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PubMed2004

[Pharmaceutical care program in HIV patients under antiretroviral treatment: methodology and documentation].

Most hospital pharmacy services in Spain have increased pharmaceutical care activities for HIV-patients under antiretroviral therapy during last years. So, it is necessary the establishment of work methods to secure the best quality of care. The pharmacy service of the general hospital of Castellón has developed a global pharmaceutical care program for these patients characterized by the systematic and individualized strategy or basic pharmaceutical care record which can be completed with additional proceedings. The basic record includes complete drug therapy registry, clinical evolution data and detection of drug related problems (DRP), evaluation and promotion of patient adherence, individualized counselling and nutritional evaluation. Additional proceedings include exhaustive DRP monitoring, additional patient adherence to treatments measurements, SOAP methodology, quality of life and perceived patient satisfaction. Our purpose integrate patient status with pharmaceutical care provided and the expected or obtained outcomes, either clinical or economic as well as activity outcomes, quality of life and satisfaction related results. The main characteristics of the purposed methodology are: clinical orientation, it permits the registry and the establishment of a systematic work methodology, is designed as a cross structure and variables are coded. According to our experience, our model can be considered useful in clinical practice and could be applied in different hospital outpatient units.

Anti-Retroviral Agents↗

PubMed2005

[Chromosomal behaviors in plant wide hybridizations and their genetic and evolutionary implications].

The wide hybridization and polyploidization play a significant role in the evolution of higher plants. On the contrary, the artificially synthesized allopolyploids are genetically unstable and fail to be used as crops. One reason for this situation may be that the allopolyploids in nature are the products of natural selection and evolution and it is difficult for human to repeat and perform the process in short periods. Another reason is that we know little about the interaction mechanisms between the genomes of different origins. So the genetics and epigenetics after allopolyploidizations are now studied by multidisciplinary approaches. The spatial separation of parental genomes in hybrid cells have been observed in some sexual and somatic hybrids, but the biological meanings remain to clarify. The abnormal chromosome behaviors in plant wide crosses, such as pseudogamy, semigamy, chromosome elimination and the mitotic and meiotic separation of parental genomes, may indicate the incompatibility of two parental species at gametic and chromosomal levels. The systematic studies at different levels on chromosomal behavior and genetics in plant hybridizations are needed to undermine the mechanisms responsible for the formation and evolution of new species.

Chromosome Mapping↗

PubMed1996

Molecular evolution of ependymin and the phylogenetic resolution of early divergences among euteleost fishes.

The rate and pattern of DNA evolution of ependymin, a single-copy gene coding for a highly expressed glycoprotein in the brain matrix of teleost fishes, is characterized and its phylogenetic utility for fish systematics is assessed. DNA sequences were determined from catfish, electric fish, and characiforms and compared with published ependymin sequences from cyprinids, salmon, pike, and herring. Among these groups, ependymin amino acid sequences were highly divergent (up to 60% sequence difference), but had surprisingly similar hydropathy profiles and invariant glycosylation sites, suggesting that functional properties of the proteins are conserved. Comparison of base composition at third codon positions and introns revealed AT-rich introns and GC-rich third codon positions, suggesting that the biased codon usage observed might not be due to mutational bias. Phylogenetic information content of third codon positions was surprisingly high and sufficient to recover the most basal nodes of the tree, in spite of the observation that pairwise distances (at third codon positions) were well above the presumed saturation level. This finding can be explained by the high proportion of phylogenetically informative nonsynonymous changes at third codon positions among these highly divergent proteins. Ependymin DNA sequences have established the first molecular evidence for the monophyly of a group containing salmonids and esociforms. In addition, ependymin suggests a sister group relationship of electric fish (Gymnotiformes) and Characiformes, constituting a significant departure from currently accepted classifications. However, relationships among characiform lineages were not completely resolved by ependymin sequences in spite of seemingly appropriate levels of variation among taxa and considerably low levels of homoplasy in the data (consistency index = 0.7). If the diversification of Characiformes took place in an "explosive" manner, over a relatively short period of time this pattern should also be observed using other phylogenetic markers. Poor conservation of ependymin's primary structure hinders the design of efficient primers for PCR that could be used in wide-ranging fish systematic studies. However, alternative methods like PCR amplification from cDNA used here should provide promising comparative sequence data for the resolution of phylogenetic relationships among other basal lineages of teleost fishes.

Amino Acid Sequence↗

PubMed1994

Further data on the occurrence and evolution of satellite DNA families in the lacertid genome.

This paper reports the isolation and characterization of two HindIII repetitive DNA families from the genome of two lacertid lizards, Podarcis sicula and Lacerta saxicola. These satellites did not appear to be related to each other. The consensus sequences of their monomeric units did not show any similarity, though both DNAs were A-T rich. Moreover, each of them was found only in closely related species. The monomeric unit of the HindIII DNA family isolated from P. sicula (pLHS) showed a close resemblance to pLCS, a centromeric satellite DNA previously isolated from the same species; it was, however, mainly localized at pericentromeric, interstitial and telomeric levels. The results also provide interesting information on the systematics of the lacertids studied.

Animals↗

PubMed1998

Evolutionary neurocontrollers for autonomous mobile robots.

In this article we describe a methodology for evolving neurocontrollers of autonomous mobile robots without human intervention. The presentation, which spans from technological and methodological issues to several experimental results on evolution of physical mobile robots, covers both previous and recent work in the attempt to provide a unified picture within which the reader can compare the effects of systematic variations on the experimental settings. After describing some key principles for building mobile robots and tools suitable for experiments in adaptive robotics, we give an overview of different approaches to evolutionary robotics and present our methodology. We start reviewing two basic experiments showing that different environments can shape very different behaviours and neural mechanisms under very similar selection criteria. We then address the issue of incremental evolution in two different experiments from the perspective of changing environments and robot morphologies. Finally, we investigate the possibility of evolving plastic neurocontrollers and analyse an evolved neurocontroller that relies on fast and continuously changing synapses characterized by dynamic stability. We conclude by reviewing the implications of this methodology for engineering, biology, cognitive science and artificial life, and point at future directions of research.

Journal Article↗

PubMed1997

An episodic change of rDNA nucleotide substitution rate has occurred during the emergence of the insect order Diptera.

We have studied the potential reasons for a conspicuous deviation of substitution rates in Dipteran ribosomal genes. Systematic pairwise relative-rate tests reveal that a significant increase in substitution rate is characteristic for Diptera, but not for the other insects analyzed. Estimation of sequence change in specific lineages reveals that most of these substitutions took place during the evolution of the Dipteran stem lineage. When related to the paleontologically documented periods of absolute time, the substitution rate in the stem lineage of the Diptera underwent an at least 20-fold increase compared to other insect groups and subsequently dropped by a factor of 10 before the diversification of the major Dipteran subgroups. Systematic comparisons of nucleotide composition show that this episodic change in substitution rate was accompanied by a significant increase in A+T content of Dipteran rDNA. Our data suggest that the episodic evolution of the Dipteran rDNA has most probably been caused by a change of directional mutation pressure which must have occurred during the evolution of the stem lineage of the Diptera.

Animals↗

PubMed2005

Epigenetics and its implications for plant biology 2. The 'epigenetic epiphany': epigenetics, evolution and beyond.

SCOPE: In the second part of a two-part review, the ubiquity and universality of epigenetic systems is emphasized, and attention is drawn to the key roles they play, ranging from transducing environmental signals to altering gene expression, genomic architecture and defence. KEY ISSUES: The importance of transience versus heritability in epigenetic marks is examined, as are the potential for stable epigenetic marks to contribute to plant evolution, and the mechanisms generating novel epigenetic variation, such as stress and interspecific hybridization. FUTURE PROSPECTS: It is suggested that the ramifications of epigenetics in plant biology are immense, yet unappreciated. In contrast to the ease with which the DNA sequence can be studied, studying the complex patterns inherent in epigenetics poses many problems. Greater knowledge of patterns of epigenetic variation may be informative in taxonomy and systematics, as well as population biology and conservation.

Arabidopsis↗

PubMed1976

A cybernetic approach to the origin of the genetic coding mechanism. I. Methodological principles.

It is postulated that some quasi-deterministic code features (universality, connectedness, systematic degeneracy, symmetry, regularity and so on) resulted from unique (and therefore universal) relization of a stochastic evolutionary process. The evolution of real genetic systems should satisfy the principle of succession; that is, loss of a feature that is necessary for a genetic system means death to its carrier. The hypothesis of unique key coincidence is proposed which indicates the mechanisms of arising of the primary correspondence between the linear structures of polynucleotides and polypeptides. If the collinear coincidence was to appear in the key positions of pra-protein with, at least, some of the primitive properties of the pra-amino-acyl-t-RNA-synthetase required for the accelerated recognition of the key positions of pra-template, the positive feed-back mechanism in the system would be most short-circuited so that the repetitive reproduction of pra-synthetase would be much accelerated.

Amino Acyl-tRNA Synthetases↗

PubMed2005

Phylogenomic study of the subfamily Caprinae by cross-species chromosome painting with Chinese muntjac paints.

Chromosomal homologies have been established between the Chinese muntjac (Muntiacus reevesi, MRE, 2n = 46) and five ovine species: wild goat (Capra aegagrus, CAE, 2n = 60), argali (Ovis ammon, OAM, 2n = 56), snow sheep (Ovis nivicola, ONI, 2n = 52), red goral (Naemorhedus cranbrooki, NCR, 2n = 56) and Sumatra serow (Capricornis sumatraensis, CSU, 2n = 48) by chromosome painting with a set of chromosome-specific probes of the Chinese muntjac. In total, twenty-two Chinese muntjac autosomal painting probes detected thirty-five homologous segments in the genome of each species. The chromosome X probe hybridized to the whole X chromosomes of all ovine species while the chromosome Y probe gave no signal. Our results demonstrate that almost all homologous segments defined by comparative painting show a high degree of conservation in G-banding patterns and that each speciation event is accompanied by specific chromosomal rearrangements. The combined analysis of our results and previous cytogenetic and molecular systematic results enables us to map the chromosomal rearrangements onto a phylogenetic tree, thus providing new insights into the karyotypic evolution of these species.

Animals↗

PubMed2006

Current status of transrectal ultrasound-guided prostate biopsy in the diagnosis of prostate cancer.

In contemporary practice, most prostate cancers are either invisible on ultrasound or indistinguishable from concurrent benign prostatic hyperplasia. Diagnosis therefore rests on prostate biopsy. Biopsies are not simply directed at ultrasonically visible lesions, as these would miss many cancers; rather the whole gland is sampled. The sampling itself is systematic, using patterns based on prostate zonal anatomy and the geographical distribution and frequency of cancer. This review explains the evolution of the prostate biopsy technique, from the classical sextant biopsy method to the more recent extended biopsy protocols (8, 10, 12, >12 and saturation biopsy protocols). Extended protocols are increasingly being used to improve diagnostic accuracy, especially in those patients who require repeat biopsy. This trend has been facilitated by the ongoing improvement in safety and acceptability of the procedure, particularly with the use of antibiotic prophylaxis and local anaesthesia. The technical details of these extended protocols are discussed, as are the current data regarding procedure-related morbidity and how this may be minimized.

Age Factors↗

PubMedDate not supplied

Significance of high-grade prostatic intraepithelial neoplasia on prostate biopsy.

The early diagnosis of prostate cancer has been facilitated by the development of serum prostate-specific antigen (PSA) testing and evolution in transrectal ultrasound-guided biopsy of the prostate. Over a decade has passed since the initial recommendations for systematic sextant sampling of the prostate to increase the accuracy of cancer detection. Subsequently, variations in the number and location of biopsies have been proposed to maximize prostate cancer detection and obtain more complete information regarding tumor grade, tumor volume, and local stage. Although current biopsy strategies provide a wide sampling of the prostate gland, biopsy histology may not be conclusive for either the presence or absence of adenocarcinoma. High-grade prostatic intraepithelial neoplasia (HGPIN) is found in a significant fraction of patients undergoing transrectal prostate biopsies. In this article, we discuss the significance of high-grade prostatic intraepithelial neoplasia and other abnormal histology findings and current evidence addressing the presence of cancer and need for additional prostate biopsies.

Adenocarcinoma↗

PubMed1998

Familial amyloid polyneuropathy type I (Portuguese): distribution and characterization of renal amyloid deposits.

Renal amyloidosis has been considered rare and late in the evolution of the transthyretin (TTR) familial amyloid polyneuropathy (FAP) of the Portuguese type (type I). Renal biopsy has been performed systematically in 14 patients with FAP type I before liver transplantation. In all patients, TTR Met30 mutation was shown. Seven had proteinuria or abnormal microalbuminuria, whereas seven others had no urinary abnormalities. All had renal amyloid deposition predominantly in the medulla. Glomerular and vascular involvement was more prominent in patients with urinary abnormalities. Patients with the most extensive renal lesions represented a subgroup with a low score of polyneuropathy disability, a high prevalence of nephropathy in the proband generation, or a late onset for relatives with nephropathy. Immunohistochemistry studies showed that the amyloid substance corresponded to transthyretin. We have shown that renal TTR-derived amyloid deposition is common in patients with FAP type I, even in the absence of urinary abnormalities. The clinical presentation of nephropathy is not a late occurrence in the disease.

Adult↗

PubMed2000

Geochemistry of the Archean Kam Group, Yellowknife Greenstone Belt, Slave Province, Canada.

The geochemistry and isotope systematics of Archean greenstone belts provide important constraints on the origin of the volcanic rocks and tectonic models for the evolution of Archean cratons. The Kam Group is a approximately 10-km-thick pile of submarine, tholeiitic mafic, and subordinate felsic volcanic rocks erupted between 2712 and 2701 Ma that forms the bulk of the Yellowknife greenstone belt in the dominantly granite-metasedimentary Slave Province. Mafic rocks range from Normal-mid-ocean range basalt-like basalts to slightly light-rare-earth-element-enriched (LREE-enriched) but Nb-depleted basaltic andesites and andesites, whereas dacitic to rhyodacitic felsic rocks are strongly LREE-enriched and highly depleted in Nb. The varepsilonTNd range from +5 to -3 in the mafic to intermediate rocks and from 0 to -5.5 in the felsic rocks. The varepsilonTNd decreases with increasing La/Sm, SiO2 and decreasing Nb/La, suggesting that as the mafic magmas evolved they were contaminated by older basement rocks. Gneissic granitoids >2.9 Ga in age, found at the base of the Kam Group, have varepsilonTNd between -6 and -9 and are excellent candidates for the contaminant. The geochemical and isotopic data, combined with the submarine eruptive setting and field evidence for existing continental basement, support a continental margin rift model for the Kam Group. Similar geochemical-isotopic studies are required on other Slave greenstone belts in order to test evolutionary models for the Slave Province.

Journal Article↗

PubMed2006

Mutation-biased adaptation in a protein NK model.

Evolutionary trends responsible for systematic differences in genome and proteome composition have been attributed to GC:AT mutation bias in the context of neutral evolution or to selection acting on genome composition. A possibility that has been ignored, presumably because it is part of neither the Modern Synthesis nor the Neutral Theory, is that mutation may impose a directional bias on adaptation. This possibility is explored here with simulations of the effect of a GC:AT bias on amino acid composition during adaptive walks on an abstract protein fitness landscape called an "NK" model. The results indicate that adaptation does not preclude mutation-biased evolution. In the complete absence of neutral evolution, a modest GC:AT bias of realistic magnitude can displace the trajectory of adaptation in a mutationally favored direction, to such a degree that amino acid composition is biased substantially and persistently. Thus, mutational explanations for evolved patterns need not presuppose neutral evolution.

Adaptation, Physiological↗

PubMed1995

The management of uraemia in the elderly: treatment choices.

The particularity of geriatric medicine and the lack of information due to the fact that geriatric nephrology dates back only 10 years explains why the management of chronic uraemia among the elderly presents itself as a succession of difficult dilemmas. (1) Should causes of chronic renal failure be systematically determined and treated? Risk-benefit assessments of the investigations and treatments involved in preventing or slowing down the evolution to end-stage renal disease (ESRD) are required to answer this question. (2) In cases of ESRD, should dialysis always be considered? The fact that life expectancy is limited for the aged does not justify depriving them of treatment. Nevertheless, in some borderline situations, conservative treatment may be preferable. (3) When should dialysis be started? Currently the mortality before the 90th day of dialysis is very high among elderly patients. To improve results it is probably necessary to determine appropriate criteria for starting treatment before complications occur. (4) What is the best method for the first treatment? There is much controversy about the respective advantages of haemodialysis and peritoneal dialysis. The choice depends on the individual's medical and social conditions. (5) Should dialysis treatment be stopped, and, if so, in this case, when? The large acceptance rate of elderly patients for dialysis implies that withdrawal of treatment must sometimes be considered. Fears linked to this dilemma probably explain why some physicians choose to exclude elderly patients from dialysis. It seems to us more ethical to treat this group of patients and assume responsibility for stopping treatment should it be necessary.

Aged↗

PubMed1998

Multilocus phylogeny of cichlid fishes (Pisces: Perciformes): evolutionary comparison of microsatellite and single-copy nuclear loci.

Among vertebrates, cichlid fishes are the paradigmatic example of adaptive radiation and ecological specialization. In turn, molecular genetic studies of cichlids have focused primarily on more recently diverged groups. Here, we present an evolutionary hypothesis of the major lineages of cichlid fishes based on DNA sequence data from two nuclear loci. One marker, Tmo-4C4, is a single-copy locus containing a region of amino acid similarity to the muscle protein TITIN. Flanking sequence from a second, microsatellite, locus Tmo-M27, shows similarity to mammalian RAS guanine nucleotide-releasing factor. We compare and combine data from these loci to evaluate phylogenetic performance. In separate and combined analyses, the sequence data support and clarify previous morphological hypotheses of cichlid major-group relationships. Indian and Malagasy cichlids form a basal, paraphyletic group. Neotropical cichlids are the sister clade to an African assemblage composed of the paraphyletic west and Pan-African lineages and a group of east African rift lake taxa. We use a consensus phylogeny of the Cichlidae to trace evolutionary changes in the microsatellite repeat motif at Tmo-M27. Analysis reveals that the repeat region was nearly lost in the ancestor to cichlids and then amplified extensively in African taxa. Results demonstrate that the two new DNA markers could be widely applied in perciform systematics. Furthermore, the comparative approach can unveil mutational dynamics of simple-sequence repeat loci over long periods of fish evolution. Simple-sequence repeat regions are increasingly being found in introns of important regulatory genes. We address issues involving their function and suggest caution in making assumptions of strict neutrality.

Animals↗

PubMed2001

The onset of nonlinearity in cosmological structure.

We discuss the progression of growth of cosmological structure, from the quasilinear evolution of nearly Gaussian fluctuations on large scales into highly non-Gaussian, strongly nonlinear structure on small scales. A systematic development in perturbation theory describes the first departures from homogeneity but fails to reproduce the fully nonlinear results. Physical insight, conceptual models, and symmetries are useful in the strong clustering regime. A phenomenological model with input information from the quasilinear regime provides enticing results for the strongly nonlinear regime.

Journal Article↗

PubMed2004

Gag non-cleavage site mutations contribute to full recovery of viral fitness in protease inhibitor-resistant human immunodeficiency virus type 1.

It is well documented that human immunodeficiency virus type 1 (HIV-1) Gag cleavage site mutations (CSMs) emerge in conjunction with various HIV-1 mutations for protease inhibitor (PI) resistance and improve viral replication capacity, which is reduced by acquisition of the resistance. However, CSMs are not the only mutations that emerge in Gag during treatment; many mutations other than CSMs (non-CSMs) have been found to accumulate in the Gag region. In the present study we demonstrate the important role of Gag non-CSMs with regard to viral fitness recovery. We selected three Gag-protease sequences with different PI resistance-associated mutations and CSMs from patients with antiretroviral treatment failure. To clarify the significance of CSMs and non-CSMs, four types of recombinant viruses with different patterns in each sequence were constructed. These were the GP type (patient-derived Gag and protease), the P type (HXB2 Gag and patient-derived protease), the GP(-c) type (CSMs removed from the GP type), and the P(+c) type (CSMs in the HXB2 Gag frame and patient-derived protease). By comparison of these four types of recombinant viruses in each patient-derived Gag-protease sequence, we found that non-CSMs, which had no systematic pattern, make a significant contribution to viral fitness recovery. Our findings demonstrate a delicate interaction between the in vivo evolution of Gag and protease to evade drug selective pressure and the importance of Gag in evaluating drug-resistant viruses.

Amino Acid Sequence↗