ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources

MOTIVATION: Heterogeneity of databases and software resources continues to hamper the integration of biological information. Top-down solutions are not feasible for the full-scale problem of integration across biological species and data types. Bottom-up solutions so far have not integrated, in a maximally flexible way, dynamic and interactive graphical-user-interface components with data repositories and analysis tools. RESULTS: We present a component-based approach that relies on a generalized platform for component integration. The platform enables independently-developed components to synchronize their behavior and exchange services, without direct knowledge of one another. An interface-based data model allows the exchange of information with minimal component interdependency. From these interactions an integrated system results, which we call ISYSf1.gif" BORDER="0">. By allowing services to be discovered dynamically based on selected objects, ISYS encourages a kind of exploratory navigation that we believe to be well-suited for applications in genomic research.     

Biotechnological Tools for Enhancing Microbial Solubilization of Insoluble Inorganic Phosphates

During recent years, many studies appeared on microbial solubilization of insoluble phosphates as an alternative of chemically based P-fertilizer production and bearing in mind the progressive increase in P-fertilizer prices based on high global P consumption and the scarcity of rock phosphate reserves. This biotechnological approach is mainly related to microbial production of organic acids such as citric, oxalic, gluconic, itaconic, and lactic acid, which react with the insoluble P-sources. The most applied and studied P-solubilizers are fungal microorganisms cultivated in conditions of submerged and solid-state fermentation systems. Therefore, the aim of this review is to summarize data on the effect of various abiotic factors on the fungal organic acid production. Nutrient medium components, fermentation process parameters, interaction between insoluble P-particles and microbial systems, and mode of fermentation are analyzed for their impact on both organic acid production and P-solubilization. Suggestions for further studies are also discussed.     

Stable carbon and nitrogen isotope ratio profiling of sperm whale teeth reveals ontogenetic movements and trophic ecology

Teeth from male sperm whales (Physeter macrocephalus) stranded in the North-eastern Atlantic were used to determine whether chronological profiles of stable isotope ratios of C (δ¹³C) and N (δ¹⁵N) across dentine growth layers could be used to detect known ontogenetic benchmarks in movements and trophic ecology. Profiles showed a general decrease in δ¹³C (median = 1.91‰) and an increase in δ¹⁵N (median = 2.42‰) with age. A marked decline in δ¹³C occurred for all 11 teeth around 9–10 years and again for six individuals around 20 years. After the early twenties the δ¹³C continued to decline with age for all teeth. These results are consistent with males segregating from natal groups in low latitudes with the onset of puberty between 4 and 15 years and gradually dispersing pole-ward into ¹³C-depleted temperate waters. Penetration into further depleted, productive high latitudes after the age of 20 might facilitate the spurt of accelerated growth rate observed around this age. Breeding migrations back to lower latitudes were not reflected in the δ¹³C profiles possibly due to being short compared to the time spent feeding in high latitudes. The timings of marked isotopic change in the δ¹⁵N profiles reflect those of the δ¹³C profiles, suggesting a link between dietary changes and movements. The observed increase in δ¹⁵N with age is likely to be caused by a trophic level increase as males grow in size, probably feeding on larger prey. An additional explanation could be that, in the higher latitudes of the North Atlantic, the main prey source is the high trophic level squid Gonatus fabricii. Also, the lower latitudes from where males disperse are depleted in basal ¹⁵N. Profiles of δ¹³C and δ¹⁵N in sperm whale teeth gathered from different regions, sexes, and periods in time, could provide a unique way to understand the ecology of this species across different oceans.     

Expression of CD64 on Circulating Neutrophils Favoring Systemic Inflammatory Status in Erythema Nodosum Leprosum

Erythema Nodosum Leprosum (ENL) is an immune reaction in leprosy that aggravates the patient´s clinical condition. ENL presents systemic symptoms of an acute infectious syndrome with high leukocytosis and intense malaise clinically similar to sepsis. The treatment of ENL patients requires immunosuppression and thus needs to be early and efficient to prevent both disabilities and permanent nerve damage. Some patients experience multiple episodes of ENL and prolonged use of immunosuppressive drugs may lead to serious adverse effects. Thalidomide treatment is extremely effective at ameliorating ENL symptoms. Several mechanisms have been proposed to explain the efficacy of thalidomide in ENL, including the inhibition of TNF production. Given its teratogenicity, thalidomide is prohibitive for women of childbearing age. A rational search for molecular targets during ENL episodes is essential to better understand the disease mechanisms involved, which may also lead to the discovery of new drugs and diagnostic tests. Previous studies have demonstrated that IFN-γ and GM-CSF, involved in the induction of CD64 expression, increase during ENL. The aim of the present study was to investigate CD64 expression during ENL and whether thalidomide treatment modulated its expression. Leprosy patients were allocated to one of five groups: (1) Lepromatous leprosy, (2) Borderline leprosy, (3) Reversal reaction, (4) ENL, and (5) ENL 7 days after thalidomide treatment. The present study demonstrated that CD64 mRNA and protein were expressed in ENL lesions and that thalidomide treatment reduced CD64 expression and neutrophil infiltrates—a hallmark of ENL. We also showed that ENL blood neutrophils exclusively expressed CD64 on the cell surface and that thalidomide diminished overall expression. Patient classification based on clinical symptoms found that severe ENL presented high levels of neutrophil CD64. Collectively, these data revealed that ENL neutrophils express CD64, presumably contributing to the immunopathogenesis of the disease.     

Evaluation of the Double Agar Gel Immunodiffusion Test and of the Enzyme-Linked Immunosorbent Assay in the Diagnosis and Follow-Up of Patients with Chronic Pulmonary Aspergillosis

The diagnosis of chronic pulmonary aspergillosis (CPA) depends on the radiologic image and the identification of specific antibodies. The present study aimed to evaluate accuracy parameters of enzyme-linked immunosorbent assay (ELISA) and of the determination of serum galactomannan level in the diagnosis of patients with CPA, comparing these results with the double agar gel immunodiffusion (DID) test. In addition, the prevalence of cross-reactivity and the serological progression after treatment were evaluated by comparing DID and ELISA. Six study groups were formed: G1: 22 patients with CPA, 17 of whom had Aspergillus fungus ball, one chronic cavitary pulmonary aspergillosis (CCPA) and four chronic fibrosing pulmonary aspergillosis (CFPA); G2: 28 patients with pulmonary tuberculosis (TB); G3: 23 patients with histoplasmosis (HST); G4: 50 patients with paracoccidioidomycosis (PCM); G5: 20 patients with cryptococcosis (CRC); and G6: 200 healthy controls. Serum antibodies were measured by DID and ELISA, with two antigen preparations—Aspergillus fumigatus (DID₁, ELISA₁) and a pool of A. fumigatus, A. flavus and A. niger antigens (DID₂, ELISA₂). The Platélia Aspergillus Enzyme Immunoassay (EIA) kit was used to measure galactomannan. The cut-off points of ELISA were determined for each antigen preparation and for the 95% and 99% confidence intervals. Despite the low sensitivity, DID was the technique of choice due to its specificity, positive and negative predictive values and positive likelihood ratio–especially with the antigen pool and due to the low frequency of cross-reactivity. ELISA₁ and a 0.090 cut-off showed high sensitivity, specificity and negative predictive value, but a high frequency of cross-reactivity with CRC. The best degree of agreement was observed between ELISA₁ and ELISA₂. The detection of serum galactomannan showed high sensitivity, comparable to ELISA₂. The immunodiffusion test showed an excellent relationship with the progression after treatment, which made it the reaction of choice for patient follow-up.     

Oxidative Stress in the Heart of Rats Infected with Trypanosoma evansi

This study was conducted to investigate the occurrence of oxidative stress in the heart tissue of rats infected with Trypanosoma evansi. Rats were divided into 2 groups (A and B) with 12 animals each, and further subdivided into 4 subgroups (A1 and A2, 6 animals/each; and B1 and B2, 6 animals/each). Animals in the groups B1 and B2 were subcutaneously inoculated with T. evansi. Thiobarbituric acid reactive substances (TBARS), superoxide dismutase activity (SOD), glutathione S-transferase activity (GST), reduced glutathione activity (GSH), and non-protein thiols (NPSH) in the heart tissue were evaluated. At day 5 and 15 post-infection (PI), an increase in the TBARS levels and a decrease in the SOD activity (P<0.05) were observed. GSH and GST activities were decreased in infected animals at day 15 PI (P<0.05). Considering the proper functioning of the heart, it is possible that the changes in the activity of these enzymes involved in the oxidative stress may be related, at least in part, in the pathophysiology of rats infected with T. evansi.     

Transfer of delayed hypersensitivity to leishmanin (Montenegro reaction).

It was possible to transfer the cutaneous leishmanin hypersensitivity (Montenegro reaction) to 7 out of 12 recipients. The diameter of the indurations observed ranged from 8 to 25 mm. Histological examination of skin biopsies from the site of three positive Montenegro reactions showed intense mononuclear infiltrate of lymphocytes and histiocytes, and one biopsy showed the feature of tuberculoid granuloma. Four recipients retested with leishmanin after 11, 22, 25, and 32 days, still showed positive reactions.     

Dose-related inhibition of gastric secretion by intraduodenal trypsinogen in dogs

It has been shown previously that trypsinogen and its activation peptide but not trypsin decreased gastric secretion. The purpose of this work was to study the dose-action relation between the intraduodenal infusion of trypsinogen and gastric secretion. Three dogs provided with gastric and duodenal Thomas fistulae were stimulated by continuous i.v. perfusion of porcine gastrin I-II (6 microgram kg-1 h-1). Pancreatic juice was diverted to the exterior and gastric secretion was collected. Upon reaching a gastric secretory plateau, porcine trypsinogen was infused intraduodenally at doses of 5, 10, 20, 40, 80 and 160 mg. Each test was continued for a further 60 min. Control was made with isotonic saline. There was a dose-related inhibition of the gastrin-stimulated gastric acid output. This inhibition reached a maximum of 50% with 40 mg of intraduodenal trypsinogen, showing no increase with higher doses.