Structural flexibility allows the functional diversity of potyvirus genome-linked protein VPg

Several viral genome-linked proteins (VPgs) of plant viruses are intrinsically disordered and undergo folding transitions in the presence of partners. This property has been postulated to be one of the factors that enable the functional diversity of the protein. We created a homology model of Potato virus A VPg and positioned the known functions and structural properties of potyviral VPgs on the novel structural model. The model suggests an elongated structure with a hydrophobic core composed of antiparallel β-sheets surrounded by helices and a positively charged contact surface where most of the known activities are localized. The model most probably represents the fold induced immediately after binding of VPg to a negatively charged lipid surface or to SDS. When the charge of the positive surface was lowered by lysine mutations, the efficiencies of in vitro NTP binding, uridylylation reaction, and unspecific RNA binding were reduced and in vivo the infectivity was debilitated. The most likely uridylylation site, Tyr63, locates to the positively charged surface. Surprisingly, a Tyr63Ala mutation did not prevent replication completely but blocked spreading of the virus. Based on the localization of Tyr119 in the model, it was hypothesized to serve as an alternative uridylylation site. Evidence to support the role of Tyr119 in replication was obtained which gives a positive example of the prediction power of the model. Taken together, our experimental data support the features presented in the model and the idea that the functional diversity is attributable to structural flexibility.     

A Genome Wide Meta-Analysis Study for Identification of Common Variation Associated with Breast Cancer Prognosis

Objective

Genome wide association studies (GWAs) of breast cancer mortality have identified few potential associations. The concordance between these studies is unclear. In this study, we used a meta-analysis of two prognostic GWAs and a replication cohort to identify the strongest associations and to evaluate the loci suggested in previous studies. We attempt to identify those SNPs which could impact overall survival irrespective of the age of onset.

Methods

To facilitate the meta-analysis and to refine the association signals, SNPs were imputed using data from the 1000 genomes project. Cox-proportional hazard models were used to estimate hazard ratios (HR) in 536 patients from the POSH cohort (Prospective study of Outcomes in Sporadic versus Hereditary breast cancer) and 805 patients from the HEBCS cohort (Helsinki Breast Cancer Study). These hazard ratios were combined using a Mantel-Haenszel fixed effects meta-analysis and a p-value threshold of 5×10⁻⁸ was used to determine significance. Replication was performed in 1523 additional patients from the POSH study.

Results

Although no SNPs achieved genome wide significance, three SNPs have significant association in the replication cohort and combined p-values less than 5.6×10⁻⁶. These SNPs are; rs421379 which is 556 kb upstream of ARRDC3 (HR = 1.49, 95% confidence interval (CI) = 1.27–1.75, P = 1.1×10⁻⁶), rs12358475 which is between ECHDC3 and PROSER2 (HR = 0.75, CI = 0.67–0.85, P = 1.8×10⁻⁶), and rs1728400 which is between LINC00917 and FOXF1.

Conclusions

In a genome wide meta-analysis of two independent cohorts from UK and Finland, we identified potential associations at three distinct loci. Phenotypic heterogeneity and relatively small sample sizes may explain the lack of genome wide significant findings. However, the replication at three SNPs in the validation cohort shows promise for future studies in larger cohorts. We did not find strong evidence for concordance between the few associations highlighted by previous GWAs of breast cancer survival and this study.     

Adenovirus-mediated gene transfer of Lp-PLA2 reduces LDL degradation and foam cell formation in vitro

Oxidation of LDL generates biologically active platelet-activating factor (PAF)-like phospholipid derivatives, which have potent proinflammatory activity. These products are inactivated by lipoprotein-associated phospholipase A2 (Lp-PLA2), an enzyme capable of hydrolyzing PAF-like phospholipids. In this study, we generated an adenovirus (Ad) encoding human Lp-PLA2 and injected 10(8), 10(9), and 10(10) plaque-forming unit doses of Adlp-PLA2 and control AdlacZ intra-arterially into rabbits to achieve overexpression of Lp-PLA2 in liver and in vivo production of Lp-PLA2-enriched LDL. As a result, LDL particles with 3-fold increased Lp-PLA2 activity were produced with the highest virus dose. Increased Lp-PLA2 activity in LDL particles decreased the degradation rate in RAW 264 macrophages after standard in vitro oxidation to 60-80% compared with LDL isolated from LacZ-transduced control rabbits. The decrease was proportional to the virus dose and Lp-PLA2 activity. Lipid accumulation and foam cell formation in RAW 264 macrophages were also decreased when incubated with oxidized LDL containing the highest Lp-PLA2 activity. Inhibition of the Lp-PLA2 activity in the LDL particles led to an increase in lipid accumulation and foam cell formation. It is concluded that increased Lp-PLA2 activity in LDL attenuates foam cell formation and decreases LDL oxidation and subsequent degradation in macrophages.     

Metformin and its sulphonamide derivative simultaneously potentiateanti-cholinesterase activity of donepezil and inhibit beta-amyloid aggregation

The aim of this study was to assess in vitro the effects of sulphenamide and sulphonamide derivatives of metformin on the activity of human acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE), establish the type of inhibition, and assess the potential synergism between biguanides and donepezil towards both cholinesterases (ChEs) and the effects on the β-amyloid aggregation. Sulphonamide 5 with para-trifluoromethyl- and ortho-nitro substituents in aromatic ring inhibited AChE in a mixed-type manner at micromolar concentrations (IC₅₀?=?212.5?±?48.3?µmol/L). The binary mixtures of donepezil and biguanides produce an anti-AChE effect, which was greater than either compound had alone. A combination of donepezil and sulphonamide 5 improved the IC₅₀ value by 170 times. Compound 5 at 200?µmol/L inhibited Aβ aggregation by ～20%. In conclusion, para-trifluoromethyl-ortho-nitro-benzenesulphonamide presents highly beneficial anti-AChE and anti-Aβ aggregation properties which could serve as a promising starting point for the design and development of novel biguanide-based candidates for AD treatment.     

Review of root dynamics in forest ecosystems grouped by climate,climatic forest type and species

Patterns of both above- and belowground biomass and production were evaluated using published information from 200 individual data-sets. Data sets were comprised of the following types of information: organic matter storage in living and dead biomass (e.g. surface organic horizons and soil organic matter accumulations), above- and belowground net primary production (NPP) and biomass, litter transfers, climatic data (i.e. precipitation and temperature), and nutrient storage (N, P, Ca, K) in above- and belowground biomass, soil organic matter and litter transfers. Forests were grouped by climate, foliage life-span, species and soil order. Several climatic and nutrient variables were regressed against fine root biomass or net primary production to determine what variables were most useful in predicting their dynamics. There were no significant or consistent patterns for above- and belowground biomass accumulation or NPP change across the different climatic forest types and by soil order. Similarly, there were no consistent patterns of soil organic matter (SOM) accumulation by climatic forest type but SOM varied significantly by soil order—the chemistry of the soil was more important in determining the amount of organic matter accumulation than climate. Soil orders which were high in aluminum, iron, and clay (e.g. Ultisols, Oxisols) had high total living and dead organic matter accumulations-especially in the cold temperate zone and in the tropics. Climatic variables and nutrient storage pools (i.e. in the forest floor) successfully predicted fine root NPP but not fine root biomass which was better predicted by nutrients in litterfall. The importance of grouping information by species based on their adaptive strategies for water and nutrient-use is suggested by the data. Some species groups did not appear to be sensitive to large changes in either climatic or nutrient variables while for others these variables explained a large proportion of the variation in fine root biomass and/or NPP.     

Solid-phase minisequencing confirmed by FISH analysis in determination of gene copy number

The solid-phase minisequencing method (Syvänen et al. 1990) allows accurate quantative determination of the ratio between two DNA or RNA sequences that are present as a mixture in a sample and differ from each other only by a single nucleotide. Here, we present another application of the minisequening method, the determination of the gene copy number in a genome. The copy number of a marker gene aspartyl glucosaminidase (AGA) located at 4qter, was determined in three patients with a chromosomal alteration involving the distal region of 4q. For the minisequencing assay an equal amount of DNA from a patient homozygous for a mutation in the AGA gene was added to the DNA samples concerned. The relative amount of the normal sequence determined in each combined sample gives the copy number of the AGA gene. Fluorescence in situ hybridization (FISH), applied in parallel as a control, produced concordant results with solid-phase minisequencing in each case. As the potential of the minisequencing lies in automation, it could be a useful tool in the screening of monosomies, trisomies or loss of heterozygosity in diagnostics.     

Sperm use economy of honeybee (Apis mellifera) queens

The queens of eusocial ants, bees, and wasps only mate during a very brief period early in life to acquire and store a lifetime supply of sperm. As sperm cannot be replenished, queens have to be highly economic when using stored sperm to fertilize eggs, especially in species with large and long‐lived colonies. However, queen fertility has not been studied in detail, so that we have little understanding of how economic sperm use is in different species, and whether queens are able to influence their sperm use. This is surprising given that sperm use is a key factor of eusocial life, as it determines the fecundity and longevity of queens and therefore colony fitness. We quantified the number of sperm that honeybee (Apis mellifera) queens use to fertilize eggs. We examined sperm use in naturally mated queens of different ages and in queens artificially inseminated with different volumes of semen. We found that queens are remarkably efficient and only use a median of 2 sperm per egg fertilization, with decreasing sperm use in older queens. The number of sperm in storage was always a significant predictor for the number of sperm used per fertilization, indicating that queens use a constant ratio of spermathecal fluid relative to total spermathecal volume of 2.364 × 10^?6 to fertilize eggs. This allowed us to calculate a lifetime fecundity for honeybee queens of around 1,500,000 fertilized eggs. Our data provide the first empirical evidence that honeybee queens do not manipulate sperm use, and fertilization failures in worker‐destined eggs are therefore honest signals that workers can use to time queen replacement, which is crucial for colony performance and fitness.     

Trends in Food Habits and Their Relation to Socioeconomic Status among Nordic Adolescents 2001/2002-2009/2010

Background

In the Nordic countries, substantial policy and intervention efforts have been made to increase adolescents'' consumption of fruit and vegetables and to reduce their intake of sweets and soft drinks. Some initiatives have been formulated in a Nordic collaboration and implemented at national level. In recent years, social inequalities in food habits have been attracted particular governmental interest and several initiatives addressing the socioeconomic gradient in food habits have been highlighted. However, few internationally published studies have evaluated how trends in adolescents'' food habits develop in the context of Nordic nutrition policy, or have compared differences between the Nordic countries.

Methods

The study was based on Danish, Finnish, Norwegian and Swedish cross-sectional data from the international Health Behaviour in School-Aged Children (HBSC) study, collected via three nationally representative and comparable questionnaire surveys in 2001/2002, 2005/2006 and 2009/2010. Food habits were identified by students'' consumption of fruit, vegetables, sweets and sugar sweetened soft drink. Socioeconomic status (SES) was measured with the Family Affluence Scale (FAS). Multilevel logistic regression was used to analyze the data.

Results

Trends in fruit consumption developed differently across countries, characterized by an increase in Denmark and Norway and more stable trends in Sweden and Finland. Vegetable consumption increased particularly in Denmark and to a lesser extent in Norway, whereas Sweden and Finland displayed stable trends. Decreased trends were observed for sweet and soft drink consumption and were similar in Norway, Sweden and Finland. Sweet consumption decreased across all survey years, whereas soft drink consumption decreased between 2001/2002–2005/2006 and was stable thereafter. Denmark displayed an increase between 2001/2002–2005/2006 followed by a similar decrease between 2005/2006–2009/2010 for both sweet and soft drink consumption. Socioeconomic inequalities in fruit and vegetable consumption were observed in all countries, with no cross-country differences, and no changes over time. Small but not significant cross-country variation was identified for SES inequalities in sweet consumption. Reduced SES inequalities were observed in Sweden between 2005/2006 and 2009/2010. SES was not associated with soft drink consumption in this study population, with the exception of Denmark for the survey year 2009/2010.

Conclusion

Different trends resulted in increased country differences in food habits during the time of observations. In survey year 2009/2010, Danish students reported a higher intake of fruit and vegetable consumption than their counterparts in the other Nordic countries. Finnish students reported the lowest frequency of sweets and soft drink consumption. Despite the positive dietary trends documented in the present study, the majority of Nordic adolescents are far from meeting national dietary recommendations. Our findings underline the need for more comprehensive initiatives targeting young people''s food habits as well as a more deliberate and focused action to close gaps in social inequalities that affect food choices.