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PubMed2006

The influence of physical activity on abdominal fat: a systematic review of the literature.

UNLABELLED: The relationship between excess abdominal adipose tissue, metabolic and cardiovascular health risk has stimulated interest in the efficacy of physical activity in specifically perturbing this adipose depot. The evolution of imaging techniques has enabled more direct measurement of changes in abdominal and visceral fat. The purpose of this summary was to systematically review the relationship between physical activity and abdominal fat. METHODS: Database searches were performed on MEDLINE, CINAHL, SPORT DISCUS and PUBMED, from 1985 to 2005 with keywords "exercise", "abdominal fat" and "visceral fat". RESULTS: Nineteen randomized controlled trials (RCTs) and eight non-randomized controlled trials were selected. In RCTs using imaging techniques to measure change in abdominal fat in overweight or obese subjects, seven out of 10 studies (including three trials with type 2 diabetics) reported significant reductions compared with controls. Reductions in visceral and total abdominal fat may occur in the absence of changes in body mass and waist circumference. Waist-to-hip ratio is not a sensitive measure of change in regional adiposity in exercise studies. No studies fulfil the Consolidated Standards of Reporting Trials (CONSORT) statement's criteria for the highest quality of randomized trial; however, many studies were in progress or published before the opportunity to comply with these recommendations. Therefore, limited evidence from a number of studies suggests a beneficial influence of physical activity on reduction in abdominal and visceral fat in overweight and obese subjects when imaging techniques are used to quantify changes in abdominal adiposity. More rigorous studies are needed to confirm these observations.

Abdominal Fat↗
PubMed2003

Structural and sequence evolution of U17 small nucleolar RNA (snoRNA) and its phylogenetic congruence in chelonians.

Vertebrate U17 RNA is an intron-encoded H/CA box containing snoRNA, which has been intensively studied in the last decade, though its precise role in ribosome biogenesis is not yet clear. A consensus secondary structure for the U17 RNA molecule has been derived from the comparative sequence and structural evolution analysis of U17 snoRNA among vertebrates. Its phylogenetic congruence above class level has been tested and preliminary data on chelonians suggest that also in this order, U17 snoRNA evolved congruently with phylogeny. We herein extend our analysis to other components of this reptile group. According to the sequence data that have also emerged from chelonians, the U17 RNA molecule can be divided into two main domains: the 5'-variable domain, which presents the sequence motifs capable of base-pairing with the 18S rRNA target and spanning STEM1, -2, and -3, and the 3'-conserved domain, consisting of STEM4. In vertebrates, the latter RNA region shows a high conservation both in secondary structure and in the presence of the three sequence motifs 5'-AUUCCUA-3', 5'-U(G/U)ACU-3', and 5'-AACCC-3'. We tested the phylogenetic congruence of U17 evolution with chelonian relationships: Our results are significantly similar to those emerging from mtDNA and morphological systematics. Some discrepancies (e.g., the position of Platysternon) need to be addressed in greater depth.

Animals↗
PubMed1982

Functional morphology of beta cells in the area centralis of the cat's retina: a model for the evolution of central retinal specializations.

The dendritic morphology of beta cells in and around the area centralis of the retinae of normally pigmented and Siamese cats is described. Individual central beta cells in the Siamese cat do not differ morphologically from central beta cells in normally pigmented cats, and in both groups of animals, there is a clear morphological continuity between central and peripheral beta cells. On the basis of systematic patterns of beta cell dendritic orientation, ther area centralis of the normal cat can be divided into a central region, approximately 200 micrometers in diameter, and a pericentral region, approximately 1,400 micrometers in diameter. In the central region, nearly all beta cells have a single large primary dendrite which descends perpendicular to the plane of inner plexiform layer, and gives rise to a dendritic tree which is vertically aligned with the cell's soma. In the pericentral region, the single primary dendrite of most cells descends obliquely through the inner plexiform layer and gives rise to a dendritic tree which is displaced laterally from the position of the soma. For most of the cells the trajectory of the dendrite is systematically related to the location of the cell relative to the area centralis such that the somas are displaced away from its center, presumably in order to minimize the thickness of the ganglion cell layer in the high acuity region. Many beta cells outside the pericentral region also have oriented single primary dendrites, but their orientation seems fairly random with respect to the location of the area centralis. In the Siamese area centralis, this systematic pattern of beta cell dendritic orientation is markedly reduced, suggesting that the pattern is under genetic control. On the basis of these observations, a model for the evolution of the area centralis and fovea is presented which involves selection for systematic for systematic patterns of dendritic orientation in regions of high ganglion cell density.

Animals↗
PubMed1995

[Evolution of the susceptibility to penicillin G of Streptococcus pneumoniae at the Limoge University Hospital Center].

A systematic detection of Streptococcus pneumoniae strains with reduced susceptibility to penicillin has been realized at Limoges Hospital during two years half. Of 302 strains isolated, 27 had reduced susceptibility to penicillin (8,9%), and, for 15 strains (5%), the MIC of penicillin G reached at least 2 mg/l. The frequency of strains with reduced susceptibility to penicillin increased from 1992 to 1994: 8,2% in 1992, 8,7% in 1993 and 12,2% in 1994. The resistance level exhibited by pneumococcus strains increased since 1992: the percentage of resistant strains (MIC mg/l > 1) was 2,7% in 1992, 6,9% in 1993 and 7,3% in 1994. Most of the strains with reduced susceptibility to penicillin belonged to serotype 23 (52%) and were isolated from blood cultures, cerebral-spinal or pleural fluids (41%).

France↗
PubMed1993

The systematics of nematodes that cause ostertagiasis in domestic and wild ruminants in North America: an update and a key to species.

Studies of medium stomach worms (Subfamily Ostertagiinae) of domestic and wild ruminants in North America have refined our understanding of the systematics, host distribution and biogeography of these nematodes. Strong support for recognition of monophyly for the Ostertagiinae has resulted from preliminary phylogenetic analyses of morphological characters among these and other trichostrongylids. Evaluation of morphological and biochemical characters in our laboratory and elsewhere has not refuted the polymorphism hypothesis where paired major and minor morphotypes are postulated to represent polymorphic species within the genera Ostertagia (Ostertagia ostertagi/Ostertagia lyrata; Ostertagia leptospicularis/Ostertagia kolchida; Ostertagia gruehneri/Ostertagia arctica; Ostertagia mossi/Ostertagia dikmansi), Teladorsagia (Teladorsagia circumcincta/Teladorsagia trifurcata (= Teladorsagia davtiani), and Marshallagia (Marshallagia marshalli/Marshallagia occidentalis). The minor morphotype of Ostertagia bisonis, recognized in Eurasia (considered to be Teladorsagia kazakhstanica), has yet to be discovered in North America. The taxonomy of these species has remained stable since an earlier overview of Ostertagia spp. and Teladorsagia spp. in North American domestic stock at the 1986 Ostertagia Workshop. Investigations since 1986 have focused on comparative morphology and the clear differentiation of Ostertagiinae, primarily from wild ruminants, that have been reported or may potentially occur in domestic bovids. Among these are species which infect wild and domestic sheep (Marshallagia marshalli/Marshallagia occidentalis), bovids (Ostertagia bisonis), and cervids (Ostertagia mossi/Ostertagia dikmansi, Ostertagia leptospicularis/Ostertagia kolchida, Ostertagia gruehneri/Ostertagia arctica, Mazamastrongylus odocoilei and Mazamastrongylus pursglovei) in North America. A key is presented for identifying 15 species of the Subfamily Ostertagiinae that are parasitic in domestic and wild ruminants of North America. Four exotic species (Camelostrongylus mentulatus, Spiculopteragia spiculoptera (= Spiculopteragia boehmi), Spiculopteragia asymmetrica and Longistrongylus curvispiculum) have been reported in North America, but only in game farms and are not included in the key. Hyostrongylus rubidus, a member of the Ostertagiinae normally parasitic in pigs and only rarely reported from domestic ruminants, is not included in the keys. Additional data from comparative morphology and molecular analyses will promote a reassessment of the generic-level systematics of the Ostertagiinae and allow an evaluation of host-parasite evolution and historical biogeography.

Animals↗
PubMed1998

Transmission pattern of hobo transposable element in transgenic lines of Drosophila melanogaster.

This study is an attempt to trace the fate of hobo elements in the genomes of E strains of Drosophila melanogaster that have been transfected with pHFL1, a plasmid containing an autonomous hobo. Such long-term population studies (over 105 generations) could be very useful for better understanding the population and genomic dynamics of transposable elements and their pattern of insertions. Molecular analyses of hobo elements in the transfected lines were performed using Southern blots of XhoI-digested genomic DNAs. The complete element was observed in all six injected lines. In two lines we observed, at generation 100, two deleted elements, which did not correspond to Th1 and Th2. The results obtained by the in situ method show that the number of hybridization sites increases in each line and prove that the hobo element may be amplified in an RM genome. The hobo activity does not seem to be systematically correlated with the number of hobo elements. After generation 85, the evolution of the hobo element's insertion site number depends on the injected line. In all lines, the total number of insertions remains quite small, between 0 and 11. Hobo elements are located on each of the chromosomal arms. We describe 'hotspots'-insertion sites present in all lines and in all generations. On the 3R arm, a short inversion appeared once at generation 85.

Animals↗
PubMed2004

Interfacial tensions from drop retraction versus pendant drop data and polydispersity effects.

Interfacial tensions sigma were measured by means of both methods for the following polymer pair: polyisobutylene (PIB 3) plus poly(dimethylsiloxane) (PDMS 152) and poly(dimethyl-co-methylphenylsiloxane) (CoP26*) plus PDMS 48. The numbers after the abbreviation state the molar masses in kilograms; the homopolymers exhibit polydispersities on the order of 2. The reliability of the method of drop retraction is backed up by systematic measurements, which demonstrate that it is possible to study the time evolution of sigma. Because of the free choice of the phases (drop or matrix) and the possibility to vary the overall composition of the system in a wide range, drop retraction yields more information than the pendant drop method. For the present systems both types of experiments yield identical results for the droplets of higher density. Experiments with the inverse blends and at higher volume fractions of the disperse phase demonstrate that the polydispersity of the components plays an important role. In the case of the system PIB 3/PDMS 152 the steady-state interfacial tension at 25 degrees C is 2.25 mN m(-1) if the drop consists of PDMS, but only 1.3 mN m(-1) if it consists of PIB. Furthermore, the time-independent sigma values are attained much more rapidly in the latter case.

Journal Article↗
PubMed2006

There is no universal molecular clock for invertebrates, but rate variation does not scale with body size.

The existence of a universal molecular clock has been called into question by observations that substitution rates vary widely between lineages. However, increasing empirical evidence for the systematic effects of different life history traits on the rate of molecular evolution has raised hopes that rate variation may be predictable, potentially allowing the "correction" of the molecular clock. One such example is the body size trend observed in vertebrates; smaller species tend to have faster rates of molecular evolution. This effect has led to the proposal of general predictive models correcting for rate heterogeneity and has also been invoked to explain discrepancies between molecular and paleontological dates for explosive radiations in the fossil record. Yet, there have been no tests of an effect in any nonvertebrate taxa. In this study, we have tested the generality of the body size effect by surveying a wide range of invertebrate metazoan lineages. DNA sequences and body size data were collected from the literature for 330 species across five phyla. Phylogenetic comparative methods were used to investigate a relationship between average body size and substitution rate at both interspecies and interfamily comparison levels. We demonstrate significant rate variation in all phyla and most genes examined, implying a strict molecular clock cannot be assumed for the Metazoa. Furthermore, we find no evidence of any influence of body size on invertebrate substitution rates. We conclude that the vertebrate body size effect is a special case, which cannot be simply extrapolated to the rest of the animal kingdom.

Animals↗
PubMed2006

Cloning and characterization of an ascidian homolog of the human 8-oxoguanine DNA glycosylase (Ogg1) that is involved in the repair of 8-oxo-7,8-dihydroguanine in DNA in Ciona intestinalis.

PURPOSE: It is of interest to perform a systematic comparative analysis of the conserved domains in DNA glycosylases and the evolution of DNA base excision repair systems. Furthermore, it is important to characterize the roles and regulation of base excision repair during the development of organisms. To address these issues, we first identified 8-oxo-7,8-dihydroguanine (8-oxoG)-DNA glycosylase (Ogg1) of the ascidian Ciona intestinalis as a good model system. MATERIALS AND METHODS: A cDNA clone coding for a peptide with homology to human Ogg1 was identified in the expressed sequence tag (EST) database from the Ciona cDNA resources. We examined whether CiOgg1 has DNA glycosylase/AP (apurinic/apyrimidinic) lyase activities for 8-oxoG-containing oligonucleotide. Furthermore, the expression level of CiOgg1 was compared in various tissues of Ciona intestinalis. RESULTS: The CiOgg1gene encoded a protein of 351 amino acids, which shows 37% identity of amino acid sequence with human Ogg1. The Helix-hairpin-Helix motif was highly conserved. The ascidian enzyme had functional 8-oxoG-DNA glycosylase/AP lyase activities, which removed 8-oxoG opposite cytosine from DNA. Expression of the CiOgg1 significantly reduced the frequency of spontaneous G:C to T:A transversions in E. coli mutM mutY. The highest expression level was observed in testis in Ciona intestinalis. CONCLUSIONS: The structure and functions of Ogg1 are well conserved in Ciona intestinalis. CiOgg1 is involved in the repair of 8-oxoG in DNA in Ciona intestinalis.

Amino Acid Sequence↗
PubMed2000

Primordial Lithium and Big Bang Nucleosynthesis.

Recent determinations of the abundance of the light-element Li in very metal-poor stars show that its intrinsic dispersion is essentially zero and that the random error in the estimated mean Li abundance is negligible. However, a decreasing trend in the Li abundance toward lower metallicity indicates that the primordial abundance of Li can be inferred only after allowing for nucleosynthesis processes that must have been in operation in the early history of the Galaxy. We show that the observed Li versus Fe trend provides a strong discriminant between alternative models for Galactic chemical evolution of the light elements at early epochs. We critically assess current systematic uncertainties and determine the primordial Li abundance within new, much tighter limits: &parl0;Li&solm0;H&parr0;p=1.23+0.68-0.32x10-10. We show that the Li constraint on OmegaB is now limited as much by uncertainties in the nuclear cross sections used in big bang nucleosynthesis (BBN) calculations as by the observed abundance itself. A clearer understanding of systematics allows us to sharpen the comparison with 4He and deuterium and the resulting test of BBN.

Journal Article↗
PubMed2004

Genome-scale phylogeny and the detection of systematic biases.

Phylogenetic inference from sequences can be misled by both sampling (stochastic) error and systematic error (nonhistorical signals where reality differs from our simplified models). A recent study of eight yeast species using 106 concatenated genes from complete genomes showed that even small internal edges of a tree received 100% bootstrap support. This effective negation of stochastic error from large data sets is important, but longer sequences exacerbate the potential for biases (systematic error) to be positively misleading. Indeed, when we analyzed the same data set using minimum evolution optimality criteria, an alternative tree received 100% bootstrap support. We identified a compositional bias as responsible for this inconsistency and showed that it is reduced effectively by coding the nucleotides as purines and pyrimidines (RY-coding), reinforcing the original tree. Thus, a comprehensive exploration of potential systematic biases is still required, even though genome-scale data sets greatly reduce sampling error.

Genome, Fungal↗
PubMed2006

Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors?

A recent phylogenomic study reported that the animal phylogeny was unresolved despite the use of 50 genes. This lack of resolution was interpreted as "a positive signature of closely spaced cladogenetic events." Here, we propose that this lack of resolution is rather due to the mutual cancellation of the phylogenetic signal (historical) and the nonphylogenetic signal (due to systematic errors) that results from inadequate taxon sampling and/or model of sequence evolution. Starting with a data set of comparable size, we use 3 different strategies to reduce the nonphylogenetic signal: 1) increasing the number of species; 2) replacing a fast-evolving species by a slowly evolving one; and 3) using a better model of sequence evolution. In all cases, the phylogenetic resolution is markedly improved, in agreement with our hypothesis that the originally reported lack of resolution was artifactual.

Algorithms↗
PubMed1995

L1 (LINE-1) retrotransposable elements provide a "fossil" record of the phylogenetic history of murid rodents.

The single most difficult problem in phylogenetic analysis is deciding whether a shared taxonomic character is due to common ancestry or one that appeared independently due to convergence, parallelism, or reversion to an ancestral state. Mammalian L1 retrotransposons undergo periodic amplifications in which multiple copies of the elements are interspersed in the genome. Because these elements apparently are transmitted only by inheritance and are retained in the genome, a shared L1 amplification event can only be an inherited ancestral character. We propose that L1 amplification events can be an excellent tool for analyzing mammalian evolution and demonstrate here how we addressed several refractory problems in rodent systematics using L1 DNA as a taxonomic character.

Animals↗
PubMed2003

Validation of publication of new names and new combinations previously effectively published outside the IJSEM.

The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.

Bacteria↗
PubMed2005

Inhomogeneous evolution of subgraphs and cycles in complex networks.

Subgraphs and cycles are often used to characterize the local properties of complex networks. Here we show that the subgraph structure of real networks is highly time dependent: as the network grows, the density of some subgraphs remains unchanged, while the density of others increase at a rate that is determined by the network's degree distribution and clustering properties. This inhomogeneous evolution process, supported by direct measurements on several real networks, leads to systematic shifts in the overall subgraph spectrum and to an inevitable overrepresentation of some subgraphs and cycles.

Journal Article↗
PubMed2003

High-performance liquid chromatography analyses of pyoverdin siderophores differentiate among phytopathogenic fluorescent Pseudomonas Species.

The relationship of pyoverdins produced by 41 pathovars of Pseudomonas syringae and by phytopathogenic Pseudomonas species was investigated. A high-performance liquid chromatography method for analyzing the culture medium proved to be superior to isoelectric focusing for detecting pyoverdin production, for differentiating slightly different pyoverdins, and for differentiating atypical from typical Fe(III)-chelated pyoverdins. Nonfluorescent strains were found in Pseudomonas amygdali, Pseudomonas meliae, Pseudomonas fuscovaginae, and P. syringae. Pseudomonas agarici and Pseudomonas marginalis produced typical pyoverdins. Among the arginine dihydrolase-negative fluorescent Pseudomonas species, spectral, amino acid, and mass spectrometry analyses underscored for the first time the clear similarities among the pyoverdins produced by related species. Within this group, the oxidase-negative species Pseudomonas viridiflava and Pseudomonas ficuserectae and the pathovars of P. syringae produced the same atypical pyoverdin, whereas the oxidase-positive species Pseudomonas cichorii produced a similar atypical pyoverdin that contained a glycine instead of a serine. The more distantly related species Pseudomonas asplenii and Pseudomonas fuscovaginae both produced a less similar atypical pyoverdin. The spectral characteristics of Fe(III)-chelated atypical pyoverdins at pH 7.0 were related to the presence of two beta-hydroxyaspartic acids as iron ligands, whereas in typical pyoverdins one of the ligands is always ornithine based. The peptide chain influenced the chelation of iron more in atypical pyoverdins. Our results demonstrated that there is relative pyoverdin conservation in the amino acids involved in iron chelation and that there is faster evolution of the other amino acids, highlighting the usefulness of pyoverdins in systematics and in identification.

Amino Acids↗