Biomedical subjects

G Grillo

Publications and source records attributed to G Grillo.

At least 19 recordsLinked to original sources

PubMed2000

Analysis of oligonucleotide AUG start codon context in eukariotic mRNAs.

The AUG start codon context features have been investigated by analyzing eukaryotic mRNAs belonging to various taxonomic groups. The functional relevance of each specific position surrounding the AUG start codon has been established as a function of the measured shift between base composition observed at that particular position, and base composition averaged over all the 5'untranslated regions. A more detailed analysis carried out on human genes belonging to different isochores showed significant isochore-specific fea-tures that cannot be explained only by a mutational bias effect. The most represented heptamers spanning from position -3 to +4 with respect to the initiator AUG have been determined for mRNAs belonging to different taxonomic groups and a web page utility has been set up (http://bigarea.area.ba.cnr.it:8000/BioWWW/ATG.html) to determine the relative abundance of a user submitted oligonucleotide context in a given species or taxon.

5' Untranslated Regions↗

PubMed2000

MitoNuc and MitoAln: two related databases of nuclear genes coding for mitochondrial proteins.

Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many degenerative diseases. All functions of mitochondria depend on the interaction of nuclear and organellar genomes. Mitochondrial genomes have been extensively sequenced and analysed and the data collected in several specialised databases. In order to collect information on nuclear coded mitochondrial proteins we developed MitoNuc and MitoAln, two related databases containing, respectively, detailed information on sequenced nuclear genes coding for mitochondrial proteins in Metazoa and yeast, and the multiple alignments of the relevant homologous protein coding regions. MitoNuc and MitoAln retrieval through SRS at http://bio-www.ba.cnr.it:8000/srs6/ can easily allow the extraction of sequence data, subsequences defined by specific features and nucleotide or amino acid multiple alignments.

Databases, Factual↗

PubMed2000

UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs.

The 5' and 3' untranslated regions of eukaryotic mRNAs may play a crucial role in the regulation of gene expression controlling mRNA localization, stability and translational efficiency. For this reason we developed UTRdb, a specialized database of 5' and 3' untranslated sequences of eukaryotic mRNAs cleaned from redundancy. UTRdb entries are enriched with specialized information not present in the primary databases including the presence of nucleotide sequence patterns already demonstrated by experimental analysis to have some functional role. All these patterns have been collected in the UTRsite database so that it is possible to search any input sequence for the presence of annotated functional motifs. Furthermore, UTRdb entries have been annotated for the presence of repetitive elements. All internet resources implemented for retrieval and functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs are accessible at http://bigarea.area.ba.cnr.it:8000/EmbIT/UTRH ome/

3' Untranslated Regions↗

PubMed2000

Disodium clodronate in painful nonresponsive periarthropathy of the hip.

This article identifies and describes a small group of patients with trochanteric tendinitis and bursitis in whom all modes of traditional therapy failed. We hypothesized that obstinate pain could be due to an increase in bone turnover associated with the formation of marginal bony outgrowths or enthesophytes. Injectable disodium clodronate is known to be highly efficacious in inhibiting bone reabsorption and is able to reduce several types of bone pain. The aim of the study was to evaluate the effectiveness of disodium clodronate in periarticular pathology of the hip in a group of patients resistant to traditional treatments and who were hypothesized to have a component of bone pain in their pain syndrome. Periarticular ultrasound examination is a useful method for detecting soft tissue alterations and is of interest in the study of these patients. In this study ultrasound examination showed periarticular alterations even when results of radiography were negative. Reduction in the hyperechoic ultrasound image, which confirms periarticular calcification, was observed in 75% of the patients treated with disodium clodronate vs. 33% of those treated with paracetamol. At the end of the study, all patients treated with disodium clodronate had a reduction in spontaneous and provoked pain > or = 1/3 vs. the basal visual analogue scale, unlike those treated with paracetamol.

Acetaminophen↗

PubMed1999

UTRdb: a specialized database of 5' and 3' untranslated regions of eukaryotic mRNAs.

The 5' and 3' untranslated regions of eukaryotic mRNAs may play a crucial role in the regulation of gene expression controlling mRNA localization, stability and translational efficiency. For this reason we developed UTRdb (http://bigarea.area.ba.cnr.it:8000/BioWWW/#U TRdb), a specialized database of 5' and 3' untranslated sequences of eukaryotic mRNAs cleaned from redundancy. UTRdb entries are enriched with specialized information not present in the primary databases including the presence of nucleotide sequence patterns already demonstrated by experimental analysis to have some functional role. All these patterns have been collected in the UTRsite database so that it is possible to search any input sequence for the presence of annotated functional motifs. Furthermore, UTRdb entries have been annotated for the presence of repetitive elements.

3' Untranslated Regions↗

PubMed1999

Ciliary motility at light microscopy: a screening technique for ciliary defects.

To verify whether or not ciliary motility can be reliably assessed by light microscopy alone, we examined the nasal brushings of 53 patients with suspected ciliary dyskinesia and 10 healthy controls. The results of light microscopy were compared with cilia ultrastructure assessed with electron microscopy. Ciliary motility was significantly related with cilia ultrastructure. However, eight cases of lung disease due to bronchiectasis of unknown origin had immotile cilia on light microscopy, but normal ciliary ultrastructure on electron microscopy. Instances of normal and abnormal ultrastructure were detected in one case with motile cilia. There was an 83% agreement between electron microscopy and light microscopy. Sensitivity and specificity of light microscopy were 92% and 80%, respectively. In conclusion, light microscopy evaluation of ciliary motility does not appear to be a reliable screening test for ciliary dyskinesia because it does not quantify ciliary beat activity, which is a criterion for deranged ciliary motion. A complete evaluation of ciliary ultrastructure together with in vivo, if applicable, or in vitro function test (namely, the analysis of ciliary beat frequencies and/or waveform) is required for a definite diagnosis of ciliary dyskinesia.

Adolescent↗

PubMed1998

UTRdb: a specialized database of 5'- and 3'-untranslated regions of eukaryotic mRNAs.

The important role the untranslated regions of eukaryotic mRNAs may play in gene regulation and expression is now widely acknowledged. For this reason we developed UTRdb, a specialized database of 5'- and 3'-untranslated sequences of eukaryotic mRNAs cleaned from redundancy. UTRdb entries are enriched with specialized information not present in the primary databases, including the presence of functional patterns already demonstrated by experimental analysis to have some functional role. A collection of such patterns is being collected in UTRsite database (http://bio-www.ba.cnr.it:8000/srs5/) which can also be used with appropriate computational tools to detect known functional patterns contained in mRNA untranslated regions.

Animals↗

PubMed1998

Relationships of serum leptin to body composition and resting energy expenditure.

Body weight (BW), body mass index (BMI), body fat, serum leptin concentration and resting energy expenditure (REE) were fitted in a multiple linear regression model in a group of individuals with stable body weight. While serum leptin concentration was well related to BW, to BMI and to body fat, no correlations with the REE values were found. This suggests that serum leptin concentration would represent an index of adiposity and poorly reflects energy metabolism.

Adipose Tissue↗

PubMed1998

Pulmonary manifestations of Gaucher disease: an increased risk for L444P homozygotes?

Pulmonary disease is a complication of Gaucher disease (GD), a lysosomal disorder due to the deficiency of glucocerebrosidase. Lung involvement was investigated through chest radiography, high-resolution computed tomography of the chest, pulmonary function tests (PFT), and oxygen saturation (SaO2) at 21% FI(O2) in 13 Italian GD patients, six homoallelic for the L444P mutation (Group A), seven with various genotypes (Group B). Echocardiography and transcutaneous oxygen tension measurement at room air and after breathing 100% oxygen were performed to exclude pulmonary hypertension and/or intrapulmonary shunts. A score index (SI) including lung involvement evaluated the severity of GD. In three Group A patients with respiratory symptoms and in an asymptomatic male interstitial involvement was demonstrated; one child died of aspiration pneumonia. Group B patients had no signs of lung damage; PFT were normal in all cases but one. SaO2 was normal in both groups. Pulmonary vascular disease was ruled out in three cases with respiratory symptoms. In Groups A and B the median SI were 22 and 13, respectively (p < 0.01). L444P homozygotes appear at major risk for developing pulmonary disease, even at earlier ages. A comprehensive evaluation of lung involvement is recommended primarily in these subjects.

Adolescent↗

PubMed1998

Cystic fibrosis: when should high-resolution computed tomography of the chest Be obtained?

OBJECTIVE: To provide indications for high-resolution computed tomography (HRCT) of the chest in patients with cystic fibrosis (CF). DESIGN: We compared the HRCT and conventional chest radiography (CCR) scores and assessed their correlation with clinical scores and pulmonary function tests. SETTING: Department of Pediatrics, Federico II University, Naples, Italy. SUBJECTS: A total of 30 patients with CF 6.75 to 24 years of age. RESULTS: CCR scores correlated highly with HRCT (r = -0.8) and clinical (r = 0.5) scores, whereas total HRCT scores were not related to clinical scores. Of all the specific HRCT findings, only bronchiectasis appeared related significantly to the clinical score (r = 0.6). Most pulmonary function tests were related to CCR and total HRCT scores, but not to HRCT scoring of specific changes. Forced vital capacity and CCR scores appeared the best predictors of the HRCT score (multiple R = 0.58 and 0.79, respectively). In patients with mild lung disease, HRCT detected bronchiectasis and air trapping in 57% and 71% of the cases, respectively. In patients with more abnormal chest radiographs, bronchiectasis and air trapping were demonstrated on HRCT in all cases. CONCLUSIONS: These findings suggest that HRCT of the chest is most useful in the identification of early lung abnormalities in patients with CF with mild respiratory symptoms, whereas for established disease, CCR is still the first-line imaging technique. The advantage of detecting early changes on CT imaging awaits additional confirmation, at least until early therapeutic interventions affecting significantly the final outcome of the disease are demonstrated. In patients with advanced disease, HRCT may be useful in the evaluation of specific lung changes when more aggressive treatment such as chest surgical interventions is indicated. Given the cost of the procedure and the high radiation dosage compared with CCR, a careful assessment of the cost:benefit ratios of HRCT is strongly recommended in CF.

Adolescent↗

PubMed1998

GeneUp: a program to select short PCR primer pairs that occur in multiple members of sequence lists.

A computer program is presented that selects a small set of short primer pairs for PCR to sample all the sequences in a user-specified list of mRNAs. Such primer pairs could be used to increase the probability of sampling mRNAs of particular interest in differential display and to generate simplified hybridization probes for DNA chips or arrays. The program uses simulated PCR to find pairs of primers that sample more than one sequence in the list. A small set of such primer pairs is selected that give maximal coverage of the sequences in the list. Primer pairs are excluded that: (i) generate simulated PCR products of the same size from a number of sequences in the list, (ii) can easily form primer dimers, (iii) are outside a specified range of G + C content or (iv) occur in another list of undesirable sequences, such as rRNAs and Alu repeats. Five lists consisting of from 48-285 cDNA sequences were used to test the program. A small number of pairs of primers, 8-10 bases in length, were selected that fit the above criteria and that generate one or more simulated PCR products in all or most of the cDNAs in each list.

Base Sequence↗

PubMed1997

Structural and compositional features of untranslated regions of eukaryotic mRNAs.

The important role of 5' and 3' untranslated regions of eukaryotic mRNAs in gene regulation and expression is now widely accepted. In order to study the general structural and compositional features of these sequences we developed UTRdb, a specialized database of 5' and 3'-UTR sequences from seven different taxonomic groups of eukaryotic mRNAs cleaned of redundancy. The analysis of the UTR sequences contained in this database showed that 5'-UTR sequences, on average 200 nucleotides long, are 1.5-3 times shorter than the corresponding 3'-UTR sequences in the various taxonomic groups considered here. As to their compositional properties on average 5'-UTR sequences resulted in all cases GC richer than 3'-UTR sequences, and significant correlations were found between the GC content of 5' and 3'-UTR sequences and the GC content of the third silent codon positions of the corresponding protein coding genes. The dinucleotide analysis showed a differential depletion of CpG in vertebrate 5' and 3'-UTR, with 5'-UTR sequences being more CpG-rich, and a generalized depletion of TpA in both 5' and 3'-UTR was observed in all eukaryotic sequence collections.

Base Composition↗

PubMed1997

Alteration of interleukin-2 (IL-2) and soluble IL-2 receptor secretion in the sera and urine of patients with rickettsial boutonneuse fever.

Sera and urine samples from 115 Sicilian patients with boutonneuse fever (BF), obtained at the time of diagnosis and after clinical recovery, were analyzed for concentrations of interleukin (IL)-2 and soluble IL-2 receptor (sIL-2R). There were significantly high levels of sIL-2R in the urine and sera of patients with acute BF compared with healthy controls, and the values returned to normal following successful chemotherapy. The data indicate that the sIL-2R urine concentrations correlated directly with the sIL-2R sera levels. In contrast, in all tested sera and urine samples, IL-2 levels were normal. Furthermore, a reduction in IL-2 production by peripheral blood mononuclear cells from acute BF patients was also observed. sIL-2R represents an unspecific marker useful to monitor the evolution of BF.

Boutonneuse Fever↗

PubMed1997

Prevalence and clinical correlates of microalbuminuria in essential hypertension: the MAGIC Study. Microalbuminuria: A Genoa Investigation on Complications.

The prevalence of microalbuminuria and its relationship with several cardiovascular risk factors and target organ damage were evaluated in a cohort of 787 untreated patients with essential hypertension. Albuminuria was measured as the albumin-to-creatinine ratio in three nonconsecutive, first morning urine samples. The prevalence of microalbuminuria was 6.7%. Albuminuric patients were more likely to be men and to be characterized by higher blood pressure, body mass index, and uric acid levels and lower HDL cholesterol and HDL cholesterol-to-LDL cholesterol ratio. Piecewise linear regression analysis demonstrated that uric acid and diastolic blood pressure significantly influence albuminuria and together account for a large part of its variations. K-means cluster analysis performed on the entire cohort of patients confirmed that microalbuminuria is associated with a worse cardiovascular risk profile. Furthermore, microalbuminuria was associated with the presence of target organ damage (eg, electrocardiographic [ECG] abnormalities and retinal vascular changes). Age and the presence of microalbuminuria act as independent risk factors for the development of ECG abnormalities and retinal vascular changes. Cluster analysis allowed us to identify three subgroups of patients who differed in the presence or absence of microalbuminuria, retinopathy, and ECG abnormalities. We conclude that the prevalence of microalbuminuria in essential hypertension is lower than previously reported. Increased urinary albumin excretion is associated with a worse cardiovascular risk profile and is a concomitant indicator of early target organ damage.

Adolescent↗

PubMed1997

[Rare tumor of the stomach: leiomyoblastoma].

The Authors report a case of gastric leiomyoblastoma presenting a dyspeptic and painful symptomatology and microcytic hyposideremic anaemia. The patient underwent elsewhere gastric resection and was discharged with the diagnosis of "gastric leiomyoma characterized by bizarre cells". After a review of the literature, the Authors emphasize the anatomo-pathological and clinical aspects pointing out the diagnostic difficulties in this malignancy. The correct treatment is based on predicted factors of malignancy.

Female↗

PubMed1997

[Surgical treatment of obesity: our experience].

The surgical treatment of morbid obesity is reserved to patients non responding to medical and dietetical therapy. The Authors suggest for these patients a sequential surgical treatment: a vertical gastroplasty, followed by an abdominoplasty. In the Authors experience, this approach offers good results in terms of weight loss and aesthetics. In this paper, the results obtained in 19 patients, operated for morbid obesity in the past three years, are reported.

Adult↗

PubMed1996

Databases of mRNA untranslated regions for metazoa.

The important role that untranslated regions of mRNAs (UTR) may play in gene regulation and expression is now widely accepted. For this reason we developed UTRDB, a specialized database of 5'- and 3'-UTR of eukaryotic mRNAs cleaned of redundancy. This paper describes the composition and the general feature of UTRDB. The analysis of UTRDB by using suitable statistical methods could provide useful information for guiding the experimental work aimed at delucidating the role of UTR sequences in gene regulation and expression.

Algorithms↗

PubMed1996

CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases.

A key concept in comparing sequence collections is the issue of redundancy. The production of sequence collections free from redundancy is undoubtedly very useful, both in performing statistical analyses and accelerating extensive database searching on nucleotide sequences. Indeed, publicly available databases contain multiple entries of identical or almost identical sequences. Performing statistical analysis on such biased data makes the risk of assigning high significance to non-significant patterns very high. In order to carry out unbiased statistical analysis as well as more efficient database searching it is thus necessary to analyse sequence data that have been purged of redundancy. Given that a unambiguous definition of redundancy is impracticable for biological sequence data, in the present program a quantitative description of redundancy will be used, based on the measure of sequence similarity. A sequence is considered redundant if it shows a degree of similarity and overlapping with a longer sequence in the database greater than a threshold fixed by the user. In this paper we present a new algorithm based on an "approximate string matching' procedure, which is able to determine the overall degree of similarity between each pair of sequences contained in a nucleotide sequence database and to generate automatically nucleotide sequence collections free from redundancies.

Algorithms↗