Long and short term variations in suspended particulate material: the influence on light available to the phytoplankton community

The magnitude and frequency of events leading to changes in turbidity have been studied in a large (61 km²), shallow (mean depth 3.4 m) wind-exposed lake basin at the western end of Lake Mälaren, Sweden. In this paper we couple changes in suspended particulate inorganic material (SPIM) resulting from wind driven sediment resuspension, and variations in the discharge and sediment load, to spectral variations in subsurface light and estimates of photosynthetically active radiation (PAR). To accomplish this we use a semi-analytical model which predicts the spectral variations in downwelling irradiance (E _d()) and the attenuation coefficient of downwelling irradiance (K _d()), as a function of the concentrations of chlorophyll, dissolved yellow substances, and suspended inorganic and organic particulate material. Unusually high river discharge, led to large inputs of yellow substances and large in lake yellow substance concentrations (a _ys(420) 20 m^–1), causing variations in yellow substance concentration to have the greatest role in influencing temporal trends in the attenuation of PAR and variations in the depth of the euphotic zone (Z _eup). In spite of this, variations in SPIM could account for approximately 60% of the variation in Z _eup attributed to changes in yellow substances alone. Our results show that changes in suspended sediment concentration leads to both long-term and short-term changes in the attenuation of PAR, even in the presence of high concentrations of dissolved yellow substances.     

Structure of the O-polysaccharide from the lipopolysaccharide from Vibrio cholerae O6

The O-polysaccharide from Vibrio cholerae O6 was isolated from the LPS by mild-acid hydrolysis and has been investigated by sugar and methylation analysis and NMR spectroscopy. The polysaccharide was also depolymerized with aqueous hydrofluoric acid to give the repeating unit and multiples thereof. The O-polysaccharide had the following tetrasaccharide repeating unit. Two O-acetyl groups are present, one of them making the GlcNAc residue fully substituted and the steric crowding considerable at the branching residue.     

Confidence measures for protein fold recognition

MOTIVATION: We present an extensive evaluation of different methods and criteria to detect remote homologs of a given protein sequence. We investigate two associated problems: first, to develop a sensitive searching method to identify possible candidates and, second, to assign a confidence to the putative candidates in order to select the best one. For searching methods where the score distributions are known, p-values are used as confidence measure with great success. For the cases where such theoretical backing is absent, we propose empirical approximations to p-values for searching procedures. RESULTS: As a baseline, we review the performances of different methods for detecting remote protein folds (sequence alignment and threading, with and without sequence profiles, global and local). The analysis is performed on a large representative set of protein structures. For fold recognition, we find that methods using sequence profiles generally perform better than methods using plain sequences, and that threading methods perform better than sequence alignment methods. In order to assess the quality of the predictions made, we establish and compare several confidence measures, including raw scores, z-scores, raw score gaps, z-score gaps, and different methods of p-value estimation. We work our way from the theoretically well backed local scores towards more explorative global and threading scores. The methods for assessing the statistical significance of predictions are compared using specificity--sensitivity plots. For local alignment techniques we find that p-value methods work best, albeit computationally cheaper methods such as those based on score gaps achieve similar performance. For global methods where no theory is available methods based on score gaps work best. By using the score gap functions as the measure of confidence we improve the more powerful fold recognition methods for which p-values are unavailable. AVAILABILITY: The benchmark set is available upon request.     

Tree size frequency distributions, plant density, age and community disturbance

We show that explicit mathematical and biological relationships exist among the scaling exponents and the allometric constants (α and β, respectively) of log–log linear tree‐community size frequency distributions, plant density N_T, and minimum, maximum and average stem diameters (D_min, D_max, and , respectively). As individuals grow in size and D_max increases, N_T is predicted to decrease as reflected by a decrease in the numerical value of α and an increase in the value of β. Our derivations further show that N_T decreases as increases even if D_min or D_max remain unchanged. Because D_max and the age of the largest individuals in a community are correlated, albeit weakly, we argue that the interdependent relationships among the numerical values of α, β, N_T, and shed light on the extent to which communities have experienced recent global disturbance. These predicted relationships receive strong statistical support using two large datasets spanning a broad spectrum of tree‐dominated communities.     

WIND POLLINATION OF TAXUS CUSPIDATA

The air disturbance patterns created by and around the ovules of Taxus cuspidata are quantified for various orientations to the direction of ambient airflow, and are shown to largely dictate the motion (vectoral trajectories) and mode of deposition of windborne pollen on ovule surfaces. Perpendicular orientation to the direction of airflow results in two regions characterized by high densities of adhering pollen — one on the windward surface of the ovule, resulting from direct inertial collision, and another on the leeward surface resulting from non-inertial sedimentation. Parallel and inclined orientations of the ovule to the direction of airflow produce quantitative and qualitative variations in the pattern of adhering pollen resulting from inertial and non-inertial deposition. Direct collision of windborne pollen grains with the micropylar ends of ovules occurs for all orientations to wind direction. The aerodynamics of the ovulate shoot complex of Taxus cuspidata is related to that previously described for conifer ovulate cones, cycad megastrobili, and simulated wind tunnel analyses of archaic Paleozoic ovules based on scale models. Water transport of pollen (adhering to integument and bract surfaces) to micropyles quantitatively alters the distribution of adhering pollen grains on ovule surfaces. Although there is no evidence that pollen grains of this species are osmotically ruptured, observations do not preclude the possibility that water transport of pollen may reduce the number of viable pollen grains reaching the micropyle.     

A Revised Time Tree of the Asterids: Establishing a Temporal Framework For Evolutionary Studies of the Coffee Family (Rubiaceae)

Divergence time analyses in the coffee family (Rubiaceae) have all relied on the same Gentianales crown group age estimate, reported by an earlier analysis of the asterids, for defining the upper age bound of the root node in their analyses. However, not only did the asterid analysis suffer from several analytical shortcomings, but the estimate itself has been used in highly inconsistent ways in these Rubiaceae analyses. Based on the original data, we here reanalyze the divergence times of the asterids using relaxed-clock models and 14 fossil-based minimum age constraints. We also expand the data set to include an additional 67 taxa from Rubiaceae sampled across all three subfamilies recognized in the family. Three analyses are conducted: a separate analysis of the asterids, which completely mirrors the original asterid analysis in terms of taxon sample and data; a separate analysis of the Gentianales, where the result from the first analysis is used for defining a secondary root calibration point; and a combined analysis where all taxa are analyzed simultaneously. Results are presented in the form of a time-calibrated phylogeny, and age estimates for asterid groups, Gentianales, and major groups of Rubiaceae are compared and discussed in relation to previously published estimates. Our updated age estimates for major groups of Rubiaceae provide a significant step forward towards the long term goal of establishing a robust temporal framework for the divergence of this biologically diverse and fascinating group of plants.     

Histone Deacetylase Inhibition Enhances Tissue Plasminogen Activator Release Capacity in Atherosclerotic Man

The expression of the tissue plasminogen activator (t-PA) gene appears to be under epigenetic control and can be affected by histone deacetylation inhibition. The study aimed to test if histone deacetalyase inhibitor treatment lead to increased t-PA release or reduced exhaustion in t-PA release in response to stimulation, as well as change in plasminogen activator inhibitor-1 (PAI-1) in subjects with coronary disease. In this clinical study, 16 post-myocardial infarction subjects, the perfused forearm model was used with isoprenaline provocation during 20 minutes, to stimulate local t-PA release. Each subject was measured twice on the same day (repeated stimuli sequences) as well as on two different occasions, without treatment and after four weeks of treatment with valproic acid (500 mg, twice daily). Net forearm release for t-PA in response to isoprenaline at minutes 1.5, 3, 6, 9, 12, 15 and 18 was measured, allowing assessment of cumulative t-PA release. There was a reduction in the exhaustion of cumulative t-PA release during repeated and prolonged stimulation with valproic acid treatment compared to non-treatment. Plasma PAI-1 antigen was decreased following treatment compared to non-treatment (18.4 ± 10.0 vs. 11.0 ± 7.1 nanograms/ml respectively, mean with 95% confidence interval). These findings demonstrate that histone deacetylation inhibition increases the capacity for endogenous t-PA release in subjects with vascular disease. Furthermore, the fibrinolytic balance is favored with suppressed PAI-1 levels. More studies are needed to establish the clinical relevance of these findings.

Trial registration

EU Clinical Trials Register 2012-004950-27     

Time Trends in Incidence and Mortality of Acute Myocardial Infarction,and All-Cause Mortality following a Cardiovascular Prevention Program in Sweden

Background

In 1988, a cardiovascular prevention program which combined an individual and a population-based strategy was launched within primary health-care in Sollentuna, a municipality in Stockholm County. The aim of this study was to investigate time trends in the incidence of and mortality from acute myocardial infarction and all-cause mortality in Sollentuna compared with the rest of Stockholm County during a period of two decades following the implementation of a cardiovascular prevention program.

Materials and Methods

The average population in Sollentuna was 56,589 (49% men) and in Stockholm County (Sollentuna included) 1,795,504 (49% men) during the study period of 1987–2010. Cases of hospitalized acute myocardial infarction and death were obtained for the population of Sollentuna and the rest of Stockholm County using national registries of hospital discharges and deaths. Acute myocardial infarction incidence and mortality were estimated using the average population of Sollentuna and Stockholm in 1987–2010.

Results

During the observation period, the incidence of acute myocardial infarction decreased more in Sollentuna compared with the rest of Stockholm County in women (-22% vs. -7%; for difference in slope <0.05). There was a trend towards a greater decline in Sollentuna compared to the rest of Stockholm County in the incidence of acute myocardial infarction (in men), acute myocardial mortality, and all-cause mortality but the differences were not significant.

Conclusion

During a period of steep decline in acute myocardial infarction incidence and mortality in Stockholm County the municipality of Sollentuna showed a stronger trend in women possibly compatible with favorable influence of a cardiovascular prevention program.

Trial Registration

ClinicalTrials.gov NCT02212145