Swarming strategies for cooperative species

In this paper, we propose a model to investigate the relative efficiency of simple swarming strategies based on the interplay between spontaneous and recruitment-based emigration. We conduct a dynamical study of the model which combines inverse density dependence, saturation effects and induced vs. diffusion-like population transfer. The influence of the most relevant parameters is explored on a systematic basis, and transition values for which qualitative changes occur in the system's behaviour are given. The model is then used to study colonization of a multiple sites environment, as well as confrontation between species featuring different swarming strategies. Simulation results indicate that cooperative organisms should have an interest in evolving recruitment-based emigration. The corresponding population transfer patterns prove more efficient in invading new territories, eliminating competitors in the process. We suggest that this advantage could have promoted a simple form of coordinated swarming in species featuring a primitive type of cooperation.     

Fixed response thresholds and the regulation of division of labor in insect societies

We introduce a simple mathematical model of regulation of division of labor in insect societies based on fixed-response thresholds. Individuals with different thresholds respond differently to task-associated stimuli. Low-threshold individuals become involved at a lower level of stimulus than high-threshold individuals. We show that this simple model can account for experimental observations of Wilson (1984), extend the model to more complicated situations, explore its properties, and study under what conditions it can account for temporal polyethism.     

酵母双杂交系统筛选与RapGAP相互作用的蛋白质

目的筛选与Rap GAP相互作用的蛋白质,为进一步研究人源Rap1GAP介导的信号转导通路、揭示其与肿瘤的关系提供实验依据。方法选用与Rap1GAP同源的来自美丽线虫的Rap GAP作为饵蛋白,以来源于美丽线虫的c DNA文库作为靶蛋白,应用p PC97、p PC86组成的酵母双杂交系统筛选c DNA文库中与Rap GAP相互作用的蛋白质。结果通过营养缺陷平板(-LTH)筛选出63个拟似阳性菌落。经过Lac Z鉴定,19个菌落为阳性,其中7个为强阳性。提取来自19个酵母菌落中的重组DNA,经PCR扩增,12个菌落出现阳性结果。将该19个重组DNA分别电转化入DH5α细菌,涂板培养后,每板挑取4~10个克隆,通过Sal I和Not I双酶切鉴定进行阳性克隆筛选。将阳性克隆的重组DNA进行序列测定。测序结果与Gen Bank比较,其中4个克隆的DNA片段为Y39b6a基因片段、2个为Rap GAP、1个为苯丙氨酸-4-羟化酶、1个为细胞色素C氧化酶,还有1个DNA片段编码美丽线虫特有的小分子蛋白的基因片段,其余11个DNA片段不编码已知蛋白质。结论初步筛选出与Rap GAP相互作用的蛋白质,特别是其中有2个克隆为Rap GAP,提示Rap GAP可能以二聚体的方式存在。     

Genomic and experimental evidence for multiple metabolic functions in the RidA/YjgF/YER057c/UK114 (Rid) protein family

Background

It is now recognized that enzymatic or chemical side-reactions can convert normal metabolites to useless or toxic ones and that a suite of enzymes exists to mitigate such metabolite damage. Examples are the reactive imine/enamine intermediates produced by threonine dehydratase, which damage the pyridoxal 5''-phosphate cofactor of various enzymes causing inactivation. This damage is pre-empted by RidA proteins, which hydrolyze the imines before they do harm. RidA proteins belong to the YjgF/YER057c/UK114 family (here renamed the Rid family). Most other members of this diverse and ubiquitous family lack defined functions.

Results

Phylogenetic analysis divided the Rid family into a widely distributed, apparently archetypal RidA subfamily and seven other subfamilies (Rid1 to Rid7) that are largely confined to bacteria and often co-occur in the same organism with RidA and each other. The Rid1 to Rid3 subfamilies, but not the Rid4 to Rid7 subfamilies, have a conserved arginine residue that, in RidA proteins, is essential for imine-hydrolyzing activity. Analysis of the chromosomal context of bacterial RidA genes revealed clustering with genes for threonine dehydratase and other pyridoxal 5''-phosphate-dependent enzymes, which fits with the known RidA imine hydrolase activity. Clustering was also evident between Rid family genes and genes specifying FAD-dependent amine oxidases or enzymes of carbamoyl phosphate metabolism. Biochemical assays showed that Salmonella enterica RidA and Rid2, but not Rid7, can hydrolyze imines generated by amino acid oxidase. Genetic tests indicated that carbamoyl phosphate overproduction is toxic to S. enterica cells lacking RidA, and metabolomic profiling of Rid knockout strains showed ten-fold accumulation of the carbamoyl phosphate-related metabolite dihydroorotate.

Conclusions

Like the archetypal RidA subfamily, the Rid2, and probably the Rid1 and Rid3 subfamilies, have imine-hydrolyzing activity and can pre-empt damage from imines formed by amine oxidases as well as by pyridoxal 5''-phosphate enzymes. The RidA subfamily has an additional damage pre-emption role in carbamoyl phosphate metabolism that has yet to be biochemically defined. Finally, the Rid4 to Rid7 subfamilies appear not to hydrolyze imines and thus remain mysterious.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1584-3) contains supplementary material, which is available to authorized users.     

Optimizing Human Synovial Fluid Preparation for Two-Dimensional Gel Electrophoresis

Background

Prenatal screening for Down Syndrome (DS) would benefit from an increased number of biomarkers to improve sensitivity and specificity. Improving sensitivity and specificity would decrease the need for potentially risky invasive diagnostic procedures.

Results

We have performed an in depth two-dimensional difference gel electrophoresis (2D DIGE) study to identify potential biomarkers. We have used maternal plasma samples obtained from first and second trimesters from mothers carrying DS affected fetuses compared with mothers carrying normal fetuses. Plasma samples were albumin/IgG depleted and expanded pH ranges of pH 4.5 - 5.5, pH 5.3 - 6.5 and pH 6 - 9 were used for two-dimensional gel electrophoresis (2DE). We found no differentially expressed proteins in the first trimester between the two groups. Significant up-regulation of ceruloplasmin, inter-alpha-trypsin inhibitor heavy chain H4, complement proteins C1s subcomponent, C4-A, C5, and C9 and kininogen 1 were detected in the second trimester in maternal plasma samples where a DS affected fetus was being carried. However, ceruloplasmin could not be confirmed as being consistently up-regulated in DS affected pregnancies by Western blotting.

Conclusions

Despite the in depth 2DE approach used in this study the results underline the deficiencies of gel-based proteomics for detection of plasma biomarkers. Gel-free approaches may be more productive to increase the number of plasma biomarkers for DS for non-invasive prenatal screening and diagnosis.     

Individual preferences and social interactions determine the aggregation of woodlice

Background

The aggregation of woodlice in dark and moist places is considered an adaptation to land life and most studies are focused on its functionality or on the behavioural mechanisms related to the individual''s response to abiotic factors. Until now, no clear experimental demonstration was available about aggregation resulting from inter-attraction between conspecifics.

Methodology/Main Findings

We present the dynamics of aggregation, not previously described in detail in literature, as being independent of the experimental conditions: homogeneous and heterogeneous environments with identical or different shelters. Indeed whatever these conditions, the aggregation is very quick. In less than 10 minutes more than 50% of woodlice were aggregated in several small groups in the homogeneous environment or under shelters in the heterogeneous environment. After this fast aggregation, woodlice progressively moved into a single aggregate or under one shelter.

Conclusions/Significance

Here we show for the first time that aggregation in woodlice implies a strong social component and results from a trade-off between individual preferences and inter-attraction between individuals. Moreover, our results reveal that the response to the heterogeneities affects only the location of the aggregates and not the level of aggregation, and demonstrate the strong inter-attraction between conspecifics which can outweigh individual preferences. This inter-attraction can lead to situations that could seem sub-optimal.     

Amplification of individual preferences in a social context: the case of wall-following in ants

Amplification processes are an essential component of the collective phenomena observed in social and gregarious species. In this paper, we tested the hypothesis that a weak individual wall-following tendency in ants can be amplified by communication through chemical trails, leading to a response to the spatial heterogeneities at the collective level. In our experiments, ants had to cross a diamond-shaped bridge along either of two branches of equal length to get from their nest to a food source. Two types of bridge were used: control bridges without a wall, and experimental bridges equipped with a wall along the inner edge of one of their branches. On the control bridges, ants collectively chose either branch of the bridge in most experiments, whereas on the experimental bridges, the branch with the wall was selected almost systematically. A mathematical model is proposed to assess, in various conditions, the importance of the amplification effect of the chemical trail on the wall-following tendency observed at the individual level. The model highlights the fact that the amplification process can lead to an overestimation of individual capabilities and, thus, that the results of experiments investigating individual preferences at group level in animals must be interpreted with caution.     

A specific increase in inositol 1,4,5-trisphosphate 3-kinase B expression upon differentiation of human embryonic stem cells

Human embryonic stem cells (hESCs) are of great hope for regenerative medicine due to their dual pluripotency and self-renewal properties. We report a comparison of inositol phosphate (InsP(s)) production in undifferentiated, differentiated hESCs and in two cancer cell lines, Ntera2 cells, a human embryonal carcinoma cell (hECC) line and HeLa cells. To evaluate the potential impact of InsP(s) in differentiation, hESCs were spontaneously differentiated in culture for two weeks. The distribution of the different InsP(s) was affected upon differentiation: the level of highly phosphorylated InsP(s) was decreased. In contrast, the total level of phosphoinositides (PI) was increased. Using real time quantitative PCR (qPCR), the mRNA expression of several enzymes of the metabolism of InsP(s) was determined: a specific increase in inositol 1,4,5-trisphosphate 3-kinase A and B (ITPKA and ITPKB) was observed upon hESCs spontaneous differentiation. Ins(1,4,5)P(3) 3-kinase activity, undetectable in undifferentiated hESCs, increased upon differentiation. The same observation was made by Western blotting using an antibody directed against human ITPKB. This is the first report showing the potential implication of soluble InsP(s) in hESCs and possible function of isoenzymes of the inositol trisphosphate 3-kinase family in differentiation.     

Self-assemblage and quorum in the earthworm Eisenia fetida (Oligochaete, Lumbricidae)

Despite their ubiquity and ecological significance in temperate ecosystems, the behavioural ecology of earthworms is not well described. This study examines the mechanisms that govern aggregation behaviour specially the tendency of individuals to leave or join groups in the compost earthworm Eisenia fetida, a species with considerable economic importance, especially in waste management applications. Through behavioural assays combined with mathematical modelling, we provide the first evidence of self-assembled social structures in earthworms and describe key mechanisms involved in cluster formation. We found that the probability of an individual joining a group increased with group size, while the probability of leaving decreased. Moreover, attraction to groups located at a distance was observed, suggesting a role for volatile cues in cluster formation. The size of earthworm clusters appears to be a key factor determining the stability of the group. These findings enhance our understanding of intra-specific interactions in earthworms and have potential implications for extraction and collection of earthworms in vermicomposting processes.