Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping

BACKGROUND

Protein-protein interaction (PPI) data are widely used to generate network models that aim to describe the relationships between proteins in biological systems. The fidelity and completeness of such networks is primarily limited by the paucity of protein interaction information and by the restriction of most of these data to just a few widely studied experimental organisms. In order to extend the utility of existing PPIs, computational methods can be used that exploit functional conservation between orthologous proteins across taxa to predict putative PPIs or 'interologs'. To date most interolog prediction efforts have been restricted to specific biological domains with fixed underlying data sources and there are no software tools available that provide a generalised framework for 'on-the-fly' interolog prediction.

RESULTS

We introduce Bio::Homology::InterologWalk, a Perl module to retrieve, prioritise and visualise putative protein-protein interactions through an orthology-walk method. The module uses orthology and experimental interaction data to generate putative PPIs and optionally collates meta-data into an Interaction Prioritisation Index that can be used to help prioritise interologs for further analysis. We show the application of our interolog prediction method to the genomic interactome of the fruit fly, Drosophila melanogaster. We analyse the resulting interaction networks and show that the method proposes new interactome members and interactions that are candidates for future experimental investigation.

CONCLUSIONS

Our interolog prediction tool employs the Ensembl Perl API and PSICQUIC enabled protein interaction data sources to generate up to date interologs 'on-the-fly'. This represents a significant advance on previous methods for interolog prediction as it allows the use of the latest orthology and protein interaction data for all of the genomes in Ensembl. The module outputs simple text files, making it easy to customise the results by post-processing, allowing the putative PPI datasets to be easily integrated into existing analysis workflows. The Bio::Homology::InterologWalk module, sample scripts and full documentation are freely available from the Comprehensive Perl Archive Network (CPAN) under the GNU Public license.

COMPARISON OF SINE VERSUS PULSE WAVEFORM EFFECTS ON FATIGUE CRACK GROWTH BEHAVIOR OF NR, SBR, AND BR COMPOUNDS

Fatigue crack growth experiments on carbon black-filled rubber compounds have been carried out to evaluate the influence of testing conditions over different compound formulations. Investigations on the influence of waveform, data acquisition, and compound formulation have been performed on strip-tensile specimens reproducing the mode I of crack opening. The response of three different compound formulations (based on either natural rubber, butadiene rubber, or styrene-butadiene rubber) to the application of two different waveforms, pulse and sine, has been analyzed, showing significant differences in fatigue behavior and ranking of the various compounds. Compared to the sinusoidal waveform, the use of a pulse waveform provided an improved correlation of the tearing energy with the crack propagation speed. This difference was particularly evident in the case of natural rubber and butadiene rubber, while it resulted negligible in the case of styrene-butadiene rubber. Such a different behavior could be attributed to differences in macromolecular chains orientation. Fine-tuning of video acquisition parameters provided an accurate observation of the crack growth process, as confirmed by the low standard deviation of the estimated tearing energy and crack growth rate.

Spot urinary iodine concentration as a measure of dietary iodine, evaluated in over 3800 young male subjects undergoing medical check-up preliminary to military enrolment in Piemonte and Aosta Valley (Italy)

The aim of the study was to assess iodine status in over 3800 young male subjects aged 18, living in 6 different provinces of Piemonte and in Aosta Valley, Italy. A cross-sectional study on 3837 young male subjects undergoing medical evaluation preliminary to military enrolment was performed. Spot urine samples were obtained in the morning hours and urinary iodine was measured by a colorimetric method. As outcome measure iodine status, based on spot urinary iodine median concentration, categorised as sufficient (>99 microg/l), mild deficiency (50-99 microg/l), moderate deficiency (20-49 microg/l) and severe deficiency (<20 microg/l), was obtained. Median urinary iodine concentration was 101.8 microg/l in our sample. Moderate-to-severe iodine deficiency was found in <10% of all subjects. Mild iodine deficiency was found in <40% of the subjects, with greater variability within the provinces considered. For each geographical area significant differences can be observed in more than 50% of the comparisons of the confidence intervals related to the frequencies of samples with spot urinary iodine concentration below 100 microg/l. The high frequency of mild iodine deficiency found in our sample suggests that dietary sources of iodine in Piemonte, Italy, have improved since the last evaluation 25 yr ago (2) but may still be insufficient. Further population studies are required.

[Intact whole bioactive parathormone: problems arising from comparing different methods]

BACKGROUND

Parathyroid hormone (PTH) has important applications in the nephrological clinical practice. Because assays of Intact PTH (I-PTH) are liable to interferences by N-truncated fragments, a novel method for whole-(1-84) PTH has been proposed. This study is aimed at comparing the latter with some of the previous I-PTH assays. For each method the results are referred to pertinent markers of mineral metabolism.

METHODS

We enrolled 171 subjects, including 56 healthy controls (C), 65 calcium stone- formers (CaSF), 40 haemodialysis patients (HD), 10 with primary hyperparathyroidism (PHP). On blood samples we measured: I-PTH by four methods (N-Tact, Advantage, Elecsys, Scantibodies), whole-(1-84) PTH, defined as CAP (Cyclase Activating PTH), total and ionised calcium, phosphate, vitamin D, osteocalcin and Crosslaps. The difference between I-PTH and CAP Scantibodies is defined as CIP (Cyclase Inhibiting PTH).

RESULTS

Despite relating to each other (r>0.97) PTH values varied remarkably among methods. For all methods, the reference intervals differed from those provided by the producer. Assuming these new ranges, 10 CaSF had over-range values not always associated with abnormalities of mineral metabolism. One of the PHP patients was normal for I-PTH with 2/4 methods. In HD the differences among methods were even greater, there were inverse (p<0.05) and direct (p<0.001) relationships with ionised calcium and osteocalcin-crosslaps, respectively. The CAP/CIP ratio was lower in low bone turnover patients, but the two subgroups widely overlapped.

CONCLUSIONS

This study indicates that the reliability of I-PTH assays is still unsatisfactory, and none of the four methods emerged as the best. Assay for CAP only improves diagnostic efficiency, whereas the CAP/CIP ratio does not exhibit powerful discriminating capacity. Our suggestion is that each Centre should establish its own reference ranges. PTH assay should always be coupled with measurements of other markers of mineral metabolism as well as renal function.

Bone turnover in hyperthyroidism before and after thyrostatic management

Hyperthyroidism is associated with enhanced osteoblastic and osteoclastic activity, and patients frequently have low bone mineral density and high bone turnover. The aim of this study was to examine the bone formation and resorption markers trend in 12 female patients, before and after normalization of thyroid activity. The following measurements were made at baseline and 1 and 6 months after hormone normalization induced by methimazole treatment: total alkaline phosphatase (ALP), bone alkaline phosphatase (BALP), collagen type C-terminal propeptide (PICP), osteocalcin (BGP), telopeptide (ICTP), urinary-hydroxyproline/urinary creatinine (uOHP/uCreat), urinary calcium/urinary creatinine (uCa/uCreat) and deoxypyridinoline crosslinks (D-Pyr). Compared with controls, all of these parameters were significantly increased (ALP p = 0.014; BALP p = 0.0001; PICP p = 0.013; BGP p = 0.009; ICTP p = 0.0001; uOHP/uCreat p = 0.002; uCa/uCreat p = 0.044; crosslinks p = 0.0001). After treatment the values of ALP, BALP and PICP in hyperthyroid patients showed an initial slight increase and then a significant downwards trend (ALP p = 0.008, BAP p = 0.001, PICP p = 0.026). Furthermore, resorption markers showed a significant decrease (uOHP/ uCreat p < 0.005 and D-Pyr p < 0.008). As regards lumbar BMD patients, measurements were significantly reduced in comparison with the control group (p = 0.005). Six months after serum thyroid hormones level normalization, we observed a significant increase (p=0.014 vs baseline). Both neoformation and resorption markers are useful to assess pathological bone turnover and bone involvement in hyperthyroidism. They could also be employed to monitor the effect of antithyroid treatment on bone and to indicate if bone antiresorption therapy should be considered.

Thrombosis-free survival and life expectancy in 187 consecutive patients with essential thrombocythemia

A total of 187 consecutive patients with essential thrombocythemia (ET) were diagnosed and followed by our Hematology Department in the period October 1980-November 1994. The overall follow-up was 773 patient-years. Thrombosis-free survival and overall survival were calculated for the whole cohort; the same parameters were then calculated after arbitrary division of the cohort into two groups, according to the median age at diagnosis (55 years). Fifty percent of the patients had at least one thrombotic episode within 9 years after diagnosis. The thrombosis-free survival curves calculated for patients younger or older than 55 years at diagnosis were comparable. About 85% of the patients were alive 10 years after diagnosis. The survival curves for patients younger and older than 55 years at diagnosis were not significantly different in the observation period, and the observed mortality (seven patients) among patients younger than 55 years at diagnosis was significantly higher than expected (1.68 cases). The relative risk of death was four times greater (SMR = 4.17, 95% C.I. 1.6-8.6, p<0.01) than for healthy, age-matched people living in the same area. Age at diagnosis, smoking, sex, hypercholesterolemia, peak number of platelets, hypertension, and diabetes were not significant prognostic cardiovascular risk factors in our cohort. In conclusion, our data show that ET has to be considered a serious disease that significantly decreases both quality of life (expected life without thrombosis) and life expectancy for younger patients.

Impact of glycaemic control, hypertension and insulin treatment on general and cause-specific mortality: an Italian population-based cohort of type II (non-insulin-dependent) diabetes mellitus

The aims of this study were to assess the impact of diabetes and associated variables (fasting plasma glucose, blood pressure, antidiabetic treatment, body mass index) on general and cause-specific mortality in an Italian population-based cohort with Type II (non-insulin-dependent) diabetes mellitus, comprising mainly elderly patients. The patients (n = 1967) who had Type II diabetes were identified in 1988 with an 80% estimated completeness of ascertainment. In 1995, a mortality follow-up (98% completeness) of the cohort was done amounting to a total of 11153 person-years. Observed and expected number of deaths were 577 and 428.7, respectively, giving a standardized mortality ratio (SMR) of 1.35 (95% CI 1.24-1.46). The most common underlying causes of death were malignant neoplasm, ischaemic heart disease and cerebrovascular diseases, which accounted for 18%, 17.8% and 17.5% of deaths, respectively. Cardiovascular disease as a whole (international classification of disease ICD-9 390-459) accounted for 260 of 577 deaths (SMR 1.21, 95% CI 1.07-1.36). In internal analysis, the most important predictors of general mortality were insulin-treatment (relative risk [RR] 1.72, 95% CI 1.19-2.49) and a fasting plasma glucose greater than 8.89 mmol/l ([RR] 1.29, 95 % CI 1.04-1.60), whereas the most important predictors of cardiovascular diseases were insulin-treatment and hypertension. In conclusion, this population-based study showed: 1) slight mortality excess of 35% in Type II diabetes being associated with 2) a 30% increased mortality in subjects with baseline fasting glucose greater than 8.89 mmol/l and 3) a 40% increased risk of death from cardiovascular diseases in hypertensive patients.

Association between an R338L mutation in the thyroid hormone receptor-beta gene and thyrotoxic features in two unrelated kindreds with resistance to thyroid hormone

Resistance to thyroid hormone (RTH) is a rare syndrome characterized by reduced sensitivity to thyroid hormone due to thyroid hormone receptor-beta (TRbeta) gene mutations or deletion. RTH has been classified on the basis of clinical features into generalized (GRTH) and pituitary (PRTH) resistance. There is, however, overlap of clinical and biochemical findings in patients with the two forms of resistance, and similar TRbeta gene mutations have been identified in both. The 2 subtypes of RTH, therefore, are considered to be different manifestations of a single genetic entity. We report a mutation of the TRbeta gene, an arginine to leucine substitution at codon 338 (R338L), in 2 unrelated RTH kindreds of northern Italian ancestry. The same mutation was already reported in a single unrelated kindred affected by PRTH. Five individuals, 3 in the first and 2 in the second family, were clinically evaluated and followed for 3-11 years. During the long-term follow-up, the patients manifested symptoms and signs of hyperthyroidism including palpitations, fine tremors, heat intolerance, increased sweating, increased deep tendon reflexes, moist and warm skin, cardiac rhythm abnormalities, reduced body weight, and reduced bone mineral density. The clinical features of these kindreds are consistent with a predominant PRTH phenotype.

Thyroid cancer histotype changes as observed in a major general hospital in a 21-year period

The existing registries of thyroid carcinoma are seldom comparable as far as epidemiological data, diagnostic criteria and histopatological description are concerned. Epidemiological studies report a progressive increase in the incidence of thyroid carcinoma in the last twenty years and in both sexes this increase of incidence has been referred to papillary histotype. Data collected from surgical series show a rate of thyroid carcinomas from 7 to 20% of total thyroid surgeries. The present study was designed in order to obtain a retrospective review of the distribution of thyroid carcinoma's different histotypes in the last 21 years in a major General Hospital. Detailed analysis of patients with histologically confirmed thyroid carcinoma admitted between 1974 and 1994 to the Surgery Department of Mauriziano Hospital of Torino, Italy showed an overall 11.8% prevalence of thyroid cancer out of the total thyroid surgeries. The rate of papillary carcinoma was the highest (54.3%) followed by follicular carcinoma (27.6%), anaplastic carcinoma (11.1%), medullary carcinoma (4.6%) and others (2.4%). The papillary-to-follicular ratio varied from 0.60 in 1974-76 to 6.88 in 1992-94. Female to male ratio of all thyroid carcinoma histotypes was 2.0 or more; papillary and follicular histotypes had the highest ratio. The variations of the histotype rate observed may be consequence of the silent increase of daily iodine intake throughout the subsequent years, while improved diagnostic tools available and increased experience of the medical staff have probably increased the number on thyroid ablations performed. Our data confirm the changing epidemiology of thyroid carcinoma, reported by international literature.

Incidence of second primary malignancies after a malignant tumor in childhood: a population-based survey in Piedmont (Italy)

We have studied the frequency of second primary malignancies (SPM) among the 2,328 children registered in 1967-1969 at the Childhood Cancer Registry of Piedmont, the largest population-based childhood cancer registry in Southern Europe. Since the population of Piedmont is not served by a conventional cancer registry covering all ages, SPMs were identified through a number of ad hoc surveys within a variety of sources. Eighteen SPM (all histologically diagnosed) were observed after a thorough survey conducted in the ontological departments in Piedmont and after a postal questionnaire addressed to general practitioners. Death certificates were also examined. The crude incidence rate was 116.5 per 100,000 person-years. Risk was higher among children whose first malignancy was diagnosed more recently (SIR = 9.8 for diagnoses in 1983-1989 vs. 4.5 for diagnoses in 1967-1974). The same tendency was confirmed in analyses restricted to children in whom leukemia was diagnosed as the first cancer. Clinical data regarding the treatment of the first malignancy were available for 16 children out of 18: 15 had received chemotherapy and 12 radiotherapy (9 SPM originated in the irradiation field). The interest of measuring the risk of SPM on a population basis (and not only in clinical series) and the advantage of close cooperation between epidemiologists and clinical oncologists are underlined.

[Pancreatic beta-cell hyperplasia in adults. A clinical case]

The author describe a rare case of pancreatic beta-cell hyperplasia. The patient was referred to us because of serious hypoglycemic crises. During hospitalization, endogenous hyperinsulinism was confirmed by hematochemical and instrumental tests. AngioCT of the pancreas evidenced a small lesion of the corpus, suspected of insulinoma. The patient underwent a corpus caudalis pancreatectomy: a small nodule with histologic neuroendocrine traits was ablated. A few days after the operation, new symptomatic hypoglycemia appeared. The hormonal tests confirmed a recurrence of endogenous hyperinsulinism. The patient underwent a new operation for pancreaticoduodenectomy: histological examination confirmed a pancreatic beta-cells hyperplasia. This condition has to be taken into account in the differential diagnosis of post prandial hypoglycemia. Besides, the observation of an insulinoma doesn't exclude the presence of a diffused disorder of islet cells as in the case above described.

Procoagulant activity of mononuclear cells is increased in myeloproliferative and myelodysplastic diseases

Procoagulant activity (PCA) of peripheral mononuclear cells (PMC) was evaluated in patients with primary thrombocythemia (PT, group A), polycythemia vera (PV), idiopathic myelofibrosis (IM) and myelodysplastic syndromes (group B), and in 15 healthy subjects as control group. PCA of PMC was assayed under basal conditions and after agonist-induced stimulation: bacterial lipopolysaccharide, glycosylated granulocyte-macrophage colony-stimulating factor, recombinant alpha-interferon. PCA was similar in the control group and group A when no stimulation was used, while PCA was found significantly higher in group B patients in the same conditions. In group A patients and in the control group, but not in group B patients, a lower PCA expression was found when PMC were simultaneously coincubated with LPS and alpha-interferon with respect to LPS incubation alone.

[Analysis of right electrocardiographic leads in 195 normal subjects]

AIM

The aim of the present study was to analyse age-related differences in the morphology of QRS complex and ST-T segment of right-sided chest ECG leads (V3R-V6R) in normal subjects.

METHODS

One hundred ninety-five subjects evaluated for competitive sport training were divided into 2 groups according to age: group A (18-35 years) 77 subjects; group B (36-65 years) 118 subjects. All subjects underwent a complete clinical examination, conventional 12-lead ECG with right-sided chest leads, spirometric tests, a maximal stress-test (Bruce protocol), and a cardiac ultrasound study. None had signs or symptoms of cardiopulmonary disease nor of thoracic abnormalities, and all had normal standard ECGs.

RESULTS

An rS morphology in V3R-V4R was observed in 92%-84% and 92%-81% of subjects in groups A and B, respectively (p = NS). The QS morphology in V6R was observed in 15% of subjects in group A and in 11% in group B (p = NS). Negative T-waves in V6R were more often observed in group A than B (94% vs 85%, p < 0.03). Isoelectric T-waves in V3R were found in 10% of subjects in group A and 21% in group B (p < 0.04). The amplitude of R-wave was always higher in group A (p < 0.01). An upsloping ST-T segment (0.5-1 mm) was observed only in V3R-V4R, with a prevalence of 23% in group A and 13% in group B in V3R (p < 0.05).

CONCLUSIONS

No significant differences were observed between the 2 groups as to QRS complex of the right-sided ECG leads. A QS morphology may be observed even in normal subjects. The polarity of T-wave is quite variable, but in V6R it is most often negative among young people. Elevation of ST-T segment may be observed only in V3R and V4R, and more often in young subjects in the former lead.

The risk associated with poisonings in children

The risk associated with poisonings in children was assessed on 6175 subjects admitted to the pediatric hospitals of 3 regions of Northern Italy between 1975 and 1990. The frequency of exposures and the severity of sequelae allowed high- and low-risk substances to be identified. Risks were studied separately in the 0-4, 5-9 and 10-13 y age group to determine age-related differences. A decrease in drug-related poisonings and an increase of those caused by household products, particularly in the first 2 y of life, were observed in 1983-90 as against 1975-82 in association with the introduction of safety caps and containers for drugs. Our study points out the need to strengthen active primary prevention through health education and parental and adolescent information, and to improve passive prevention through the extension of safety closures to household products.

Multiple myeloma: 'early' plasma cell phenotype identifies patients with aggressive biological and clinical characteristics

The immunological phenotype of bone marrow myeloma cells and peripheral blood lymphocytes was evaluated in 38 untreated myeloma patients. A striking increase of monotypic cells expressing the same light chain as the M component was observed in bone marrow from 18/38 (47%) patients. A two-colour analysis clarified that the majority of myeloma cells co-expressed plasma cell and B lymphocyte markers (cyIg, CD38, CD56 and sIg), and were regarded as early-plasma cells (early-PC). In the remaining patients, myeloma cells expressed plasma cell markers only (late-PC). Phenotype corresponded to a distinct morphological pattern: early-PC showed a lympho-plasmocytoid feature with significantly lower diameters than late-PC (12.1 v 14.8 microns, P < 0.007). Moreover, the plasma cell labelling index was significantly increased in early-PC patients (1.2 v 0.5%, P < 0.04). In peripheral blood from patients with early-PC, monotypic cells co-expressing sIg and CD38, CD56, but not CD19, were also detected. These data suggest a recirculation of early-PC. Myeloma cells maintained their phenotypic pattern during the course of the disease. This observation suggests that the degree of maturation is an intrinsic characteristic of the myeloma cell population in individual patients. The evaluation of prognostic factors, such as beta 2-microglobulin, C-reactive protein and neopterin, showed a statistically significant increase in the early-PC patients, suggesting a poor outcome. In conclusion, myeloma cell phenotype allows identification of a myeloma variant with aggressive biological and clinical characteristics.

Interferon plus glucocorticoids as intensified maintenance therapy prolongs tumor control in relapsed myeloma

Interferon-alpha-2b (IFN) has been demonstrated to prolong remission duration and survival in responding multiple myeloma (MM) patients. The aim of this study was to intensity maintenance therapy adding glucocorticoids (GLU) to the standard IFN therapy. Twenty-eight relapsed MMs with stable disease or response after conventional chemotherapy received IFN+GLU. The treatment included 3 megaunits of IFN 3 times a week continuously until relapse, plus 4 days pulsed high-dose dexamethasone (40 mg/day for 4 days every 28 days for 6 consecutive months every 12 months) in patients < 70 years, or oral prednisone (PDN, 50 mg 3 times a week) in patients > 70 years, both until relapse. Conventional chemotherapy induced a response in 12/28 MMs. For all patients the actuarial median progression-free survival from relapse was 24 months and the survival from relapse 42 months with no difference between responding and nonresponding patients. The first duration of tumor control, i.e. the interval from diagnosis to first relapse, was shorter than the period between first and second relapse in 11/28 patients (40%). Toxicity was mild and oral PDN significantly increased the subjective tolerability of IFN. These findings indicate that IFN+GLU after induction chemotherapy may prolong the duration of tumor control in relapsed MM.