The Physiome Model Repository 2

MOTIVATION: The Physiome Model Repository 2 (PMR2) software was created as part of the IUPS Physiome Project (Hunter and Borg, 2003), and today it serves as the foundation for the CellML model repository. Key advantages brought to the end user by PMR2 include: facilities for model exchange, enhanced collaboration and a detailed change history for each model. AVAILABILITY: PMR2 is available under an open source license at http://www.cellml.org/tools/pmr/; a fully functional instance of this software can be accessed at http://models.physiomeproject.org/.     

Plankton community dynamics during decay of a cyanobacteria bloom: a mesocosm experiment

The aim of the work was to study the effects of a decaying cyanobacteria bloom on nutrient dynamics, plankton community development and production rates of bacteria and primary producers. It was hypothesised that the system would turn more heterotrophic following the decay of the bloom. A 10-day outdoors mesocosm experiment was performed in early June in a brackish-water environment. Non-toxic filamentous cyanobacteria Aphanizomenon flos-aquae were added to the treatment, whereas the control lacked cyanobacteria. A. flos-aquae decayed rapidly, and was absent from the units by day 2. Significantly higher bacteria abundances, lower nanoflagellate densities and higher ciliate abundances were found, suggesting a bottom-up regulated process in the treatments bags. N:P ratios were low (6?C12), suggesting N-limitation. Bacteria correlated negatively with numbers of heterotrophic nanoflagellates (HNF), suggesting grazing on bacteria by HNF. Primary production correlated positively with irradiance, chlorophyll a and inorganic nutrients in all units. The rapidly decaying A. flos-aquae biomass imposed a significant bottom-up regulation in the treatment mesocosms, and the system turned from autotrophic into more heterotrophic with time. The rapid decay also caused some similarities and parallel changes between the treatment and the control.     

A new method to uncover signatures of divergent and stabilizing selection in quantitative traits

While it is well understood that the pace of evolution depends on the interplay between natural selection, random genetic drift, mutation, and gene flow, it is not always easy to disentangle the relative roles of these factors with data from natural populations. One popular approach to infer whether the observed degree of population differentiation has been influenced by local adaptation is the comparison of neutral marker gene differentiation (as reflected in FST) and quantitative trait divergence (as reflected in QST). However, this method may lead to compromised statistical power, because FST and QST are summary statistics which neglect information on specific pairs of populations, and because current multivariate tests of neutrality involve an averaging procedure over the traits. Further, most FST-QST comparisons actually replace QST by its expectation over the evolutionary process and are thus theoretically flawed. To overcome these caveats, we derived the statistical distribution of population means generated by random genetic drift and used the probability density of this distribution to test whether the observed pattern could be generated by drift alone. We show that our method can differentiate between genetic drift and selection as a cause of population differentiation even in cases with FST=QST and demonstrate with simulated data that it disentangles drift from selection more accurately than conventional FST-QST tests especially when data sets are small.     

Aerobic oral and rectal bacteria of free-ranging Steller sea lion pups and juveniles (Eumetopias jubatus) in Alaska

Bacteriologic cultures from oral, rectal, and lesion samples from free-ranging Steller sea lion (SSL, Eumetopias jubatus) pups and juveniles in Alaska (2001-2005) were examined to determine frequency of infection by a specific subset of common and pathogenic aerobic bacteria. Associations between isolated bacteria and age, sex, body condition, location, and sampling season were investigated. Salmonella spp. isolates were further evaluated to determine spatial clustering (n=48) and to identify serovars (n=13) and antimicrobial susceptibility patterns (n=11). We sampled 356 SSL pups (n=272) and juveniles (n=84), and identified 988 isolates of 13 bacterial genera of specific interest. Pasteurella spp. (43.8%), beta-hemolytic Streptococcus spp. (30.6%), and Mannheimia spp. (18.2%) were the most commonly isolated oral bacteria (n=499 isolates), whereas Escherichia coli (47.6%), beta-hemolytic E. coli (32.4%), Salmonella spp. (10.4%), and Campylobacter spp. (7.8%) were the most frequently isolated rectal bacteria (n=460 isolates). Salmonella was most commonly found in pups from western stocks and in samples collected during fall/winter seasons. A significant Salmonella cluster was detected at the Perry Island haulout. Five serovars were isolated: Enteritidis, Infantis, Newport, Reading, and Stanley. Pulsed-field gel electrophoresis provided evidence that Salmonella isolates were most likely being maintained within the SSL population in Alaska.     

High frequency one-step gene replacement in Trichoderma reesei. II. Effects of deletions of individual cellulase genes

Four cellulase genes of Trichoderma reesei, cbh1, cbh2, egl1 and egl2, have been replaced by the amdS marker gene. When linear DNA fragments and flanking regions of the corresponding cellulase locus of more than 1 kb were used, the replacement frequencies were high, ranging from 32 to 52%. Deletion of the major cellobiohydrolase 1 gene led to a 2-fold increase in the production of cellobiohydrolase II; however, replacement of the cbh2 gene did not affect the final cellulase levels and deletion of egl1 or egl2, slightly increased production of both cellobiohydrolases. Based on our results, endoglucanase II accounts for most of the endoglucanase activity produced by the hypercellulolytic host strain. Furthermore, loss of the egl2, gene causes a significant drop in the filter paper-hydrolysing activity, indicating that endoglucanase II has an important role in the total hydrolysis of cellulose.     

Standardised Resting Time Prior to Blood Sampling and Diurnal Variation Associated with Risk of Patient Misclassification: Results from Selected Biochemical Components

BackgroundAccording to current recommendations, blood samples should be taken in the morning after 15 minutes’ resting time. Some components exhibit diurnal variation and in response to pressures to expand opening hours and reduce waiting time, the aims of this study were to investigate the impact of resting time prior to blood sampling and diurnal variation on biochemical components, including albumin, thyrotropin (TSH), total calcium and sodium in plasma.MethodsAll patients referred to an outpatient clinic for blood sampling were included in the period Nov 2011 until June 2014 (opening hours: 7am–3pm). Each patient’s arrival time and time of blood sampling were registered. The impact of resting time and the time of day for all components was analysed using simple linear regression. The “maximum allowable bias” was used as quality indicator for the change in reference interval.ResultsSignificant diurnal variation was found for albumin (n = 15,544; p<2×10⁻¹⁶), TSH (n = 20,019; p<2×10⁻¹⁶), calcium (n = 13,588; p = 2.8×10⁻¹²) and sodium (n = 51,917; p<2×10⁻¹⁶). Further significant influence for resting time was found for albumin (p = 2.6×10⁻⁴), TSH (p = 0.004), calcium (p = 8.9×10⁻⁷) and sodium (p = 8.7×10⁻¹⁶). Only TSH and albumin were clinically significantly influenced by diurnal variation. Resting time had no clinically significant effect.ConclusionsWe found no need for resting 15 minutes prior to blood sampling. However, diurnal variation was found to have a significant and considerable impact on TSH and, to a minor degree, albumin. This has to be taken into account to ensure that reference intervals provided by the laboratory are valid on a 24-hour basis.     

Allelopathy of Baltic Sea cyanobacteria: no evidence for the role of nodularin

Extracts of Aphanizomenon flos-aquae and Nodularia spumigena,the two most common cyanobacteria forming recurrent blooms inthe Baltic Sea, decrease the abundance of some phytoplanktonspecies via the release of allelopathic substances. We investigatedhow cell-free filtrates of the two cyanobacteria, as well aspurified hepatotoxin nodularin, produced by N. spumigena affectedcell numbers, chlorophyll a content and ¹⁴CO₂ uptake of thecryptophyte Rhodomonas sp. Both cyanobacterial filtrates significantlyretarded the growth of Rhodomonas sp., A. flos-aquae filtrateup to 46%, whereas purified nodularin showed no significanteffect on any of the growth parameters of the cryptophyte. Theseresults suggest that the allelopathic effect of N. spumigenais most probably due to metabolite(s) other than nodularin,possibly acting via the damage of the target cells.     

Bioflocculation of Euglena gracilis via direct application of fungal filaments: a rapid harvesting method

Journal of Applied Phycology - The high cost and environmental impact of traditional microalgal harvesting methods limit commercialization of microalgal biomass. Fungal bioflocculation of...