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PubMed2026

Genetic Tools in the Nakaseomyces clade for Evolutionary Comparisons of Signal Transduction Pathways.

The genus Nakaseomyces provides four species that are closely related but have different characteristics. For example, N. glabratus (formerly known as Candida glabrata) is a common human pathogen, whereas N. bracarensis and N. nivariensis have been isolated in clinical settings but are not common human pathogens. N. delphensis was isolated from fruit and there is no evidence it is pathogenic. Given the differences, we developed the clade as a molecular genetic system where we could introduce plasmids and assess transcriptional output from cloned promoters. We engineered a CRISPR/Cas9 plasmid that allows for rapid Gibson cloning of gRNAs, generated auxotrophic strains for amino acids and nucleotides, and introduced plasmids into each species. We used promoter-YFP plasmids to determine that while there are differences between the species, each species likely has intact thiamine and phosphate (THI and PHO) signal transduction pathways, and that gene expression in N. glabratus and N. bracarensis is more similar to one another than to the other two species. Finally, we determine that N. glabratus, N. bracarensis, and N. nivariensis persist in a murine macrophage for 24 h, whereas N. delphensis does not. This work describes new molecular tools for genetic manipulation in the Nakaseomyces clade and allows for evolutionary questions to be explored.

Signal Transduction↗
PubMed1999

Brain-derived neurotrophic factor immunoreactivity in the limbic system of rats after acute seizures and during spontaneous convulsions: temporal evolution of changes as compared to neuropeptide Y.

Seizures increase the synthesis of brain-derived neurotrophic factor in forebrain areas, suggesting this neurotrophin has biological actions in epileptic tissue. The understanding of these actions requires information on the sites and extent of brain-derived neurotrophic factor production in areas involved in seizures onset and their spread. In this study, we investigated by immunocytochemistry the changes in brain-derived neurotrophic factor in the hippocampus, entorhinal and perirhinal cortices of rats at increasing times after acute seizures eventually leading to spontaneous convulsions. We also tested the hypothesis that seizure-induced changes in brain-derived neurotrophic factor induce later modifications in neuropeptide Y expression by comparing, in each instance, their immunoreactive patterns. As early as 100 min after seizure induction, brain-derived neurotrophic factor immunoreactivity increased in CA1 pyramidal and granule neurons and in cells of layers II-III of the entorhinal cortex. At later times, immunoreactivity progressively decreased in somata while increasing in fibres in the hippocampus, the subicular complex and in specific layers of the entorhinal and perirhinal cortices. Changes in neuropeptide Y immunoreactivity were superimposed upon and closely followed those of brain-derived neurotrophic factor. One week after seizure induction, brain-derived neurotrophic factor and neuropeptide Y immunoreactivities were similar to controls in 50% of rats. In rats experiencing spontaneous convulsions, brain-derived neurotrophic factor and neuropeptide Y immunoreactivity was strongly enhanced in fibres in the hippocampus/parahippocampal gyrus and in the temporal cortex. In the dentate gyrus, changes in immunoreactivity depended on sprouting of mossy fibres as assessed by growth-associated protein-43-immunoreactivity. These modifications were inhibited by repeated anticonvulsant treatment with phenobarbital. The dynamic and temporally-linked alterations in brain-derived neurotrophic factor and neuropeptide Y in brain regions critically involved in epileptogenesis suggest a functional link between these two substances in the regulation of network excitability.

Acute Disease↗
PubMed2001

Structure of the induced antibacterial protein from tasar silkworm, Antheraea mylitta. Implications to molecular evolution.

The crystal structure of an antibacterial protein of immune origin (TSWAB), purified from tasar silkworm (Antheraea mylitta) larvae after induction by Escherichia coli infection, has been determined. This is the first insect lysozyme structure and represents induced lysozymes of innate immunity. The core structure of TSWAB is similar to c-type lysozymes and alpha-lactalbumins. However, TSWAB shows significant differences with respect to the other two proteins in the exposed loop regions. The catalytic residues in TSWAB are conserved with respect to the chicken lysozyme, indicating a common mechanism of action. However, differences in the noncatalytic residues in the substrate binding groove imply subtle differences in the specificity and the level of activity. Thus, conformational differences between TSWAB and chicken lysozyme exist, whereas functional mechanisms appear to be similar. On the other hand, alpha-lactalbumins and c-type lysozymes exhibit drastically different functions with conserved molecular conformation. It is evident that a common molecular scaffold is exploited in the three enzymes for apparently different physiological roles. It can be inferred on the basis of the structure-function comparison of these three proteins having common phylogenetic origin that the conformational changes in a protein are minimal during rapid evolution as compared with those in the normal course of evolution.

Amino Acid Sequence↗
PubMed1999

The dynamics of chromosome evolution in birds and mammals.

Comparative mapping, which compares the location of homologous genes in different species, is a powerful tool for studying genome evolution. Comparative maps suggest that rates of chromosomal change in mammals can vary from one to ten rearrangements per million years. On the basis of these rates we would expect 84 to 600 conserved segments in a chicken comparison with human or mouse. Here we build comparative maps between these species and estimate that numbers of conserved segments are in the lower part of this range. We conclude that the organization of the human genome is closer to that of the chicken than the mouse and by adding comparative mapping results from a range of vertebrates, we identify three possible phases of chromosome evolution. The relative stability of genomes such as those of the chicken and human will enable the reconstruction of maps of ancestral vertebrates.

Animals↗
PubMed2003

The evolution of the music faculty: a comparative perspective.

We propose a theoretical framework for exploring the evolution of the music faculty from a comparative perspective. This framework addresses questions of phylogeny, adaptive function, innate biases and perceptual mechanisms. We argue that comparative studies can make two unique contributions to investigations of the origins of music. First, musical exposure can be controlled and manipulated to an extent not possible in humans. Second, any features of music perception found in nonhuman animals must not be part of an adaptation for music, and must rather be side effects of more general features of perception or cognition. We review studies that use animal research to target specific aspects of music perception (such as octave generalization), as well as studies that investigate more general and shared systems of the mind/brain that may be relevant to music (such as rhythm perception and emotional encoding). Finally, we suggest several directions for future work, following the lead of comparative studies on the language faculty.

Animals↗
PubMed2000

Comparative fluorescence in situ hybridization mapping of a 431-kb Arabidopsis thaliana bacterial artificial chromosome contig reveals the role of chromosomal duplications in the expansion of the Brassica rapa genome.

Comparative genome studies are important contributors to our understanding of genome evolution. Most comparative genome studies in plants have been based on genetic mapping of homologous DNA loci in different genomes. Large-scale comparative physical mapping has been hindered by the lack of efficient and affordable techniques. We report here the adaptation of fluorescence in situ hybridization (FISH) techniques for comparative physical mapping between Arabidopsis thaliana and Brassica rapa. A set of six bacterial artificial chromosomes (BACs) representing a 431-kb contiguous region of chromosome 2 of A. thaliana was mapped on both chromosomes and DNA fibers of B. rapa. This DNA fragment has a single location in the A. thaliana genome, but hybridized to four to six B. rapa chromosomes, indicating multiple duplications in the B. rapa genome. The sizes of the fiber-FISH signals from the same BACs were not longer in B. rapa than those in A. thaliana, suggesting that this genomic region is duplicated but not expanded in the B. rapa genome. The comparative fiber-FISH mapping results support that chromosomal duplications, rather than regional expansion due to accumulation of repetitive sequences in the intergenic regions, played the major role in the evolution of the B. rapa genome.

Arabidopsis↗
PubMed2001

The phylogenetic placement of chondrichthyes: inferences from analysis of multiple genes and implications for comparative studies.

Elasmobranch fishes (sharks and rays) have proven valuable for inferring general and specific properties of molecular evolution through comparative studies with crown group vertebrates because they are the most ancient group of gnathostomes. Recent studies have questioned the conventional phylogenetic placement of sharks in the vertebrate tree, however. In this paper I review the importance of the basal position of Chondrichthyes for comparative biology and compile evidence from multiple, independent genes to evaluate the phylogenetic placement of sharks. The results suggests that alternative phylogenetic hypotheses of the relationships among the Chondrichthyes, Actinopterygii and Sarcopterygii can not be refuted with available data, implying that the assumption of the basal placement of sharks in the vertebrate tree is suspect. Resolving the phylogeny of basal vertebrates is important for testing hypotheses about the evolution of vertebrates, and the current lack of a robust phylogeny limits evolutionary inferences that can be gained from comparative studies that include sharks and rays.

Animals↗
PubMed2000

The rice R gene family: two distinct subfamilies containing several miniature inverted-repeat transposable elements.

The R and B genes of maize regulate the anthocyanin biosynthetic pathway and constitute a small gene family whose evolution has been shaped by polyploidization and transposable element activity. To compare the evolution of regulatory genes in the distinct but related genomes of rice and maize, we previously isolated two R homologues from rice (Oryza sativa). The Ra1 gene on chromosome 4 can activate the anthocyanin pathway, whereas the Rb gene, of undetermined function, maps to chromosome 1. In this study, rice R genes have been further characterized. First, we found that an Rb cDNA can induce pigmentation in maize suspension cells. Second, another rice R homologue (Ra2) was identified that is more closely related to Ra1 than to Rb. Domesticated rice and its wild relatives harbor multiple Ra-like and Rb-like genes despite the fact that rice is a true diploid with the smallest genome of all the grass species analyzed to date. Finally, several miniature inverted-repeat transposable elements (MITEs) were found in R family members. Their possible role in hastening the divergence of R genes is discussed.

Amino Acid Sequence↗
PubMed1981

Simulation of protein evolution by random fixation of allowed codons.

Computer simulation of protein evolution is based on a simple model consisting of random fixation of allowed codons (RFAC). Random replacement of single nucleotides occurs in a DNA sequence. If this results in any of the synonomous codons for allowed amino acids the mutation is fixed, if not, there is no change in the DNA and the cycle is repeated. Multiple fixations at the same nucleotide site, back mutations, degenerate fixations and coincidental identity of amino acids all occur. RFAC simulation begins with a single DNA sequence and follows a phylogeny based on the fossil record. The rate of fixation at the level of DNA is constant. The model upon which RFAC simulation is based is the same as the neutral theory of molecular evolution. The simulation is therefore a test of this theory. The results of simulated and real evolution are compared for fibrinopeptides A in mammals and cytochromes C and hemoglobin alpha and beta chains in vertebrates. In each case the allowed variation at each site has been set equal to that observed, twice that observed and all protein amino acids. Rates of fixation vary from 2.4 X 10(-10) to 10(-8) accepted nucleotide fixations per codon per year. There is some, although never excellent, agreement between real and simulated evolution, the better fits are obtained in the cases of fibrinopeptides A and cytochromes C. The major source of discrepancy between real evolution and simulation is irregularities in the rates of real evolution. RFAC simulation is compared with the random evolutionary hit (REH) model, augmented maximum parsimony and the accepted point mutations (PAM) approach.

Amino Acids↗
PubMed1992

Comparative variation of morphological and molecular evolution through geologic time: 28S ribosomal RNA versus morphology in echinoids.

The comparatively good fossil record of post-Palaeozoic echinoids allows rates of morphological change to be estimated over the past 260 million years and compared with rates of molecular evolution. Parsimony analysis of morphological data, based predominantly on skeletal characteristics, and parsimony, distance and maximum likelihood analyses of molecular data, from the first 380 bases from the 5' end of the 28S rRNA molecule, for 10 species of echinoid produce congruent phylogenies. The molecular sequence chosen is demonstrably far from saturation and sister groups have divergence times ranging from about 15 to 260 Ma. Parsimony analysis allows the great majority of molecular and morphological apomorphies to be placed in one of 18 independent geological time intervals, providing a direct measure of rates of evolution for periods in the geological past. Because most molecular fixed point mutations in our sequences cannot be polarized unambiguously by outgroup comparison (making the outgroup states effectively random), distance and parsimony analyses both tend spuriously to root the echinoid tree on the longest internal branch. A topology identical to that derived from morphological data is, however, obtained using Maximum Likelihood and also parsimony analysis where outgroup rooting is restricted to more conserved regions. This is taken as the correct topology for assessing rates of evolution. Overall, both morphological and molecular changes show a moderately strong correlation with time elapsed, but a weaker correlation with one another. Statistically significant differences in evolutionary rate are found between some, but not all, pair-wise comparisons of sister lineages for both molecular and morphological data. The molecular clock rate for echinaceans is three times faster than that for cidaroids and irregular echinoids. Spearman's rank correlation test, which requires only relative magnitude of changes to be known, suggests that morphological change has a slightly better correlation with time than does molecular change, averaged over all ten species. However, when just echinaceans are considered an extremely good correlation is found between the number of molecular changes and time elapsed, whereas morphological change remains poorly correlated. Thus, molecular rates approximate to a clocklike model within restricted echinoid clades, but vary significantly between clades. Averaging results over all echinoids produces a correlation that is no better than the correlation between morphological change and time elapsed.

Animals↗
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↗