LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage

The scale of genetic-variation datasets has increased enormously and the linkage equilibrium (LD) structure of these polymorphisms, particularly in whole-genome association studies, is of great interest. The significant computational complexity of calculating single- and multiple-marker correlations at a genome-wide scale remains challenging. We have developed a program that efficiently characterizes whole-genome LD structure on large number of SNPs in terms of single- and multiple-marker correlations. AVAILABILITY: LdCompare is licensed under the GNU General Public License (GPL). Source code, documentation, testing datasets and precompiled executables are available for download at: http://www.affymetrix.com/support/developer/tools/devnettools.affx     

Use of horseradish peroxidase to block nonspecific enzyme uptake in immunoperoxidase microscopy.

Intrinsic tissue peroxidase activity can be more or less successfully destroyed by methanol-H2O2 treatment. It has been found, however, in our laboratory that horseradish peroxidase (HRP) coupled to antibody will bind to some tissue components on a nonspecific basis and remain to take part in the histochemical stain. This contributes considerably to the background. This difficulty can be largely overcome if the tissues are pretreated with a solution of horseradish peroxidase which binds with nonspecific tissue sites. The adsorbed enzyme, along with the intrinsic peroxidase, can then be successfully inactivated by methanol-H2O2 treatment. By this method of blocking, there is considerable reduction in background staining.     

Wood growth response of Calluna vulgaris (L.) Hull to elevated N deposition and drought

Ring diameters and ring number counts were recorded from Calluna stem cross-sections harvested during an N manipulation experiment. The application of dendrochronological methods permitted accurate ageing of shrubs growing in a heathland of known age. Linear regression analyses demonstrated a highly significant association between increasing levels of N input and stem diameter in both watered and droughted plots (droughted in 1997 only). N inputs were identified as the most significant environmental stressor, appearing to speed ageing vis the Calluna growth cycle. Drought sensitivity was noted in the high N treatment plots (120 kg N ha⁻¹ yr⁻¹) with decreased stem diameters. This may have implications in the response of Calluna growth under current climate change scenarios.     

Aquaporin 1 is important for maintaining secretory granule biogenesis in endocrine cells

Aquaporins (AQPs), a family of water channels expressed in epithelial cells, function to transport water in a bidirectional manner to facilitate transepithelial fluid absorption and secretion. Additionally, AQP1 and AQP5 are found in pancreatic zymogen granules and synaptic vesicles and are involved in vesicle swelling and exocytosis in exocrine cells and neurons. Here, we show AQP1 is in dense-core secretory granule (DCSG) membranes of endocrine tissue: pituitary and adrenal medulla. The need for AQP1 in endocrine cell function was examined by stable transfection of AQP1 antisense RNA into AtT20 cells, a pituitary cell line, to down-regulate AQP1 expression. These AQP1-deficient cells showed more than 60% depletion of DCSGs and significantly decreased DCSG protein levels, including proopiomelanocotin/pro-ATCH and prohormone convertase 1/3, but not non-DCSG proteins. Pulse-chase studies revealed that whereas DCSG protein synthesis was unaffected, approximately 50% of the newly synthesized proopiomelanocortin was degraded within 1 h. Low levels of ACTH were released upon stimulation, indicating that the small number of DCSGs that were made in the presence of the residual AQP1 were functionally competent for exocytosis. Analysis of anterior pituitaries from AQP1 knockout mice showed reduced prohormone convertase 1/3, carboxypeptidase E, and ACTH levels compared to wild-type mice demonstrating that our results observed in AtT20 cells can be extended to the animal model. Thus, AQP1 is important for maintaining DCSG biogenesis and normal levels of hormone secretion in pituitary endocrine cells.     

Psychiatric morbidity in men one week after first acute myocardial infarction.

One week after a first myocardial infarction 35 out of 100 consecutive men patients aged under 65 were found by standardised clinical interview to have psychiatric morbidity. In 16 the morbidity had been evident before the infarct, and these patients showed a wider range of psychopathology than those whose symptoms had been precipitated by the infarct. The results suggest that psychiatric morbidity in patients with heart disease is not necessarily a result of the disease process. Thus characterising psychiatric morbidity and identifying the patients'' individual needs are important if rehabilitation is to be effective.     

Effect of homomeric P450-P450 complexes on P450 function

Previous studies have shown that the presence of one P450 enzyme can affect the function of another. The goal of the present study was to determine if P450 enzymes are capable of forming homomeric complexes that affect P450 function. To address this problem, the catalytic activities of several P450s were examined in reconstituted systems containing NADPH-POR (cytochrome P450 reductase) and a single P450. CYP2B4 (cytochrome P450 2B4)-, CYP2E1 (cytochrome P450 2E1)- and CYP1A2 (cytochrome P450 1A2)-mediated activities were measured as a function of POR concentration using reconstituted systems containing different concentrations of P450. Although CYP2B4-dependent activities could be explained by a simple Michaelis-Menten interaction between POR and CYP2B4, both CYP2E1 and CYP1A2 activities generally produced a sigmoidal response as a function of [POR]. Interestingly, the non-Michaelis behaviour of CYP1A2 could be converted into a simple mass-action response by increasing the ionic strength of the buffer. Next, physical interactions between CYP1A2 enzymes were demonstrated in reconstituted systems by chemical cross-linking and in cellular systems by BRET (bioluminescence resonance energy transfer). Cross-linking data were consistent with the kinetic responses in that both were similarly modulated by increasing the ionic strength of the surrounding solution. Taken together, these results show that CYP1A2 forms CYP1A2-CYP1A2 complexes that exhibit altered catalytic activity.     

Expression and activity of NOX5 in the circulating malignant B cells of hairy cell leukemia

Hairy cells (HCs) are mature malignant B cells that contain a number of constitutively active signaling molecules including GTP-bound Rac1, protein kinase C, and Src family kinases. Because Rac1 is a component of the reactive oxidant species (ROS)-generating NADPH oxidase system, we investigated the role of this GTPase in ROS production in HCs. In this study, we show that ROS production in HCs involves a flavin-containing oxidase dependent on Ca2+, but not on GTP-Rac1 or protein kinase C. This suggests the involvement of the nonphagocytic NADPH oxidase NOX5, an enzyme found in lymphoid tissues, but not in circulating lymphocytes. By using RT-PCR and Southern and Western blotting and by measuring superoxide anion production in membrane fractions in the absence of cytosolic components, we demonstrate for the first time that HCs (but not circulating normal B cells or some other lymphoid cell types) express NOX5. We also demonstrate that inhibition of NADPH oxidase in HCs results in a selective increase in the activity of Src homology region 2 domain-containing phosphatase 1 (SHP-1). Furthermore, SHP-1 in HCs coimmunoprecipitates with tyrosine phosphorylated CD22 and localizes in the same cellular compartment as NOX5. This allows the inactivation of SHP-1 by NOX5-generated ROS and contributes to the maintenance of the constitutive activation of HCs.     

Synthesis and characterization of the first potent inhibitor of yapsin 1. Implications for the study of yapsin-like enzymes

The potent peptidic inhibitor, Y1, of the basic residue-specific yeast aspartyl protease, yapsin 1, was synthesized and characterized. The inhibitor was based on the peptide sequence of a cholecystokinin(13-33) analog that yapsin 1 cleaved with an efficiency of 5.2 x 10(5) m(-1) s(-1) (Olsen, V., Guruprasad, K., Cawley, N. X., Chen, H. C., Blundell, T. L., and Loh, Y. P. (1998) Biochemistry 37, 2768-2777). The apparent K(i) of Y1 for the inhibition of yapsin 1 was determined to be 64.5 nm, and the mechanism is competitive. Y2 was also developed as an analog of Y1 for coupling to agarose beads. The resulting inhibitor-coupled agarose beads were successfully used to purify yapsin 1 to apparent homogeneity from conditioned medium of a yeast expression system. Utilization of this new reagent greatly facilitates the purification of yapsin 1 and should also enable the identification of new yapsin-like enzymes from mammalian and nonmammalian sources. In this regard, Y1 also efficiently inhibited Sap9p, a secreted aspartyl protease from the human pathogen, Candida albicans, which has specificity for basic residues similar to yapsin 1 and might provide the basis for the prevention or control of its virulence. A single-step purification of Sap9p from conditioned medium was also accomplished with the inhibitor column. N-terminal amino acid sequence analysis yielded two sequences indicating that Sap9p is composed of two subunits, designated here as alpha and beta, similar to yapsin 1.     

Acute Choline Supplementation In Vivo Enhances Acetylcholine Synthesis In Vitro when Neurotransmitter Release Is Increased by Potassium

The main objective of these studies was to determine whether the acute administration of choline to rats provides supplemental precursor that can be used to support acetylcholine synthesis when the demand for choline is increased by increasing neurotransmitter release. For these experiments, hippocampal and striatal slices were prepared form rats that had received saline or an acute injection of choline. Slices were incubated in a choline-free buffer containing 4.74-35 mM KCl, and acetylcholine synthesis and release and choline production were measured. The initial tissue contents of acetylcholine and choline did not differ between experimental groups for either brain region. When hippocampal slices from the controls were incubated for 10 min with depolarizing concentrations of KCl, acetylcholine release increased and the tissue content decreased in a concentration-dependent fashion; no net synthesis of acetylcholine occurred. In contrast, hippocampal slices from the choline-injected animals maintained their tissue content in the presence of high concentrations of KCl, despite an increase in acetylcholine release that was similar in magnitude to that of the controls; positive net synthesis of acetylcholine resulted. Although the molar concentration of choline achieved in the incubation media at the end of the 10-min period did not differ between groups, the mobilization of free choline from bound stores was significantly greater in hippocampal slices from the choline-injected group than the controls. In addition, the synthesis of acetylcholine by hippocampal slices from the choline-injected group was prevented by the presence of hemicholinium-3 (1 microM) in the media.(ABSTRACT TRUNCATED AT 250 WORDS)     

Psychogenic facial pain: presentation and treatment.

Ninety three patients took part in a two centre double blind controlled clinical trial designed to assess the efficacy of dothiepin (Prothiaden) as compared with placebo and a soft biteguard in the treatment of psychogenic facial pain. The results showed the superiority of dothiepin over placebo in achieving pain relief; 71% of patients were pain free in the dothiepin group at nine weeks compared with 47% in the placebo group. The biteguard conferred no benefit and compliance in its use was poor. Out of 84 patients followed up for 12 months, 68 (81%) became pain free. An adverse life event before development of pain, minimal previous surgical treatment, and freedom from pain at nine weeks were strong prognostic indicators for successful treatment. These results are clear evidence of the efficacy of dothiepin in psychogenic facial pain, though the drug may be needed for up to a year.