Conformational changes induced by nucleotide binding in Cdc6/ORC from Aeropyrum pernix

Archaea contain one or more proteins with homology to eukaryotic ORC/Cdc6 proteins. Sequence analysis suggests the existence of at least two subfamilies of these proteins, for which we propose the nomenclature ORC1 and ORC2. We have determined crystal structures of the ORC2 protein from the archaeon Aeropyrum pernix in complexes with ADP or a non-hydrolysable ATP analogue, ADPNP. Between two crystal forms, there are three crystallographically independent views of the ADP complex and two of the ADPNP complex. The protein molecules in the three complexes with ADP adopt very different conformations, while the two complexes with ADPNP are the same. These structures indicate that there is considerable conformational flexibility in ORC2 but that ATP binding stabilises a single conformation. We show that the ORC2 protein can bind DNA, and that this activity is associated with the C-terminal domain of the protein. We present a model for the interaction of the winged helix (WH) domain of ORC2 with DNA that differs from that proposed previously for Pyrobaculum aerophilum ORC/Cdc6.     

Design of a bio-inspired controller for dynamic soaring in a simulated unmanned aerial vehicle

This paper is inspired by the way birds such as albatrosses are able to exploit wind gradients at the surface of the ocean for staying aloft for very long periods while minimizing their energy expenditure. The corresponding behaviour has been partially reproduced here via a set of Takagi-Sugeno-Kang fuzzy rules controlling a simulated glider. First, the rules were hand-designed. Then, they were optimized with an evolutionary algorithm that improved their efficiency at coping with challenging conditions. Finally, the robustness properties of the controller generated were assessed with a view to its applicability to a real platform.     

DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays

Mapping DNase I hypersensitive sites is an accurate method of identifying the location of gene regulatory elements, including promoters, enhancers, silencers and locus control regions. Although Southern blots are the traditional method of identifying DNase I hypersensitive sites, the conventional manual method is not readily scalable to studying large chromosomal regions, much less the entire genome. Here we describe DNase-chip, an approach that can rapidly identify DNase I hypersensitive sites for any region of interest, or potentially for the entire genome, by using tiled microarrays. We used DNase-chip to identify DNase I hypersensitive sites accurately from a representative 1% of the human genome in both primary and immortalized cell types. We found that although most DNase I hypersensitive sites were present in both cell types studied, some of them were cell-type specific. This method can be applied globally or in a targeted fashion to any tissue from any species with a sequenced genome.     

Differential effects of postconditioning on myocardial stunning and infarction: a study in conscious dogs and anesthetized rabbits

Postconditioning, i.e., brief intermittent episodes of myocardial ischemia-reperfusion performed at the onset of reperfusion, reduces infarct size after prolonged ischemia. Our goal was to determine whether postconditioning is protective against myocardial stunning. Accordingly, conscious chronically instrumented dogs (sonomicrometry, coronary balloon occluder) were subjected to a control sequence (10 min coronary artery occlusion, CAO, followed by coronary artery reperfusion, CAR) and a week apart to postconditioning with four cycles of brief CAR and CAO performed at completion of the 10 min CAO. Three postconditioning protocols were investigated, i.e., 15 s CAR/15 s CAO (n=5), 30 s CAR/30 s CAO (n=7), and 1 min CAR/1 min CAO (n=6). Left ventricular wall thickening was abolished during CAO and similarly reduced during subsequent stunning in control and postconditioning sequences (e.g., at 1 h CAR, 33+/-4 vs. 34+/-4%, 30+/-4 vs. 30+/-4%, and 33+/-4 vs. 32+/-4% for 15 s postconditioning, 30 s postconditioning, and 1 min postconditioning vs. corresponding control, respectively). We confirmed this result in anesthetized rabbits by demonstrating that shortening of left ventricular segment length was similarly depressed after 10 min CAO in control and postconditioning sequences (4 cycles of 30 s CAR/30 s CAO). In additional rabbits, the same postconditioning protocol significantly reduced infarct size after 30 min CAO and 3 h CAR (39+/-7%, n=6 vs. 56+/-4%, n=7 of the area at risk in postconditioning vs. control, respectively). Thus, contrasting to its beneficial effects on myocardial infarction, postconditioning does not protect against myocardial stunning in dogs and rabbits. Conversely, additional episodes of ischemia-reperfusion with postconditioning do not worsen myocardial stunning.     

Seasonal Variation in the Chemical Composition of Tropical Australian Marine Macroalgae

The proximate chemical composition (ash, soluble carbohydrate, lipid and protein) was determined in 30 common species of tropical Australian marine macroalgae from Darwin Harbour (12^∘26′S, 130^∘51′E), in summer (hot and wet) and winter (cool and dry). There was a wide diversity of species in both seasons (19 species in summer and 20 species in winter). In most species, the major component was soluble carbohydrate (chlorophytes range 2.5–25.8% dry weight (dw), phaeophytes range 8.4–22.2% dw, rhodophytes range 18.7–39.2% dw) with significantly higher (p < 0.05) percentages only in winter season rhodophytes. Highest percentages of protein were found in rhodophytes collected in the summer (range 4.8–12.8% dw), with significantly lower percentages (p < 0.05) during winter. All species had lipid contents within the range 1.3–7.8% dw, with highest percentages in summer phaeophytes, but no significant differences between species or season. Most species had moderate to high ash contents (24.2–89.7% dw), with the highest percentages during summer. Compared with summer samples, macroalgae collected in winter had higher energy value and slightly lower percentages of inorganic matter. The variation of algal groups and chemical composition may influence the availability of the food source for the majority of herbivores, which in turn is likely to effect their ecology and community structure.     

Nematode and macrofaunal diversity in central Arctic Ocean benthos

Deep-sea diversity studies have revealed intriguing patterns on both local and regional scales, but there is insufficient evidence with which to evaluate these trends in the Arctic Ocean basin. We collected data on the diversity of benthic macrofauna and meiofaunal nematodes along two transects from the shelf margin to the North Pole. Contrary to prevailing paradigms, there was no change in diversity with depth between 1000 and 4273 m. There was a trend, however, toward reduced taxonomic richness for both macrofauna and nematodes with increasing latitude. Regional (β-) diversity differences were not observed for nematodes, but significant contrasts in Bray-Curtis similarity-based community structure of macrofauna were seen between the Eurasian and Amerasian Basins, as well as between the Lomonosov and Mendeleev Ridges. Since fauna within the deep Arctic Ocean appear to represent a single species pool, we suggest that both local (α-) and β-diversity may be determined by ecological processes in the Arctic, and are not the consequence of historical or evolutionary processes. Furthermore, insights gained from studies of benthic-pelagic coupling, known to play a significant role in determining benthic community structure and function at high latitudes, may also be useful in investigations of Arctic biodiversity. This model may be valuable in designing future studies of biodiversity, and for predicting potential impacts of climate change on diversity patterns.     

Molecular divergences of the Ornithodoros sonrai soft tick species, a vector of human relapsing fever in West Africa

The soft tick Ornithodoros sonrai is recognized as the only vector of Borrelia crocidurae causing human relapsing fever in West Africa. Its determination has been exclusively based on morphological features, geographical distribution and vector competence. Some ambiguities persist in its systematics and may cause misunderstanding about West African human relapsing fevers epidemiology. By amplifying and aligning 16S and 18S rDNA genes in O. sonrai specimens collected from 14 distinct sites in Senegal and Mauritania, we showed the existence of four genetically different subgroups that were morphologically and ecologically identified as belonging to the same species. Within O. sonrai, intraspecific polymorphism was high (pairwise divergence from 0.2% to 16.4%). In all cases, these four subgroups formed a monophyletic clade sharing a common ancestor with East African soft ticks that transmit Borrelia duttoni human relapsing fever. From amplification of the flagellin gene of B. crocidurae we verified that all subgroups of O. sonrai were infected by B. crocidurae and may constitute vectors for this pathogen. All flagellin sequences were identical, refuting the hypothesis suggesting parallel evolution between O. sonrai and B. crocidurae. However, differences in infection rates were significant, suggesting different vector competences between subgroups of O. sonrai.     

Mechanism of RecA-mediated homologous recombination revisited by single molecule nanomanipulation

The mechanisms of RecA-mediated three-strand homologous recombination are investigated at the single-molecule level, using magnetic tweezers. Probing the mechanical response of DNA molecules and nucleoprotein filaments in tension and in torsion allows a monitoring of the progression of the exchange in real time, both from the point of view of the RecA-bound single-stranded DNA and from that of the naked double-stranded DNA (dsDNA). We show that strand exchange is able to generate torsion even along a molecule with freely rotating ends. RecA readily depolymerizes during the reaction, a process presenting numerous advantages for the cell's 'protein economy' and for the management of topological constraints. Invasion of an untwisted dsDNA by a nucleoprotein filament leads to an exchanged duplex that remains topologically linked to the exchanged single strand, suggesting multiple initiations of strand exchange on the same molecule. Overall, our results seem to support several important assumptions of the monomer redistribution model.     

BDNF and DYRK1A Are Variable and Inversely Correlated in Lymphoblastoid Cell Lines from Down Syndrome Patients

Down syndrome or trisomy 21 is the most common genetic disorder leading to mental retardation. One feature is impaired short- and long-term spatial memory, which has been linked to altered brain-derived neurotrophic factor (BDNF) levels. Mouse models of Down syndrome have been used to assess neurotrophin levels, and reduced BDNF has been demonstrated in brains of adult transgenic mice overexpressing Dyrk1a, a candidate gene for Down syndrome phenotypes. Given the link between DYRK1A overexpression and BDNF reduction in mice, we sought to assess a similar association in humans with Down syndrome. To determine the effect of DYRK1A overexpression on BDNF in the genomic context of both complete trisomy 21 and partial trisomy 21, we used lymphoblastoid cell lines from patients with complete aneuploidy of human chromosome 21 (three copies of DYRK1A) and from patients with partial aneuploidy having either two or three copies of DYRK1A. Decreased BDNF levels were found in lymphoblastoid cell lines from individuals with complete aneuploidy as well as those with partial aneuploidies conferring three DYRK1A alleles. In contrast, lymphoblastoid cell lines from individuals with partial trisomy 21 having only two DYRK1A copies displayed increased BDNF levels. A negative correlation was also detected between BDNF and DYRK1A levels in lymphoblastoid cell lines with complete aneuploidy of human chromosome 21. This finding indicates an upward regulatory role of DYRK1A expression on BDNF levels in lymphoblastoid cell lines and emphasizes the role of genetic variants associated with psychiatric disorders.     

Macrophage mesenchymal migration requires podosome stabilization by filamin A

Filamin A (FLNa) is a cross-linker of actin filaments and serves as a scaffold protein mostly involved in the regulation of actin polymerization. It is distributed ubiquitously, and null mutations have strong consequences on embryonic development in humans, with organ defects which suggest deficiencies in cell migration. We have reported previously that macrophages, the archetypal migratory cells, use the protease- and podosome-dependent mesenchymal migration mode in dense three-dimensional environments, whereas they use the protease- and podosome-independent amoeboid mode in more porous matrices. Because FLNa has been shown to localize to podosomes, we hypothesized that the defects seen in patients carrying FLNa mutations could be related to the capacity of certain cell types to form podosomes. Using strategies based on FLNa knock-out, knockdown, and rescue, we show that FLNa (i) is involved in podosome stability and their organization as rosettes and three-dimensional podosomes, (ii) regulates the proteolysis of the matrix mediated by podosomes in macrophages, (iii) is required for podosome rosette formation triggered by Hck, and (iv) is necessary for mesenchymal migration but dispensable for amoeboid migration. These new functions assigned to FLNa, particularly its role in mesenchymal migration, could be directly related to the defects in cell migration described during the embryonic development in FLNa-defective patients.