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PubMed1991

Comparative methods for explaining adaptations.

The ways that taxonomic differences in morphology, behaviour or life history are related to each other and to differences in lifestyle have been used regularly to test ideas about the selective forces involved in their evolution. Such comparative tests have been transformed recently by using increased statistical rigour. The realization that the statistical model against which comparisons are made is a model of how evolution proceeds, forms the basis of a new generation of comparative tests that are grounded properly on phylogenetic reconstruction.

Adaptation, Physiological↗
PubMed1994

[Long-term evolution of immunologic and thyroid function in Graves disease according different therapeutic options].

BACKGROUND: A prospective study was carried out to compare the evolution of thyroid hormones, thyroglobulin (Tg) and immunoglobulins inhibiting the binding of thyrotropin to its receptor (TBII) in patients with Graves disease treated with antithyroid drugs, radioactive iodine and subtotal thyroidectomy. METHODS: Ninety-five patients with Graves disease were studied, being distributed according to clinical criteria: Group I (n = 35) patients treated with antithyroid drugs; Group II (n = 30) patients who received 131I; and Group III (n = 30) patients treated with subtotal thyroidectomy. The thyroid hormones, Tg, antithyroglobulin antibodies and TBII were determined by radioimmunoassay (RIA), prior to treatment, and at 1, 3, 6, 12, 24, and 36 months of follow up, except in those patients from Group III who were followed up to 24 months. RESULTS: The rate of reactivation at 12 months did not significantly differ among the three groups. At 24 months a higher percentage of reactivations was observed in Group I (42%), versus Group II (16%, p < 0.001) and Group III (13%, p < 0.005). At 36 months reactivation was 30% in Group I, versus 5% in Group II (p < 0.01). Upon comparison of the TBII values among the three groups, the highest basal values corresponded to Group III with significant differences being found versus Group I (p < 0.05) and Group II (p < 0.001). TBII concentrations in the three groups studied remained high at 6 and 12 months with no significant differences being observed. Negativization was shown in the TBII at 24 months in Group II with a significant difference being seen versus Group I and III. At 36 months negativization was seen in the TBII in Group I with significant differences with respect to Group II. CONCLUSIONS: The rate of reactivation following antithyroid treatment is greater to that obtained in groups treated with iodine or surgery. The earliest negativization of TBII was obtained with radioiodine.

Adolescent↗
PubMed2001

Automatic method for evaluating the activity of sourdough strains based on gas pressure measurements.

A new method is proposed for the evaluation of the activity of sourdough strains, based on gas pressure measurements in closed air-tight reactors. Gas pressure and pH were monitored on-line during the cultivation of commercial yeasts and heterofermentative lactic acid bacteria on a semi-synthetic medium with glucose as the major carbon source. Relative gas pressure evolution was compared both to glucose consumption and to acidification and growth. It became obvious that gas pressure evolution is related to glucose consumption kinetics. For each strain, a correlation was made between maximum gas pressure variation and amount of glucose consumed. The mass balance of CO2 in both liquid and gas phase demonstrated that around 90% of CO2 was recovered. Concerning biomass production, a linear relationship was found between log colony-forming units/ml and log pressure for both yeasts and bacteria during the exponential phase; and for yeasts, relative gas pressure evolution also followed optical density variation.

Carbon Dioxide↗
PubMed2026

Comparative genomic characterization and antimicrobial resistance of bacteremia-causing Enterococcus faecium and Enterococcus faecalis in a Chinese hospital.

Enterococci are common commensals of the human gut and important opportunistic pathogens, with Enterococcus faecium and Enterococcus faecalis being the most clinically prevalent species. A significant epidemiological shift has emerged with an increasing clinical burden of E. faecium. To compare genomic evolution of E. faecium and E. faecalis, we performed whole-genome sequencing on 93 E. faecium and 32 E. faecalis isolates causing bloodstream infections at a single hospital (2022-2024). Analysis of patient demographics revealed that E. faecium infections originated from fewer sources than E. faecalis, with a higher proportion deriving from intra-abdominal infections. Multilocus sequence typing identified ST78 and ST789 as the predominant sequence types for E. faecium, whereas ST16 and ST179 were most common for E. faecalis. E. faecium carried more antimicrobial resistance genes and putative virulence marker (PVM)-type virulence genes than E. faecalis, with vancomycin resistance predominantly mediated by vanHAX (33/93, 35.5%) and a single E. faecalis isolate also carrying vanHAX (1/32, 3.1%); the structurally incomplete vanHMX gene cluster was detected in 11 E. faecium isolates. Pan-genome analysis indicated a larger core genome in E. faecalis compared to E. faecium, consistent with greater plasmid replicon diversity in the latter. Intra-host comparisons showed that two E. faecalis pairs from the same patient were clonally related, with one isolate acquiring a vanHAX plasmid conferring vancomycin resistance. In contrast, E. faecium isolates exhibited marked genomic diversity even among clonally related pairs. These findings suggest that E. faecium possesses greater genomic plasticity and adaptive potential to the clinical environment.IMPORTANCEThis study provides a detailed comparison of clinical and genomic features between Enterococcus faecium and Enterococcus faecalis from the same hospital setting. We show that E. faecium isolates, mainly ST78/ST789, carry more antimicrobial resistance genes and a higher number of putative virulence marker (PVM) genes than E. faecalis, reflecting their hospital-adapted nature. E. faecium also exhibits a smaller core genome and greater diversity of plasmid replicon types, indicating higher genomic plasticity and capacity for horizontal gene transfer. By contrast, E. faecalis retains a larger core genome and a set of classical virulence factors, and its within-host isolates are clonally related. These distinct genomic profiles help to understand how the two species adapt to clinical environments and may inform more targeted infection control strategies and resistance surveillance.

Enterococcus faecium↗
PubMed2003

Sexual isolation evolves faster than hybrid inviability in a diverse and sexually dimorphic genus of fish (Percidae: Etheostoma).

Theory predicts that sexual (or behavioral) isolation will be the first form of reproductive isolation to evolve in lineages characterized by sexual selection. Here I directly compare the rate of evolution of sexual isolation with that of hybrid inviability in a diverse and sexually dimorphic genus of freshwater fish. The magnitude of both sexual isolation and hybrid inviability were quantified for multiple pairs of allopatric species. Rates of evolution were inferred by comparing genetic distances of these species pairs with the magnitude of each form of reproductive isolation: the slope of the regression of genetic distance on the magnitude of reproductive isolation represents the rate of evolution. Of the two forms of isolation, the magnitude of sexual isolation exhibited the steeper slope of regression, indicating that sexual isolation will tend to evolve to completion earlier than hybrid inviability, strictly as a by-product of evolution in geographically isolated populations. Additional evidence from the literature is used to qualitatively compare rates of evolution of sexual isolation with that of other forms of reproductive isolation. Preliminary comparisons support the prediction that sexual isolation will evolve more rapidly than other forms. Because Etheostoma is characterized by striking sexual dimorphism, these results are consistent with the hypothesis that sexual selection for exaggerated mate-recognition characters causes the relatively rapid evolution of sexual isolation.

Animals↗
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↗
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↗