Measuring genome divergence in bacteria: a case study using chlamydian data

We have studied the relative contribution of inversions, transpositions, deletions, and nucleotide substitutions to the evolution of Chlamydia trachomatis and Chlamydia pneumoniae. The minimal number of rearrangement events required for converting the gene order structure of one genome into that of the other was estimated to 59 +/- 6 events, including 13% inversions, 38% short inversions, and 49% transpositions. In contrast to previous findings, no examples of horizontal gene transfer subsequent to species divergence were identified, nor any evidence for an excessive number of tandem gene duplications. A statistical model was used to compare nucleotide frequencies for a set of genes uniquely present in one species to a set of orthologous genes present in both species. The two data sets were not significantly different, which is indicative of a low frequency of horizontal gene transfer events. This is based on the assumption that a foreign gene of different nucleotide content will not have become completely ameliorated, as verified by simulations of the amelioration rate at twofold and fourfold degenerate codon sites. The frequencies of nucleotide substitutions at twofold and fourfold degenerate sites, deletions, inversions, and translocations were estimated to 1.42, 0.62, 0.18, 0.01, and 0.01 per site, respectively.     

Comparative analyses of the effect of triacontanol on photosynthesis,photorespiration and growth of tomato (C3-plant) and maize (C4-plant)

Tomato (C₃-plants) and maize (C₄-plants) were grown in a nutrient solution to which triacontanol was added twice a week. After about 4 weeks the triacontanol treatment caused a significant increase in the dry weight of the tomato plants. Leaf area and dry weight measurements of tomato leaves at different stages of development showed that the largest increase in growth was obtained when triacontanol treatment was initiated before bud formation. In maize, no effect of the triacontanol treatment on dry wieght was observed. Photosynthesis was inhibited by 27% in young leaves from triacontanol-treated tomato plants and 39% in the controls, when the oxygen concentration was raised from 2% to 21%. In maize no change in photosynthesis could be observed, neither after altered oxygen concentration nor after triacontanol treatment. The difference in the response of C₃- and C₄-plants to triacontanol indicates that it regulates processes related to photosynthesis.     

The Impact of Health Behaviours on Incident Cardiovascular Disease in Europeans and South Asians – A Prospective Analysis in the UK SABRE Study

Background

There is consistent evidence on the impact of health behaviours on risk of cardiovascular disease (CVD) in European populations. As South Asians in the UK have an excess risk of CVD and coronary heart disease (CHD) compared to Europeans, we investigated whether a similar association between combined health behaviours and risk of CVD and CHD among this high-risk group exists, and estimated the population impact.

Methods and Findings

In a prospective cohort of 1090 Europeans and 1006 South Asians (40–69 y) without prevalent CVD at baseline (1988–1990), followed up for 21 years to 2011, there were 601 incident CVD events [Europeans n = 255; South Asians n = 346] of which 520 were CHD events [n = 207 and 313 respectively]. Participants scored between 0 to 4 points for a composite score including four baseline healthy behaviours (non-smoker, moderate alcohol intake, physically active, frequent fruit/vegetable intake). Adjusted hazard ratios (95% confidence intervals) for incident CHD in Europeans who had three, two, one, and zero compared to four health behaviours were 1.33 (0.78–2.29), 1.96 (1.15–3.33), 1.36 (0.74–2.48) and 2.45 (1.18–5.10), respectively, p-trend = 0.025. In South Asians, corresponding HRs were 2.88 (1.33–6.24), 2.28 (1.06–4.91), 3.36 (1.53–7.39) and 3.48 (1.38–8.81), p-trend = 0.022. The results were similar for incident CVD; Europeans HR 2.12 (1.14–3.94), p–trend = 0.014; South Asians HR 2.73 (1.20–6.21), p-trend = 0.018. The population attributable fraction in Europeans was 43% for CHD and 28% for CVD. In South Asians it was 63% and 51% respectively.

Conclusions

Lack of adherence to four combined health behaviours was associated with 2 to 3-fold increased risk of incident CVD in Europeans and South Asians. A substantial population impact in the South Asian group indicates important potential for disease prevention in this high-risk group by adherence to healthy behaviours.     

Aircrew Fatigue in Trans‐Atlantic Morning and Evening Flights

The aim of the investigation was to compare sleepiness and sleep on westward morning and evening flights. Seven morning‐crew pilots and seven evening‐crew pilots participated. Data were collected before, during, and after outward‐bound (westward) and homeward‐bound (eastward) flights across six time zones. A sleep/wake diary (with repeated sleepiness and performance ratings) and wrist actigraphy were used for data collection. Maximum sleep was obtained after return and minimum sleep before the outward‐bound flights. Actigraphy measures and sleep efficiency over the course of the study showed no significant differences between the morning and evening crews. There was a trend for a significant effect of morning vs. evening flight for time with heavy eyelids, with the homeward‐bound flight showing more time with heavy eyelids. There were no significant differences between morning and evening crews with regard to napping during the flight. The duration of wakefulness was longer for the evening flight crew. There were significant interactions for Karolinska sleepiness scale (KSS) self‐ratings on both the outward‐bound and homeward‐bound flights, and KSS was elevated during a considerable portion of the evening flights. Rated performance showed a significant time effect, but there was no difference in self‐ratings between morning and evening crews. Evening flights involve higher levels of sleepiness than morning flights, presumably because of the close proximity in time to the circadian trough of alertness.     

Predictors of Intelligence at the Age of 5: Family,Pregnancy and Birth Characteristics,Postnatal Influences,and Postnatal Growth

Parental education and maternal intelligence are well-known predictors of child IQ. However, the literature regarding other factors that may contribute to individual differences in IQ is inconclusive. The aim of this study was to examine the contribution of a number of variables whose predictive status remain unclarified, in a sample of basically healthy children with a low rate of pre- and postnatal complications. 1,782 5-year-old children sampled from the Danish National Birth Cohort (2003–2007) were assessed with a short form of the Wechsler Preschool and Primary Scale of Intelligence – Revised. Information on parental characteristics, pregnancy and birth factors, postnatal influences, and postnatal growth was collected during pregnancy and at follow-up. A model including study design variables and child’s sex explained 7% of the variance in IQ, while parental education and maternal IQ increased the explained variance to 24%. Other predictors were parity, maternal BMI, birth weight, breastfeeding, and the child’s head circumference and height at follow-up. These variables, however, only increased the explained variance to 29%. The results suggest that parental education and maternal IQ are major predictors of IQ and should be included routinely in studies of cognitive development. Obstetrical and postnatal factors also predict IQ, but their contribution may be of comparatively limited magnitude.     

Detection of nodavirus in seawater from rearing facilities for Atlantic halibut Hippoglossus hippoglossus larvae

We used (1) ultracentrifugation followed by RT-PCR and (2) real-time RT-PCR to detect and quantify nodaviruses in seawater in which Atlantic halibut Hippoglossus hippoglossus larvae/fry had been held at rearing facilities. Evaluated against in vitro propagated viruses, the viral concentration corresponded to 1.6 x 10(4) TCID50 (50% tissue culture infectious dose) ml(-1). Evaluated against in vitro transcribed RNA, the concentration was estimated at 2 x 10(7) virus particles ml(-1) seawater.     

Fortuitous Encounters between Seagliders and Adult Female Northern Fur Seals (Callorhinus ursinus) off the Washington (USA) Coast: Upper Ocean Variability and Links to Top Predator Behavior

Behavioral responses by top marine predators to oceanographic features such as eddies, river plumes, storms, and coastal topography suggest that biophysical interactions in these zones affect predators'' prey, foraging behaviors, and potentially fitness. However, examining these pathways is challenged by the obstacles inherent in obtaining simultaneous observations of surface and subsurface environmental fields and predator behavior. In this study, migratory movements and, in some cases, diving behavior of 40 adult female northern fur seals (NFS; Callorhinus ursinus) were quantified across their range and compared to remotely-sensed environmental data in the Gulf of Alaska and California Current ecosystems, with a particular focus off the coast of Washington State (USA) – a known foraging ground for adult female NFS and where autonomous glider sampling allowed opportunistic comparison of seal behavior to subsurface biophysical measurements. The results show that in these ecosystems, adult female habitat utilization was concentrated near prominent coastal topographic, riverine, or inlet features and within 200 km of the continental shelf break. Seal dive depths, in most ecosystems, were moderated by surface light level (solar or lunar), mirroring known behaviors of diel vertically-migrating prey. However, seal dives differed in the California Current ecosystem due to a shift to more daytime diving concentrated at or below the surface mixed layer base. Seal movement models indicate behavioral responses to season, ecosystem, and surface wind speeds; individuals also responded to mesoscale eddies, jets, and the Columbia River plume. Foraging within small scale surface features is consistent with utilization of the inner coastal transition zone and habitats near coastal capes, which are known eddy and filament generation sites. These results contribute to our knowledge of NFS migratory patterns by demonstrating surface and subsurface behavioral responses to a spatially and temporally dynamic ocean environment, thus reflecting its influence on associated NFS prey species.