Context-dependent navigation in a collectively foraging species of ant, Messor cephalotes

More than 100 years of scientific research has provided evidence for sophisticated navigational mechanisms in social insects. One key role for navigation in ants is the orientation of workers between food sources and the nest. The focus of recent work has been restricted to navigation in individually foraging ant species, yet many species do not forage entirely independently, instead relying on collectively maintained information such as persistent trail networks and/or pheromones. Harvester ants use such networks, but additionally, foragers often search individually for food either side of trails. In the absence of a trail, these ‘off-trail’ foragers must navigate independently to relocate the trail and return to the nest. To investigate the strategies used by ants on and off the main trails, we conducted field experiments with a harvester ant species, Messor cephalotes, by transferring on-trail and off-trail foragers to an experimental arena. We employed custom-built software to track and analyse ant trajectories in the arena and to quantitatively compare behaviour. Our results indicate that foragers navigate using different cues depending on whether they are travelling on or off the main trails. We argue that navigation in collectively foraging ants deserves more attention due to the potential for behavioural flexibility arising from the relative complexity of journeys between food and the nest.     

A Small Set of Succinct Signature Patterns Distinguishes Chinese and Non-Chinese HIV-1 Genomes

The epidemiology of HIV-1 in China has unique features that may have led to unique viral strains. We therefore tested the hypothesis that it is possible to find distinctive patterns in HIV-1 genomes sampled in China. Using a rule inference algorithm we could indeed extract from sequences of the third variable loop (V3) of HIV-1 gp120 a set of 14 signature patterns that with 89% accuracy distinguished Chinese from non-Chinese sequences. These patterns were found to be specific to HIV-1 subtype, i.e. sequences complying with pattern 1 were of subtype B, pattern 2 almost exclusively covered sequences of subtype 01_AE, etc. We then analyzed the first of these signature patterns in depth, namely that L and W at two V3 positions are specifically occurring in Chinese sequences of subtype B/B'' (3% false positives). This pattern was found to be in agreement with the phylogeny of HIV-1 of subtype B inside and outside of China. We could neither reject nor convincingly confirm that the pattern is stabilized by immune escape. For further interpretation of the signature pattern we used the recently developed measure of Direct Information, and in this way discovered evidence for physical interactions between V2 and V3. We conclude by a discussion of limitations of signature patterns, and the applicability of the approach to other genomic regions and other countries.     

Evaluation of developmental toxicity induced by anticholinesterase insecticide,diazinon in female rats

Developmental toxicities, including birth defects, are significant public health problems. This study was planned to assess the cholinergic and developmental potentials of diazinon that is widely used as an organophosphate insecticide. Pregnant female Sprague‐Dawley rats were given diazinon orally at doses of 0, 1.9, 3.8, and 7.6 mg/kg body weight (b.w.)/day on gestation days 6 to 15. Maternal brain acetylcholinesterase activities, measured on gestation day20, were significantly decreased at 3.8 and 7.6 mg/kg b.w./day, but fetal acetylcholinesterase activity was not altered. Maternal toxicities, as evidenced by cholinergic symptoms including diarrhea, tremors, weakness, salivation, and decreased activities, were observed at the 3.8 and 7.6 mg/kg b.w./day dose groups. Net gravid uterine weight was decreased at a dose of 7.6 mg/kg b.w./day. No maternal effects were apparent in the 1.9 mg/kg b.w./day dose group. Maternal toxicity at a dose of 3.8 mg/kg b.w./day did not induce fetotoxicity or teratogeneicity. However, 7.6 mg/kg b.w./day doses significantly resulted in fetal toxicity and malformations in addition to maternal toxicity in animals. In conclusion, teratogenic disorders only outlined by doses that produced marked maternal toxicity. Since the malformations were not morphologically related, they were considered to be secondary to maternal toxicity; hence, the malformations were not related to cholinesterase inhibition. Birth Defects Res (Part B) 92:534–542, 2011. © 2011 Wiley Periodicals, Inc.     

Representative transcript sets for evaluating a translational initiation sites predictor

Background  

Translational initiation site (TIS) prediction is a very important and actively studied topic in bioinformatics. In order to complete a comparative analysis, it is desirable to have several benchmark data sets which can be used to test the effectiveness of different algorithms. An ideal benchmark data set should be reliable, representative and readily available. Preferably, proteins encoded by members of the data set should also be representative of the protein population actually expressed in cellular specimens.     

The association between leukocytes and sperm quality is concentration dependent

Background  

To evaluate the association between leukocytes (polymorphonuclear granulocytes -PMNL) and semen parameters at different leukocyte concentrations.     

Combined effect of salinity and pH on lipid content and fatty acid composition of Tisochrysis lutea

The haptophyte microalga Tisochrysis lutea was heterotrophically grown in F2 medium with different combinations of pH and salinity. Growth, oil content and fatty acids (FAs) profile were determined under each set of conditions. The salinity was adjusted using NaCl at concentrations of 0.4, 0.6, 0.8, or 1.0 M, while pH was adjusted at 7, 8, or 9, and heterotrophic growth was performed using organic carbon in the form of sugar cane industry waste (CM). Fatty acid methyl esters (FAMEs) were identified by gas chromatography. The results showed that pH of 8.0 was the optimal for dry weight and oil production, regardless of the salinity level. At pH 8.0, growth at a salinity of 0.4 M NaCl was optimal for biomass accumulation (1.185 g L^-1). Under these conditions, the maximum growth rate was 0.055 g L^-1 d^-1, with a doubling time of 17.5 h and a degree of multiplication of 2.198. Oil content was maximal (34.87%) when the salinity was 0.4 M and the pH was 9.0. The ratio of saturated to unsaturated FAs was affected by the pH value and salinity, in that unsaturated FAs increased to 58.09% of the total FAs, considerably greater than the value of 40.59% obtained for the control (0.4 M NaCl and pH 8.0).     

Protein network-based Lasso regression model for the construction of disease-miRNA functional interactions

BackgroundThere is a growing body of evidence associating microRNAs (miRNAs) with human diseases. MiRNAs are new key players in the disease paradigm demonstrating roles in several human diseases. The functional association between miRNAs and diseases remains largely unclear and far from complete. With the advent of high-throughput functional genomics techniques that infer genes and biological pathways dysregulted in diseases, it is now possible to infer functional association between diseases and biological molecules by integrating disparate biological information.ResultsHere, we first used Lasso regression model to identify miRNAs associated with disease signature as a proof of concept. Then we proposed an integrated approach that uses disease-gene associations from microarray experiments and text mining, and miRNA-gene association from computational predictions and protein networks to build functional associations network between miRNAs and diseases. The findings of the proposed model were validated against gold standard datasets using ROC analysis and results were promising (AUC=0.81). Our protein network-based approach discovered 19 new functional associations between prostate cancer and miRNAs. The new 19 associations were validated using miRNA expression data and clinical profiles and showed to act as diagnostic and prognostic prostate biomarkers. The proposed integrated approach allowed us to reconstruct functional associations between miRNAs and human diseases and uncovered functional roles of newly discovered miRNAs.ConclusionsLasso regression was used to find associations between diseases and miRNAs using their gene signature. Defining miRNA gene signature by integrating the downstream effect of miRNAs demonstrated better performance than the miRNA signature alone. Integrating biological networks and multiple data to define miRNA and disease gene signature demonstrated high performance to uncover new functional associations between miRNAs and diseases.     

Influence of the protonation,deprotonation and transition metal ions on the fluorescence of 8-hydroxyquinoline: a computational study

8-Hydroxyquinoline (8HyQ) and its derivatives are the important constituents in a variety of pharmaceutical compounds. The effect of protonation and deprotonation of 8HyQ on its electronic structure and fluorescence was investigated using B3LYP/6-311G** level of theory. We also investigated the interaction of chemosensor, 8HyQ, with different transition metals (Zn²⁺, Fe²⁺, Ni²⁺ and Co²⁺) at the same level. Our results revealed that 8HyQ displays an unusual fluorescence intensity–proton transfer relationship with diminished emission in a protonated form but enhanced emission in a deprotonated form. The Zn²⁺, Fe²⁺, Ni²⁺ and Co²⁺ complexes of 8HyQ, which were investigated at the same level of theory, showed that the order of binding energies was 8HyQ-Ni²⁺>8HyQ-Zn²⁺>8HyQ-Co²⁺>8HyQ-Fe²⁺. Time-dependent density functional theory calculations indicated that Zn ion enhances the fluorescence of 8HyQ as a consequence of the inhibition of the proton transfer. The results are in good agreement between the predicted properties of transition metal complexes of 8HyQ and previously published experimental and theoretical results. A natural bond orbital analysis was performed to understand the nature of hydrogen-bonding interaction in 8HyQ and also to reveal the inter-relations between electronic structure and other properties.