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J Alves

Publications and source records attributed to J Alves.

At least 19 recordsLinked to original sources
PubMed2005

Differential expression of NF-kappaB pathway genes among peripheral T-cell lymphomas.

Nuclear factor kappa B (NF-kappaB) is one important pathway in T-cell proliferation and survival. In a previously reported microarray study, we found NF-kappaB pathway genes differentially expressed between peripheral (PTCL) and lymphoblastic lymphomas. Here, we investigated the expression of NF-kappaB pathway genes using cDNA microarrays in a group of 62 PTCL and in reactive lymph nodes. We found two different subgroups of PTCL based on the expression of NF-kappaB pathway genes. One-third of PTCL showed clearly reduced expression of NF-kappaB genes, while the other group was characterized by high expression of these genes. This distinction was found among all T-cell lymphoma categories analyzed (PTCL unspecified, angioimmunoblastic, cutaneous and natural killer/T lymphomas) with the exception of anaplastic lymphomas (ALCL), which were characterized by reduced NF-kappaB expression in anaplastic cells. Quantitative RT-PCR and immunohistochemical analysis of NF-kappaB-p65 protein confirmed these differences among PTCL subgroups. Importantly, we found that differentiation between NF-kappaB-positive and -negative PTCL could be of clinical interest. The expression profile associated to reduced expression of NF-kappaB genes was significantly associated with shorter survival of patients and seems to be an independent prognostic factor in a multivariate analysis.

Adult↗
PubMed2005

CaSPredictor: a new computer-based tool for caspase substrate prediction.

MOTIVATION: In vitro studies have shown that the most remarkable catalytic features of caspases, a family of cysteineproteases, are their stringent specificity to Asp (D) in the S1 subsite and at least four amino acids to the left of scissile bound. However, there is little information about the substrate recognition patterns in vivo. The prediction and characterization of proteolytic cleavage sites in natural substrates could be useful for uncovering these structural relationships. RESULTS: PEST-like sequences rich in the amino acids Ser (S), Thr (T), Pro (P), Glu or Asp (E/D), including Asn (N) and Gln (Q) are adjacent structural/sequential elements in the majority of cleavage site regions of the natural caspase substrates described in the literature, supporting its possible implication in the substrate selection by caspases. We developed CaSPredictor, a software which incorporated a PEST-like index and the position-dependent amino acid matrices for prediction of caspase cleavage sites in individual proteins and protein datasets. The program predicted successfully 81% (111/137) of the cleavage sites in experimentally verified caspase substrates not annotated in its internal data file. Its accuracy and confidence was estimated as 80% using ROC methodology. The program was much more efficient in predicting caspase substrates when compared with PeptideCutter and PEPS software. Finally, the program detected potential cleavage sites in the primary sequences of 1644 proteins in a dataset containing 9986 protein entries. AVAILABILITY: Requests for software should be made to Dr José E. Belizário SUPPLEMENTARY INFORMATION: Supplementary information is available for academic users at site http://icb.usp.br/~farmaco/Jose/CaSpredictorfiles.

Algorithms↗
PubMed2003

Responses of soybean to oxygen deficiency and elevated root-zone carbon dioxide concentration.

Root flooding is damaging to the growth of crop plants such as soybean (Glycine max L.). Field flooding for 3 d often results in leaf chlorosis, defoliation, cessation of growth and plant death. These effects have been widely attributed solely to a lack of oxygen in the root-zone. However, an additional damaging factor may be CO(2), which attains levels of 30 % (v/v) of total dissolved gases. Accordingly, the effects of root-zone CO(2) on oxygen-deficient soybean plants were investigated in hydroponic culture. Soybean plants are shown to be very tolerant of excess water and anaerobiosis. No oxygen (100 % N(2) gas) and low oxygen (non-aerated) treatments for 14 d had no effect on soybean survival or leaf greenness, but plants became severely chlorotic and stunted when the roots were exposed to no oxygen together with CO(2) concentrations similar to those in flooded fields (equilibrium concentrations of 30 %). When root-zone CO(2) was increased to 50 %, a quarter of soybean plants died. Those plants that survived showed severe symptoms of chlorosis, necrosis and root death. In contrast, rice (Oryza sativa L.) plants were not affected by the combination of no oxygen and elevated root-zone CO(2.) A concentration of 50 % CO(2) did not affect rice plant survival or leaf colour. These results suggest that the high susceptibility of soybean to soil flooding, compared with that of rice, is an outcome of its greater sensitivity to CO(2).

Adaptation, Physiological↗
PubMed2002

Personality, brain asymmetry, and neuroendocrine reactivity in two immune-mediated disorders: a preliminary report.

Development of some immune-mediated disorders may depend on dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis. To explore neuropsychologic mechanisms in relation to the abnormal endocrine reactivity in patients with systemic lupus erythematosus (SLE) and chronic hepatitis C (CHC) we used the corticotropin releasing hormone (CRH) test, the Minnesota Multiphasic Personality Inventory (MMPI), and the Edinburgh Inventory of Manual Preference Inventory (EIMP). Compared to controls, the adrenocorticotrophic hormone (ACTH) response to CRH was reduced in CHC, while SLE presented reduced baseline dehydroepiandrosterone sulfate levels; higher neurotic scores were found in SLE and higher behavior deviant scores in CHC. Peak ACTH levels were a significant factor for the MMPI profile variability, while the manual preference score was a significant factor for the ACTH response. Personality and manual preference contribute to neuroendocrine abnormalities. Different behavioral and neuroimmunoendocrine models emerge for these disorders.

Adrenocorticotropic Hormone↗
PubMed2001

[Is ambulatory blood pressure monitoring reliable in hypertensive patients with atrial fibrillation?].

Atrial fibrillation (AF) is commonly seen in patients (pts) with systemic hypertension. They are usually excluded from ambulatory blood pressure monitoring (ABPM) because its accuracy is unknown. The aim of our study was to determine if ABPM can be used to assess 24 hour BP in pts with AF. We included hypertensive pts with chronic (> 6 months) AF, controlled heart rate (60-100 c.p.m), under therapy and also hypertensive pts in sinus rhythm (control group--CG). They were submitted to 24 hour ABPM (Spacelabs 90207). Manual BP with a standard mercury sphygmomanometer was taken during 3 visits (office BP) and on the day of ambulatory monitoring. Simultaneous measurements with a T-Tube were also performed. Thirty pts with chronic AF (63% males), mean age 73 +/- 8 years (52-85) and 18 pts in sinus rhythm (CG) were studied. The age, gender, office BP, ambulatory BP and proportion of successful measurements was similar in the 2 groups. In CG systolic and diastolic office BP did not differ from day ambulatory BP (148 +/- 14/84 +/- 7 vs 138 +/- 18/76 +/- 11 mmHg) and the same was seen in pts in AF (table). In this group, only the systolic BP taken immediately before the ambulatory device was put on, was significantly different from day ambulatory BP (148 +/- 21 vs 137 +/- 19 mmHg, p = 0.04). The proportion of successful measurements in AF group was 94 +/- 8 (65-98) with 93% > 80%. In 64 simultaneous measurements the differences were 6 +/- 5 and 5 +/- 5 mmHg for systolic and diastolic BP. Casual and ambulatory heart rate was also similar in the two groups (76 +/- 7/76 +/- 12--AF group; 78 +/- 10/78 +/- 8--control group). In conclusion, this study demonstrates that ABPM can be used to assess BP in patients with atrial fibrillation. There was a high percentage of successful recordings (93%). As in patients in sinus rhythm, there was no significantly difference in mean office blood pressure and daytime ambulatory blood pressure.

Aged↗
PubMed2000

Preventing the spread of vancomycin-resistant enterococci in a long-term care facility.

OBJECTIVES: To test the hypothesis that infection control practices can prevent the spread of vancomycin-resistant enterococci (VRE) to residents of a long-term care facility (LCF) from an affiliated acute care facility with a high endemic rate of colonization. DESIGN: Point prevalence study of the rate of rectal colonization. SETTING: A state-supported veterans nursing home and an acute care veterans hospital. PARTICIPANTS: Residents in a state veterans home. INTERVENTIONS: Identification of patients with rectal colonization by VRE before transfer to the state veterans home, contact isolation for colonized veterans, use of oral bacitracin to eliminate colonization. MEASUREMENTS: Rectal swab and culture for VRE, review of clinical records and recording of presumptive risk factors for VRE colonization. The risk factors were age, gender, length of stay at nursing home, treatment with vancomycin or oral antibiotics, prior hospitalization at the acute care facility during the prior year, use of indwelling urethral catheters, presence of diarrhea, and fecal or urinary incontinence. RESULTS: Sixty-nine of 200 residents were cultured in the first study (1996) and 130 of 230 residents were cultured in the second study (1998). Residents who consented to culture differed from those who did not only with regards to gender (2 vs 7, P = .012). In neither study were any residents found to be colonized with VRE who had not already been identified as positive on admission. CONCLUSIONS: Adherence to infection control practices by the patient care staff of the LTCF was associated with the absence of transmission of VRE colonization among its residents. The presence of rectal colonization with VRE in an acute care patient should not be a barrier to acceptance in a nursing home.

Administration, Oral↗
PubMed2000

Antioxidant susceptibility of pathogenic pathways in subjects with antiphospholipid antibodies: a pilot study.

The pathogenesis of antiphospholipid antibody (aPL) related thrombosis is multifactorial and includes, amongst others, enhanced coagulation activation measured as prothrombin fragment 1 + 2 (F1 + 2), elevated plasma levels of von Willebrand factor (vWF), plasminogen activator inhibitor (PAI) and endothelin-1 (ET-1) as well as heightened thromboxane generation and lipid peroxidation. To evaluate the antioxidant susceptibility of some of the above pathways, probucol (500 mg/d orally, a cholesterol lowering agent bearing antioxidant properties) was administered for a three week period to 14 subjects with aPL and to seven healthy controls. At baseline aPL participants showed higher plasma levels of vWF (P = 0.006), ET-1 (P = 0.0002) and enhanced urinary excretion of 11-dehydro-thromboxane-B2 (TXB2) (P = 0.0004), F2-isoprostanes (marker of lipid peroxidation) (P = 0.02) and albumin (P = 0.04) than controls. In the aPL group baseline IgG anticardiolipin (aCL) titre positively related with urinary TXB2 (r2 = 0.43, P = 0.01) and inversely with urinary NOx (r2 = -0.6, P = 0.005) whereas urinary NOx and TXB2 were negatively correlated (r2 = -0.42, P = 0.01). After the treatment period significant decreases from baseline values were noted for PAI (P = 0.01), ET-1 (P = 0.006), TXB2 (P = 0.02), F2-isoprostanes (P = 0.01) and albuminuria (P = 0.01) in aPL participants but not in controls. These pilot data support oxidative sensitive mechanisms and a potential role for antioxidant treatment in the pathogenesis of aPL induced vasculopathy.

Adult↗
PubMed2000

Fibrinogen in systemic lupus erythematosus: more than an acute phase reactant?

OBJECTIVE: To investigate whether plasma fibrinogen (FNG) measured longitudinally in a cohort of patients with systemic lupus erythematosus (SLE) increased over observational time faster than in a control group, and whether its increase might depend upon age, disease duration, disease activity, and medications. METHODS: Hospital based retrospective study with repeated measurements of plasma FNG and C-reactive protein (CRP) for patients and controls and erythrocyte sedimentation rate (ESR) and lupus activity index (LAI) for patients only. Study groups included patients with SLE: n = 96 (95% female), and healthy controls: n = 39 (95% female). Of the patients, 42% had SLE only, 23% had SLE with antiphospholipid antibodies (aPL), and 34% had SLE with aPL related thrombosis. RESULTS: Median baseline FNG was higher in patients (357 mg/dl; 95% CI 339-375) than in controls (271 mg/dl; 95% CI 251-291) by 86 mg/dl (95% CI 56-115, p < 0.001); in older subjects than younger (in patients and in controls); in patients with thrombosis than in other patient groups (by an average of 35 mg/dl; 95% CI 9-61 mg/dl): and in patients with longer disease duration (p = 0.05). Mean FNG increased faster in patients (19 mg/dl/year; 95% CI 12-26 mg/dl) than in controls (2.6 mg/dl/year; 95% CI 2.0-3.2 mg/dl). The increase was faster than the age effect and independent of patient group and disease activity. CONCLUSION: Plasma FNG in patients with SLE increases throughout followup regardless of disease activity, mimicking the age related increment observed in population based studies. The rapidity of the increment may reflect the prematurity of vascular disease typical of SLE.

Acute-Phase Proteins↗
PubMed1999

A clonal Plasmodium falciparum population in an isolated outbreak of malaria in the Republic of Cabo Verde.

We present the first parasitological, molecular and longitudinal analysis of an isolated outbreak of malaria. This outbreak occurred on Santiago Island (Republic of Cabo Verde), a region where malaria is hypoendemic and controlled, and thus the population is considered non-immune. Blood samples were collected from the inhabitants over 1 month and during cross-sectional surveys in the following year. The presence and nature of the parasites was determined by PCR. Plasmodium falciparum was the only species detected. Genetic analysis revealed that the circulating parasites were genetically homogeneous, and probably clonal. Gametocytes were found throughout this period. Our data suggest that this represented a focal outbreak, resulting in the infection of at least 40% of the villagers with a clonal parasite line. Thus, P. falciparum infections can persist for at least 1 year in a substantial proportion (10%) of the hosts. Implications for malaria control and the interpretation of epidemiological data are discussed.

Africa, Western↗
PubMed1999

Oxidative stress in systemic lupus erythematosus and allied conditions with vascular involvement.

OBJECTIVE: To evaluate the occurrence and clinical significance of lipid peroxidation (oxidative stress) in rheumatic diseases characterized by vascular involvement. PATIENTS AND METHODS: Plasma 8-epi-PGF2alpha (oxidative stress marker) was measured by gas chromatography-mass spectrometry in 36 patients with systemic lupus erythematosus (SLE), 13 with systemic sclerosis (SSc), 13 with systemic vasculitis [Wegener's granulomatosis (WG), n = 4; Churg Strauss syndrome (CSS), n = 3; Behcet syndrome, n = 6], 12 with rheumatoid arthritis (RA) and in 23 healthy controls (n = 23). RESULTS: 8-epi-PGF2alpha levels were higher in patients with SLE (P = 0.007), SSc (P < 0.001) and vasculitis (P = 0.001) than in controls. In SLE, a positive Coombs' test and arterial hypertension independently predicted 8-epi-PGF2alpha concentrations (P = 0.004 and P = 0.001, respectively). SLE patients not taking prednisolone showed higher 8-epi-PGF2alpha concentrations than SLE patients on prednisolone (P = 0.02). In the latter group, a dose response relationship was noted between 8-epi-PGF2alpha and steroid dosage (r = 0.6, P = 0.0003). In WG and CSS, 8-epi-PGF2alpha concentrations correlated with disease activity (r = 0.8, P = 0.01) and were higher than in patients with Behcet disease (P = 0.003). CONCLUSIONS: Oxidative stress may be pathogenetically relevant in some autoimmune rheumatic diseases with vascular involvement. Amelioration of some clinical manifestations of these diseases may be envisaged by targeting lipid peroxidation with dietary or pharmacological antioxidants.

Adult↗
PubMed1998

Asn141 is essential for DNA recognition by EcoRI restriction endonuclease.

The amino acid residue Asn141 of the restriction endonuclease EcoRI was proposed to make three hydrogen bonds to both adenine residues within the recognition sequence -GAATTC-. We have mutated Asn141 to alanine, aspartate, serine, and tyrosine. Only the serine mutant is active under normal buffer conditions although 1000-fold less than wild-type EcoRI. The alanine and aspartate mutants can be activated by Mn2+. At acidic pH the latter mutant becomes even more active than the wild-type enzyme in the presence of Mn2+. We conclude that Asn141 is essential for DNA recognition and that serine can partly substitute it.

Adenine↗
PubMed1998

Single-tube nested competitive PCR with homologous competitor for quantitation of DNA target sequences: theoretical description of heteroduplex formation, evaluation of sensitivity, precision and linear range of the method.

Competitive PCR is a frequently used technique for quantitation of DNA and mRNA. However, the application of the most favourable homologous mutated competitors is impeded by the formation of heteroduplex molecules which complicates the data evaluation and may lead to quantitation errors. Moreover, in most cases a single quantitation of an unknown sample requires multiple competitive reactions for identification of the equivalence point. In the present study, a highly efficient and reliable method as well as the underlying theoretical model is described. The mathematical solutions of this model provide the basis for single-tube quantitation using a homologous mutated competitor. For quantitation of Human Papilloma Virus 16-DNA, it is shown that single tube quantitations using simple PAGE separation and video evaluation for signal analysis permit linear detection within more than two orders of magnitude. In addition, repeated single-tube competitive PCRs exhibited good precision (average standard deviation 5%), even if carried out as nested high cycle PCR for quantitation of low abundant sequences (intraassay sensitivity <2 x 10(2) copies). This evaluation method can be applied to any DNA separation and detection method which is capable of resolving the heteroduplex fraction from both homoduplex molecules.

Animals↗
PubMed1998

Coronal leakage: endotoxin penetration from mixed bacterial communities through obturated, post-prepared root canals.

Coronal leakage has been considered as one of the major causes of failure in root canal treatment. Bacteria have been shown to penetrate the root canal obturating materials and influence the periapical tissues. Endotoxin, a component of Gram-negative bacteria, is a potent inflammatory agent and may be able to penetrate obturating materials faster than bacteria. This in vitro study examined the possible penetration of post-prepared canals by endotoxin and bacterial cells derived from mixed bacterial communities. Results showed that both bacteria and endotoxin were able to penetrate the obturating materials in post-prepared canals; however, endotoxin penetration was faster than bacterial. If one speculates that a similar sequence of events occurs clinically, then such a rapid penetration of endotoxin could lead to an early periapical reaction, with subsequent treatment failure and need for retreatment or periapical surgery. The need for an immediate and proper coronal restoration after root canal treatment is therefore reinforced.

Analysis of Variance↗
PubMed1997

Sequence context influencing cleavage activity of the K130E mutant of the restriction endonuclease EcoRI identified by a site selection assay.

We have generated several EcoRI mutants which exhibit a decreased cleavage rate on one of the five specific cleavage sites in bacteriophage lambda-DNA. To study the influence of the sequence context on the cleavage rate in more detail, we developed a site selection assay. From a complete set of 4096 plasmid substrates, differing in three bases on both sides of a recognition sequence, optimal (best cut) and unfavorable (worst cut) sequences were selected by repeated limited digestion, separation, and in vivo amplification of cleaved and uncleaved plasmids. In order to compare the sequence preferences of the inner arm mutant K130E and the wild type enzyme, the cleavage rates and sequences of individual plasmids from the resulting pools were determined. The inner arm mutant K130E selected pools with clearly defined consensus sequences and a high amount of palindromic sequences. The cleavage rates of the selected sequences are specific for the K130E mutant as is shown by their cleavage with other mutants. In contrast, wild type EcoRI does not lead to a selection in this assay. Pre-steady state kinetics show that preferences for a certain sequence context are a result of differences in the dissociation rates of the wild type enzyme. EcoRI is evolved to efficiently recognize and cleave each nonmethylated DNA invading the cell. Therefore, a fast dissociation after cleavage is not mandatory.

Deoxyribonuclease EcoRI↗
PubMed1997

Influence of divalent cations on inner-arm mutants of restriction endonuclease EcoRI.

To understand the functional role of the inner arm region of EcoRI for the interaction with its DNA substrate, we mutated each of the positively charged amino acid residues Lys130 and Arg131 to Ala or Glu. The resulting cleavage activities are only about tenfold reduced but DNA binding in the absence of divalent cations is totally disrupted for three of the mutants ([Ala130]EcoRI, [Glu130]EcoRI and [Glu131]EcoRI). The binding can be rescued by adding 1 mM Ca2+. This binding behaviour resembles that of the blunt end cutter EcoRV. Furthermore, the cleavage activity of the [Glu130]EcoRI is stimulated by Ca2+. Therefore, a second metal binding site is involved in [Glu130]EcoRI catalyzed DNA cleavage. Its location is postulated to be in the inner arm region at positions 133 and 135 presenting an Asp-Xaa-Asp motif typical for Ca2+ binding. A net positive charge at the tip of the inner arm due to the basic amino acids Lys130 and Arg131 in the wild-type enzyme or due to binding of a divalent cation in the mutants is important for DNA recognition by EcoRI. However, a direct phosphate contact providing an indirect readout is not observed. Implications of the binding and cleavage behaviour with regard to mechanistic differences between blunt end and sticky end cutters and a general catalytic mechanism of restriction enzymes are discussed.

Binding Sites↗
PubMed1997

The coagulation/fibrinolysis balance in systemic sclerosis: evidence for a haematological stress syndrome.

Systemic sclerosis (SSc) is a disease characterized by progressive microvascular occlusion and fibrosis resulting in irreversible organ damage, the pathogenesis of which is felt to be of vascular origin. To gain a comprehensive view of the coagulation/fibrinolytic balance in SSc, a number of haemostatic and fibrinolytic variables were measured in 26 SSc patients (11 limited, 15 diffuse) and in 22 control subjects. Of the coagulation activation markers, the mean plasma level of prothrombin fragment 1 + 2 (F1 + 2), but not of thrombin-antithrombin complexes (TAT), was higher in SSc patients than in controls (P < 0.001). Plasma levels of fibrin split product D-dimer (DD), fibrinogen (FNG) and von Willebrand factor (vWF) were higher amongst patients than controls (P < 0.001). vWF and FNG levels were positively correlated (P < 0.001). Mean levels of DD and vWF were more elevated in patients with diffuse than limited disease (P = 0.001 and P = 0.04, respectively). On the fibrinolytic side, defective tissue plasminogen activator (tPA) release (venous occlusion test, stimulated level < basal level) was noted in 46% (12/26) of SSc patients, but only in 4% (1/22) of controls. Patients had higher mean levels of tPA inhibitor (PAI) than controls (P < 0.001), levels being more elevated amongst patients with diffuse than limited disease (P = 0.01). An abnormally high lipoprotein (a) [Lp(a)] level was found in 9% (2/20) of control subjects, but in 30% (8/26) of SSc patients (P = 0.04) where it clustered with fibrinolytic defects. Altogether, these data suggest that patients with SSc are in a hypercoagulable state characterized by elevated plasma levels of FNG and vWF, by a dual hypofibrinolytic pattern (defective tPA release and elevated PAI), and by increased thrombin generation with enhanced fibrin formation. Higher levels of vWF, DD and PAI in patients with diffuse disease are consistent with more extensive (micro)vascular involvement, although no causal relationship can be inferred. The lack of a parallel increase of TAT with F1 + 2, in the presence of normal levels of antithrombin III (ATIII), indirectly suggests an impairment of the heparan sulphate-ATIII system which would favour thrombin generation. Since thrombin may act as a mitogen for fibroblasts, may upregulate vWF, PAI and endothelin production by endothelial cells, and may promote fibrin deposition on the vessel wall leading to worsening of microvascular occlusions, limitation of thrombin generation, besides fibrinolytic enhancement, could represent a possible coadjuvant interventional strategy.

Adult↗