Genetic diversity and phylogenetic relationships of bacteria belonging to the Ochrobactrum-Brucella group by recA and 16S rRNA gene-based comparative sequence analysis

The genetic diversity and phylogenetic interrelationships among 106 Ochrobactrum strains (O. anthropi: 72, O. intermedium: 22, O. tritici: 5, O. oryzae: 2, O. grignonense: 2, O. gallinifaecis: 1, O. lupini: 2), the type strains of the eight Brucella species and other closely related taxa were studied by recA and rrs gene (16S rRNA) comparative sequence analysis. Both markers correctly delineated the various Ochrobactrum species; however, resolution at the subspecies level was considerably higher in the recA gene-based approach. Phylogenetic analyses using neighbor-joining, parsimony, and maximum likelihood algorithms generated trees with similar topologies but the overall branching order, and also the order of the subclades, were not stable in either assay, which could be explained by generally high recA and rrs sequence similarities. Ochrobactrum and Pseudochrobactrum formed separate clades distinct from other Alphaproteobacteria with Bartonella, Agrobacterium, and Rhizobium as the closest relatives. O. gallinifaecis was the most distinct member, when compared to the type species O. anthropi, with rrs and recA similarities of 96.2% and 81.4%. Brucella species were indistinguishable, exhibiting high rrs and recA gene similarities of 98.6% and 85.5% compared with Ochrobactrum intermedium. At the protein level, all RecA sequences among the various Ochrobactrum species and between Ochrobactrum and Brucella were highly similar with only a few amino acid substitutions. O. anthropi and O. tritici were indistinguishable by means of their RecA proteins. A set of initially biochemically classified strains did not cluster within their assigned species and they either grouped within other known species or grouped as potential novel Ochrobactrum species. In further investigations, these strains were reclassified and described as novel species. In summary, Ochrobactrum is a highly diverse genus comprising several novel species. We recommend recA- in addition to rrs gene-analysis for correct species allocation and subtyping of novel Ochrobactrum isolates.     

Analysis and modeling of time-variant amplitude–frequency couplings of and between oscillations of EEG bursts

Low-frequency (0.5-2.5 Hz) and individually defined high-frequency (7-11 or 8-12 Hz; 11-15 or 14-18 Hz) oscillatory components of the electroencephalogram (EEG) burst activity derived from thiopental-induced burst-suppression patterns (BSP) were investigated in seven sedated patients (17-26 years old) with severe head injury. The predominant high-frequency burst oscillations (>7 Hz) were detected for each patient by means of time-variant amplitude spectrum analysis. Thereafter, the instantaneous envelope (IE) and the instantaneous frequency (IF) were computed for these low- and high-frequency bands to quantify amplitude-frequency dependencies (envelope-envelope, envelope-frequency, and frequency-frequency correlations). Time-variant phase-locking, phase synchronization, and quadratic phase couplings are associated with the observed amplitude-frequency characteristics. Additionally, these time-variant analyses were carried out for modeled burst patterns. Coupled Duffing oscillators were adapted to each EEG burst and by means of these models data-based burst simulations were generated. Results are: (1) strong envelope-envelope correlations (IE courses) can be demonstrated; (2) it can be shown that a rise of the IE is associated with an increase of the IF (only for the frequency bands 0.5-2.5 and 7-11 or 8-12 Hz); (3) the rise characteristics of all individually averaged envelope-frequency courses (IE-IF) are strongly correlated; (4) for the 7-11 or 8-12 Hz oscillation these associations are weaker and the variation between the time courses of the patients is higher; (5) for both frequency ranges a quantitative amplitude-frequency dependency can be shown because higher IE peak maxima are accompanied by stronger IF changes; (6) the time range of significant phase-locking within the 7-11 or 8-12 Hz frequency bands and of the strongest quadratic phase couplings (between 0.5-2.5 and 7-11 or 8-12 Hz) is between 0 and 1,000 ms; (7) all phase coupling characteristics of the modeled bursts accord well with the corresponding characteristics of the measured EEG burst data. All amplitude-frequency dependencies and phase locking/coupling properties described here are known from and can be discussed using coupled Duffing oscillators which are characterized by autoresonance properties.     

Evaluation of the efficacy and effectiveness of a structured disorder tailored psychotherapy in ADHD in adults: study protocol of a randomized controlled multicentre trial

ADHD is a serious risk factor for co-occurring psychiatric disorders and negative psychosocial consequences in adulthood. Previous trials on psychotherapeutic concepts for adult ADHD are based on behavioural (cognitive behavioural and dialectical behavioural) psychotherapeutic approaches and showed significant effects. The aim of our study group (COMPAS) is to carry out a first randomized and controlled multicentre study to evaluate the effects of a disorder tailored psychotherapy in adult ADHD compared to clinical management in combination with psychopharmacological treatment or placebo. A total of 448 adults with ADHD according to DSM-IV will be treated at seven university sites in Germany. In a four-arm design, patients are randomized to a manualized dialectical behavioural therapy (DBT) based group programme plus methylphenidate or placebo or clinical management plus methylphenidate or placebo with weekly sessions in the first 12 weeks and monthly sessions thereafter. Therapists are graduated psychologists or physicians. Treatment integrity is established by independent supervision. Primary endpoint (ADHD symptoms measured by the Conners Adult Rating Scale) is rated by interviewers blind to the treatment allocation. Intention-to-treat analysis will be performed within a linear regression model (Current Controlled Trials ISRCTN54096201). The trial is funded by the German Federal Ministry of Research and Education (01GV0606) and is part of the German network for the treatment of ADHD in children and adults (ADHD-NET).     

Mass Occurrence and Dominant Behavior of the European Ant Species <Emphasis Type="Italic">Formica fuscocinerea</Emphasis> (Forel)

Recently, masses of the ant Formica (Serviformica) fuscocinerea (Forel) have been occurring at numerous sites in Southern Germany. Although F. fuscocinerea is native to Southern Germany, these mass occurrences resemble ant invasions in density and dominance. This study aimed to investigate the underlying mechanisms that promote sudden mass occurrence of a previously inconspicuous ant species within its native range. To estimate the competitive dominance of F. fuscocinerea, species occurrence and abundance considering biotic and abiotic parameters were studied in a natural habitat where F. fuscocinerea co-occurred with two other common ant species, Myrmica ruginodis (Nylander) and Lasius niger (Linnaeus). To understand the species’ distribution in the field, laboratory experiments on interspecific competition were conducted. Finally, the colony structure of F. fuscocinerea was investigated with intraspecific aggression tests. Formica fuscocinerea dominated an area that, as indicated by strongly frequented foraging trails on the trees, provided important food sources, e.g. trophobionts, to the ants. Other ant species coexisted only at the periphery of the F. fuscocinerea range. Laboratory experiments revealed F. fuscocinerea as highly dominant species. Additionally, F. fuscocinerea showed a complete lack of intraspecific aggression between ants originating from distances up to 58 km, indicating weak or nonexistent behavioral boundaries among ants of physically separated nests. Since extraordinarily high worker densities, strong interspecific dominance and a lack of colony boundaries within supercolonies are considered to be important traits of several invasive ant species we conclude that the same traits also promote the dominance of F. fuscocinerea.     

Polymorphism in developmental timing: intraspecific heterochrony in a Lake Victoria cichlid

SUMMARY Biologists measure developmental time by dividing development into arbitrary time blocks called "stages." This is a reasonable approach, provided that developmental timing is precisely controlled within a species. However, the degree of this precision is unknown. This is unfortunate because precision in developmental timing at the population level is a central issue to the whole research program of heterochrony. To examine this issue, we apply Ontogenetic Sequence Analysis to 261 embryos of the Lake Victoria cichlid Haplochromis piceatus . The result of our analysis can be mapped as a complex web of 26,880 equally parsimonious developmental sequences. This topology reflects timing polymorphism (intraspecific heterochrony) among embryos of this species. Because of this timing polymorphism, it is not possible to define discrete "stages" in this cichlid (although there is sufficient sequence signal to assess the maturity of embryos). More generally, we show that sequence polymorphism creates uncertainty about how a given embryo will develop implying that the mechanisms controlling developmental timing in embryos lack precision. For this reason, it is imperative to consider patterns of embryonic variability when measuring developmental time.     

Ecology of Staphylococcus aureus: characterization of strains from chicken

The majority of S. aureus strains isolated from beak-swabs and pathological processes in chicken shows coagulation of human plasma (not of bovine plasma), crystal violet-type A, hemolysine-type A, formation of fibrinolysin, not formation of DNase and reactions with the experimental phage A1591. Because of the absence of DNase-formation and the reaction-specificity for phage A1591 we propose to designate these strains as host-specific variety gallinae of S. aureus. The strains from chicken are compared with strains of human, bovine, and ovine origin. An ecological study in a chicken farm has shown that S. aureus strains from chicken are not found in man and vice versa.     

Surveillance of R-plasmids.

The surveillance of R-plasmids consists of: (1.) Ecological and epidemiological investigations. (1.1.) Prevalence of R-plasmids in pathogenic and apathogenic bacteria occurring in the biotic environment (man, animal); in the abiotic environment (sewage, food, feed); under high selection pressure (hospital, animal production, plant production). (2.) Biological investigations. (2.1.) Genetic properties of R-plasmids: (2.2.) Plasmid induced variations of the properties of the host bacteria (virulence, phage pattern, antigenic pattern, serological properties). The problems resulting from plasmid-mediated drug resistance call for a strict chemotherapeutic drug policy with the regard to ecological processes.     

A Timescale for Evolution,Population Expansion,and Spatial Spread of an Emerging Clone of Methicillin-Resistant Staphylococcus aureus

Due to the lack of fossil evidence, the timescales of bacterial evolution are largely unknown. The speed with which genetic change accumulates in populations of pathogenic bacteria, however, is a key parameter that is crucial for understanding the emergence of traits such as increased virulence or antibiotic resistance, together with the forces driving pathogen spread. Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of hospital-acquired infections. We have investigated an MRSA strain (ST225) that is highly prevalent in hospitals in Central Europe. By using mutation discovery at 269 genetic loci (118,804 basepairs) within an international isolate collection, we ascertained extremely low diversity among European ST225 isolates, indicating that a recent population bottleneck had preceded the expansion of this clone. In contrast, US isolates were more divergent, suggesting they represent the ancestral population. While diversity was low, however, our results demonstrate that the short-term evolutionary rate in this natural population of MRSA resulted in the accumulation of measurable DNA sequence variation within two decades, which we could exploit to reconstruct its recent demographic history and the spatiotemporal dynamics of spread. By applying Bayesian coalescent methods on DNA sequences serially sampled through time, we estimated that ST225 had diverged since approximately 1990 (1987 to 1994), and that expansion of the European clade began in 1995 (1991 to 1999), several years before the new clone was recognized. Demographic analysis based on DNA sequence variation indicated a sharp increase of bacterial population size from 2001 to 2004, which is concordant with the reported prevalence of this strain in several European countries. A detailed ancestry-based reconstruction of the spatiotemporal dispersal dynamics suggested a pattern of frequent transmission of the ST225 clone among hospitals within Central Europe. In addition, comparative genomics indicated complex bacteriophage dynamics.     

Coverage and power in genomewide association studies

The ability of genomewide association studies to decipher genetic traits is driven in part by how well the measured single-nucleotide polymorphisms "cover" the unmeasured causal variants. Estimates of coverage based on standard linkage-disequilibrium measures, such as the average maximum squared correlation coefficient (r2), can lead to inaccurate and inflated estimates of the power of genomewide association studies. In contrast, use of the "cumulative r2 adjusted power" measure presented here gives more-accurate estimates of power for genomewide association studies.