mediates adhesion of a human breast carcinoma cell line to collagen type IV through a p38 MAP kinase-dependent pathway

Adhesion of metastatic human mammary carcinoma MDA-MB-435 cells to the basement membrane protein collagen type IV can be activated by treatment with arachidonic acid. We initially observed that this arachidonic acid-mediated adhesion was inhibited by the tyrosine kinase inhibitor genistein. Therefore, we examined the role of the mitogen-activated protein (MAP) kinase family tyrosine phosphorylation-regulated pathways in arachidonic acid-stimulated cell adhesion. Arachidonic acid stimulated the phosphorylation of p38, the activation of MAP kinase-activated protein kinase 2 (MAPKAPK2, a downstream substrate of p38), and the phosphorylation of heat shock protein 27 (a downstream substrate of MAP kinase-activated protein kinase 2). Treatment with the p38 inhibitor PD169316 completely and specifically inhibited arachidonic acid-mediated cell adhesion to collagen type IV. p38 activity was specifically associated with arachidonic acid-stimulated adhesion; this was demonstrated by the observation that 12-O-tetradecanoylphorbol 13-acetate-activated cell adhesion was not blocked by inhibiting p38 activity. Extracellular signal-regulated protein kinases (ERKs) 1 and 2 were also activated by arachidonic acid; however, cell adhesion to collagen type IV was not highly sensitive to PD98059, an inhibitor of MAP kinase kinase/ERK kinase 1 (MEK1) that blocks activation of the ERKs. c-Jun NH(2)-terminal kinase was not activated by arachidonic acid treatment of these cells. Together, these data suggest a novel role for p38 MAP kinase in regulating adhesion of breast cancer cells to collagen type IV.