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PubMed2001

Molecular evolution of the ocnus and janus genes in the Drosophila melanogaster species subgroup.

Genes involved in male fertility are potential targets for sexual selection, and their evolution may play a role in reproductive isolation and speciation. Here we describe a new Drosophila melanogaster gene, ocnus (ocn), that encodes a protein abundant in testes nuclear extracts. RT-PCR indicates that ocn transcription is limited to males and is specific to testes. ocn shares homology with another testis-specific gene, janusB (janB), and is located just distal to janB on chromosome 3. The two genes also share homology with the adjacent janusA (janA) gene, suggesting that multiple duplication events have occurred within this region of the genome. We cloned and sequenced these three genes from species of the D. melanogaster species subgroup. Phylogenetic analysis based on protein-encoding sequences predicts a duplication pattern of janA --> janA janB --> janA janB ocn, with the latter event occurring after the divergence of the D. melanogaster and Drosophila obscura species groups. We found significant heterogeneity in the rates of evolution among the three genes within the D. melanogaster species subgroup as measured by the ratio of nonsynonymous to synonymous substitutions, suggesting that diversification of gene function followed each duplication event and that each gene evolved under different selective constraints. All three genes showed faster rates of evolution than genes encoding proteins with metabolic function. These results are consistent with previous studies that have detected an increased rate of evolution in genes with reproductive function.

Animals↗

PubMed2004

Differential correlates of diet and phylogeny on the shape of the premaxilla and anterior tooth in sparid fishes (Perciformes: Sparidae).

We explore the correlational patterns of diet and phylogeny on the shape of the premaxilla and anterior tooth in sparid fishes (Perciformes: Sparidae) from the western Mediterranean Sea. The premaxilla is less variable, and in spite of the presence of species-specific features, a common structural pattern is easily recognizable in all species (i.e. the ascending and the articular processes are fused in a single branch, as in many percoid fishes). In contrast, tooth shape is more variable, and different structural types can be recognized (e.g. canine-like or incisive). Coupling geometric morphometric and comparative methods we found that the relationship between shape, diet and phylogeny also differs between premaxilla and tooth. Thus, the shape of the premaxilla is significantly correlated with food type, whereas the shape of the teeth is not correlated with diet, and probably reflects the species phylogenetic relationships. Two biological roles, resistance against compressive forces generated in the buccal cavity and the size of the oral gape, would explain the ecomorphological patterns of the premaxilla. The premaxilla and anterior tooth appear to evolve at different rates (mosaic evolution) and represent an example of morphological traits belonging to the same functional unit but following uncoupled evolutionary pathways.

Adaptation, Biological↗

PubMed2006

Efficient estimation of detailed single-neuron models.

Biophysically accurate multicompartmental models of individual neurons have significantly advanced our understanding of the input-output function of single cells. These models depend on a large number of parameters that are difficult to estimate. In practice, they are often hand-tuned to match measured physiological behaviors, thus raising questions of identifiability and interpretability. We propose a statistical approach to the automatic estimation of various biologically relevant parameters, including 1) the distribution of channel densities, 2) the spatiotemporal pattern of synaptic input, and 3) axial resistances across extended dendrites. Recent experimental advances, notably in voltage-sensitive imaging, motivate us to assume access to: i) the spatiotemporal voltage signal in the dendrite and ii) an approximate description of the channel kinetics of interest. We show here that, given i and ii, parameters 1-3 can be inferred simultaneously by nonnegative linear regression; that this optimization problem possesses a unique solution and is guaranteed to converge despite the large number of parameters and their complex nonlinear interaction; and that standard optimization algorithms efficiently reach this optimum with modest computational and data requirements. We demonstrate that the method leads to accurate estimations on a wide variety of challenging model data sets that include up to about 10(4) parameters (roughly two orders of magnitude more than previously feasible) and describe how the method gives insights into the functional interaction of groups of channels.

Algorithms↗

PubMed1993

Construct validation and the Rasch model: functional ability of healthy elderly people.

The purpose of this study was to test the construct validity of a measure of functional ability, developed with the intention of achieving a high degree of variability and capacity for discriminating among a group of healthy elderly people. Data were collected from 734 70-year-old people in Denmark in the county of Copenhagen. Functional ability was measured with the traditional activities of daily living and with a classification system developed specially for healthy elderly people. Construct validity was tested by the Rasch model for item analysis, addressing specifically the internal validity by assessing the homogeneity of items under different conditions. The results show that the proposed measure of functional ability is a combination of six different dimensions, divided into 3 types: mobility function, lower limb function and upper limb function. With regard to these three types decreased functional ability can appear by either tiredness or reduced speed.

Activities of Daily Living↗

PubMed2005

Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study.

BACKGROUND: Completed genomes and environmental genomic sequences are bringing a significant contribution to understanding the evolution of gene families, microbial metabolism and community eco-physiology. Here, we used comparative genomics and phylogenetic analyses in conjunction with enzymatic data to probe the evolution and functions of a microbial nitrilase gene family. Nitrilases are relatively rare in bacterial genomes, their biological function being unclear. RESULTS: We examined the genetic neighborhood of the different subfamily genes and discovered conserved gene clusters or operons associated with specific nitrilase clades. The inferred evolutionary transitions that separate nitrilases which belong to different gene clusters correlated with changes in their enzymatic properties. We present evidence that Darwinian adaptation acted during one of those transitions and identified sites in the enzyme that may have been under positive selection. CONCLUSION: Changes in the observed biochemical properties of the nitrilases associated with the different gene clusters are consistent with a hypothesis that those enzymes have been recruited to a novel metabolic pathway following gene duplication and neofunctionalization. These results demonstrate the benefits of combining environmental genomic sampling and completed genomes data with evolutionary and biochemical analyses in the study of gene families. They also open new directions for studying the functions of nitrilases and the genes they are associated with.

Aminohydrolases↗

PubMed1989

Determination of characteristic parameters of human postural dynamics.

Posture control performance was quantified in three variables (swiftness, stiffness, damping). Subjects were tested with a force platform recording body sway induced by vibrators attached to the calf muscles. Parameter estimation was made with identification of a transfer function representing the stabilized inverted pendulum. It is conjectured that the state feedback parameters identified are suitable for use in assessing ability to maintain posture.

Adult↗

PubMed2006

Utility of the detection of Plasmodium parasites for the diagnosis of malaria in endemic areas.

BACKGROUND: In populations where the prevalence of infection with Plasmodium parasites is high, blood tests that identify Plasmodium parasites in patients with fever may lead to false positive diagnosis of malaria-disease. We characterised the diminishing value of the parasite detection test as a function of the prevalence of infection. METHODS: We computed the ability of the parasite detection test to identify malaria at various levels of prevalence (0% to 90%), assuming plausible estimates of sensitivity (95% and 85%) and specificity (99% and 95%) for the detection of parasites. In each situation, we computed likelihood ratios of malaria (or absence of malaria) for positive and negative parasite detection tests. Likelihood ratios were classified as clinically useful (> or = 10), intermediate (5-10), or unhelpful (<5). RESULTS: Likelihood ratios of positive tests were strongly related to the prevalence of infection in the general population: a positive test was unhelpful when the prevalence was 20% or more, and useful only when prevalence was 5% or less. The sensitivity and specificity of the test had little influence on these results. Likelihood ratios of negative tests were clinically useful when prevalence was 70% or less, but only for high levels of sensitivity (95%). If sensitivity was low (85%), the negative test was at best of intermediate utility, and was unhelpful if the prevalence of asymptomatic infection exceeded 30%. CONCLUSION: Identification of Plasmodium parasites supports a diagnosis of malaria only in areas where the prevalence of Plasmodium infection is low. Wherever this prevalence exceeds about 20%, a positive test is clinically unhelpful.

Animals↗

PubMed2006

Probabilistic dietary exposure assessment taking into account variability in both amount and frequency of consumption.

Probabilistic dietary exposure assessments that are fully based on Monte Carlo sampling from the raw intake data may not be appropriate. This paper shows that the data should first be analysed by using a statistical model that is able to take the various dimensions of food consumption patterns into account. A (parametric) model is discussed that takes into account the interindividual variation in (daily) consumption frequencies, as well as in amounts consumed. Further, the model can be used to include covariates, such as age, sex, or other individual attributes. Some illustrative examples show how this model may be used to estimate the probability of exceeding an (acute or chronic) exposure limit. These results are compared with the results based on directly counting the fraction of observed intakes exceeding the limit value. This comparison shows that the latter method is not adequate, in particular for the acute exposure situation. A two-step approach for probabilistic (acute) exposure assessment is proposed: first analyse the consumption data by a (parametric) statistical model as discussed in this paper, and then use Monte Carlo techniques for combining the variation in concentrations with the variation in consumption (by sampling from the statistical model). This approach results in an estimate of the fraction of the population as a function of the fraction of days at which the exposure limit is exceeded by the individual.

Adolescent↗

PubMed2004

Nonneutral evolution of the transcribed pseudogene Makorin1-p1 in mice.

Pseudogenes are nonfunctional relics of formerly functional genes and are thought to evolve neutrally. In some pseudogenes, however, the molecular evolutionary patterns are atypical of neutrally evolving sequences, exhibiting sequence conservation, codon-usage bias, and other features associated with functional genes. Makorin1-p1 is a transcribed pseudogene first identified in the mouse Mus musculus. The transcript of Makorin1-p1 can regulate the stability of the transcript of its paralogous functional gene Makorin1. Specifically, the half-life of Makorin1 mRNA increases significantly in the presence of Makorin1-p1 transcript, and targeted deletion of Makorin1-p1 is lethal in mice. Here, we show that Makorin1-p1 originated after the separation of Mus and Rattus but before the divergence of M. musculus and M. pahari. The transcribed region of Makorin1-p1 exhibits rates of point and indel substitutions that are two to four times lower than those in the untranscribed region, suggesting that the transcribed region is under functional constraint and is not evolving neutrally. Although the transcript of Makorin1-p1 likely functions by its sequence similarity to Makorin1, we find no evidence of gene conversion between them, indicating that functional conservation alone is sufficient to maintain their coordinated evolution. A duplication-degeneration model is proposed to explain how Makorin1-p1 was co-opted into the regulatory system of Makorin1. There are over 10,000 pseudogenes in a typical mammalian genome, and it is plausible that many functional but untranslatable pseudogenes exist. Our results illustrate the potential of using evolutionary analysis to identify such pseudogenes from genome sequences.

Animals↗

PubMed2004

Joint analysis of time-to-event and multiple binary indicators of latent classes.

Multiple categorical variables are commonly used in medical and epidemiological research to measure specific aspects of human health and functioning. To analyze such data, models have been developed considering these categorical variables as imperfect indicators of an individual's "true" status of health or functioning. In this article, the latent class regression model is used to model the relationship between covariates, a latent class variable (the unobserved status of health or functioning), and the observed indicators (e.g., variables from a questionnaire). The Cox model is extended to encompass a latent class variable as predictor of time-to-event, while using information about latent class membership available from multiple categorical indicators. The expectation-maximization (EM) algorithm is employed to obtain maximum likelihood estimates, and standard errors are calculated based on the profile likelihood, treating the nonparametric baseline hazard as a nuisance parameter. A sampling-based method for model checking is proposed. It allows for graphical investigation of the assumption of proportional hazards across latent classes. It may also be used for checking other model assumptions, such as no additional effect of the observed indicators given latent class. The usefulness of the model framework and the proposed techniques are illustrated in an analysis of data from the Women's Health and Aging Study concerning the effect of severe mobility disability on time-to-death for elderly women.

Aged↗

PubMed2005

A note on P-values under group sequential testing and nonproportional hazards.

Group sequential designs are often used for periodically assessing treatment efficacy during the course of a clinical trial. Following a group sequential test, P-values computed under the assumption that the data were gathered according to a fixed sample design are no longer uniformly distributed under the null hypothesis of no treatment effect. Various sample space orderings have been proposed for computing proper P-values following a group sequential test. Although many of the proposed orderings have been compared in the setting of time-invariant treatment effects, little attention has been given to their performance when the effect of treatment within an individual varies over time. Our interest here is to compare two of the most commonly used methods for computing proper P-values following a group sequential test, based upon the analysis time (AT) and Z-statistic orderings, with respect to resulting power functions when treatment effects on survival are delayed. Power under the AT ordering is shown to be heavily influenced by the presence of a delayed treatment effect, while power functions corresponding to the Z-statistic ordering remain robust under time-varying treatment effects.

Algorithms↗

PubMed2001

Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation.

We have developed a formalism and a computational method for analyzing the potential functional consequences of non-synonymous single nucleotide polymorphisms. Our approach uses a structural model and phylogenetic information to derive a selection of structure and sequence-based features serving as indicators of an amino acid polymorphim's effect on function. The feature values can be integrated into a probabilistic assessment of whether an amino acid polymorphism will affect the function or stability of a target protein. The method has been validated with data sets of unbiased mutations in the lac repressor and lysoyzyme. Applying our methodology to recent surveys of genetic variation in the coding regions of clinically important genes, we estimate that approximately 26-32 % of the natural non-synonymous single nucleotide polymorphisms have effects on function. This estimate suggests that a typical person will have about 6240-12,800 heterozygous loci that encode proteins with functional variation due to natural amino acid polymorphism.

Amino Acids↗

PubMed2005

[Determination of placebo effect in irritable bowel syndrome].

BACKGROUND AND OBJECTIVE: The determinants of the placebo effect are not well established. Goal of this study was to explore likely predictive factors in an already published data set. METHODS: We re-analysed data from a study in 120 patients with the irritable bowel syndrome (IBS) that were randomly assigned to three arms of the study to receive (double-blind) either a drug (mebeverin) (n = 40) or placebo (n = 40), or (in an open trial) dietary treatment (fibre) (n = 40) for up to 16 week. Treatment was conducted by 3 different doctors (A, B, C) with 44, 27, and 18 patients, resp. A fourth group (n = 31) was treated by different varying physicians. Symptoms were assessed every 4 weeks, and the degree of patient compliance and the number of drop-outs, the number of patients improved/not improved (in %), symptom severity (Kruis Score) at enrolment, and age and gender as covariates were included into the analysis. RESULTS: Drop-out rate was 30 % for placebo, 30 % for mebeverin, and 15 % for the diet. For the patients remaining in the study, average compliance was 75 % with placebo, but 89 % for the drug and 82 % for the diet. Response rates were 39 % for placebo, but 20 % for the drug; response rate for the diet (open trial) was 43 % under all doctors. Response rates for drug and placebo combined were 32 % for doctor A (female,43 years), but 19 % for doctors B and C together (both males, 32 and 40 years)); this effect was not significant. Placebo responders were more often women (47 %) than men (28 %), while age effects were only found with dietary treatment: responders were younger. Placebo responders had an overall lower Kruis Score than non-responders (45 vs 52 points), but this was also true for drug (52 vs. 62 points) and diet responders (56 vs 68 points). CONCLUSION: The major factors contributing to the placebo response are the treating physician (gender, training), and the patients gender (female). Patients with lower Kruis score (more likely non-functionally disordered) may be prone to higher (placebo) response rates.

Adult↗

PubMedDate not supplied

DNA segmentation through the Bayesian approach.

We present a new approach to DNA segmentation into compositionally homogeneous blocks. The Bayesian estimator, which is applicable for both short and long segments, is used to obtain the measure of homogeneity. An exact optimal segmentation is found via the dynamic programming technique. After completion of the segmentation procedure, the sequence composition on different scales can be analyzed with filtration of boundaries via the partition function approach.

Algorithms↗

PubMed2003

Expressed sequence tags from the Closterium peracerosum-strigosum-littorale complex, a unicellular charophycean alga, in the sexual reproduction process.

We obtained genetic information on sexual reproduction of the Closterium peracerosum-strigosum-littorale complex, a unicellular charophycean alga. Normalized cDNA libraries were constructed from cells in the sexual reproduction process, and a total of 1190 5'-end expressed sequence tags were established. Since 604 of these ESTs were classified into 174 non-redundant sequences, these 1190 ESTs include 760 unique sequences. Similarity search against a public non-redundant protein database indicated that 390 unique sequences had significant similarity to registered sequences. Among these 390 sequences, 3 were identical to and 4 were homologous to previously identified sex-pheromone genes. According to our study, 370 of 760 unique sequences are likely to be novel transcripts. These cDNA clones and EST sequence information may would be helpful for future functional analyses using DNA array technologies.

Amino Acid Sequence↗

PubMed2000

Origin and evolution of eukaryotic chaperonins: phylogenetic evidence for ancient duplications in CCT genes.

Chaperonins are oligomeric protein-folding complexes which are divided into two distantly related structural classes. Group I chaperonins (called GroEL/cpn60/hsp60) are found in bacteria and eukaryotic organelles, while group II chaperonins are present in archaea and the cytoplasm of eukaryotes (called CCT/TriC). While archaea possess one to three chaperonin subunit-encoding genes, eight distinct CCT gene families (paralogs) have been characterized in eukaryotes. We are interested in determining when during eukaryotic evolution the multiple gene duplications producing the CCT subunits occurred. We describe the sequence and phylogenetic analysis of five CCT genes from TRICHOMONAS: vaginalis and seven from GIARDIA: lamblia, representatives of amitochondriate protist lineages thought to have diverged early from other eukaryotes. Our data show that the gene duplications producing the eight CCT paralogs took place prior to the organismal divergence of TRICHOMONAS: and GIARDIA: from other eukaryotes. Thus, these divergent protists likely possess completely hetero-oligomeric CCT complexes like those in yeast and mammalian cells. No close phylogenetic relationship between the archaeal chaperonins and specific CCT subunits was observed, suggesting that none of the CCT gene duplications predate the divergence of archaea and eukaryotes. The duplications producing the CCTdelta and CCTepsilon subunits, as well as CCTalpha, CCTbeta, and CCTeta, are the most recent in the CCT gene family. Our analyses show significant differences in the rates of evolution of archaeal chaperonins compared with the eukaryotic CCTs, as well as among the different CCT subunits themselves. We discuss these results in light of current views on the origin, evolution, and function of CCT complexes.

Amino Acid Sequence↗

PubMed2002

Worldwide mutation spectrum in cartilage-hair hypoplasia: ancient founder origin of the major70A-->G mutation of the untranslated RMRP.

Pleiotropic, recessively inherited cartilage-hair hypoplasia (CHH) is due to mutations in the untranslated RMRP gene on chromosome 9p13-p12 encoding the RNA component of RNase MRP endoribonuclease. We describe 36 different mutations in this gene in 91 Finnish and 44 non-Finnish CHH families. Based on their nature and localisation, these mutations can be classified into three categories: mutations affecting the promoter region, small changes of conserved nucleotides in the transcript, and insertions and duplications in the 5' end of the transcript. The only known functional region that seemed to avoid mutations was a nucleolar localisation signal region between nucleotides 23-62. The most common mutation in CHH patients was a base substitution G for A at nucleotide 70. This mutation contributed 92% of the mutations in the Finnish CHH patients. Our results using linkage disequilibrium based maximum likelihood estimates with close markers, genealogical studies, and haplotype data suggested that the mutation was introduced to Finland some 3900-4800 years ago, and before the expansion of the population. The same major mutation accounted for 48% of the mutations among CHH patients from other parts of Europe, North and South America, the Near East, and Australia. In the non-Finnish CHH families, the A70G mutation segregated with the same major haplotype, although shorter, as in most of the Finnish families. In 23 out of these 27 chromosomes, the common region extended over 60 kb, and, therefore, all the chromosomes most likely arose from a solitary event many thousands of years ago.

Cartilage Diseases↗

PubMed2004

Adaptive evolution drives the diversification of zinc-finger binding domains.

The human genome is estimated to contain 700 zinc-finger genes, which perform many key functions, including regulating transcription. The dramatic increase in the number of these genes as we move from yeast to C. elegans to Drosophila and to humans, as well as the clustered organization of these genes in humans, suggests that gene duplication has played an important role in expanding this family of genes. Using likelihood methods developed by Yang and parsimony methods introduced by Suzuki and Gojobori, we have investigated four clusters of zinc-finger genes on human chromosome 19 and found evidence that positive selection was involved in diversifying the family of zinc-finger binding motifs.

Adaptation, Biological↗