Biomedical subjects

J Palau

Publications and source records attributed to J Palau.

At least 19 recordsLinked to original sources

PubMed2001

[Infection in patients with neutropenia that undergo an autologous peripheral blood stem cell transplant due to breast cancer].

BACKGROUND: The extent and duration of neutropenia and the characteristics of the underlying disease are determinant factors for the prognosis of febrile syndromes. Despite the fact that traditionally the peripheral blood stem cell transplantation (PBSCT) were considered to cause high risk neutropenia, in all probability the neutropenia observed in the PBSCT in some solid tumours could be considered moderate risk. Febrile episodes in patients with these characteristics were evaluated. METHODS: We prospectively analysed 132 autologus PBSCT in patients with breast cancer (1994-1999). Conditioning regime: STAMP V. Antibacterial prophylaxis: ofloxacin (400 mg/12 hrs PO). Classification of the febrile syndrome: bacteremia, microbiologically documented infection withut bacteremia, clinical infection and a fever of unknown origin. RESULTS: 122 patients had a fever (92%), mean age: 45 years (range: 27-61). There were 32 (26%) bacteremias, 13 (11%) microbiologically documented infections without bacteremia and 54 (44%) clinical infections. The mean number of days with a neutrophil count of <1x109/1 was 14 (range: 11-20). In the 74 patients (61%) that had a granulocyte colony stimulating factor (G-CSF), the mean number of days to reach a 0,5x109/I neutrophil count (7,6) and the average number of days in hospital (26) were significantly less. There was a main infectious point in 80 patients (65%): the most frequent being oropharynx in 33 cases (46%) and digestive in 29 cases (41%). 48 gram negative (GN) 29 gram positive (GP) bacteria were isolated (71% of the GN's were resistant to ofloxacin). Between 1997-1999 the GN/GP ratio was 2,3. There were no deaths related to the infection. CONCLUSIONS: Given the excellent evolution of our patients we can consider their neutropenia to be moderate or low risk, and they are a long way from the death rates caused by infections published by other types of hemopoietic transplants. The predominance of GN over the last few years and their limited sensitivity to quinolones means that their prophylactic use in these patients should be reconsidered.

Acyclovir↗

PubMed2001

Evolution of alpha-amylases: architectural features and key residues in the stabilization of the (beta/alpha)(8) scaffold.

We provide a comprehensive analysis of the current enzymes with alpha-amylase activity (AAMYs) that belong to family 13 glycoside hydrolase (GH-13; 144 Archaea, Bacteria, and Eukaryota sequences from 87 different species). This study aims to further knowledge of the evolutionary molecular relationships among the sequences of their A and B domains with special emphasis on the correlation between what is observed in the structures and protein evolution. Multialignments for the A domain distinguish two clusters for sequences from Archaea organisms, eight for sequences from Bacteria organisms, and three for sequences from Eukaryota organisms. The clusters for Bacteria do not follow any strict taxonomic pathway; in fact, they are rather scattered. When we compared the A domains of sequences belonging to different kingdoms, we found that various pairs of clusters were significantly similar. Using either sequence similarity with crystallized structures or secondary-structure prediction methods, we identified in all AAMYs the eight putative beta-strands that constitute the beta-sheet in the TIM barrel of the A domain and studied the packing in its interior. We also discovered a "hidden homology" in the TIM barrel, an invariant Gly located upstream in the sequence before the conserved Asp in beta-strand 3. This Gly precedes an alpha-helix and is actively involved in capping its N-terminal end with a capping box. In all cases, a Schellman motif caps the C-terminal end of this helix.

Cluster Analysis↗

PubMed2001

Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site.

Soybean beta-amylase (EC 3.2.1.2) has been crystallized both free and complexed with a variety of ligands. Four water molecules in the free-enzyme catalytic cleft form a multihydrogen-bond network with eight strategic residues involved in enzyme-ligand hydrogen bonds. We show here that the positions of these four water molecules are coincident with the positions of four potential oxygen atoms of the ligands within the complex. Some of these waters are displaced from the active site when the ligands bind to the enzyme. How many are displaced depends on the shape of the ligand. This means that when one of the four positions is not occupied by a ligand oxygen atom, the corresponding water remains. We studied the functional/structural role of these four waters and conclude that their presence means that the conformation of the eight side chains is fixed in all situations (free or complexed enzyme) and preserved from unwanted or forbidden conformational changes that could hamper the catalytic mechanism. The water structure at the active pocket of beta-amylase is therefore essential for providing the ligand recognition process with plasticity. It does not affect the protein active-site geometry and preserves the overall hydrogen-bonding network, irrespective of which ligand is bound to the enzyme. We also investigated whether other enzymes showed a similar role for water. Finally, we discuss the potential use of these results for predicting whether water molecules can mimic ligand atoms in the active center.

Binding Sites↗

PubMed2000

Horizontal gene transfer of glycosyl hydrolases of the rumen fungi.

By combining analyses of G + C content and patterns of codon usage and constructing phylogenetic trees, we describe the gene transfer of an endoglucanase (celA) from the rumen bacteria Fibrobacter succinogenes to the rumen fungi Orpinomyces joyonii. The strong similarity between different glycosyl hydrolases of rumen fungi and bacteria suggests that most, if not all, of the glycosyl hydrolases of rumen fungi that play an important role in the degradation of cellulose and other plant polysaccharides were acquired by horizontal gene transfer events. This acquisition allows fungi to establish a habitat within a new environmental niche: the rumen of the herbivorous mammals for which cellulose and plant hemicellulose constitute the main raw nutritive substrate.

Animals↗

PubMed2000

Horizontal gene transfer in bacterial and archaeal complete genomes.

There is growing evidence that horizontal gene transfer is a potent evolutionary force in prokaryotes, although exactly how potent is not known. We have developed a statistical procedure for predicting whether genes of a complete genome have been acquired by horizontal gene transfer. It is based on the analysis of G+C contents, codon usage, amino acid usage, and gene position. When we applied this procedure to 17 bacterial complete genomes and seven archaeal ones, we found that the percentage of horizontally transferred genes varied from 1.5% to 14.5%. Archaea and nonpathogenic bacteria had the highest percentages and pathogenic bacteria, except for Mycoplasma genitalium, had the lowest. As reported in the literature, we found that informational genes were less likely to be transferred than operational genes. Most of the horizontally transferred genes were only present in one or two lineages. Some of these transferred genes include genes that form part of prophages, pathogenecity islands, transposases, integrases, recombinases, genes present only in one of the two Helicobacter pylori strains, and regions of genes functionally related. All of these findings support the important role of horizontal gene transfer in the molecular evolution of microorganisms and speciation.

Amino Acids↗

PubMed2000

[Cost of antibiotic therapy in neutropenic patients undergoing peripheral blood stem cell transplantation for breast cancer].

The increase in pharmaceutical costs, especially for expensive procedures such as bone marrow transplants, has led to the study of the economic impact of febrile neutropenia in peripheral blood stem cell transplantation (PBSCT). We analyzed 89 consecutive patients with breast cancer who underwent PBSCT. All patients developed febrile neutropenia and were administered an empirical intravenous regimen based on the combination of piperacillin-tazobactam and amikacin. We analyzed the direct costs of this treatment and grouped them into drug acquisition cost, administration costs (cost of the additional material), and preparation costs (time employed for the preparation and administration of the drug). We found that the overall cost was $1,110, 65% of which corresponded to the initial therapy and the rest (35%) to the use of additional antibiotics. This higher cost was especially related to the use of vancomycin or teicoplanin (50%). The acquisition costs accounted for 90% of the overall treatment costs. Thirty-six patients (40%) did not need additional antibiotics and the cost in this group was less ($663). We concluded that knowledge of the costs of pharmacological therapy for infection in PBSCT is indispensable for the appropriate development of treatment units, especially in terms of optimizing resources and comparing different therapeutic or prophylactic approaches.

Amikacin↗

PubMed1999

Structural features of single amino acid repeats in proteins.

Single amino acid repeats are found in different kinds of proteins. Some of these repeats are pathogenic. It is striking that some amino acids are able to form such repeats, but other amino acids are not. We suggest an explanation for this fact based on the different tendency of each amino acid to form aggregates. Aggregation may be due to the formation of incipient lamellar crystals as they have been described in poly-alpha-amino acids and in most synthetic polymers.

Amino Acids↗

PubMed1999

DNA-interacting proteins in the spermiogenesis of the mollusc Murex brandaris.

Sperm chromatin of Murex brandaris (a neogastropod mollusc) undergoes a series of structural transitions during spermiogenesis. The DNA-interacting proteins responsible for these changes as well as the mature protamines present in the ripe sperm nucleus have been characterized. The results reveal that spermiogenic nuclear proteins are protamine precursors that are subjected to a substantial number of small N-terminal deletions that gradually modify their overall charge. The composition of mature protamines is remarkably simple in turn, promoting an efficient and extremely tight packaging of DNA. The pattern of spermiogenic chromatin condensation in M. brandaris clearly departs from that corresponding to vertebrate chromatin.

Amino Acid Sequence↗

PubMed1999

Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis.

Glycosyl hydrolase (GH) genes from Escherichia coli and Bacillus subtilis were used to search for cases of horizontal gene transfer. Such an event was inferred by G + C content, codon usage analysis, and a phylogenetic congruency test. The codon usage analysis used is a procedure based on a distance derived from a Pearson linear correlation coefficient determined from a pairwise codon usage comparison. The distances are then used to generate a distance-based tree with which we can define clusters and rapidly compare codon usage. Three genes (yagH from E. coli and xynA and xynB from B. subtilis) were determined to have arrived by horizontal gene transfer and were located in E. coli CP4-6 prophage, and B. subtilis prophages 6 and 5, respectively. In this study, we demonstrate that with codon usage analysis, the proposed horizontally transferred genes can be distinguished from highly expressed genes.

Bacillus subtilis↗

PubMed1998

Circular permutants in beta-glucosidases (family 3) within a predicted double-domain topology that includes a (beta/alpha)8-barrel.

By predicting the general secondary structure for beta-glucosidases (family 3), in conjunction with existing knowledge of the circular permutants present in B. fibrisolvens and R. albus, we were able to find the canonical elements of the secondary structure. The way these elements are linked suggests that there is a double-domain topology made up of a (beta/alpha)8-barrel domain and a "mainly all-beta" domain. A number of already known conserved motifs are located within (or near) the C-terminal part of the putative parallel beta-strands of the (bet/alpha)8-barrel, which is consistent with what is known about the location of catalytical sites for enzymes that have this domain topology. Within the circular permutants, two beta/alpha units are located at the N-terminal part of the molecule, whereas the other six beta/alpha units are located at the C-terminal end. In this way, the circular permutants can be seen to have a putative discontinuous double-domain topology.

Amino Acid Sequence↗

PubMed1998

[Invasive fungal infections in patients with blood disorders].

BACKGROUND: Invasive fungal infections (IFI) are severe infectious complications frequently observed in patients with hematological disorders. The aims of this study were to analyse the characteristics of this particular type of infection in a large series of a single institution and to determine the factors associated with the outcome and therapeutic response. PATIENTS AND METHODS: This study reviews the clinical and microbiological features of 155 IFI occurred among 144 patients with hematologic disorders throughout a period of 17 years in a single institution. RESULTS: In 118 cases (82%) the diagnosis was acute leukemia. The main risk factors for developing IFI included a persistent and profound granulocytopenia, the use of broad-spectrum antibacterial agents, indwelling central venous catheters and the damage of normal host barriers following intensive cytotoxic chemotherapy. Candida (65 cases [44%]) and Aspergillus (38 cases [26%]) species were the most common fungal species isolated. An increasing number of IFI were caused by fungi previously considered as contaminants or harmless colonizers. The outcome of IFI was favourable in 78 cases (50%). The most important prognostic factors for the outcome of the IFI were the phase of cytotoxic chemotherapy (p = 0.005), the response of the underlying disease to the cytotoxic chemotherapy (p < 0.00001), and the recovery of neutropenia during the infection course (p < 0.00001). An earlier use of empirical antifungal therapy was also associated with a better outcome. CONCLUSIONS: In spite of earlier treatment and regardless the development of new antifungal agents, the prognosis of IFI in patients with hematological malignancies remains poor. The use of hematopoietic growth factors, through their impact in the duration and severity of neutropenia, may prove valuable the management of IFI in this setting.

Acute Disease↗

PubMed1998

Deciphering the structural code for proteins: helical propensities in domain classes and statistical multiresidue information in alpha-helices.

We made several statistical analyses in a large sample of nearly 4,000 helices (from 546 redundancy-controlled PDB protein subunits), which give new insights into the helical properties of globular proteins. In a first experiment, the amino acid composition of the whole sample was compared with the composition of two helical sample subgroups (the "mainly-alpha" and the "(alpha/beta)8 barrel" domain classes); we reached the conclusion that composition-based helical propensities for secondary structure prediction do not depend on the structural class. Running a five-residue window through the whole sample, the positional composition revealed that positive and negative residues are located throughout the helices and tend to neutralize the macrodipole effect. On this basis, we analyzed charged triplets using a running five-residue window. The conclusion was that only mixed charged residues [positive (+) and negative (-)] located at positions 1-2-5 and 1-4-5 are clearly favored. In these locations the most abundant are (- -..+) and (-..+ +), and this shows the existence of side chain microdipoles, which neutralize the large macrodipole of the helix. We made a systematic statistical analysis of charged, dipolar, and hydrophobic + aromatic residues, which enabled us to work out rules that should be useful for modeling and design purposes. Finally, we analyzed the relative abundance of all the different amphipathic double-arcs that are present in helices formed by octapeptides (8) and nonapeptides (18). All of the double-arcs that make up Schiffer and Edmundson's classical helical wheel are found in abundance in the sample.

Chemical Phenomena↗

PubMed1998

The antiemetic efficacy of granisetron plus dexamethasone, haloperidol and loracepam in breast cancer patients treated with high-dose chemotherapy with peripheral blood stem-cell support.

There has recently been a marked trend to increasing dose intensity in cancer chemotherapy, with or without peripheral blood stem-cell support, which has been associated with a higher frequency of nausea and vomiting. Antiemetic treatment in this setting has not been extensively analysed. From October 1995 to January 1997, prevention of emesis with granisetron 3 mg/12 h i.v., dexamethasone 12 mg/24 h i.v., haloperidol 0.5 mg/12 h p.o., and loracepam I mg/24 h p.o. was instituted in 30 breast cancer patients treated with high-dose chemotherapy (a 4-day intravenous continuous infusion of cyclophosphamide 1500 mg/m2 per day, thio-TEPA 125 mg/m2 per day and carboplatin 200 mg/m2 per day).A total of 30% of the patients (9/30) obtained complete or major protection on the 4 days of chemotherapy treatment (96.7% (29/30) on day 1, 86.7% (26/30) on day 2, 70% (21/30) on day 3, and 50% (15/30) on day 4). On the days following chemotherapy, 46.7% (14/30) presented fewer than two emetic episodes on day 5, 70% (21/30) on day 6, 83.4% (25/30) on day 7 and, 93.3% (28/30) on day 8. This energic antiemetic combination treatment has hardly any effect in the prevention of emesis, providing complete or major protection of 30% for the 4 days of chemotherapy treatment. Further investigation aimed at improving antiemetic treatment results is necessary.

Adult↗

PubMed1998

Nuclear receptors, nuclear-receptor factors, and nuclear-receptor-like orphans form a large paralog cluster in Homo sapiens.

We studied a human protein paralog cluster formed by 38 nonredundant sequences taken from the Swiss-Prot database and its supplement, TrEMBL. These sequences include nuclear receptors, nuclear-receptor factors and nuclear-receptor-like orphans. Working separately with both the central cysteine-rich DNA-binding domain and the carboxy-terminal ligand-binding domain, we performed multialignment analyses that included drawings of paralog trees. Our results show that the cluster is highly multibranched, with considerable differences in the amino acid sequence in the ligand-binding domain (LBD), and 17 proximal subbranches which are identifiable and fully coincident when independent trees from both domains are compared. We identified the six recently proposed subfamilies as groups of neighboring clusters in the LBD paralog tree. We found similarities of 80%-100% for the N-terminal transactivation domain among mammalian ortholog receptors, as well as some paralog resemblances within diverse subbranches. Our studies suggest that during the evolutionary process, the three domains were assembled in a modular fashion with a nonshuffled modular fusion of the LBD. We used the EMBL server PredictProtein to make secondary-structure predictions for all 38 LBD subsequences. Amino acid residues in the multialigned homologous domains--taking the beginning of helix H3 of the human retinoic acid receptor-gamma as the initial point of reference--were substituted with H or E, which identify residues predicted to be helical or extended, respectively. The result was a secondary structure multialignment with the surprising feature that the prediction follows a canonical pattern of alignable alpha-helices with some short extended elements in between, despite the fact that a number of subsequences resemble each other by less than 25% in terms of the similarity index. We also identified the presence of a binary patterning in all of the predicted helices that were conserved throughout the 38-sequence sample. Our results fit well with a recently proposed evolutionary model that combines protein secondary structure and amino acid replacement. We propose a new hypothesis for molecular evolution, in which chaperones--acting as an endogenous cellular device for selection--play a crucial role in preserving protein secondary structure.

Amino Acid Sequence↗

PubMed1998

IMASIS. A multicenter hospital information system--experience in Barcelona.

The present study aimed to analyse physicians' attitudes towards IMASIS, and their potential influence on IMASIS medical record project. IMAS (Institut Municipal d'Assistència Sanitària) is the health care organisation of the City Council of Barcelona. IMAS hospital information system (IMASIS), which first applications were designed and implemented in 1984, is currently facing a new phase, focused on clinical information management. Our approach included a personal interview with representatives of every hospital unit, and a self-administered questionnaire distributed to every clinician. Both provided a worthy insight into the cultural patterns to be considered in the HIS implementation process. Moreover, the results helped to define the subsequent steps of IMASIS evolution. Our experience is proposed as a tool to assess clinical informations systems from a user point of view.

Adult↗

PubMed1997

Anatomy of a conformational transition of beta-strand 6 in soybean beta-amylase caused by substrate (or inhibitor) binding to the catalytical site.

A computational study of the five soybean beta-amylase X-ray structure reported so far revealed a peculiar conformational transition after substrate (or inhibitor) binding, which affects a segment of the beta-strand 6 (residues 341-343) in the (beta/alpha)8 molecular scaffold. Backbone distortions that involve considerable changes in the phi and psi angles were observed, as well as two sharp rotamer transitions for the Thr342 and Cys343 side chains. These changes caused the outermost CA-layer (at the C-terminal side of the barrel), which is involved in the catalysis, to shrink. Our observations strongly suggest that the 341FTC343 residue conformations in the free enzyme are not optimal for protein stability. Furthermore, as a result of conformational transitions in the ligand-binding process, there is a negative enthalpy change for these residues (-27 and -34 kcal/mol, after substrate or inhibitor binding, respectively). These findings support the proposed "stability-function" hypothesis for proteins that recognize a ligand (Shoichet BK, Baase WA, Kuroki R, Matthews BW. 1995. A relationship between protein stability and protein function. Proc Natl Acad Sci USA 92:452-456). They are also in good agreement with other experimental results in the literature that describe the role of the 341-343 segment in beta-amylase activity. Site-directed mutagenesis focused on these residues could be useful for undertaking functional studies of beta-amylase.

Binding Sites↗

PubMed1996

Evolution of beta-amylase: patterns of variation and conservation in subfamily sequences in relation to parsimony mechanisms.

Soybean and sweet potato beta-amylases are structured as alpha/beta barrels and the same kind of folding may account for all known beta-amylases. We provide a comprehensive analysis of both protein and DNA (coding region) sequences of beta-amylases. The aim of the study is to contribute to the knowledge of the evolutionary molecular relationships among all known beta-amylases. Our approach combines the identification of the putative eightfold structural core formed by beta-strands with a complete multi-alignment analysis of all known sequences. Comparing putative beta-amylase (alpha/beta)8 cores from plants and microorganisms, two differentiated versions of residues at the packing sites, and a unique set of eight identical residues at the C-terminal catalytical site are observed, indicating early evolutionary divergence and absence of localized three-dimensional evolution, respectively. A new analytical approach has been developed in order to work out conserved motifs for beta-amylases, mostly related with the enzyme activity. This approach appears useful as a new routine to find sets of motifs (each set being known as a fingerprint) in protein families. We demonstrate that the evolutionary mechanism for beta-amylases is a combination of parsimonious divergence at three distinguishable rates in relation to the functional signatures, the barrel scaffold, and alpha-helix-containing loops.

Amino Acid Sequence↗

PubMed1996

[Levels of cytokeratin CK19 expression in mononuclear blood cells evaluated using a reverse PCR (RT-PCR)].

AIMS: The sensitivity and specificity of a reverse transcription PCR method (RT-PCR) to detect cytokeratin K19 (CK19) expression was evaluated with the purpose of assessing its capability to detect the presence of breast cancer tumour cells in peripheral blood progenitor cell collection that had to be reinfused to breast cancer patients submitted to intensive chemotherapy as haematopoietic support. PATIENTS AND METHODS: Two breast cancers as positive samples were used and 34 samples of mononucleated blood cells as negative controls: 18 peripheral blood samples from normal subjects, 14 from different types of leukaemias (M3, M4Eo, M2, etc.) and two from two patients with Hodgkin's lymphoma. The method studied is a nested RT-PCR that amplifies the CK19 expression from the sample RNA extracted following the method of phenol-chloroform. RESULTS: The right performance of the method is demonstrated by observing the detection of CK19 transcripts in the breast cancer RNA and by obtaining good blank results both with non transcribed RNA and with DNA. Moreover, the method has an excellent sensitivity such as to allow the detection of CK19 transcripts in a 10(-6) dilution of cDNA reverse transcribed from 1 microgram of breast cancer RNA. The CK19 transcripts were also detected in the 64% of RNA obtained from the mononucleated blood cells controls, although the percentage of positivities was lower (47%) in the RNA from peripheral blood samples. Nevertheless it should be remarked that the levels of CK19 expression in the blood mononucleated cells is almost negligible since it used to extinguish at 1:5 cDNA dilution. CONCLUSIONS: The method studied is specific and has a high sensitivity that explains the detection of CK19 illegitimate expression approximately a half in mononucleated blood cells negative controls. However, the levels of CK19 expression in mononucleated blood cells were almost negligible and it used to extinguish at 1:5 cDNA dilution, therefore it could be concluded that the method might be useful to detect breast cancer occult tumours cells in mononucleated blood cell collection, always provided that a lower amount of cDNA is taken, thus decreasing to nil almost the false positive samples and keeping always a good sensitivity.

Biomarkers, Tumor↗