Superior activity of the type C class of ISS in vitro and in vivo across multiple species

CpG-C are a novel class of CpG motif-containing immunostimulatory sequences (ISS) that includes both a 5'-TCG element and a CpG-containing palindrome. CpG-C drive all known ISS activities and, in particular, are potent enhancers of IFN-alpha from plasmacytoid dendritic cells (PDCs). In our examination of CpG-C sequence requirements, we determined that optimal IFN-alpha-inducing activity could be achieved with longer palindromes. Longer palindromes also correlated with maintenance of the double-stranded (ds) form despite concentration and pH changes, indicating a preference for ds oligodeoxynucleotides (ODNs) by the ISS-induced signaling mechanism for IFN-alpha synthesis. This correlation did not hold for all arms of the ISS-induced immune response, since we did not observe increased B cell activity with the longer palindrome CpG-C ODNs. We further demonstrated that CpG-C retained activity in an in vitro primate system and induced the expression of several cytokines and IFN-alpha-inducible genes when CpG-C were administered in vivo to mice and primates. In conclusion, we have shown CpG-C to exert several types of immune functions across multiple species, and this novel class is thus an attractive candidate for ISS-based therapeutic strategies.     

A fuzzy inference system to evaluate contract service provider performance

This paper puts forward a fuzzy inference system for evaluating the quality performance of service contract providers. An Application Service Provider was designed and put online, featuring surveys to establish the most useful indicators to evaluate the quality of the service. This model was implemented in 10 separate hospitals. As a result, the service cost-acquisition cost ratio in these cases was reduced from 16.14% to 6.09% in the period 2001-January 2003.     

Characterization of the long-wavelength opsin from Mecoptera and Siphonaptera: does a flea see?

Mecoptera and Siphonaptera represent two insect orders that have largely been overlooked in the study of insect vision. Recent phylogenetic evidence demonstrates that Mecoptera (scorpionflies) is paraphyletic, with the order Siphonaptera (fleas) nesting as sister to the family Boreidae (snow fleas), showing an evolutionary trend towards reduction in gross eye morphology within fleas. We provide the first molecular characterization of long-wavelength opsins from these three lineages (opsin gene from fleas [FL-Opsin], the Boreidae [B-Opsin], and a mecopteran family [M-Opsin]) and assess the effects of loss of visual acuity on the structure and function of the opsin gene. Phylogenetic analysis implies a physiological sensitivity in the red-green spectrum for these opsins. Analysis of intron splice sites reveals a high degree of similarity between FL-Opsin and B-Opsin as well as conserved splice sites across insect blue-green and long-wavelength opsins. Calculated rates of evolution and tests for destabilizing selection indicate that FL-Opsin, B-Opsin, and M-Opsin are evolving at similar rates with no radical selective pressures, implying conservative evolution and functional constraint across all three lineages.     

Crotalus durissus terrificus venom interferes with morphological, functional, and biochemical changes in murine macrophage

Crotalus durissus terrificus venom (Cdt) is toxic for a variety of eukaryotic cells, especially at high concentrations. However its effects on host immune cells are not well known. The purpose of this study was to determine the effect of Cdt on functional status and the mediators production in peritoneal macrophages. The effects of Cdt were analyzed in vitro and were detected using functional status of macrophages as determined by the H(2)O(2) release, spreading percentage, phagocytic index, vacuole formation, and mediators production. Several functional bioassays were employed: cytotoxicity was determined by taking the lyses percentage and the presence of hydrogen peroxide (H(2)O(2)) in macrophages, using the horseradish peroxidase-dependent oxidation of phenol red and nitric oxide (NO) in the supernatants of macrophages by the Griess reaction. The tumor necrosis factor (TNF) activity was detected by measuring its cytotoxic activity on L929 cells, and the production the level of other cytokines was assayed using enzyme-linked immunosorbent assay. In vitro studies revealed that Cdt produced (a) a discrete increase in the release of H(2)O(2) and vacuole formation; (b) a decrease in spreading percentage and in the phagocytic index; and (c) an increment in the mediators production. More pronounced increments of IL-6 and TNF were observed after 24 and 48 hours, respectively. Maximum levels of IFN-gamma and NO were observed after 96 hours. Interestingly, levels of all mediators presented a discreet decrease, as the amount of Cdt was increased. In contrast, the IL-10 levels observed for all doses studied here did not alter. The IL-6/IL-10 ratio may possibly reflect the balance of pro- and anti-inflammatory cytokines in macrophages, which may be manifested in the inflammatory status during the envenoming processes. Taken together, these data indicate that Cdt have a differential effect on macrophage activation and that this venom is a potent inhibitor of anti-inflammatory response.     

Naltrexone plus benzodiazepine aids abstinence in opioid-dependent patients

Naltrexone (NTX) is widely used to prevent relapse of opioid-dependent patients but its association with insomnia and "hyperexcitability" can result in treatment withdrawal. We evaluated whether NTX combined with the benzodiazepine prazepam was more effective than NTX in keeping patients opioid-free. We determined the relapse rate over 6 months in 56 opioid-dependent subjects, divided into 4 equal groups. All groups received psychological support and underwent urine tests for drug metabolites twice weekly. Group 1 did not receive pharmacological treatment (controls). Group 2 received NTX alone (one 50-mg tablet daily); group 3 received NTX (one 50-mg tablet daily) plus placebo (one tablet twice daily); and group 4 received NTX (one 50-mg tablet daily) plus prazepam (one 10-mg tablet twice daily). Ten patients of group 1 relapsed within 3 months, one after 6 months and three remained opioid-free. Six patients of group 2 relapsed within three months, two after 6 months, and six remained opioid-free. Seven patients of group 3 relapsed three months, one after 6 months and six patients remained opioid-free. In group 4, one patient relapsed within 3 months and one patient after 6 months; 12 patients of this group remained opioid-free. At urine tests, a significantly higher percent patients of group 4 remained free of Delta(9)-tetrahydrocannabinol versus patients of groups 2 and 3. In conclusion, many patients remained opioid-free on NTX alone or combined with prazepam, with a significant advantage for the NTX plus prazepam group.     

Genome-wide estimation of gender differences in the gene expression of human livers: Statistical design and analysis

Background

Gender differences in gene expression were estimated in liver samples from 9 males and 9 females. The study tested 31,110 genes for a gender difference using a design that adjusted for sources of variation associated with cDNA arrays, normalization, hybridizations and processing conditions.

Results

The genes were split into 2,800 that were clearly expressed (expressed genes) and 28,310 that had expression levels in the background range (not expressed genes). The distribution of p-values from the 'not expressed' group was consistent with no gender differences. The distribution of p-values from the 'expressed' group suggested that 8 % of these genes differed by gender, but the estimated fold-changes (expression in males / expression in females) were small. The largest observed fold-change was 1.55. The 95 % confidence bounds on the estimated fold-changes were less than 1.4 fold for 79.3 %, and few (1.1%) exceed 2-fold.

Conclusion

Observed gender differences in gene expression were small. When selecting genes with gender differences based upon their p-values, false discovery rates exceed 80 % for any set of genes, essentially making it impossible to identify any specific genes with a gender difference.

     

Differences in in vitro plant regeneration ability among four Arabidopsis thaliana ecotypes

Summary The Arabidopsis ecotypes Columbia (Col), Landsberg erecta (Ler), Cape Verde Island (Cvi) and Wassilewskija (WS) have been tested for their regeneration response in vitro. A characteristic morphology of leaf-derived calluses has been found for each ecotype. Differences in regeneration ability have been detected depending on the plant strain. the explant source and on the culture medium composition. In CIR/SIR media, which contain 0.5 mg l⁻¹ (2.26 μM) of 2,4-dichlorophenoxyacetic acid (2,4-D) and glucose, root explants from the four ecotypes are able to reach a considerable regeneration level, while leaf explants do not regenerate beyond a basal level (5% approximately). In CIH/SIH media, which contain 2.2 mg l⁻¹ (9.95 μM) of 2,4-D and suerose, leaf explants from all the ecotypes, with the exception of Col, are able to regenerate, but they do it at variable levels (Ler 5.75%, WS 75.09%, and Cvi 27.53% as regeneration rates). With these media all root explants are able to regenerate, but again the four ecotypes show different rates (Col 27.7%, Ler 57.25%, WS 98.54%, and Cvi 42.25%). The variation of the different medium components affects differentially the regeneration ability of the four ecotypes depending also on the kind of explant. Thus, when the 2,4-D concentration is raised WS duplicates its regeneration rate in both leaf and root explants. Changing glucose for sucrose in CIR/SIR media diminishes to the basal level the regeneration of Cvi root explants, while the CIH/SIH salts and vitamin concentration permit the regeneration of leaf explants from all the ecotypes except Col. The genes responsible for those observed differences in regeneration ability could be identified and mapped by analyzing the in vitro regeneration behavior of the recombinant inbred lines (RILs) obtained by crossing these ecotypes.     

A therapeutic target for hormone-independent estrogen receptor-positive breast cancers

BACKGROUND: The action of the steroid hormone estradiol (E2) is mediated via interaction with a specific receptor (ER) that initiates a series of events downstream, leading to the modulation of hormone-responsive genes and cell proliferation. Antihormones also bind, but do not confer the active configuration to ER, thereby, blocking the transmission of E2-ER-initiated signals for cell proliferation. Although these compounds qualify for successful therapy of ER-positive [ER (+)] breast cancer patients, only a fraction of patients responds to antihormone treatment. In this study, the functional status of ER is determined to identify alternative targets for therapy of antihormone-resistant ER (+) breast cancers. METHOD: The interaction of ER with a specific DNA sequence, designated as E2 response element (ERE), was targeted to assess the functional state of ER. ER-ERE complex formation was measured by electrophoretic mobility shift assay (EMSA) and by a newly developed technique, based on the preferential binding of DNA-protein complex to a nitrocellulose membrane (NMBA) that measures both total and functional fraction of ER. RESULTS: The NMBA assay identified functional variants of ER among ER (+) breast cancer cell lines and breast tumor biopsy specimens. ER of (21PT) cells did not bind E2 and these cells were tamoxifen (TAM) resistant. However 21PT cells were sensitive to a calmodulin (CaM) antagonist, W7, that blocked ERE-ER complex formation. CONCLUSIONS: ER variants of the 21PT type were detected among breast cancer biopsy specimens, emphasizing the significance of an alternative therapeutic target for TAM-resistant ER (+) human breast cancers with compounds such as W7.     

A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction

A classification model of a DNA-binding protein chain was created based on identification of alpha helices within the chain likely to bind to DNA. Using the model, all chains in the Protein Data Bank were classified. For many of the chains classified with high confidence, previous documentation for DNA-binding was found, yet no sequence homology to the structures used to train the model was detected. The result indicates that the chain model can be used to supplement sequence based methods for annotating the function of DNA-binding. Four new candidates for DNA-binding were found, including two structures solved through structural genomics efforts. For each of the candidate structures, possible sites of DNA-binding are indicated by listing the residue ranges of alpha helices likely to interact with DNA.