Gardening by the psychomyiid caddisfly Tinodes waeneri: evidence from stable isotopes

Sedentary species face a trade-off between the benefits of exploiting food close to their homes and the cost of defending it. In aquatic systems, it has been suggested that some sedentary grazers can increase the range of circumstances under which they are at an advantage over mobile grazers by enhancing food resources within their feeding territories through ‘gardening’. We examined this for the retreat-building sedentary larvae of the caddis Tinodes waeneri, which are often dominant in the littoral of lakes. We hypothesised that T. waeneri gardens by fertilising its retreat (a fixed ‘gallery’ on which algae and other microorganisms grow), and that gardening would be more important in lower productivity lakes. We tested this by analysing the carbon and nitrogen stable isotope ratios of larvae, their galleries and the general background epilithon, collected from rocks in the littoral zones of six lakes spread across a natural nutrient gradient. We found evidence of nutrient recycling within the Tinodes gallery community in all lakes. Galleries were ¹⁵N-depleted compared to the epilithon, suggesting that algae on galleries preferentially assimilated ¹⁴N from larval excretions that were themselves ¹⁵N-depleted relative to the larval food source. Mixing model results indicate that galleries formed an important larval carbon and nitrogen source, with mean gallery dietary contributions of over 40% in at least one sample period in all lakes studied. Gallery contributions were greater between April and October than in January and, contrary to our initial hypothesis, greater in the more productive lakes of those surveyed. Nevertheless, T. waeneri galleries do act as a fertilised garden. ‘Gardening’ appears to be widespread in this species, and may affect productivity and patterns of nitrogen retention within the stony littoral of lakes.     

Acid-sensing ion channel 3 mediates peripheral anti-hyperalgesia effects of acupuncture in mice inflammatory pain

Background  

Peripheral tissue inflammation initiates hyperalgesia accompanied by tissue acidosis, nociceptor activation, and inflammation mediators. Recent studies have suggested a significantly increased expression of acid-sensing ion channel 3 (ASIC3) in both carrageenan- and complete Freund's adjuvant (CFA)-induced inflammation. This study tested the hypothesis that acupuncture is curative for mechanical hyperalgesia induced by peripheral inflammation.     

Protein structure similarity from principle component correlation analysis

Background  

Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD) in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities.     

Adrenocorticotropic Hormone Suppresses Gonadotropin-Stimulated Estradiol Release from Zebrafish Ovarian Follicles

While stress is known to impact reproductive performance, the pathways involved are not entirely understood. Corticosteroid effects on the functioning of the hypothalamus-pituitary-gonadal axis are thought to be a key aspect of stress-mediated reproductive dysfunction. A vital component of the stress response is the pituitary secretion of adrenocorticotropic hormone (ACTH), which binds to the melanocortin 2 receptor (MC2R) in the adrenal glands and activates cortisol biosynthesis. We recently reported MC2R mRNA abundance in fish gonads leading to the hypothesis that ACTH may be directly involved in gonadal steroid modulation. Using zebrafish (Danio rerio) ovarian follicles, we tested the hypothesis that acute ACTH stimulation modulates cortisol and estradiol (E₂) secretion. ACTH neither affected cortisol nor unstimulated E₂ release from ovarian follicles. However, ACTH suppressed human chorionic gonadotropin (hCG)-stimulated E₂ secretion in a dose-related manner, with a maximum decrease of 62% observed at 1 I.U. ACTH mL⁻¹. This effect of ACTH on E₂ release was not observed in the presence of either 8-bromo-cAMP or forskolin, suggesting that the mechanism(s) involved in steroid attenuation was upstream of adenylyl cyclase activation. Overall, our results suggest that a stress-induced rise in plasma ACTH levels may initiate a rapid down-regulation of acute stimulated E₂ biosynthesis in the zebrafish ovary, underscoring a novel physiological role for this pituitary peptide in modulating reproductive activity.     

Conditional random pattern model for copy number aberration detection

Background  

DNA copy number aberration (CNA) is very important in the pathogenesis of tumors and other diseases. For example, CNAs may result in suppression of anti-oncogenes and activation of oncogenes, which would cause certain types of cancers. High density single nucleotide polymorphism (SNP) array data is widely used for the CNA detection. However, it is nontrivial to detect the CNA automatically because the signals obtained from high density SNP arrays often have low signal-to-noise ratio (SNR), which might be caused by whole genome amplification, mixtures of normal and tumor cells, experimental noise or other technical limitations. With the reduction in SNR, many false CNA regions are often detected and the true CNA regions are missed. Thus, more sophisticated statistical models are needed to make the CNAs detection, using the low SNR signals, more robust and reliable.     

Golgi-Cox studies on the central nervous system of a gastropod mollusc

Summary Complete neurones were impregnated in the brain of the pulmonate gastropod pond snail, Lymnaea stagnalis L. using the Golgi-Cox method. Mapping of small to medium sized neurones identified in living preparations by the position of the perikarya was possible. Simple monopolar and bifurcating monopolar neurones with varying lateral patterns of short fine fibres were common in the pond snail brain. Larger neurones have more complex and numerous branches originating from axons close to the perikarya than smaller ones. Stem processes originating on the cell body were observed on neurones above 30 in somal diameter. Possible sites for the location of chemical synapses were suggested. Functional types of neurones were difficult to separate on morphological grounds. Giant or very large neurones are small in number in pond snail ganglia, compared with medium or small neurones.The authors wish to thank Mr. Colin Atherton for photographic assistance and the U.K. Science Research Council for a grant to P. R. B.     

Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces

Background

Predicting drug-protein interactions from heterogeneous biological data sources is a key step for in silico drug discovery. The difficulty of this prediction task lies in the rarity of known drug-protein interactions and myriad unknown interactions to be predicted. To meet this challenge, a manifold regularization semi-supervised learning method is presented to tackle this issue by using labeled and unlabeled information which often generates better results than using the labeled data alone. Furthermore, our semi-supervised learning method integrates known drug-protein interaction network information as well as chemical structure and genomic sequence data.

Results

Using the proposed method, we predicted certain drug-protein interactions on the enzyme, ion channel, GPCRs, and nuclear receptor data sets. Some of them are confirmed by the latest publicly available drug targets databases such as KEGG.

Conclusions

We report encouraging results of using our method for drug-protein interaction network reconstruction which may shed light on the molecular interaction inference and new uses of marketed drugs.

     

Temporal changes in stress and tissue-specific metabolic responses to municipal wastewater effluent exposure in rainbow trout

Sub-chronic exposure to municipal wastewater effluent (MWWE) in situ was recently shown to impact the acute response to a secondary stressor in rainbow trout (Oncorhynchus mykiss). However, little is known about whether MWWE exposure in itself is stressful to the animal. To address this, we carried out a laboratory study to examine the organismal and cellular stress responses and tissue-specific metabolic capacity in trout exposed to MWWE. Juvenile rainbow trout were exposed to 0, 20 and 90% MWWE (from a tertiary wastewater treatment plant), that was replenished every 2d, for 14 d. Fish were sampled 2, 8 or 14 d post-exposure. Plasma cortisol, glucose and lactate levels were measured as indicators of organismal stress response, while inducible heat shock protein 70 (hsp70), constitutive heat shock protein 70 (hsc70) and hsp90 expression in the liver were used as markers of cellular stress response. Impact of MWWE on cortisol signaling was ascertained by determining glucocorticoid receptor protein (GR) expression in the liver, brain and, heart, and metabolic capacity was evaluated by measuring liver glycogen content and tissue-specific activities of key enzymes in intermediary metabolism. Plasma glucose and lactate levels were unaffected by exposure to MWWEs, whereas cortisol showed a transient increase in the 20% group at 8d. Liver hsc70 and hsp90, but not hsp70 expression, were higher in the 90% MWWE group after 8d. There was a temporal change in GR expression in the liver and heart, but not brain of trout exposed to MWWE. Liver glycogen content and activities liver gluconeogenic enzyme phosphoenolpyruvate carboxykinase (PEPCK), and alanine aminotransferase (AlaAT) were significantly affected by MWWE exposure. The glycolytic enzymes pyruvate kinase (PK) and hexokinase (HK) activities were significantly higher temporally by MWWE exposure in the gill and heart, but not in the liver and brain. Overall, a 14 d exposure to MWWE evokes a cellular stress response and perturbs the cortisol stress response in rainbow trout. The tissue-specific temporal changes in the metabolic capacity suggest enhanced energy demand in fish exposed to MWWE, which may eventually lead to reduced fitness.