BlastR--fast and accurate database searches for non-coding RNAs

We present and validate BlastR, a method for efficiently and accurately searching non-coding RNAs. Our approach relies on the comparison of di-nucleotides using BlosumR, a new log-odd substitution matrix. In order to use BlosumR for comparison, we recoded RNA sequences into protein-like sequences. We then showed that BlosumR can be used along with the BlastP algorithm in order to search non-coding RNA sequences. Using Rfam as a gold standard, we benchmarked this approach and show BlastR to be more sensitive than BlastN. We also show that BlastR is both faster and more sensitive than BlastP used with a single nucleotide log-odd substitution matrix. BlastR, when used in combination with WU-BlastP, is about 5% more accurate than WU-BlastN and about 50 times slower. The approach shown here is equally effective when combined with the NCBI-Blast package. The software is an open source freeware available from www.tcoffee.org/blastr.html.     

Social Network Influences Decision Making During Collective Movements in Brown Lemurs (<Emphasis Type="Italic">Eulemur fulvus fulvus</Emphasis>)

Many animal species live as a group and must therefore move as such. Several authors have suggested that the mechanisms underlying collective movements in primate species appear to rely on complex cognitive skills, given their high level of cognitive abilities. However, recent studies have highlighted the fact that complex patterns do not necessarily imply complex mechanisms. We used a modeling approach to investigate the patterns of collective movement in a semi-free-ranging group of brown lemurs. We recorded via digital video cameras the order and joining latencies of the 11 individuals of the group during the departure time of spontaneous group movements. We then assessed whether mimetic mechanisms or the existence of a leader were underlying conditions for the joining process by testing 5 computer models relying respectively on 5 hypotheses: the independence of individuals, an anonymous mimetism, a mimetism according to kinship, a mimetism according to affiliation, and eventually the existence of a leader. We found that departure latencies, associations, and the order of individuals at departure time could all be explained by the mimetism according to affiliation model. Thus, an individual’s decision to join the collective movement or not depended on the decision taken by its preferred social partners. These results show the importance of social parameters in primate decision making and that the high cohesion displayed by the group members might not be constrained merely by ecological factors such as predation or foraging consideration.     

Reaching a Consensus: Terminology and Concepts Used in Coordination and Decision-Making Research

Research on coordination and decision-making in humans and nonhuman primates has increased considerably throughout the last decade. However, terminology has been used inconsistently, hampering the broader integration of results from different studies. In this short article, we provide a glossary containing the central terms of coordination and decision-making research. The glossary is based on previous definitions that have been critically revised and annotated by the participants of the symposium “Where next? Coordination and decision-making in primate groups” at the XXIIIth Congress of the International Primatological Society (IPS) in Kyoto, Japan. We discuss a number of conceptual and methodological issues and highlight consequences for their implementation. In summary, we recommend that future studies on coordination and decision-making in animal groups do not use the terms “combined decision” and “democratic/despotic decision-making.” This will avoid ambiguity as well as anthropocentric connotations. Further, we demonstrate the importance of 1) taxon-specific definitions of coordination parameters (initiation, leadership, followership, termination), 2) differentiation between coordination research on individual-level process and group-level outcome, 3) analyses of collective action processes including initiation and termination, and 4) operationalization of successful group movements in the field to collect meaningful and comparable data across different species.     

Oleuropein and derivatives from olives as Tau aggregation inhibitors

Tau isoforms constitute a family of microtubule-associated proteins that are mainly expressed in neurons of the central nervous system. They promote the assembly of tubulin monomers into microtubules and modulate their stability, thus playing a key structural role in the distal portion of axons. In Alzheimer's disease and related tauopathies, Tau aggregation into fibrillary tangles contributes to intraneuronal and glial lesions. We report herein the ability of three natural phenolic derivatives obtained from olives and derived food products to prevent such Tau fibrillization in vitro, namely hydroxytyrosol, oleuropein, and oleuropein aglycone. The latter was found to be more active than the reference Tau aggregation inhibitor methylene blue on both wild-type and P301L Tau proteins, inhibiting fibrillization at low micromolar concentrations. These findings might provide further experimental support for the beneficial nutritional properties of olives and olive oil as well as a chemical scaffold for the development of new drugs aiming at neurodegenerative tauopathies.     

Waixenicin A inhibits cell proliferation through magnesium-dependent block of transient receptor potential melastatin 7 (TRPM7) channels

Transient receptor potential melastatin 7 (TRPM7) channels represent the major magnesium-uptake mechanism in mammalian cells and are key regulators of cell growth and proliferation. They are expressed abundantly in a variety of human carcinoma cells controlling survival, growth, and migration. These characteristics are the basis for recent interest in the channel as a target for cancer therapeutics. We screened a chemical library of marine organism-derived extracts and identified waixenicin A from the soft coral Sarcothelia edmondsoni as a strong inhibitor of overexpressed and native TRPM7. Waixenicin A activity was cytosolic and potentiated by intracellular free magnesium (Mg(2+)) concentration. Mutating a Mg(2+) binding site on the TRPM7 kinase domain reduced the potency of the compound, whereas kinase deletion enhanced its efficacy independent of Mg(2+). Waixenicin A failed to inhibit the closely homologous TRPM6 channel and did not significantly affect TRPM2, TRPM4, and Ca(2+) release-activated Ca(2+) current channels. Therefore, waixenicin A represents the first potent and relatively specific inhibitor of TRPM7 ion channels. Consistent with TRPM7 inhibition, the compound blocked cell proliferation in human Jurkat T-cells and rat basophilic leukemia cells. Based on the ability of the compound to inhibit cell proliferation through Mg(2+)-dependent block of TRPM7, waixenicin A, or structural analogs may have cancer-specific therapeutic potential, particularly because certain cancers accumulate cytosolic Mg(2+).     

Structure and DNA-binding properties of the Bacillus subtilis SpoIIIE DNA translocase revealed by single-molecule and electron microscopies

SpoIIIE/FtsK are a family of ring-shaped, membrane-anchored, ATP-fuelled motors required to segregate DNA across bacterial membranes. This process is directional and requires that SpoIIIE/FtsK recognize highly skewed octameric sequences (SRS/KOPS for SpoIIIE/FtsK) distributed along the chromosome. Two models have been proposed to explain the mechanism by which SpoIIIE/FtsK interact with DNA. The loading model proposes that SpoIIIE/FtsK oligomerize exclusively on SpoIIIE recognition sequence/orienting polar sequences (SRS/KOPS) to accomplish directional DNA translocation, whereas the target search and activation mechanism proposes that pre-assembled SpoIIIE/FtsK hexamers bind to non-specific DNA, reach SRS/KOPS by diffusion/3d hopping and activate at SRS/KOPS. Here, we employ single-molecule total internal reflection imaging, atomic force and electron microscopies and ensemble biochemical methods to test these predictions and obtain further insight into the SpoIIIE–DNA mechanism of interaction. First, we find that SpoIIIE binds DNA as a homo-hexamer with neither ATP binding nor hydrolysis affecting the binding mechanism or affinity. Second, we show that hexameric SpoIIIE directly binds to double-stranded DNA without requiring the presence of SRS or free DNA ends. Finally, we find that SpoIIIE hexamers can show open and closed conformations in solution, with open-ring conformations most likely resembling a state poised to load to non-specific, double-stranded DNA. These results suggest how SpoIIIE and related ring-shaped motors may be split open to bind topologically closed DNA.