Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families

In this study, we address the issue of performing meaningful pK(a) calculations using homology modeled three-dimensional (3D) structures and analyze the possibility of using the calculated pK(a) values to detect structural defects in the models. For this purpose, the 3D structure of each member of five large protein families of a bacterial nucleoside monophosphate kinases (NMPK) have been modeled by means of homology-based approach. Further, we performed pK(a) calculations for the each model and for the template X-ray structures. Each bacterial NMPK family used in the study comprised on average 100 members providing a pool of sequences and 3D models large enough for reliable statistical analysis. It was shown that pK(a) values of titratable groups, which are highly conserved within a family, tend to be conserved among the models too. We demonstrated that homology modeled structures with sequence identity larger than 35% and gap percentile smaller than 10% can be used for meaningful pK(a) calculations. In addition, it was found that some highly conserved titratable groups either exhibit large pK(a) fluctuations among the models or have pK(a) values shifted by several pH units with respect to the pK(a) calculated for the X-ray structure. We demonstrated that such case usually indicates structural errors associated with the model. Thus, we argue that pK(a) calculations can be used for assessing the quality of the 3D models by monitoring fluctuations of the pK(a) values for highly conserved titratable residues within large sets of homologous proteins.     

Genome-scale metabolic modelling when changes in environmental conditions affect biomass composition

Genome-scale metabolic modeling is an important tool in the study of metabolism by enhancing the collation of knowledge, interpretation of data, and prediction of metabolic capabilities. A frequent assumption in the use of genome-scale models is that the in vivo organism is evolved for optimal growth, where growth is represented by flux through a biomass objective function (BOF). While the specific composition of the BOF is crucial, its formulation is often inherited from similar organisms due to the experimental challenges associated with its proper determination.A cell’s macro-molecular composition is not fixed and it responds to changes in environmental conditions. As a consequence, initiatives for the high-fidelity determination of cellular biomass composition have been launched. Thus, there is a need for a mathematical and computational framework capable of using multiple measurements of cellular biomass composition in different environments. Here, we propose two different computational approaches for directly addressing this challenge: Biomass Trade-off Weighting (BTW) and Higher-dimensional-plane InterPolation (HIP).In lieu of experimental data on biomass composition-variation in response to changing nutrient environment, we assess the properties of BTW and HIP using three hypothetical, yet biologically plausible, BOFs for the Escherichia coli genome-scale metabolic model iML1515. We find that the BTW and HIP formulations have a significant impact on model performance and phenotypes. Furthermore, the BTW method generates larger growth rates in all environments when compared to HIP. Using acetate secretion and the respiratory quotient as proxies for phenotypic changes, we find marked differences between the methods as HIP generates BOFs more similar to a reference BOF than BTW. We conclude that the presented methods constitute a conceptual step in developing genome-scale metabolic modelling approaches capable of addressing the inherent dependence of cellular biomass composition on nutrient environments.     

The influence of mitonuclear genetic variation on personality in seed beetles

There is a growing awareness of the influence of mitochondrial genetic variation on life-history phenotypes, particularly via epistatic interactions with nuclear genes. Owing to their direct effect on traits such as metabolic and growth rates, mitonuclear interactions may also affect variation in behavioural types or personalities (i.e. behavioural variation that is consistent within individuals, but differs among individuals). However, this possibility is largely unexplored. We used mitonuclear introgression lines, where three mitochondrial genomes were introgressed into three nuclear genetic backgrounds, to disentangle genetic effects on behavioural variation in a seed beetle. We found within-individual consistency in a suite of activity-related behaviours, providing evidence for variation in personality. Composite measures of overall activity of individuals in behavioural assays were influenced by both nuclear genetic variation and by the interaction between nuclear and mitochondrial genomes. More importantly, the degree of expression of behavioural and life-history phenotypes was correlated and mitonuclear genetic variation affected expression of these concerted phenotypes. These results show that mitonuclear genetic variation affects both behavioural and life-history traits, and they provide novel insights into the maintenance of genetic variation in behaviour and personality.     

Turnover of DNA-P and phospholipid-P in lake sediments

Identifying and quantifying the forms of phosphorus (P) in lake sediments is a prerequisite for understanding lake trophic status and possible exports of P downstream. Organic P is one of the most important P forms found in the sediment, where orthophosphate diesters, including DNA and phospholipids, represent a degradable P pool that can support primary production and eutrophication. In this study, sediment cores from the eutrophic Lake Erken and the oligotrophic Lake Ånnsjön, both in steady state regarding long-term P input revealed trends in the degradation of DNA-P and PL-P with sediment depth. Comparisons were performed based on the differentiation of essentially permanent or recalcitrant P and temporary, potentially mobile P for the respective fractions. The temporary P pool was defined as the part of the total P pool calculated for values higher than the level at which the measured P concentration converged to a constant value and the recalcitrant pool was defined as the difference between the total and the temporary. The temporary diester-P pool comprised over 20 % of the total temporary P in Lake Erken and around 4 % in Lake Ånnsjön. The decrease in P concentrations with depth was more rapid for DNA-P compared to PL-P in both lakes, suggesting that DNA-P has a more prominent role in internal loading. The study shows that P mobilization potential can be different for different P fractions, which is important when assessing their contribution to internal loading of P within an aquatic system.     

Enhancing immunomodulation on innate immunity by shape transition among RNA triangle,square and pentagon nanovehicles

Modulation of immune response is important in cancer immunotherapy, vaccine adjuvant development and inflammatory or immune disease therapy. Here we report the development of new immunomodulators via control of shape transition among RNA triangle, square and pentagon. Changing one RNA strand in polygons automatically induced the stretching of the interior angle from 60° to 90° or 108°, resulting in self-assembly of elegant RNA triangles, squares and pentagons. When immunological adjuvants were incorporated, their immunomodulation effect for cytokine TNF-α and IL-6 induction was greatly enhanced in vitro and in animals up to 100-fold, while RNA polygon controls induced unnoticeable effect. The RNA nanoparticles were delivered to macrophages specifically. The degree of immunostimulation greatly depended on the size, shape and number of the payload per nanoparticles. Stronger immune response was observed when the number of adjuvants per polygon was increased, demonstrating the advantage of shape transition from triangle to pentagon.     

Manipulation of a VEGF-Notch signaling circuit drives formation of functional vascular endothelial progenitors from human pluripotent stem cells

Human pluripotent stem cell (hPSC)-derived endothelial lineage cells constitutes a promising source for therapeutic revascularization, but progress in this arena has been hampered by a lack of clinically-scalable differentiation protocols and inefficient formation of a functional vessel network integrating with the host circulation upon transplantation. Using a human embryonic stem cell reporter cell line, where green fluorescent protein expression is driven by an endothelial cell-specific VE-cadherin (VEC) promoter, we screened for > 60 bioactive small molecules that would promote endothelial differentiation, and found that administration of BMP4 and a GSK-3β inhibitor in an early phase and treatment with VEGF-A and inhibition of the Notch signaling pathway in a later phase led to efficient differentiation of hPSCs to the endothelial lineage within six days. This sequential approach generated > 50% conversion of hPSCs to endothelial cells (ECs), specifically VEC⁺CD31⁺CD34⁺CD14⁻KDR^high endothelial progenitors (EPs) that exhibited higher angiogenic and clonogenic proliferation potential among endothelial lineage cells. Pharmaceutical inhibition or genetical knockdown of Notch signaling, in combination with VEGF-A treatment, resulted in efficient formation of EPs via KDR⁺ mesodermal precursors and blockade of the conversion of EPs to mature ECs. The generated EPs successfully formed functional capillary vessels in vivo with anastomosis to the host vessels when transplanted into immunocompromised mice. Manipulation of this VEGF-A-Notch signaling circuit in our protocol leads to rapid large-scale production of the hPSC-derived EPs by 12- to 20-fold vs current methods, which may serve as an attractive cell population for regenerative vascularization with superior vessel forming capability compared to mature ECs.     

Time-Wise Change in Neck Pain in Response to Rehabilitation with Specific Resistance Training: Implications for Exercise Prescription

Purpose

To determine the time-wise effect of specific resistance training on neck pain among industrial technicians with frequent neck pain symptoms.

Methods

Secondary analysis of a parallel-group cluster randomized controlled trial of 20 weeks performed at two large industrial production units in Copenhagen, Denmark. Women with neck pain >30 mm VAS (N = 131) were included in the present analysis. The training group (N = 77) performed specific resistance training for the neck/shoulder muscles three times a week, and the control group (N = 54) received advice to stay active. Participants of both groups registered neck pain intensity (0–100 mm VAS) once a week.

Results

Neck pain intensity was 55 mm (SD 23) at baseline. There was a significant group by time interaction for neck pain (F-value 2.61, P<0.001, DF = 19). Between-group differences in neck pain reached significance after 4 weeks (11 mm, 95% CI 2 to 20). The time-wise change in pain showed three phases; a rapid decrease in the training group compared with the control group during the initial 7 weeks, a slower decrease in pain during the following weeks (week 8–15), and a plateau during the last weeks (week 16–20). Adherence to training followed a two-phase pattern, i.e. weekly participation rate was between 70–86% during the initial 7 weeks, dropping towards 55–63% during the latter half of the training period.

Conclusion

Four weeks of specific resistance training reduced neck pain significantly, but 15 weeks is required to achieve maximal pain reduction. The time-wise change in pain followed a three-phase pattern with a rapid effect during the initial 7 weeks followed by a slower but still positive effect, and finally a plateau from week 15 and onwards. Decreased participation rate may explain the decreased efficacy during the latter phase of the intervention.     

Educational Inequalities in Acute Myocardial Infarction Incidence in Norway: A Nationwide Cohort Study

Background

Increasing differences in cardiovascular disease (CVD) mortality across levels of education have been reported in Norway. The aim of the study was to investigate educational inequalities in acute myocardial infarction (AMI) incidence and whether such inequalities have changed during the past decade using a nationwide longitudinal study design.

Methods

Data on 141 332 incident (first) AMIs in Norway during 2001–2009 were obtained through the Cardiovascular Disease in Norway (CVDNOR) project. Educational inequalities in AMI incidence were assessed in terms of age-standardised incidence rates stratified on educational level, incidence rate ratios (IRR), relative index of inequality (RII) and slope index of inequality (SII). All calculations were conducted in four gender and age strata: Men and women aged 35–69 and 70–94 years.

Results

AMI Incidence rates decreased during 2001–2009 for all educational levels except in women aged 35–69 among whom only those with basic education had a significant decrease. In all gender and age groups; those with the highest educational level had the lowest rates. The strongest relative difference was found among women aged 35–69, with IRR (95% CI) for basic versus tertiary education 3.04 (2.85–3.24)) and RII (95% CI) equal to 4.36 (4.03–4.71). The relative differences did not change during 2001–2009 in any of the four gender and age groups, but absolute inequalities measured as SII decreased among the oldest men and women.

Conclusions

There are substantial educational inequalities in AMI incidence in Norway, especially for women aged 35–69. Relative inequalities did not change from 2001 to 2009.     

Population size, female fecundity, and sex ratio variation in gynodioecious Plantago maritima

Theory predicts that the sex ratio of gynodioecious populations (in which hermaphrodites and females coexist) will be affected by the relative female fitness of females and hermaphrodites, and by founder events and genetic drift in small populations. We documented the sex ratio and size of 104 populations of the gynodioecious, perennial herb Plantago maritima in four archipelagos in eastern Sweden and western Finland (from latitude 53 to 64 degrees N). The sex ratio varied significantly both among and within archipelagos (range 0-70% females, median 6.3% females). The frequency of females was highest in the northernmost archipelago and lowest in the southernmost archipelago. As predicted, females were more frequently missing from small than from large populations, and the variance in sex ratio increased with decreasing population size. The relative fecundity of female plants (mean seed output per female/mean seed output per hermaphrodite) ranged from 0.43 to 2.16 (median 1.01, n = 12 populations). Among the 12 populations sampled for seed production (four in each of three archipelagos), the frequency of females was positively related to relative fecundity of females and negatively related to population size. The results suggest that the local sex ratio is influenced both by the relative fecundity of females and hermaphrodites and by stochastic processes in small populations.