Effects of growth rates on the otolith increments deposition rate in capelin larvae (Mallotus villosus)

Otolith microstructure analysis was applied to known age capelin larvae (Mallotus villosus) in order to examine the formation of daily increments. In two validation experiments, newly hatched yolk sac larvae were stocked into eight 10 m³ plastic bags where environmental conditions were kept as natural as possible. The bags were terminated after 35-79 days, the surviving larvae were collected and the otoliths were analysed. Survival in the bags varied between 39 - 71% with average individual length growth rates of 0.25 mm day^- 1. The ages of most larvae were underestimated and the accuracy in age estimation was generally low. Highest accuracy was found for fast growing larvae. On average, the larvae started to form increments about 12 days after hatching, and the increment width increased with age and/or length of the larvae. Larvae showing low body growth rates had fast otolith growth relative to body length.     

A Gene Panel,Including LRP12, Is Frequently Hypermethylated in Major Types of B-Cell Lymphoma

Epigenetic modifications and DNA methylation in particular, have been recognized as important mechanisms to alter gene expression in malignant cells. Here, we identified candidate genes which were upregulated after an epigenetic treatment of B-cell lymphoma cell lines (Burkitt''s lymphoma, BL; Follicular lymphoma, FL; Diffuse large B-cell lymphoma, DLBCL activated B-cell like, ABC; and germinal center like, GCB) and simultaneously expressed at low levels in samples from lymphoma patients. Qualitative methylation analysis of 24 candidate genes in cell lines revealed five methylated genes (BMP7, BMPER, CDH1, DUSP4 and LRP12), which were further subjected to quantitative methylation analysis in clinical samples from 59 lymphoma patients (BL, FL, DLBCL ABC and GCB; and primary mediastinal B-cell lymphoma, PMBL). The genes LRP12 and CDH1 showed the highest methylation frequencies (94% and 92%, respectively). BMPER (58%), DUSP4 (32%) and BMP7 (22%), were also frequently methylated in patient samples. Importantly, all gene promoters were unmethylated in various control samples (CD19+ peripheral blood B cells, peripheral blood mononuclear cells and tonsils) as well as in follicular hyperplasia samples, underscoring a high specificity. The combination of LRP12 and CDH1 methylation could successfully discriminate between the vast majority of the lymphoma and control samples, emphasized by receiver operating characteristic analysis with a c-statistic of 0.999. These two genes represent promising epigenetic markers which may be suitable for monitoring of B-cell lymphoma.     

Habitat heterogeneity and mammalian predator–prey interactions

• 1 In predator–prey theory, habitat heterogeneity can affect the relationship between kill rates and prey or predator density through its effect on the predator's ability to search for, encounter, kill and consume its prey. Many studies of predator–prey interactions include the effect of spatial heterogeneity, but these are mostly based on species with restricted mobility or conducted in experimental settings.
• 2 Here, we aim to identify the patterns through which spatial heterogeneity affects predator–prey dynamics and to review the literature on the effect of spatial heterogeneity on predator–prey interactions in terrestrial mammalian systems, i.e. in freely moving species with high mobility, in non‐experimental settings. We also review current methodologies that allow the study of the predation process within a spatial context.
• 3 When the functional response includes the effect of spatial heterogeneity, it usually takes the form of predator‐dependent or ratio‐dependent models and has wide applicability.
• 4 The analysis of the predation process through its different stages may further contribute towards identifying the spatial scale of interest and the specific spatial mechanism affecting predator–prey interactions.
• 5 Analyzing the predation process based on the functional response theory, but separating the stages of predation and applying a multiscale approach, is likely to increase our insight into how spatial heterogeneity affects predator–prey dynamics. This may increase our ability to forecast the consequences of landscape transformations on predator–prey dynamics.

     

Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study

Background  

A method to evaluate and analyze the massive data generated by series of microarray experiments is of utmost importance to reveal the hidden patterns of gene expression. Because of the complexity and the high dimensionality of microarray gene expression profiles, the dimensional reduction of raw expression data and the feature selections necessary for, for example, classification of disease samples remains a challenge. To solve the problem we propose a two-level analysis. First self-organizing map (SOM) is used. SOM is a vector quantization method that simplifies and reduces the dimensionality of original measurements and visualizes individual tumor sample in a SOM component plane. Next, hierarchical clustering and K-means clustering is used to identify patterns of gene expression useful for classification of samples.     

An early cell shape transition drives evolutionary expansion of the human forebrain

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In thrombin stimulated human platelets Citalopram, Promethazine, Risperidone, and Ziprasidone, but not Diazepam, may exert their pharmacological effects also through intercalation in membrane phospholipids in a receptor-independent manner

Intercalation of drugs in the platelet membrane affects phospholipid-requiring enzymatic processes according to the drugs’ intercalation capability. We investigated effects of Promethazine, Citalopram, Ziprasidone, Risperidone, and Diazepam on phospholipase A₂ (PLA₂) and polyphosphoinositide (PPI) metabolism in thrombin-stimulated human platelets. We also examined effects of the drugs on monolayers of glycerophospholipids using the Langmuir technique. Diazepam did not influence PLA ₂ activity, had no effects on PPI cycle, and caused no change in mean molecular area of phospholipid monolayers. The remaining psychotropic drugs affected these parameters in different ways and levels of potency suggesting that they act by being intercalated between the molecules of adjacent membrane phospholipids, thus causing changes in substrate availability for phospholipid-hydrolyzing enzymes (PLA₂ and Phospholipase C). We show that several psychotropic drugs can also have other cellular effects than receptor antagonism. These effects may be implicated in the psychotropic effects of the drugs and/or their side effects.     

Distinct Roles of Myosin Va in Membrane Remodeling and Exocytosis of Secretory Granules

Hormone‐ and neuropeptide‐containing secretory granules (SGs) of neuroendocrine PC12 cells are formed at the trans‐ Golgi network as immature SGs. These intermediates are converted to mature SGs in a complex maturation process, including matrix condensation, processing of cargo proteins and removal of proteins and membrane in clathrin‐coated vesicles. The resulting mature SGs undergo Ca²⁺‐dependent exocytosis upon an appropriate stimulus. We here show that the motor protein myosin Va is implicated in a maturation step of SGs, their binding to F‐actin and their stimulated exocytosis. Interference with myosin Va function blocked the removal of the transmembrane protein furin from maturing SGs without affecting condensation and processing of proteins of the SG lumen. Furthermore, the ATP‐inhibited binding of SGs to F‐actin decreased with progressive maturation and upon interference with myosin Va function. Moreover, the expression of a dominant‐negative myosin Va‐tail or shRNA‐based downregulation of myosin Va interfered with stimulated exocytosis of SGs. In summary, our data suggest an essential function of myosin Va in the membrane remodeling of SGs during maturation and a role in their exocytosis.     

An empirical test for a zone of canalization in thermal reaction norms

Theoretical models on the evolution of phenotypic plasticity predict a zone of canalization where reaction norms cross, and genetic variation is minimized in the environment a population most frequently encounter. Empirical tests of this prediction are largely missing, in particular for life‐history traits. We addressed this prediction by quantifying thermal reaction norms of three life‐history traits (somatic growth rate, age and size at maturation) of a Norwegian population of Daphnia magna and testing for the occurrence of an intermediate temperature (T_m) at which genetic variance in the traits is minimized. Size at maturation changed relatively little with temperature compared to the other traits, and there was no genetic variance in the shape of the reaction norm. Consequently, age at maturation and somatic growth rate were strongly negatively correlated. Both traits showed a strong genotype–environment interaction, and the estimated T_m was 14 °C for both age at maturation and growth rate. This value of T_m corresponds well with mean summer temperatures experienced by the population and suggests that the population has evolved under stabilizing selection in temperatures that fluctuate around this mean temperature. These results suggest local adaptation to temperature in the studied population and allow predicting evolutionary trajectories of thermal reaction norms under changing thermal regimes.     

Wolf reintroduction to Scotland: public attitudes and consequences for red deer management

Reintroductions are important tools for the conservation of individual species, but recently more attention has been paid to the restoration of ecosystem function, and to the importance of carrying out a full risk assessment prior to any reintroduction programme. In much of the Highlands of Scotland, wolves (Canis lupus) were eradicated by 1769, but there are currently proposals for them to be reintroduced. Their main wild prey if reintroduced would be red deer (Cervus elaphus). Red deer are themselves a contentious component of the Scottish landscape. They support a trophy hunting industry but are thought to be close to carrying capacity, and are believed to have a considerable economic and ecological impact. High deer densities hamper attempts to reforest, reduce bird densities and compete with livestock for grazing. Here, we examine the probable consequences for the red deer population of reintroducing wolves into the Scottish Highlands using a structured Markov predator-prey model. Our simulations suggest that reintroducing wolves is likely to generate conservation benefits by lowering deer densities. It would also free deer estates from the financial burden of costly hind culls, which are required in order to achieve the Deer Commission for Scotland's target deer densities. However, a reintroduced wolf population would also carry costs, particularly through increased livestock mortality. We investigated perceptions of the costs and benefits of wolf reintroductions among rural and urban communities in Scotland and found that the public are generally positive to the idea. Farmers hold more negative attitudes, but far less negative than the organizations that represent them.