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Results for “variational inference”

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PubMed1992

Vitamin C and the common cold.

The effect of vitamin C on the common cold has been the subject of several studies. These studies do not support a considerable decrease in the incidence of the common cold with supplemental vitamin C. However, vitamin C has consistently decreased the duration of cold episodes and the severity of symptoms. The benefits that have been observed in different studies show a large variation and, therefore, the clinical significance may not be clearly inferred from them. The biochemical explanation for the benefits may be based on the antioxidant property of vitamin C. In an infection, phagocytic leucocytes become activated and they produce oxidizing compounds which are released from the cell. By reacting with these oxidants, vitamin C may decrease the inflammatory effects caused by them. Scurvy, which is caused by a deficiency in vitamin C, is mostly attributed to the decreased synthesis of collagen. However, vitamin C also participates in several other reactions, such as the destruction of oxidizing substances. The common cold studies indicate that the amounts of vitamin C which safely protect from scurvy may still be too low to provide an efficient rate for other reactions, possibly antioxidant in nature, in infected people.

Antioxidants↗

PubMed2000

Seasonal variation in heart rate variability in asthmatic children.

Asthma is a "seasonal disease" with symptoms either aggravated by environmental changes during specific seasons or prevalent at certain times of the year for other reasons. We examined whether the heart rate variability (HRV) of asthmatic children changes by season. The HRV during a portion of one night (00:00-04:00) and day (12:00-16:00) and the entire 24h period (00:00-24:00) during each of the four seasons was analyzed. The data of 95 children with asthma and 106 healthy children, as controls, were assessed. In children with asthma during the 24h period, seasonal variation in the low-frequency (LF) band (0.04-0.15 Hz) and the high-frequency (HF) band (0.15-0.4 Hz) were detected (HF: F=6.81, p=.0003; LF: F=4.18, p= .008). The HF value in the summer was significantly higher than in autumn and spring (Scheffe test: autumn vs. summer, s = 4.46, p < .001: spring vs. summer, s = 2.86, p < .05), while the LF value in autumn was significantly lower than in summer (s = 3.42, p < .01). In the control group, no seasonal variation in HF, LF, or LF/HF was detected. The findings infer the HRV, a surrogate measure of autonomic nervous system function, of asthmatic children is more susceptible to seasonal changes brought about by either endogenous annual rhythms or environmental weather phenomena.

Adolescent↗

PubMed2001

Curved tails in polymerization-based bacterial motility.

The curved actin "comet-tail" of the bacterium Listeria monocytogenes is a visually striking signature of actin polymerization-based motility. Similar actin tails are associated with Shigella flexneri, spotted-fever Rickettsiae, the Vaccinia virus, and vesicles and microspheres in related in vitro systems. We show that the torque required to produce the curvature in the tail can arise from randomly placed actin filaments pushing the bacterium or particle. We find that the curvature magnitude determines the number of actively pushing filaments, independent of viscosity and of the molecular details of force generation. The variation of the curvature with time can be used to infer the dynamics of actin filaments at the bacterial surface.

Actins↗

PubMed2006

Population structure and gene evolution in Saccharomyces cerevisiae.

The fully sequenced genomes of four species within the Saccharomyces sensu stricto complex provide a wealth of information for molecular-evolutionary inference. Yet virtually nothing is known about population-genetic variation within these species, including the molecular-biological and genetic-model organism S. cerevisiae. Here we investigate the population-genetic variation and population structure of S. cerevisiae by sequencing the four loci CDC19, PHD1, FZF1 and SSU1 in 27 strains. Sequence analysis demonstrates a distinct population structure in S. cerevisiae, distinguishing strains collected from a Pennsylvanian oak forest and strains collected from vineyards, perhaps due to ecological rather than geographic factors. The low level of conflict observed between the gene trees estimated for each locus implies moderate recombination in nature. High polymorphism in the gene SSU1 provides evidence of diversifying selection on its protein product, a sulfite exporter, perhaps associated with the use of sulfur-based fungicides in vineyards. FZF1, encoding a transcription factor regulating the expression level of SSU1, displays even greater polymorphism. This, the first multilocus sequence study of population structure in natural isolates of S. cerevisiae, is the first study to demonstrate population structure within S. cerevisiae, and the first study to detect historical selection on a locus important to the natural history of wine yeast.

Cloning, Molecular↗

PubMed2001

Variations of concentric hair cells in a Cnidarian sensory epithelium (Coryne tubulosa).

In capitate hydropolyps, the spherical end-knobs of the short tentacles present an exceptional concentration of sensory functions in one of the evolutionarily oldest nervous systems. The tentacular spheres are the basis of sensation and discrimination of objects and of capturing of prey-objects by the discharge of nematocytes (stinging cells). Recent electrophysiological studies of the spheres revealed combined chemo/mechanosensory functioning of the nematocytes and mechanosensitivity of further types of cells. The present electron microscopical study made use of the small size of the spheres of Coryne tubulosa to characterize all cells of some spheres. Five types of ectodermal cells were found to have sensory structural features and to be separated by or enclosed in supporting cells: 1) nematocytes of the stenotele type; 2) short and 3) long ciliated concentric hair cells, which carry a cilium-stereovilli bundle, similar to the cnidocil apparatus of nematocytes; 4) cells having a recessed cilium-microvilli complex equipped with a thick cell-traversing rootlet (rootlet cells); and 5) cells having a recessed short cilium with no microvilli and only a short rootlet and containing, apically as well as basally, aggregations of dense-core vesicles (vesicle-rich cells). Types 1-4 vary the configuration of a concentric cilium-microvilli complex (variations of a concentric hair bundle) and were demonstrated or inferred to be mechanosensitive. Apical exocytotic activity, which is well known for the nematocytes (discharge of their cnidocyst), is indicated by ultrastructure for the nematocyte-resembling concentric hair cells and for the vesicle-rich cells. The tentacular spheres are considered an early paradigm of a sensory epithelium. Its synaptic structures and extensive connectivity are the subject of a subsequent paper.

Animals↗

PubMed1997

Quantitative genetic analysis of arterial oxygen saturation in Tibetan highlanders.

This study was designed to test the hypothesis that genetic differences inferred from biological kinship relationships among individuals contribute to individual variation in percentage of oxygen saturation of arterial hemoglobin (SaO2) in a high-altitude native population. SaO2 data were obtained by pulse oximetry from 354 nonpregnant, healthy Tibetan residents of Pen-Dri, two rural agropastoral villages at 3800-4065 m altitude in Lhasa Municipal District, Tibet Autonomous Region, China. Statistical analyses of these data from 46 pedigrees tested the hypothesis of a significant genetic contribution to SaO2 variation. The average SaO2 was 89.4 +/- 0.2%, with a range of 76-97%. Additive genetic effects account for 44% of the interindividual phenotypic variation in SaO2 in the sample. Complex segregation analysis and variance decomposition analysis determined that 21% of the total phenotypic variation could be explained by a major gene influencing SaO2. Homozygotes for the low-SaO2 allele have a mean SaO2 of 83.6%, whereas heterozygotes and homozygotes for the high-SaO2 allele have means of 87.6% and 88.3%, respectively. This confirms findings in another Tibetan sample and extends the known geographic distribution of the major gene. These results suggest the hypothesis that individuals with the dominant allele for higher SaO2 have a selective advantage in their high-altitude hypoxic environment.

Adaptation, Physiological↗

PubMed1999

Exposure assessment strategies for work-related risk factors for musculoskeletal disorders.

The design of assessment strategies depends on the risk factors of interest, features of the measurement device, feasibility considerations, and variation at the workplace. The selection of variables should permit specific etiologic inferences. Several researchers have combined different methods into a broad array of exposure measures. Other authors have converted inputs from disparate methods into a common exposure metric, varying from subjective ratings to quantitative measures such as compression forces in the lumbar back. The parameterization of an exposure variable should address the 3 principal exposure dimensions intensity, frequency, and duration. Standardized expressions of variation patterns of exposure have been suggested. An alternative approach is the modeling of exposure variability that allows for exposure assessment at the individual level. A related topic is the critical time window of risk factors for musculoskeletal disorders. This window not only requires detailed information of exposure events over time, but also appropriate characterization of episodic musculoskeletal problems.

Environmental Monitoring↗

PubMed2000

Evolution of balanced genetic polymorphism.

Extreme genetic polymorphism maintained by balancing selection (so called because many alleles are maintained in a balance by a mechanism of rare allele advantage) is intimately associated with the important task of self/non-self-discrimination. Widely disparate self-recognition systems of plants, animals and fungi share several general features, including the maintenance of large numbers of alleles at relatively even frequency, and persistence of this variation over very long time periods. Because the evolutionary dynamics of balanced polymorphism are very different from those of neutral genetic variation, data on balanced polymorphism have been used as a novel source for inference of the history of populations. This review highlights the unique evolutionary properties of balanced genetic polymorphism, and the use of theoretical understanding in analysis and application of empirical data for inference of population history. However, a second goal of this review is to point out where current theory is incomplete. Recent observations suggest that entirely novel selective forces may act in concert with balancing selection, and these novel forces may be extremely potent in shaping genetic variation at self-recognition loci.

Animals↗

PubMed2006

Variation in leaf physiology of Salix arctica within and across ecosystems in the High Arctic: test of a dual isotope (Delta13C and Delta18O) conceptual model.

Leaf carbon isotope discrimination (Delta(13)C) varies with the balance between net photosynthesis (A) and stomatal conductance (g ( s )). Inferences that can be made with Delta(13)C are limited, as changes could reflect variation in A and/or g ( s ). Investigators have suggested that leaf delta(18)O enrichment above source water (Delta(18)O) may enable differentiation between sources of variation in Delta(13)C, as leaf Delta(18)O varies with transpiration rate (E), which is closely correlated with g ( s ) when leaves experience similar leaf to air vapor pressure differences. We examined leaf gas exchange of Salix arctica at eight sites with similar air temperatures and relative humidities but divergent soil temperatures and soil water contents near Pituffik, Greenland (76 degrees N, 38 degrees W). We found negative correlations at the site level between g ( s ) and Delta(18)O in bulk leaf tissue (r (2) = 0.62, slope = -17.9 per thousand/mol H(2)O m(-2) s(-1), P = 0.02) and leaf alpha-cellulose (r (2) = 0.83, slope = -11.5 per thousand mol H(2)O m(-2) s(-1), P < 0.01), consistent with the notion that leaf water enrichment declines with increasing E. We also found negative correlations at the site-level between intrinsic water-use efficiency (iWUE) and Delta(13)C in bulk leaf tissue (r (2) = 0.65, slope = -0.08 per thousand/mumol CO(2) /mol H(2)O, P = 0.02) and leaf alpha-cellulose (r (2) = 0.50, slope = -0.05 per thousand/[mumol CO(2) /mol H(2)O], P = 0.05). When increasing Delta(13)C was driven by increasing g ( s ) alone, we found negative slopes between Delta(13)C and Delta(18)O for bulk leaf tissue (-0.664) and leaf alpha-cellulose (-1.135). When both g ( s ) and A (max) increased, we found steeper negative slopes between Delta(13)C and Delta(18)O for bulk leaf tissue (-2.307) and leaf alpha-cellulose (-1.296). Our results suggest that the dual isotope approach is capable of revealing the qualitative contributions of g ( s ) and A (max) to Delta(13)C at the site level. In our study, bulk leaf tissue was a better medium than leaf alpha-cellulose for application of the dual isotope approach.

Arctic Regions↗

PubMed2005

[Linking quantitation of electrophoresis pattern and data analysis in AFLP for Oncomelania hupensis].

OBJECTIVE: To search into a method for analyzing the quantitative data in amplified fragment length polymorphism (AFLP) electrophoresis. METHODS: Oncomelania snails collected from the field were screened. Forty snails found uninfected with schistosomiasis were divided randomly into two groups and used to isolate genomic DNA. AFLP electrophoresis pattern was first transformed into quantitative data by Glyko BandScan software, and the bands were read according to different standards of band-reading to acquire the corresponding data. These data sets were analyzed by genetic statistics to get an inference set, and the analysis of this inference set was performed to reach a summary description. RESULTS: The results of genetic variation from different standards of band-reading were different With the increase of the standard value of band-reading, the indices indicating the genetic polymorphism of Oncomelania hupensis population (e.g. Shannon's information index) also increased. When the standard value reached at certain level, the values of these indices began to decrease. Compared with the above indices, the change for gene flow turned out contrary to the genetic identity. The distributions of inference results from different standards of band-reading all showed significant normal distribution. The mean value of genetic variation based on total grey was very close to that on the proportion of total grey. The average genetic identity between the "subpopulations" was 0.956 according to proportion of total grey or 0.958 from the total grey with an average genetic distance between the "subpopulations" of 0.045 and 0.043 respectively. CONCLUSION: It seems to be a reasonable and accurate method by quantifying the AFLP electrophoresis pattern followed by analyzing the data through the use of the different standards of band-reading.

Animals↗

PubMed2003

Variation in the NS3 gene and protein in South African isolates of bluetongue and equine encephalosis viruses.

Bluetongue virus (BTV) and equine encephalosis virus (EEV) are agriculturally important orbiviruses transmitted by biting midges of the genus Culicoides. The smallest viral genome segment, S10, encodes two small nonstructural proteins, NS3 and NS3A, which mediate the release of virus particles from infected cells and may subsequently influence the natural dispersion of these viruses. The NS3 gene and protein sequences of South African isolates of these viruses were determined, analysed and compared with cognate orbivirus genes from around the world. The South African BTV NS3 genes were found to have the highest level of sequence variation for BTV (20 %), while the highest level of protein variation of BTV NS3 (10 %) was found between South African and Asian BTV isolates. The inferred NS3 gene phylogeny of the South African BTV isolates grouped them with BTV isolates from the United States, while the Asian BTV isolates grouped into a separate lineage. The level of variation found in the NS3 gene and protein of EEV was higher than that found for BTV and reached 25 and 17 % on the nucleotide and amino acid levels, respectively. The EEV isolates formed a lineage independent from that of the other orbiviruses. This lineage segregated further into two clusters that corresponded to the northern and southern regions of South Africa. The geographical distribution of these isolates may be related to the distribution of the Culicoides subspecies that transmit them.

African Horse Sickness Virus↗

PubMed1997

Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony.

The rate of evolution of macromolecules such as ribosomal RNAs and proteins varies along the molecule because structural and functional constraints differ between sites. Many studies have shown that ignoring this variation in computing evolutionary distances leads to severe underestimation of sequence divergences, and thus can lead to misleading evolutionary tree inferences. We propose here a new parsimony-based method for computing evolutionary distances between pairs of sequences that takes into account this variation and estimates it from the data. This method applies to the number of substitutions per site in ribosomal RNA genes as well as to the number of nonsynonymous substitutions per codon for protein-coding genes and is especially suitable when large data sets (> or = 100 sequences) are analyzed. First, starting from a phylogeny constructed with usual distances, the maximum-parsimony method is used to infer the distribution of the number of substitutions that have occurred at each site (or codon) along this tree. This distribution is then fitted to an "invariant + truncated negative binomial" distribution that allows for invariant sites. Maximum-likelihood fitting of this distribution to different data sets showed that it agreed very well with real data. Noticeably, allowing for invariant sites seemed to be very important. Finally, two distance estimates were developed by introducing the distribution of site variability into the substitution models of Jukes and Cantor and of Kimura. The use of different numbers of aligned sequences (up to 1,000 rRNA sequences) showed that the parameters of the model are very sensitive to the number of sequences used to estimate them. However, if at least 100 sequences are considered, the two new distance estimates are quite stable with respect to the number of sequences used to fit the distribution. This stability is true for low as well as for high evolutionary distances. These new distances appeared to be much better estimates of the number of substitutions per site than the classical distances of Jukes and Cantor and of Kimura, which both greatly underestimate this number, so that they can serve as indexes to detect saturation. We conclude that the new distances are particularly suitable for phylogenetic analysis when very distantly related species and relatively large data sets are considered. Trees reconstructed using these distances are generally different from those constructed by means of the classical estimates. Using this new method, we showed that the mean evolutionary distance between Prokaryotes and Eukaryotes is substantially higher for the small-subunit than for the large-subunit rRNAs. This suggests than the former might have experienced a drastic change during the early evolution of Eukaryotes.

Algorithms↗

PubMed2005

Evolutionary history of the European whitefish Coregonus lavaretus (L.) species complex as inferred from mtDNA phylogeography and gill-raker numbers.

We compared mitochondrial DNA and gill-raker number variation in populations of the European whitefish Coregonus lavaretus (L.) species complex to illuminate their evolutionary history, and discuss mechanisms behind diversification. Using single-strand conformation polymorphism (SSCP) and sequencing 528 bp of combined parts of the cytochrome oxidase b (cyt b) and NADH dehydrogenase subunit 3 (ND3) mithochondrial DNA (mtDNA) regions, we documented phylogeographic relationships among populations and phylogeny of mtDNA haplotypes. Demographic events behind geographical distribution of haplotypes were inferred using nested clade analysis (NCA) and mismatch distribution. Concordance between operational taxonomical groups, based on gill-raker numbers, and mtDNA patterns was tested. Three major mtDNA clades were resolved in Europe: a North European clade from northwest Russia to Denmark, a Siberian clade from the Arctic Sea to southwest Norway, and a South European clade from Denmark to the European Alps, reflecting occupation in different glacial refugia. Demographic events inferred from NCA were isolation by distance, range expansion, and fragmentation. Mismatch analysis suggested that clades which colonized Fennoscandia and the Alps expanded in population size 24 500-5800 years before present, with minute female effective population sizes, implying small founder populations during colonization. Gill-raker counts did not commensurate with hierarchical mtDNA clades, and poorly with haplotypes, suggesting recent origin of gill-raker variation. Whitefish designations based on gill-raker numbers were not associated with ancient clades. Lack of congruence in morphology and evolutionary lineages implies that the taxonomy of this species complex should be reconsidered.

Animals↗

PubMed2006

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Accurate inference and estimation in population genomics.

Both intra- and interspecific genomic comparisons have revealed local similarities in the level and frequency of mutational variation, as well as in patterns of gene expression. This autocorrelation between measurements leads to violations of assumptions of independence in many statistical methods, resulting in misleading and incorrect inferences. Here I show that autocorrelation can be due to many factors and is present across the genome. Using a one-dimensional spatial stochastic model, I further show how previous results can be employed to correct for autocorrelation along chromosomes in population and comparative genomics research. When multiple hypothesis tests are autocorrelated, I demonstrate that a simple correction can lead to increased power in statistical inference. I present a preliminary analysis of population genomic data from Drosophila simulans to show the ubiquity of autocorrelation and applicability of the methods proposed here.

Animals↗

PubMed1982

Structural studies on yeast nucleosomes.

Mononucleosomes isolated from micrococcal nuclease digests of stationary phase chromatin of the yeast Saccharomyces cerevisiae were compared both compositionally and physiochemically with those from chicken and bovine calf. It was found that while yeast mononucleosomes are similar in composition, their thermal denaturation profiles and circular dichroism spectra indicate a less constrained structure. Furthermore, yeast nucleosomes were discovered to be labile in solutions of low ionic strength and could not be reconstituted by methods applicable to calf and chicken nucleosomes. On the basis of the reconstitution of a hybrid nucleosome containing calf histones H2A, H2B, and H3 and yeast histone H4, it was concluded that variations in the yeast H4 sequence are unlikely to be responsible for the apparent decrease in the stability of yeast nucleosomes. Examinations of histone-histone interactions in free solution revealed a change in the H3-H4 interaction and together with the previously published results of other researchers it was inferred that changes in the H3 sequence might be responsible for this structural variation.

Animals↗

PubMed1999

Paleolandscape variation and early pleistocene hominid activities: members 1 and 7, Olorgesailie formation, Kenya.

Paleolandscape research tests for variation in the spatial distribution of hominid artefacts and establishes the association of hominid activities with paleoenvironmental features over distances of 100s to 1000s of meters. This approach requires (1) precise definition of narrow stratigraphic intervals based on sedimentary criteria that can be documented over a broad area, and (2) excavation of these intervals in order to establish taphonomic and paleoenvironmental contexts. In this report, excavations of three target intervals within the early Pleistocene deposits (992 to 780 ka) of the Olorgesailie basin are described. Assessment of time-averaging and paleolandscape structure shows that each target interval represents a relatively brief period (</=1000 yrs) and exhibits a unique distribution of environmental features (e.g., topographic gradients, channels, soil development). Stone artefacts and fossilized animal bones are distributed nonrandomly in each interval, and include clusters that were five to 293 times more densely concentrated than the laterally equivalent background scatter. A paleosol in upper Member 1 preserves a relatively continuous distribution of artefacts and fossils, in contrast with the more patchy distribution in two intervals of lower Member 7. We infer that the difference between the two members reflects a real variation in hominid land use-either a response to local environmental differences or perhaps a change through time in hominid interaction with the environment. By expanding the comparative analysis to diverse basins, it should be possible to test for broader evolutionary change in hominid activities. Examples drawn from East African Pliocene and early Pleistocene sites suggest that evolutionary change in land use entailed (1) wider ranging of hominids and longer distances of stone transport, (2) expansion of tool-assisted behaviors to a wider diversity of environmental settings, and (3) more strongly focused placement of particular artefact forms (e.g., bifaces) in different areas of the landscape in response to specific environmental features, such as lava outcrops, stream channels, and lake margins. ¿

Animals↗

PubMed1993

Native oak chloroplasts reveal an ancient divide across Europe.

Glacial refugia and postglacial migration are major factors responsible for the present patterns of genetic variation we see in natural populations. Traditionally postglacial history has been inferred from fossil data, but new molecular techniques permit historical information to be gleaned from present populations. The chloroplast tRNA(Leu1) intron contains regions which have been highly conserved over a billion years of chloroplast evolution. Surprisingly, in one of these regions which has remained invariant for all photosynthetic organisms so far studied, we have found intraspecific site polymorphism. This polymorphism occurs in two European oaks, Quercus robur and Q. petraea, indicating hybridisation and introgression between them. Two distinct chloroplast types occur and are distributed geographically as eastern and western forms suggesting that these oaks are each derived from at least two separate glacial refugia.

Base Sequence↗

PubMed2004

SNPs, SSRs and inferences on cassava's origin.

Despite its importance as a staple food throughout the tropics, the root crop cassava (it Manihot esculenta ssp. esculenta) has traditionally not been a major focus of research. One basic question about cassava that remained unresolved until recently concerns the crop's origin. This paper describes analyses of SNPs (single nucleotide polymorphisms) and SSR (simple sequence repeat) variation as a means of tracing cassava's evolutionary and geographical origins. Genetic diversity was examined in a sample of 20 cassava varieties that are representative of germplasm diversity within the crop, and in 212 individuals collected from wild populations of two closely related Manihot species. SNP and indel variation was examined in portions of two low copy nuclear genes, BglA and Hnl. Inferences from these genes were compared to those from previously examined loci, including the low copy nuclear gene G3pdh and 5 SSR loci. For all genes examined, SNPs and SSR alleles are shared between domesticated cassava and a specific geographical subset of wild Manihot populations, which suggests the following: (1) Cassava was likely domesticated from a single wild Manihot species, M. esculenta ssp. flabellifolia, rather than from multiple hybridizing species, as traditionally believed; and (2) the crop most likely originated in the southern Amazon basin.

Aldehyde-Lyases↗