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Biomedical subjects

E Merino

Publications and source records attributed to E Merino.

At least 37 records · Page 2Linked to original sources
PubMed2000

Relationship between whole proteome aminoacid composition and static DNA curvature.

To study possible relationships between an organism's genomic DNA curvature and the aminoacid composition of its proteome, every peptidic sequence from fully determined genomes was retrotranslated using the E. coli codon preferences, and the curvature profiles of the resulting DNA sequences were calculated and compared. A clear interdependence between these two variables was observed, as each retrotranslated proteome presented a distinctive, statistically significant DNA curvature profile biased toward its natural DNA curvature profile. In addition, by comparing the profiles arising from real and randomly permuted proteomes, we also found a position-dependent contribution of the peptidic sequence to DNA curvature. The implications of these results support the idea of a possible selection toward a specific global curvature of genomes.

Amino Acids↗
PubMed2000

A Bacillus subtilis gene of previously unknown function, yhaG, is translationally regulated by tryptophan-activated TRAP and appears to be involved in tryptophan transport.

Computer analysis of the Bacillus subtilis genome sequence revealed a gene with no previously attributed function, yhaG, specifying a transcript containing a presumptive binding site for the tryptophan-activated regulatory protein, TRAP. The presumptive TRAP binding site overlaps the yhaG Shine-Dalgarno sequence and translation initiation region. TRAP was shown to regulate expression of yhaG translationally. Production of the yhaG transcript in vivo was found to compete for the binding of TRAP to other known TRAP binding sites. YhaG is likely to be a transmembrane protein involved in tryptophan transport.

Amino Acid Sequence↗
PubMed1999

[Visceral leishmaniasis: a comparative study of patients with and without human immunodeficiency virus infection].

BACKGROUND: The changes that HIV coinfection can induce in clinical symptoms, response to treatment and prognosis of visceral Leishmaniasis (VL) are not well known. METHOD: We retrospectively describe the characteristics of VL in patients with and without HIV infection, between 1988-1998. RESULTS: Fifty episodes of VL were diagnosed in 40 patients. Nineteen (47.5%) were HIV coinfected, 57.8% of them have had an aids defining illness, and the median of CD4+ lymphocytes was 50/mm3. Clinical and laboratory data were similar to patients non HIV infected, except for lower levels of LDH (437 vs 578 U/ml; p = 0.02) and total lymphocytes (665 vs 1.500/mm3; p = 0.004) and higher levels of hemoglobin (9.8 vs 8.7 gr/dl; p = 0.01) and ESR (85 vs 44 mm; p = 0.01). The first episode of VL was diagnosed in 87.5% patients through bone marrow aspirate, and the other cases were diagnosed by biopsies of gum (2), lymph node (1) or liver (1). One patient was diagnosed clinically: he had a positive serology and a good response to antileishmanial therapy. Treatment failed in nine patients (22.5%), 7 HIV-coinfected. Eight patients died (20%), 6 HIV-coinfected. Five deaths were directly attributed to VL. Six coinfected patients (31.5%) relapsed and only one (4.7%) in the other group. CONCLUSIONS: We did not find major differences in clinical manifestations or laboratory data between the two groups. Biopsies of several tissues can be particularly helpful for diagnosis in immunocompromised patients with negative bone marrow aspirates. Failures, mortality and relapses are more common in HIV infected patients. VL coinfection usually affects HIV infected patients when they develop severe immunodepression.

AIDS-Related Opportunistic Infections↗
PubMed1998

Relationship between codon usage and sequence-dependent curvature of genomes.

Static DNA curvature distributions of full-sequenced genomes and large DNA contigs from different organisms were calculated. Very distinctive differences among histogram profiles coming from archaebacteria, eubacteria, and eukaryotes were observed. Eubacterial profiles were, on average, more curved than were archaeal and eukaryotic profiles. A comparative analysis between real and randomized DNA sequences revealed that eubacterial genomes presented, overall, higher curvature values than random sequences. An opposite portrait was exhibited by archaeal and eukaryotic genomes. They displayed a lower frequency of curved regions than their corresponding randomized sequences. The contributions of coding and intergenic regions to the curvature profile were also analyzed. Intergenic regions, on average, were found to be more curved than the overall genomic sequences, especially in prokaryotic organisms. Nevertheless, because of their small size with respect to coding regions, the contribution of intergenic sequences to the overall curvature profile tended to be minor. A clear relationship between codon usage and DNA curvature was demonstrated, and a proposal of the possible coevolution of both systems is discussed. Finally, we present a procedure to quantify the deviation of a curvature profile from randomness through a formal statistical analysis.

Archaea↗
PubMed1995

trp RNA-binding attenuation protein (TRAP)-trp leader RNA interactions mediate translational as well as transcriptional regulation of the Bacillus subtilis trp operon.

Expression of the Bacillus subtilis trpEDCFBA operon has been shown to be regulated by transcription attenuation in response to the availability of L-tryptophan. Regulation is mediated by the tryptophan-activated trp RNA-binding attenuation protein, TRAP, the product of mtrB. Formation of mutually exclusive RNA anti-terminator and terminator structures within trp leader RNA determines whether transcription will terminate in the leader region of the operon. Previous studies suggested that transcripts that escape termination are subject to translational regulation via the formation of a secondary structure that blocks ribosome access to the trpE ribosome-binding site. To assess the relative importance of these postulated events in trp operon regulation, we used site-directed mutagenesis to alter the putative elements involved in transcriptional and translational control. Using a trpE'-'lacZ reporter, we measured translational yield and specific mRNA levels with various leader constructs, in both mtrB+ and mtrB strains, during growth in the presence and absence of excess tryptophan. To verify that the altered regulatory regions behaved as expected, we carried out in vitro transcription assays with the wild-type and altered leader region templates and performed oligonucleotide competition assays with an oligonucleotide complementary to a segment of the transcription terminator. Our results establish that binding of TRAP to leader RNA regulates of transcription termination in the trp operon over about an 88-fold range and regulates translation of trpE over about a 13-fold range. The roles played by different trp leader RNA segments in mediating transcriptional and translational regulation are documented by our findings.

Bacillus subtilis↗
PubMed1994

Antisense overlapping open reading frames in genes from bacteria to humans.

Long Open Reading Frames (ORFs) in antisense DNA strands have been reported in the literature as being rare events. However, an extensive analysis of the GenBank database revealed that a substantial number of genes from several species contain an in-phase ORF in the antisense strand, that overlaps entirely the coding sequence of the sense strand, or even extends beyond. The findings described in this paper show that this is a frequent, non-random phenomenon, which is primarily dependent on codon usage, and to a lesser extent on gene size and GC content. Examination of the sequence database for several prokaryotic and eukaryotic organisms, demonstrates that coding sequences with in-phase, 100% overlapping antisense ORFs are present in every genome studied so far.

Amino Acid Sequence↗
PubMed1994

[Cancer of the larynx and discriminant analysis].

In order to get the prognosis on the 5 years survival, free of disease, in a sample of 428 laryngectomies, for cancer of the larynx, the AA. have realized a discriminant analysis working out with several known factors. Only from 109 components of the group complete information could be available about the variables studied and with these a linear discriminant function was obtained. The rate of correct prediction was 78.8 percent for cancer recurrence and 77.6 percent for survival without recurrence after 5 years term. The discriminant variables were: positive lymph nodes, tumour staging using TNM classification, cord mobility and alcohol consumption.

Discriminant Analysis↗
PubMed1994

[Cancer of the larynx and 5 years survival].

Between the years 1971 and 1984, 428 patients with the diagnosis of laryngeal carcinoma were operated at the ENT Department of Virgen de la Arrixaca Hospital (Murcia, Spain). All of them submited to laryngectomy. The 5-years actuarial recurrence-free rate and its correlations with host factor are studied. That is to say: staging, histology of the primary lesion, incidence of lymph node metastasis and the treatment done. The overall 5-years actuarial recurrence free rate was 74 percent. The hard drinkers had a significative lower survival rate (53 percent) that no drinkers (81 percent). Glottic localization had better survival rate (83 percent) than supraglottic (68 percent). Both stages I and II had a survival rate of 87 percent. 70 percent stage III and only 41 percent the stage IV. Squamous cell carcinoma with good differentiation had a significative better prognosis (79 percent) in well differentiated and 58 percent when the differentiation were poor. Patients with metastasis in lymph nodes had lower survival rate (49 percent) than those without metastases (83 percent).

Adult↗
PubMed1993

Adenosquamous carcinoma of the duodenum. An immunohistochemical study.

A rare adenosquamous carcinoma of the duodenum occurred in an 84-year-old woman. Histologically the neoplasm showed evidence of glandular and squamous differentiation, and both components showed malignant characteristics. Intermediate elements sharing squamous and glandular features, were found and were immunoreactive for carcinoembryonic antigen, epithelial membrane antigen and cytokeratins of both low and high molecular weight. A review of the literature and discussion about the histogenesis is included.

Adenocarcinoma↗
PubMed1992

Carbon regulation and the role in nature of the Escherichia coli penicillin acylase (pac) gene.

Quantitative analysis of specific pac mRNA and a lacZ fusion to the 5'-terminal region of the pac gene demonstrated that both phenylacetic acid induction and catabolite repression by glucose are involved, at the transcriptional level, in the regulation of the pac gene. The studies presented here suggest that this regulation is also present in Escherichia coli transformed strains in which the pac gene was not originally present. Analysis of the nucleotide sequence of the 5'-terminal region of this gene, with a statistical algorithm, confirms that the putative promoter previously proposed by our group is the most feasible within this region. We demonstrate that penicillin acylase activity can confer on E. coli the ability to use penicillin G as a metabolic substrate, by detaching the phenylacetic group which can be used as a carbon source. Based on these data, the regulation properties of the pac gene studied in this work, and the specificity profile of the penicillin acylase enzyme we suggest a role for it in E. coli as a scavenger enzyme for phenylacetylated compounds.

Base Sequence↗