PubMed Health⌕ Search

Biomedical subjects

M A Soares

Publications and source records attributed to M A Soares.

At least 19 recordsLinked to original sources
PubMed2006

Bayesian network analysis of resistance pathways against HIV-1 protease inhibitors.

Interpretation of Human Immunodeficiency Virus 1 (HIV-1) genotypic drug resistance is still a major challenge in the follow-up of antiviral therapy in infected patients. Because of the high degree of HIV-1 natural variation, complex interactions and stochastic behaviour of evolution, the role of resistance mutations is in many cases not well understood. Using Bayesian network learning of HIV-1 sequence data from diverse subtypes (A, B, C, F and G), we could determine the specific role of many resistance mutations against the protease inhibitors (PIs) nelfinavir (NFV), indinavir (IDV), and saquinavir (SQV). Such networks visualize relationships between treatment, selection of resistance mutations and presence of polymorphisms in a graphical way. The analysis identified 30N, 88S, and 90M for nelfinavir, 90M for saquinavir, and 82A/T and 46I/L for indinavir as most probable major resistance mutations. Moreover we found striking similarities for the role of many mutations against all of these drugs. For example, for all three inhibitors, we found that the novel mutation 89I was minor and associated with mutations at positions 90 and 71. Bayesian network learning provides an autonomous method to gain insight in the role of resistance mutations and the influence of HIV-1 natural variation. We successfully applied the method to three protease inhibitors. The analysis shows differences with current knowledge especially concerning resistance development in several non-B subtypes.

Bayes Theorem↗
PubMed2006

Analysis of HIV-1 pol sequences using Bayesian Networks: implications for drug resistance.

Human Immunodeficiency Virus-1 (HIV-1) antiviral resistance is a major cause of antiviral therapy failure and compromises future treatment options. As a consequence, resistance testing is the standard of care. Because of the high degree of HIV-1 natural variation and complex interactions, the role of resistance mutations is in many cases insufficiently understood. We applied a probabilistic model, Bayesian networks, to analyze direct influences between protein residues and exposure to treatment in clinical HIV-1 protease sequences from diverse subtypes. We can determine the specific role of many resistance mutations against the protease inhibitor nelfinavir, and determine relationships between resistance mutations and polymorphisms. We can show for example that in addition to the well-known major mutations 90M and 30N for nelfinavir resistance, 88S should not be treated as 88D but instead considered as a major mutation and explain the subtype-dependent prevalence of the 30N resistance pathway.

Amino Acid Sequence↗
PubMed1999

DNA replication during amplification of the C3 puff of Rhynchosciara americana initiates at multiple sites in a 6 kb region.

Two independent two-dimensional agarose gel electrophoresis methods have been used to map the origin of replication that directs amplification of the C3 DNA puff of Rhynchosciara americana. The results of neutral/neutral two-dimensional gel electrophoresis show that DNA replication initiates at multiple sites in a zone of at least 6 kb situated immediately upstream from the promoter of the main transcription unit of this puff. The complementary neutral/alkaline two-dimensional gel electrophoresis technique shows that, within the initiation zone, forks move in both directions. In contrast, unidirectional fork movement away from the initiation zone is observed at the ends of the region, implying that it is the only place in the amplified region of the C3 puff where initiations occur. Since the initiation zone coincides with the region that is most highly amplified, amplification of the C3 puff probably occurs by an onion skin-type mechanism.

Animals↗
PubMed1999

[Perception of the meaning of the caretaker's function for a group of nurses and caretakers: convergences and divergences].

This study review the of role the caretaker at the pediatric unit while the child is in hospital. The opinions of caretaker and nurses were surveyed as for the role that the participating family member would have during their stay along with the child in hospital. Data were gathered between April and June 1997 in units allowing for children to stay together with caretaker, at state hospitals. The interviews with the groups were separated by meas of the stafement analysis, based on the studies by COSTA (1992), and FRIEDMAN (1986), which allowed us to determine six categories: Security & Protection, Caretaking, Recovery, Knowledge, Supervision and Guidance, which in turn allowed us to study, although in a modest fashion, the agreements and disagreements regarding how our interviews perceive the role of the caretaker.

Adult↗
PubMed1999

The deletions of 22q11--the Portuguese experience.

The patients with a chromosome 22q11 deletion have a variable phenotype which includes DiGeorge (DG) and Velocardiofacial (VCF) syndromes. The aim of the present study is to characterize the phenotype of DG and VCF using facial biometry in 12 portuguese patients. We found 4/12 patients with the DG phenotype: 3/4 had telecanthus, small mouth and retrognathia; 1/4 had telecanthus, short nose with bulbous tip and a normal mouth. These patients had major cardiac defects associated with hypoplastic or absent thymus and monosomy 22q11. We did not find velopharyngeal insufficiency in patients with the so called DG phenotype 8/12 patients had the VCF phenotype: typical facies with variable features. Four of these had velopharyngeal insufficiency and learning disabilities. Four patients had cardiac defects and 5/8 had monosomy 22q11. Probably this clinical variability is due to mutations in critical genes involved in embryonic development.

Adolescent↗
PubMed1999

[Nursing diagnosis and interventions in a patient with multiple organ failure -- report of a case].

This study tries to identify Nursing Diagnoses and Interventions. It was done with a patient who was in critical health condition: multiple organs failure, in an Intensive Care Unit of a general hospital in Porto Alegre. The Case Study was the methodology used. Nursing Diagnoses is described mostly using NANDA Taxonomy. They are: Risk for Aspiration, Disuse Syndrome, Diarrhea, Risk for Infection, Impaired Tissue Integrity; and a Collaborative Problem was identified: Hypoglicemia. We have elaborated 34 Nursing Interventions for those diagnoses.

Aged↗
PubMed1998

The regulation of primate immunodeficiency virus infectivity by Vif is cell species restricted: a role for Vif in determining virus host range and cross-species transmission.

The primate immunodeficiency virus Vif proteins are essential for replication in appropriate cultured cell systems and, presumably, for the establishment of productive infections in vivo. We describe experiments that define patterns of complementation between human and simian immunodeficiency virus (HIV and SIV) Vif proteins and address the determinants that underlie functional specificity. Using human cells as virus producers, it was found that the HIV-1 Vif protein could modulate the infectivity of HIV-1 itself, HIV-2 and SIV isolated from African green monkeys (SIVAGM). In contrast, the Vif proteins of SIVAGM and SIV isolated from Sykes' monkeys (SIVSYK) were inactive for all HIV and SIV substrates in human cells even though, at least for the SIVAGM protein, robust activity could be demonstrated in cognate African green monkey cells. These observations suggest that species-specific interactions between Vif and virus-producing cells, as opposed to between Vif and virus components, may govern the functional consequences of Vif expression in terms of inducing virion infectivity. The finding that the replication of murine leukemia virus could also be stimulated by HIV-1 Vif expression in human cells further supported this notion. We speculate that species restrictions to Vif function may have contributed to primate immunodeficiency virus zoonosis.

Animals↗
PubMed1997

Complementation of integrase function in HIV-1 virions.

Proviral integration is essential for HIV-1 replication and represents an important potential target for antiviral drug design. Although much is known about the integration process from studies of purified integrase (IN) protein and synthetic target DNA, provirus formation in virally infected cells remains incompletely understood since reconstituted in vitro assays do not fully reproduce in vivo integration events. We have developed a novel experimental system in which IN-mutant HIV-1 molecular clones are complemented in trans by Vpr-IN fusion proteins, thereby enabling the study of IN function in replicating viruses. Using this approach we found that (i) Vpr-linked IN is efficiently packaged into virions independent of the Gag-Pol polyprotein, (ii) fusion proteins containing a natural RT/IN processing site are cleaved by the viral protease and (iii) only the cleaved IN protein complements IN-defective HIV-1 efficiently. Vpr-mediated packaging restored IN function to a wide variety of IN-deficient HIV-1 strains including zinc finger, catalytic core and C-terminal domain mutants as well as viruses from which IN was completely deleted. Furthermore, trans complemented IN protein mediated a bona fide integration reaction, as demonstrated by the precise processing of proviral ends (5'-TG...CA-3') and the generation of an HIV-1-specific (5 bp) duplication of adjoining host sequences. Intragenic complementation between IN mutants defective in different protein domains was also observed, thereby providing the first evidence for IN multimerization in vivo.

Amino Acid Sequence↗
PubMed1997

Molecular characterization of the C-3 DNA puff gene of Rhynchosciara americana.

We have mapped a region of about 33 kb which includes the transcription unit of the C-3 DNA puff gene of Rhynchosciara americana. The C-3 TU and a region extending approximately 800 bp upstream of the C-3 promoter were characterized. The TU is composed of three exons and produces a 1.1-kb mRNA whose level in salivary glands increases with the expansion of the C-3 puff. The C-3 messenger appears to undergo rapid deadenylation resulting in an RNA of about 0.95 kb which can still be observed in gland cells 15 h after the puff has regressed. The 1.1-kb mRNA codes for a 32.4-kDa, predominantly alpha-helical polypeptide with three conserved parallel coiled-coil stretches. The aa composition and structure of this polypeptide suggests that it is secreted and contributes to the formation of the cocoon in which the larvae pupate. The region upstream of the promoter contains several A-rich sequences with similarity to the ACS of yeast which might have a role in the initiation of replication/amplification.

Amino Acid Sequence↗
PubMed1997

A full-length and replication-competent proviral clone of SIVAGM from tantalus monkeys.

African green monkeys (AGM) are classified into four distinct species (commonly termed vervet, grivet, sabaeus, and tantalus monkeys), all of which are known to be infected with simian immunodeficiency virus (SIVAGM) in the wild. Sequence analysis of partial gag and env regions has indicated that each of the four species harbors a phylogenetically distinct SIVAGM subtype. This species-specific diversity suggests that African green monkeys have been infected with SIVAGM for an extended period of time, possibly even before their speciation from a common ancestor. However, our understanding of the evolutionary history of this group of viruses is still incomplete, in part because sequence information for most isolates is limited to small subgenomic regions. There are only six SIVAGM proviruses which have been sequenced in their entirety, and these represent only three of the four SIVAGM lineages (i.e., SIVAGMgri, SIVAGMver, and SIVAGMsab). In this paper, we have generated the first full-length proviral clone for SIVAGM infecting tantalus monkeys (SIVAGMtan). Lambda phage techniques were employed to clone this provirus (TAN) as a single genomic unit from productively infected Molt 4 (clone 8) cells, and sequence analysis confirmed the integrity of all major open reading frames, except vpr which contained an in-frame stop codon. The proviral clone was also biologically active since transfection yielded replication-competent virions. Amino acid sequence comparisons of all major viral proteins indicated that TAN was roughly equidistant from previously characterized sabaeus, grivet, and vervet strains, thus confirming that it represents a fourth independent SIVAGM lineage. Given the need for well-characterized reference reagents, this full-length tantalus provirus should facilitate future studies of SIVAGM molecular biology and evolution.

Animals↗
PubMed1997

Conservation and host specificity of Vpr-mediated cell cycle arrest suggest a fundamental role in primate lentivirus evolution and biology.

The human immunodeficiency virus type 1 (HIV-1) Vpr protein prevents infected cells from passing through mitosis by arresting them in the G2 phase of the cell cycle. Vpr is conserved among all primate lentiviruses, suggesting an important role in the virus life cycle. Moreover, in this study we show that the ability to cause cell cycle arrest is also conserved in Vpr proteins from a wide variety of both tissue culture-passaged and uncultured human (HIV-1 and HIV-2), sooty mangabey (simian immunodeficiency virus SIV(SM)), African green monkey (SIV(AGM)), and Sykes' monkey (SIV(SYK)) isolates. However, this property is cell type specific and appears to depend on the particular primate species from which the cells are derived. SIV(AGM) and SIV(SYK) Vpr proteins are capable of arresting African green monkey cells but are completely inactive in human cells. By contrast, HIV-1, HIV-2, and SIV(SM) Vpr proteins function in both simian and human cell types, although SIV(SM) Vpr functions more efficiently in simian cells than it does in human cells. Neither differential protein stability nor subcellular localization explains the species-specific activities of these proteins. These results thus suggest that Vpr exerts its G2 arrest function by interacting with cellular factors that have evolved differently among the various primate species.

Animals↗
PubMed1997

Study on optic microscope of the muscle and elastic components of the aorto-iliac bifurcation septum and initial segment of the middle sacral artery.

In this work the aorto-iliac bifurcation septum and the initial segment of the middle sacral artery were analyzed through optic microscope. 20 anatomical pieces of corpses from subjects of both sexes aging from 20 to 33 years were examined. After collection of pieces and fixation in formaline for 48 hours, histological sections of 20 microns were made and stained with the methods of Weigert, Verhoeff and Picrofucsine of Van Gieson. It was observed that the middle sacral artery arises from the posterior aortic wall laterally to the aorto-iliac bifurcation septum. The sequential analysis of the sections showed that the septum is lined by a thickening of connective tissue along its length and elastic fibers predominate on its central portion. Bundles of muscle fibers prevail on the lateral and posterior regions. It was observed, above the origin of the middle sacral artery, a reorganisation of tissues which represents, more caudally, the ostium of the artery. It was verified that the middle sacral artery arises at the aorto-iliac bifurcation septum, which is a transitional region and should be classified of mixed type and called aorto-septo-sacral transition.

Adult↗
PubMed1996

Fistula between duodenum and portal vein caused by peptic ulcer disease and complicated by hemorrhage and portal vein thrombosis.

We document a patient with a penetrating peptic ulcer of the first part of the duodenum, that extended into the main portal vein forming a fistula. This is the first reported case of a duodenoportal fistula secondary to peptic ulcer disease. The fistula was complicated by massive gastrointestinal hemorrhage, extra- and intrahepatic portal vein thrombosis, hepatic parenchymal infarction, and intrahepatic portal vein foreign body granulomas containing vegetable matter.

Aged↗
PubMed1994

[Nutrition evaluation of female university students].

The self-evaluation of nutritional status, utilized as a teaching strategy of introductory nutrition course at Nursing School (São Paulo's University), gave a subsidy to this work. With this purpose, 50 female university students 3rd'semester (mean age was 21.7) were required to complete a three days food record and report their approximate height and weight. The analysis of food intake adequacy indicated that 98% of the students had insufficient intake (less than 90% of recommended of National Research Council-1980) of, at least, one of the nutrients (protein, calcium, iron, vitamin A, B1, B2, C and niacin). It was evidenced an inadequate intake (less than 90% of RDA) of calcium (80% of the students), vitamin A (72%), iron (64%), vitamin B1 (74%), vitamin B2 (56%) and vitamin C (34%). The inadequate intake was more frequently and serious (less than 60% RDA) for calcium (42%), vitamin A (20%) and iron (16%) showing a vitamins and minerals deficient diet.

Adult↗
PubMed1992

The N-terminal amino acid sequence is essential for foot-and-mouth disease virus replicase activity.

1. Foot-and-mouth disease virus replicase was expressed by fusing its cDNA to the OmpA signal peptide coding sequence present in the pIN-III ompA series vectors. 2. Two constructions were developed to express either a full-length or truncated enzyme lacking the 20 amino acids at the N-terminal end. Bacterial extracts expressing the recombinant proteins were submitted to SDS-PAGE and the presence of the replicase was revealed by immunoblotting. The truncated form exhibited a higher mobility and the relative positions of the proteins show that the signal peptide was removed. 3. The biological activity of these two molecules was tested using a poly(A)-dependent oligo(U)-primed poly(U)-polymerase assay. The full-length replicase is active. The aminoterminal truncated enzyme had 0.02% activity of the intact one. 4. This result indicates the importance of the twenty N-terminal amino acids for the activity of FMDV RNA-dependent RNA polymerase.

Amino Acid Sequence↗
PubMed1992

In vitro activities of a recombinant foot-and-mouth disease virus replicase expressed in Escherichia coli.

1. The replicase gene of foot-and-mouth disease virus (FMDV) was expressed in Escherichia coli under the control of a tac promoter. The recombinant enzyme was purified by inclusion body precipitation, elution, and poly(U) Sepharose chromatography. 2. The enzyme exhibits poly(A)-dependent oligo(U)-primed poly(U) polymerase activity. The specific activity of the purified replicase is 1.3 x 10(5). The recombinant replicase synthesizes RNA using FMDV RNA as template, as well as heterologous RNAs, such as globin RNA and synthetic RNAs, polyadenylated or not. In all polymerization reactions, RNA products twice the size of the template are formed, both in the presence and absence of an oligo(U) primer. The enzyme is also capable of incorporating [alpha 32P]UTP in all RNAs tested except the viral template. This activity does not seem to be related to the primer independent polymerization activity. 3. The products from polymerization reactions were characterized by hybridization. In the absence of primer they consist of the template and a complementary strand covalently attached, while in the presence of primer they consist of two complementary strands synthesized de novo. 4. We propose mechanisms of RNA synthesis by the recombinant FMDV replicase in the absence and presence of primer. These mechanisms are discussed in terms of models for in vitro RNA synthesis of other picornaviruses.

Aphthovirus↗
PubMed1991

Expression of an active foot-and-mouth disease virus RNA polymerase in Escherichia coli.

The expression of a native form of the foot-and-mouth disease virus RNA polymerase was obtained. Two oligonucleotides of 66 base pairs were used to rebuild the 5' end of the gene and to introduce the first methionine codon. The expression of the active polymerase in E. coli was achieved by inserting the gene before the tac promoter of the pKK223-3 plasmid.

Amino Acid Sequence↗