PaTre: a method for paralogy trees construction.

Genomes can be described as a collection of clusters, the gene families, whose members are called paralogs. Paralogs are genes that most probably share duplication history and show a significant similarity in their sequences, even if they perform slightly different biological function. Among the different mechanisms that have led to an increase of the genomic information during biological evolution, gene duplication is probably the most important. To better understand duplication events, the first step is to investigate the history of the gene families in order to detect which duplication events have taken place, and in which relative (partial) order. Here we present a method, called PaTre, that, given a gene family, attempts to construct the paralogy tree of the family. We will work under the hypothesis that every family member derives from a duplication process of another member. By the term paralogy tree, we mean a directed tree in which the root represents the most ancient paralog of the family and each oriented arc (a, b) represents the existence of a duplication event from the template gene a to its copy b. Notice that gene a survives the event and can serve as a template of more than one duplication event; in fact, there can be more than one arc leaving a. PaTre uses new algorithmic techniques motivated by the specific application at hand. The reliability of the inferential process has been tested by means of a simulator that implements different hypotheses on the duplication-with-modification paradigm and on three examples of different biological gene families, belonging either to lower and higher organisms.

Effect of fluoxetine on intraocular pressure in the rabbit.

The effects of fluoxetine, which is a selective inhibitor of serotonin reuptake (SSRI) have been studied on the intraocular pressure (IOP) in the rabbit. IOP was measured using a Perkins tonometer. Intravenous administration of fluoxetine (6.0 mg kg-1) significantly increased IOP by 7.2 +/- 1.3 mmHg (P < 0.001). Fluoxetine administration also reduced the amount of urine excreted during the 24 hr, and increased the urine concentration of 5-hydroxyindole acetic acid (5-HIAA). Topical preadministration of ketanserin prevented a rise in IOP, without there being any effects on the other parameters examined. These findings indicate that intravenous administration of fluoxetine is able to raise IOP, through increased plasma levels of serotonin, which is confirmed by elevated 5-HIAA urine excretion and reduction in diuresis. Ketanserin, a specific 5-HT2A antagonist, counteracts the IOP increase brought about by fluoxetine, thus emphasizing the role of serotonin in the regulation of IOP and stressing the importance of including ophthalmological examination in the protocol of depressed patients undergoing SSRI therapy.

Polyclonal/monoclonal ratio in kidney and bone marrow transplanted patients treated with cyclosporine.

On 296 blood samples obtained from 22 bone marrow and 21 kidney transplanted patients, the concomitant measurements of polyclonal and monoclonal cyclosporine (CsA) were performed and the relative polyclonal/monoclonal (P/M) ratios were calculated. Biochemical profiles of kidney and liver functions were also determined in all patients. For each type of transplant, biochemical data were divided into two subgroups on the basis of P/M ratio: A) data obtained in patients with P/M ratio > 3.0; B) data obtained in patients with P/M ratio < or = 3.0. While in kidney transplanted patients no difference of biochemical profiles was found between two subgroups, in bone marrow transplant recipients the subgroup A showed a worsening of hepatic function parameters as compared to subgroup B. Therefore, it appears that P/M ratio could represent in bone marrow transplantation an index of hepatic CsA toxicity.

Lack of effect of gemfibrozil on cyclosporine blood concentrations in kidney-transplanted patients.

Forty kidney-transplanted patients with hypertriglyceridemia, under treatment with cyclosporine alone or associated with other immunosuppressive drugs, were treated with gemfibrozil. This drug, for a long-term treatment (ranging from 4 to 6 months), was able to decrease hypertriglyceridemia and did not modify either polyclonal (P) and monoclonal (M) cyclosporine blood levels or P/M ratio. These data seem to exclude an effect of gemfibrozil on cyclosporine blood concentrations. Therefore, the use of gemfibrozil in kidney-transplanted patients does not require modifications of cyclosporine dose.

Effects of different routes of cyclosporin A administration on blood levels in patients undergoing bone marrow transplantation.

This follow-up study has been carried out on 15 bone marrow transplant recipients treated intravenously with cyclosporin A (CsA) as a bolus (1.25-2.5 mg/kg/12 h) or by continuous infusion (1-3 mg/kg/24 h) from -2 until the 21st day after transplantation. All patients were subsequently treated with CsA orally at a starting dose of 6.25 mg/kg/12 h; this starting dose was then adjusted on the basis of CsA blood levels until the 60th day after transplantation, followed by progressive reduction and withdrawal within 6-12 months. In whole blood, trough levels of polyclonal (P) and monoclonal (M) CsA were monitored by a FPIA method and the polyclonal/monoclonal ratio (P/M) was calculated. This ratio was lower during CsA administration as a bolus or by continuous infusion than during oral administration; the decrease was statistically significant. This difference was probably due to first-pass metabolism which occurs in the liver and gut after oral administration.

A new dry chemistry immunoassay: comparison with a fluorescence polarization system.

A new dry chemistry fluorescence immunoassay has been recently developed for therapeutic drug monitoring. In the present study we compared this new assay with a fluorescence polarization immunoassay. The drugs tested were carbamazepine, phenobarbital, phenytoin, theophylline and valproate. An high degree of correlation (coefficients ranging from 0.95 to 1.00) was obtained for all drugs tested.

Evaluation of monoclonal/polyclonal ratio in kidney-transplanted patients treated with cyclosporine.

Fifty-seven kidney-transplanted outpatients, treated with cyclosporine alone or associated with azathioprine, prednisone, or methylprednisolone, were submitted to a monthly follow-up in order to determine cyclosporine blood levels and the monoclonal/polyclonal (M/P) ratio. Only methylprednisolone was able to modify the M/P ratio. This drug increased the M/P ratio, suggesting a cyclosporine metabolic inhibition. This effect disappeared in a few months in spite of the continuation of methylprednisolone treatment.

Effects of nimodipine on psychological-stress situation in aged rats.

Female aged rats treated with nimodipine, a calcium-blocker dihydropyridine derivative, were submitted to a psychological-stress situation. Nimodipine at the doses of 3 and 6 mg/Kg antagonized the stress-related body-weight decrease and lethality. These findings seem to validate the role of Ca-mediated mechanisms in the physiopathology of stress and the protective effects of the Ca-blockers in the stress-related illnesses.

Acute increase in plasma osmolality as a cause of hyperkalemia in patients with renal failure.

These studies were performed in patients with chronic renal failure to understand the mechanism(s) of hyperkalemia secondary to hypertonic NaCl infusion. In 10 patients, after intravenous infusion of either 5% or 2.5% NaCl (6 mEq per kg body wt for 120 minutes in both solutions), the maximum increase in plasma potassium averaged 0.6 (range 0.3 to 1.3) mmol/liter (P less than 0.01) or 0.3 (range 0.2 to 0.6) mmol/liter (P less than 0.01), respectively. The rise of both plasma potassium and osmolality was significantly higher during 5% NaCl than during 2.5% NaCl infusion (P less than 0.01). A significant linear correlation (P less than 0.01) between plasma potassium and osmolality was observed. Urinary potassium excretion was increased to a similar extent by 5% NaCl and 2.5% NaCl infusion. The observed hyperkalemia, secondary to NaCl infusion, was independent of venous pH, plasma bicarbonate, anion gap, insulin levels, and urinary norepinephrine and epinephrine excretion, and was associated with a fall in plasma aldosterone concentration. In separate studies, nine patients were treated with desoxycorticosterone acetate (DOCA; 20 mg i.m. for three days) before receiving saline (5%) infusion. DOCA did not prevent the level increase in plasma potassium that remained significantly correlated with plasma osmolality (P less than 0.01). In conclusion, hypertonic NaCl infusion in patients with renal failure causes a clinically relevant hyperkalemia despite increased renal excretion of potassium. This hyperkalemia is independent of acid-base or hormonal mechanisms known to regulate extrarenal homeostasis of potassium, and is strictly correlated with a rise in plasma osmolality.

Adrenergic nervous system and left ventricular mass in primary hypertension.

A link between the activity of the adrenergic nervous system and left ventricular hypertrophy has frequently been found in hypertensives. In 16 patients with untreated primary hypertension of mild to moderate degree, we have evaluated the possible correlations between echocardiographic left ventricular mass (LVMe) and sympathetic nervous system activity, using pressor response to exogenous noradrenaline infusion, measurement of 24-h catecholamine urinary excretion and pressure response to ergometric exercise. Pressor response to noradrenaline infusion was significantly related to echocardiographic measures of left ventricular hypertrophy (correlation coefficients were: -0.60 for LVMe; -0.51 for septal thickness (ST); -0.51 for posterior wall thickness). Left ventricular mass was also related to systolic blood pressure measured during ergometric exercise (correlation coefficients were: 0.52 with LVM index, 0.51 with LVMe and 0.61 with ST). Arterial wall hypertrophy has been identified as being responsible for the vascular hyperreactivity in hypertension. A likely explanation of our findings is that the degree of left ventricular hypertrophy is associated with the degree of structural alterations of the resistance vessels and that the vascular impairment is responsible for the increased pressure response to noradrenaline.

[Pharmacokinetics and nephrotoxicity of aminoglycoside antibiotics]. / Farmacocinetica e nefrotossicità degli antibiotici aminoglucosidici.

Aminoglycoside antibiotics are characterized by a quick fall of blood levels (half-life 2-3 hours) and by a very slow urinary excretion (they can be detected in the urine up to 10-20 days after therapy is discontinued). This peculiar pharmacokinetic feature of these antibiotics may be attributed to some rapid steps of their pharmacokinetics (glomerular filtration, tubular reabsorption or uptake, storage in the renal cells) followed by a very slow step (transfer from these cells to tubular lumen with following urinary excretion). The aminoglycosides are very polar compounds and their uptake by tubular cells is mediated by an active transport. The uptake is responsible for the storage in the corticorenal cells. It is generally held that the storage, because of its long duration, is responsible for the nephrotoxicity, although the correlation between storage and nephrotoxicity is denied by some authors. Some practical implications of aminoglycoside pharmacokinetics could be: a) Kidney damage by aminoglycosides is often reversible, but the potential risk of nephrotoxicity must be considered to be still present at the time of the interruption of therapy. Therefore the measures during aminoglycoside therapy (prophylaxis of risk factors, monitoring of renal function, etc.) are to be continued also in the period immediately after the interruption of therapy. b) In animals some factors (high-calcium diet, calcium blockers, ACE inhibitors) are able to reduce aminoglycoside nephrotoxicity; some of them are operating through inhibition of uptake. It would be desirable to test the possible ability of these factors to reduce aminoglycoside nephrotoxicity in humans.

Body weight and cardiovascular response to sympathetic stimulation in childhood.

The possible relationship between cardiovascular response to adrenergic stimulation and body weight has been studied in 166 eleven-year-old students (103 male, 63 female). Resting blood pressure (BP) by random-zero machine, heart rate (HR) and body weight (BMI) were measured four times in the school at 3-week intervals. On the third visit a mental arithmetic stress was carried out and a 24 h urine specimen was collected for the measurements of catecholamine excretion. On the fourth visit students carried out an isometric exercise (handgrip). Girls were more frequently found in the last quintiles of BMI (10/33 in the first vs 19/33 in the fifth). This might be due to a more advanced sexual maturation. BP at rest significantly increased with body weight (from 105/81 +/- 11/13 mmHg in the first to 119/87 +/- 10/12 in the fifth quintile). In each quintile no sex-related difference was observed in BP or HR. A marked cardiovascular response was observed during both tests without significant difference among quintiles. The 24 h urinary excretion of total catecholamines slightly increased with body weight (from 26.2 +/- 11 micrograms/24 h in the first to 34.5 +/- 19.5 micrograms/24 h in the fifth quintile). These data in a population of 11-year-old students therefore support the hypothesis that although BP at rest is influenced by BMI, the cardiovascular response to adrenergic stimulation is independent of body weight.

Is the sympathetic nervous system altered in children with familial history of arterial hypertension?

The sympathetic nervous system has been investigated in 42 children with family history of arterial hypertension and 68 children of the same age without hypertensive relatives. Pressure responses to mental arithmetic and to isometric handgrip stress were measured in both groups, along with 24 h catecholamine excretion. Resting blood pressure and heart rate did not show any difference between groups. The increase in diastolic pressure during the mental arithmetic exercise was, however, significantly greater in children with family history of hypertension. A sharp increase in blood pressure and heart rate was observed during isometric handgrip in both groups without any significant difference. Twenty-four hour catecholamine urinary excretion was significantly higher in the group with family history of hypertension (31 +/- 15 vs. 23 +/- 13 micrograms/24 h; p less than 0.05). These results seem to indicate that an initial impairment of the sympathetic activity is already detectable in young offspring of hypertensive patients.

Effects of sodium intake on blood pressure and adrenergic vascular reactivity.

The effects of dietary sodium restriction (approximately 2 g daily) on blood pressure (BP) and vascular reactivity to norepinephrine (NE) were evaluated in 12 patients with uncomplicated primary hypertension. BP was significantly reduced at the end of the treatment both at rest (153/100 +/- 19/7 vs. 142/93 +/- 19/5 mmHg) and during an exercise test on a bicycle. The pressor response to NE was significantly lower at the end of the low sodium period (reactivity index = 0.0044 vs. 0.0031; p less than 0.05): A twofold dose of NE was needed to increase mean BP by 20 mmHg (PD20) (from 273 +/- 120 to 450 +/- 218 ng/kg/min; p less than 0.05). Twenty-four-hour NE excretion increased significantly on a low-salt diet (40 +/- 14 vs. 49 +/- 16 micrograms/24 hr; p less than 0.05). The decrease in BP was inversely related to changes in PD20 (R = -0.60; less than p0.05). These results provide the evidence that the fall in BP is, at least in part, mediated by decreased end-organ responsiveness to adrenergic stimulation.

Effects of betamethasone on theophylline disposition in man. Are saliva values predictive of serum theophylline levels?

The pharmacokinetic interaction between betamethasone (5 mg/day for 5 days) and theophylline (3.35 mg/kg orally before and after betamethasone treatment) was studied in 13 female patients evaluating saliva and serum theophylline concentrations by means of an enzyme multiplied immunoassay technique. Betamethasone treatment did not significantly change saliva and serum theophylline levels. As regards the potential usefulness of saliva theophylline levels in predicting the concomitant serum concentrations of the bronchodilator, in spite of the significant correlation found in our study (r = 0.758; P less than 0.001), we think that, using individual saliva values, there is a poor predictive value for serum theophylline concentrations.