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Results for “Comparative evolution”

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PubMed1990

The comparative biology of second sex ratio evolution within a natural population of a parasitic wasp, Nasonia vitripennis.

Correlation and regression analyses indicate that isofemale strains extracted from a population of the parasitic wasp, Nasonia vitripennis, differ in the fit of their second sex ratios (those produced in previously parasitized hosts) to the predictions of the theory of optimal facultative sex ratio adjustment. Under the theory's simple assumptions about population structure, there is significant heterogeneity of fitnesses among the isofemale strains. The reasons underlying these types of heterogeneity must be understood before we can make statements about the nature of sex ratio evolution in this species. These results suggest that comparative analyses are essential for testing the qualitative predictions of optimality models.

Animals↗

PubMed1998

Different evolution of simian immunodeficiency virus in a natural host and a new host.

To address the mechanisms of host-virus adaptation and pathogenesis of lentiviral infections, we compared the evolution of the same isolate of simian immunodeficiency virus (SIVsmm9) in two different situations: nonpathogenic infection of its natural host, the sooty mangabey, and AIDS-inducing infection of a new host, the rhesus macaque. Samples were obtained at 6, 12, and 23 or 30 months postinfection from three animals of each species. Sequences were derived from the V1 and V2 domains of the surface glycoprotein. In the macaques, we observed specific variations absent from all mangabey samples, indicating that different host species select different virus variants. In the macaques, we also observed a different shape in the phylogenetic tree, a lower divergence of sibling sequences, and a lower synonymous/nonsynonymous change ratio than in the mangabeys. This suggests that the viral population is larger and submitted to weaker selection pressures when host-virus adaptation is achieved, such as in the mangabey.

Adaptation, Physiological↗

PubMed2000

[Vogt-Koyanagi-Harada syndrome: importance of rapid diagnosis and therapeutic intervention].

AIM: The Vogt-Koyanagi-Harada (VKH) syndrome is characterized by a bilateral granulomatous uveitis with exudative retinal detachments associated with systemic manifestations such as meningeal signs, cutaneous signs (poliosis, alopecia and vitiligo) and dysacousis. VKH is relatively unfrequent in Europe and Switzerland. Therefore diagnosis is often reached with some delay. Our aim here was to analyze the 3 patients for whom the diagnosis was reached less than 15 days after the first signs and compare their evolution to seven patients for whom diagnosis was known one month or more after the first signs. PATIENTS AND METHODS: Retrospective and partially prospective study of patients seen at uveitis clinic in Lausanne from 1990 to 1999 for whom an ICG angiographic work-up had been performed in addition to the usual clinical and fluoresceinic work-up. The frequency of VKH in our collective was calculated; symptoms and signs, paraclinical investigations, laboratory work-up, delay from first signs to diagnosis, the management and the evolution were the criteria analyzed. In particular the patients with early diagnosis and early treatment were analyzed and compared to the rest of the collective. Diagnosis was based on the criteria of the American Uveitis Society. Between 1990 and 1999, 14 patients with the diagnosis of VKH were seen (1.2% of our collective of uveitis patients). The 10 patients having had a work-up including ICG angiography in addition to the classical work-up were included in this study. RESULTS: The diagnosis was reached in less than 2 weeks in 3 patients. In all 3 patients inflammation was controlled after treatment. Two patients with a follow-up without recurrence of respectively 36 and 54 months were considered as healed. The last case had no recurrence after nine months but still was under therapy. Whereas clinical examination and fluorescein angiography failed to show any sequels in the 2 "healed" patients, ICG angiography showed numerous zones of hypofluorescence indicating choroidal scarring. For the 7 other cases, the diagnosis was reached one month or more after the first symptoms or signs and they all evolved in the chronic recurrent fashion. ICG angiography contributed to the rapid diagnosis in 2/3 patients with early diagnosis and was an essential parameter for the choroidal follow-up in 9/10 patients. CONCLUSION: This study shows that it is essential to rapidly reach the diagnosis of VKH and treat the patients vigorously without delay. By showing choroidal lesions not seen by the clinical examination or fluorescein angiography. ICG angiography is essential for a correct work-up and follow-up of choroidal lesions in VKH. In our two "healed" patients it was the only mean to show choroidal sequellae.

Adult↗

PubMed2003

Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation.

We have performed a large-scale analysis of amino acid sequence evolution after gene duplication by comparing evolution after gene duplication with evolution after speciation in over 1,800 phylogenetic trees constructed from manually curated alignments of protein domains downloaded from the PFAM database. The site-specific rate of evolution is significantly altered by gene duplication. A significant increase in the proportion of amino acid substitutions at constrained (slowly evolving) sites after duplication was observed. An increase in the proportion of replacements at normally constrained amino acid sites could result from relaxation of purifying selective pressure. However, the proportion of amino acid replacements involving radical changes in amino acid properties after duplication does not appear to be significantly increased by relaxed selective pressure. The increased proportion of replacements at constrained sites was observed over a relatively large range of protein change (up to 25% amino acid replacements per site). These findings have implications for our understanding of the nature of evolution after duplication and may help to shed light on the evolution of novel protein functions through gene duplication.

Algorithms↗

PubMed2000

Evolution of leukotriene B4, peptide leukotrienes, and interleukin-8 plasma concentrations in patients at risk of acute respiratory distress syndrome and with acute respiratory distress syndrome: mortality prognostic study.

OBJECTIVE: To compare the evolution of plasma concentrations of leukotriene (LT) B4, LTC4, LTD4, and interleukin (IL)-8 in patients with acute respiratory distress syndrome (ARDS) and in patients at risk of ARDS and to assess the value of these mediators in predicting mortality rate from ARDS. DESIGN: A case-control study comparing ARDS patients and patients at risk of ARDS as well as survivors and nonsurvivors with ARDS. SETTING: Hospital intensive care unit, laboratory, and department of hematology. PATIENTS: Twenty-one patients with ARDS and 14 patients at risk of ARDS. INTERVENTION: Arterial blood samples were collected on days 0, 1, and 5 after admission to the intensive care unit. MEASUREMENTS AND MAIN RESULTS: LTs were extracted, separated by high-pressure liquid chromatography and quantified by enzyme immunoassay. IL-8 was analyzed by ELISA. Plasma concentrations of LTB4 and LTC4 plus LTD4 were significantly higher in ARDS patients than in patients at risk of ARDS during the first 24 hrs. Concentrations of IL-8 were also higher in ARDS patients than in patients at risk throughout the study, although the differences between the two groups were only significant on day 5. Only the plasma concentration of LTB4 on day 1 was a marker of ARDS (72.2% sensitivity, 84.6% specificity). A logistic regression analysis showed that LTB4 and IL-8, on day 1, were markers of mortality rate in patients with ARDS (70.0% sensitivity, 87.5% specificity). CONCLUSIONS: LTs are elevated during the early phases of ARDS, whereas IL-8 increases throughout the study. The evaluation of LTB4 and IL-8 may be useful prognostic indices in patients with early phase ARDS after admission to the intensive care unit.

Biomarkers↗

PubMed1998

Gridded genomic libraries of different chordate species: a reference library system for basic and comparative genetic studies of chordate genomes.

The use of genomic libraries maintained in arrayed format is becoming a more and more popular tool for the analysis of molecular evolution and comparative molecular development. Being able to use already existing reference libraries considerably reduces the work load, and if results are made publicly available, it will facilitate in silica experiments in the future. Here we describe the construction and preliminary characterization of six cosmid libraries of different chordate species, Ciona intestinalis (Hemichordate), Branchiostoma floridae (Cephalochordate), Lampetra fluviatilis (Cyclostoma), Xiphophorus maculatus, and Danio rerio (Osteichthyes) in Lawrist7 and Fugu rubripes in Lawrist4.

Animals↗

PubMed1998

Interspecies comparative genome hybridization and interspecies representational difference analysis reveal gross DNA differences between humans and great apes.

Comparative chromosome G-/R-banding, comparative gene mapping and chromosome painting techniques have demonstrated that only few chromosomal rearrangements occurred during great ape and human evolution. Interspecies comparative genome hybridization (CGH), used here in this study, between human, gorilla and pygmy chimpanzee revealed species-specific regions in all three species. In contrast to the human, a far more complex distribution of species-specific blocks was detected with CGH in gorilla and pygmy chimpanzee. Most of these blocks coincide with already described heterochromatic regions on gorilla and chimpanzee chromosomes. Representational difference analysis (RDA) was used to subtract the complex genome of gorilla against human in order to enrich gorilla-specific DNA sequences. Gorilla-specific clones isolated with this technique revealed a 32-bp repeat unit. These clones were mapped by fluorescence in situ hybridization (FISH) to the telomeric regions of gorilla chromosomes that had been shown by interspecies CGH to contain species-specific sequences.

Animals↗

PubMed2002

[At what care level are cyclo-oxygenase-2 inhibitors prescribed?].

OBJECTIVES: To find the evolution in the billing of prescriptions for selective cyclooxygenase-2 (COX-2) inhibitors since they came on the market and to compare this evolution in primary care (PC) and specialist care (SC).Design. Cross-sectional, descriptive study. SETTING: Toledo Health Area. Main measurements. Data were obtained from the System of Drug Information (SIFAR) to analyse the monthly turnover of NSAID prescriptions (M01A group in the official classification of medicines, including rofecoxib and celecoxib) issued by doctors in PC and SC between January 2000 and June 2001. RESULTS: In our area during the study period, 583,558 NSAID packages were prescribed; 6.61% were COX-2 inhibitors, which represented 29.08% of NSAID expenditure. 98.23% of NSAID packages and 94.61% of COX-2 inhibitors were prescribed in PC. The use of COX-2 inhibitors in SC rose from 10.03% of the total NSAIDs in February 2000 to 29.79% in June 2001; whilst in PC it rose from 1.52% to 10.78%. Rofecoxib and celecoxib were third and fifth in the lists of most prescribed NSAIDs (number of packages) in SC, and ninth and twelfth in PC. In terms of cost of prescription, they were first and second in SC, and first and fourth in PC. CONCLUSIONS: COX-2 inhibitors have become the main NSAIDs prescribed. The appearance of these drugs had a different impact on SC and PC doctors, with greater use of them and a more rapid introduction in SC.

Cross-Sectional Studies↗

PubMed1997

[Current treatment of candidemia in non-neutropenic patients. Amphotericin B or fluconazole? A retrospective study of 62 consecutive patients].

BACKGROUND: To analyze the epidemiologic characteristics of non-neutropenic patients with candidemia in a general hospital and the advantages and disadvantages of treatment with amphotericin B or fluconazole. PATIENTS AND METHODS: A total of 62 adult non-neutropenic patients with candidemia and treated with amphotericin B (n = 35) or fluconazole (n = 27) were studied. All episodes were considered to be associated with infection in a vein catheter. The demographic characteristics, risk factors for the development of candidemia, Candida species recovered from blood culture, underlying diseases, and clinical manifestations in both groups were compared. The evolution regarding secondary effects developed with both drugs, therapy failures, long term complications, and overall mortality rate associated with candidemia were analyzed. RESULTS: Both groups were comparable with the exception of the percentage of patients infected with species different from Candida albicans, which was higher in the group of patients who received amphotericin B (57%) than in the fluconazole group (26%) (p = 0.02), and in that patients with severe renal failure or AIDS had received preferentially fluconazole. There were no statistically significant differences regarding the evolution of patients treated with amphotericin B or fluconazole with the following factors: therapy failure (27% versus 19%; p = 0.7), overall mortality rate (40% versus 44%; p = 0.6), and mortality directly related to candidemia (33% versus 30%). Mortality was significantly higher among patients who had not their vein catheters removed early (78%) compared with those who had their vein catheters removed early (34%) (p = 0.01). Sixty-six percent of patients treated with amphotericin developed some severe secondary effect, whereas no patient in the fluconazole group developed such effects. CONCLUSIONS: Both amphotericin B and fluconazole seem to be effective drugs for the treatment of vein catheter related candidemia in the non-neutropenic patient, although fluconazole is far less toxic. The early removal of the vein catheter plays a prognostic role with at least the same relevance than the type of antifungal therapy chosen.

Adult↗

PubMed2004

Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes.

Molecular adaptation, as characterized by the detection of positive selection, was quantified in a number of genes from different human immunodeficiency virus type 1 (HIV-1) group M subtypes, group O, and an HIV-2 subtype using the codon-based maximum-likelihood method of Yang and coworkers (Z. H. Yang, R. Nielsen, N. Goldman, and A. M. K. Pedersen, Genetics 155:431-449, 2000). The env gene was investigated further since it exhibited the strongest signal for positive selection compared to those of the other two major HIV genes (gag and pol). In order to investigate the pattern of adaptive evolution across env, the location and strength of positive selection in different HIV-1 sequence alignments was compared. The number of sites having a significant probability of being positively selected varied among these different alignment data sets, ranging from 25 in HIV-1 group M subtype A to 40 in HIV-1 group O. Strikingly, there was a significant tendency for positively selected sites to be located at the same position in different HIV-1 alignments, ranging from 10 to 16 shared sites for the group M intersubtype comparisons and from 6 to 8 for the group O to M comparisons, suggesting that all HIV-1 variants are subject to similar selective forces. As the host immune response is believed to be the dominant driving force of adaptive evolution in HIV, this result would suggest that the same sites are contributing to viral persistence in diverse HIV infections. Thus, the positions of the positively selected sites were investigated in reference to the inferred locations of different epitope types (antibody, T helper, and cytotoxic T lymphocytes) and the positions of N and O glycosylation sites. We found a significant tendency for positively selected sites to fall outside T-helper epitopes and for positively selected sites to be strongly associated with N glycosylation sites.

Adaptation, Physiological↗

PubMed1999

Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.

Comparative analysis of the protein sequences encoded in the four euryarchaeal species whose genomes have been sequenced completely (Methanococcus jannaschii, Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, and Pyrococcus horikoshii) revealed 1326 orthologous sets, of which 543 are represented in all four species. The proteins that belong to these conserved euryarchaeal families comprise 31%-35% of the gene complement and may be considered the evolutionarily stable core of the archaeal genomes. The core gene set includes the great majority of genes coding for proteins involved in genome replication and expression, but only a relatively small subset of metabolic functions. For many gene families that are conserved in all euryarchaea, previously undetected orthologs in bacteria and eukaryotes were identified. A number of euryarchaeal synapomorphies (unique shared characters) were identified; these are protein families that possess sequence signatures or domain architectures that are conserved in all euryarchaea but are not found in bacteria or eukaryotes. In addition, euryarchaea-specific expansions of several protein and domain families were detected. In terms of their apparent phylogenetic affinities, the archaeal protein families split into bacterial and eukaryotic families. The majority of the proteins that have only eukaryotic orthologs or show the greatest similarity to their eukaryotic counterparts belong to the core set. The families of euryarchaeal genes that are conserved in only two or three species constitute a relatively mobile component of the genomes whose evolution should have involved multiple events of lineage-specific gene loss and horizontal gene transfer. Frequently these proteins have detectable orthologs only in bacteria or show the greatest similarity to the bacterial homologs, which might suggest a significant role of horizontal gene transfer from bacteria in the evolution of the euryarchaeota.

Amino Acid Sequence↗

PubMed2002

Comparative phylogenetic analysis of the evolution of semelparity and life history in salmonid fishes.

The selective pressures involved in the evolution of semelparity and its associated life-history traits are largely unknown. We used species-level analyses, independent contrasts, and reconstruction of ancestral states to study the evolution of body length, fecundity, egg weight, gonadosomatic index, and parity (semelparity vs. degree of iteroparity) in females of 12 species of salmonid fishes. According to both species-level analysis and independent contrasts analysis, body length was positively correlated with fecundity, egg weight, and gonadosomatic index, and semelparous species exhibited a significantly steeper slope for the regression of egg weight on body length than did iteroparous species. Percent repeat breeding (degree of iteroparity) was negatively correlated with gonadosomatic index using independent contrasts analysis. Semelparous species had significantly larger eggs by species-level analysis, and the egg weight contrast for the branch on which semelparity was inferred to have originated was significantly larger than the other egg weight contrasts, corresponding to a remarkable increase in egg weight. Reconstruction of ancestral states showed that egg weight and body length apparently increased with the origin of semelparity, but fecundity and gonadosomatic index remained more or less constant or decreased. Thus, the strong evolutionary linkages between body size, fecundity, and gonadosomatic index were broken during the transition from iteroparity to semelparity. These findings suggest that long-distance migrations, which increase adult mortality between breeding episodes, may have been necessary for the origin of semelparity in Pacific salmon, but that increased egg weight, leading to increased juvenile survivorship, was crucial in driving the transition. Our analyses support the life-history hypotheses that a lower degree of repeat breeding is linked to higher reproductive investment per breeding episode, and that semelparity evolves under a combination of relatively high juvenile survivorship and relatively low adult survivorship.

Animals↗

PubMed1984

Study of the evolution of acute phase reactants and of thromboxane and prostacyclin during calcium pyrophosphate-induced pleurisy in the rat.

By using a clearly defined model of acute inflammation in rats, CaPP-induced pleurisy, we compared the evolution of four APR levels (Hp, HpX, alpha 2M, SAP) at a local and peripheral site. At the same time we studied thromboxane and prostacyclin concentrations in pleural exudate. The levels of APR have shown a progressive increase up to 24 h. For alpha 2M, Hp, HpX the increase in serum concentration was more rapid than in exudate, whereas the evolution of SAP level was parallel in the intra and extra-vascular compartments. On the other hand the levels of albumin and transferrin which are not APR remained constant in serum and also in exudate from 6 h to 24 h. Thromboxane and prostacyclin levels reached a peak during the first two hours of the inflammatory reaction followed by a rapid decreased. These prostanoids may be considered as early and transient mediators of acute inflammation, whereas the acute phase proteins studied have a more prolonged role in the inflammatory reaction.

Acute-Phase Proteins↗

PubMed2000

Current awareness on comparative and functional genomics [bibliography].

In order to keep subscribers up-to-date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly-published material on comparative and functional genomics. Each bibliography is divided into 16 sections. 1 Reviews & symposia; 2 General; 3 Large-scale sequencing and mapping; 4 Genome evolution; 5 Comparative genomics; 6 Gene families and regulons; 7 Pharmacogenomics; 8 Large-scale mutagenesis programmes; 9 Functional complementation; 10 Transcriptomics; 11 Proteomics; 12 Protein structural genomics; 13 Metabolomics; 14 Genomic approaches to development; 15 Technological advances; 16 Bioinformatics. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted

Animals↗

PubMed2000

Current awareness.

Animals↗

PubMed1999

Anti-HIV-1/2 Antibody Detection by Dot-ELISA in Oral Fluid of HIV Positive/AIDS Patients and Voluntary Blood Donors.

Serology is the primary means for identifying patients with HIV infection and Acquired Immunodeficiency Syndrome (AIDS). Testing of serum by serologic methods has been extensively used since 1985, not only for clinical diagnosis but also for epidemiological surveillance and donor screening in blood banks. Fast serological diagnostic techniques are now being developed, using urine and oral fluid, as an alternative for anti-HIV antibody screening, and many parallel studies are proving its accuracy. The purpose of this study was to evaluate the sensitivity, specificity, accuracy, positive predictive value (PPV) and negative predictive value (NPV) of the ImmunoComb II HIV 1&2 Saliva((R)) test from Orgenics (Dot-ELISA) compared to the routine exams (ELISA and Western Blot) of HIV positive/AIDS patients, undergoing antiretroviral treatment or not, in different stages of the disease's evolution, and compared to serologic testing of known HIV negative patients by the use of serum ELISA (blood donors). To accomplish this, patients of the Immunogenic Deficiencies Control Center (CCDI) and voluntary blood donors of the Blood Bank Center of the Medical School of S&atilde:o Paulo/Federal University of São Paulo (EPM-UN I FESP) were evaluated. Sensitivity of Dot-ELISA in oral fluid was 100%, specificity 97.08%, PPV 96.66% and NPV 100%. The method used in this case study was shown to be highly sensitive and specific, being useful particularly in epidemiological surveillance and screening.

Journal Article↗

PubMed1996

Evolution of photochemically induced focal cerebral ischemia in the rat. Magnetic resonance imaging and histology.

BACKGROUND AND PURPOSE: Magnetic resonance imaging (MRI) is increasingly used to study the pathophysiological evolution of cerebral ischemia in humans and animals. We have investigated photochemically induced (rose bengal) focal cerebral ischemia, a relatively noninvasive, reproducible model for stroke, and compared the evolution of the ischemic response in vivo and postmortem with MRI and histology, respectively. METHODS: MR images weighted for T2, diffusion, and T2* and parallel histological sections stained with cresyl fast violet (CFV) and for glial fibrillary acid protein were obtained from 34 adult male Hooded Lister rats at seven time points (3.75 to 196 hours) after bilateral ischemia induction. From CFV histology, lesion volumes and cell counts were calculated; from diffusion-weighted and T2-weighted images, apparent diffusion coefficients and lesion volumes were determined. RESULTS: Both MRI and histology revealed a well-defined lesion at 3.75 hours after irradiation and a consistent pattern of temporal evolution; lesion apparent diffusion coefficients decreased significantly by 3.75 hours, increased significantly by day 2, and correlated strikingly with the decline in lesion CFV-positive cell numbers. After day 2, astrocytes and connective tissue cells invaded the infarct. Throughout the time course, lesion volumes determined in vivo and postmortem (after shrinkage correction) agreed well. CONCLUSIONS: MRI changes quantitatively reflect histopathology, revealing reproducible primary and secondary damage characteristics noninvasively. These changes essentially replicate those reported for other animal stroke models and clinically, emphasizing the value both of MRI and the photochemically induced focal cerebral ischemia model in stroke research.

Animals↗

PubMed1997

Comparative primate energetics and hominid evolution.

There is currently great interest in developing ecological models for investigating human evolution. Yet little attention has been given to energetics, one of the cornerstones of modern ecosystem ecology. This paper examines the ecological correlates of variation in metabolic requirements among extant primate species, and uses this information to draw inferences about the changes in energy demands over the course of human evolution. Data on body size, resting metabolism, and activity budgets for selected anthropoid species and human hunter-gatherers are used to estimate total energy expenditure (TEE). Analyses indicate that relative energy expenditure levels and day ranges are positively correlated with diet quality; that is, more active species tend to consume more energy-rich diets. Human foragers fall at the positive extremes for modern primates in having high expenditure levels, large ranges, and very high quality diets. During hominid evolution, it appears that TEE increased substantially with the emergence of Homo erectus. This increase is partly attributable to larger body size as well as likely increases in day range and activity level. Assuming similar activity budgets for all early hominid species, estimated TEE for H. erectus is 40-45% greater than for the australopithecines. If, however, it is assumed that the evolution of early Homo was also associated with a shift to a more "human-like" foraging strategy, estimated expenditure levels for H. erectus are 80-85% greater than in the australopithecines. Changing patterns of resource distribution associated with the expansion of African savannas between 2.5 and 1.5 mya may been the impetus for a shift in foraging behavior among early members of the genus Homo. Such ecological changes likely would have made animal foods a more attractive resource. Moreover, greater use of animal foods and the resulting higher quality diet would have been important for supporting the larger day ranges and greater energy requirements that appear to have been associated with the evolution of a human-like hunting and gathering strategy.

Animals↗