BIODIVERSITY RESEARCH: Fidelity to foraging sites,consistency of migration routes and habitat modulation of home range by sea turtles

Aim Resources can shape patterns of habitat utilization. Recently a broad foraging dichotomy between oceanic and coastal sites has been revealed for loggerhead sea turtles (Caretta caretta). Since oceanic and coastal foraging sites differ in prey availability, we might expect a gross difference in home‐range size across these habitats. We tested this hypothesis by equipping nine adult male loggerhead sea turtles with GPS tracking devices. Location National Marine Park of Zakynthos (NMPZ) Greece, central and eastern Mediterranean (Adriatic, Ionian and Aegean seas). Methods In 2007, 2008 and 2009, Fastloc GPS‐Argos transmitters were attached to nine male loggerheads. In addition, a Sirtrack PTT unit was attached to one male in 2007. Four of the turtles were tracked on successive years. We filtered the GPS data to ensure comparable data volumes. Route consistency between breeding and foraging sites of the four re‐tracked turtles was conducted. Foraging site home range areas and within site movement patterns were investigated by the fixed kernel density method. Results Foraging home range size ranged between circa 10 km² at neritic habitats (coastal and open‐sea on the continental shelf) to circa 1000 km² at oceanic sites (using 90% kernel estimates), the latter most probably reflecting sparsely distributed oceanic prey. Across different years individuals did not follow exactly the same migration routes, but did show fidelity to their previous foraging sites, whether oceanic or neritic, with accurate homing in the final stages of migration. Main conclusions The broad distribution and diverse life‐history strategies of this population could complicate the identification of priority marine protected areas beyond the core breeding site.     

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project

Between July 18(th) and 24(th) 2010, 26 leading microbial ecology, computation, bioinformatics and statistics researchers came together in Snowbird, Utah (USA) to discuss the challenge of how to best characterize the microbial world using next-generation sequencing technologies. The meeting was entitled "Terabase Metagenomics" and was sponsored by the Institute for Computing in Science (ICiS) summer 2010 workshop program. The aim of the workshop was to explore the fundamental questions relating to microbial ecology that could be addressed using advances in sequencing potential. Technological advances in next-generation sequencing platforms such as the Illumina HiSeq 2000 can generate in excess of 250 billion base pairs of genetic information in 8 days. Thus, the generation of a trillion base pairs of genetic information is becoming a routine matter. The main outcome from this meeting was the birth of a concept and practical approach to exploring microbial life on earth, the Earth Microbiome Project (EMP). Here we briefly describe the highlights of this meeting and provide an overview of the EMP concept and how it can be applied to exploration of the microbiome of each ecosystem on this planet.     

Clearance of technetium-99m-DTPA and HRCT findings in the evaluation of patients with Idiopathic Pulmonary Fibrosis

Background

Different lung function equipment and different respiratory manoeuvres may produce different Peak Expiratory Flow (PEF) results. Although the PEF is the most common lung function test, there have been few studies of these effects and no previous study has evaluated both factors in a single group of patients.

Methods

We studied 36 subjects (PEF range 80–570 l/min). All patients recorded PEF measurements using a short rapid expiration following maximal inspiration (PEF technique) or a forced maximal expiration to residual volume (FVC technique). Measurements were made using a Wright's peak flow meter, a turbine spirometer and a Fleisch pneumotachograph spirometer.

Results

The mean PEF was 8.7% higher when the PEF technique was used (compared with FVC technique, p < 0.0001). The mean PEF recorded with the turbine spirometer was 5.5% lower than the Wright meter reading. The Fleisch spirometer result was 19.5% lower than the Wright reading. However, adjustment of the Wrights measurements from the traditional Wright's scale to the new EU Peak Flow scale produced results that were only 7.2% higher than the Fleisch pneumotachograph measurements.

Conclusion

Peak flow measurements are affected by the instruction given and by the device and Peak Flow scale used. Patient management decisions should not be based on PEF measurement made on different instruments.     

The structural basis of the TIM10 chaperone assembly

Tim9 and Tim10 are essential components of the "small Tim" family of proteins that facilitate insertion of polytopic proteins at the inner mitochondrial membrane. The small Tims are themselves imported from the cytosol and are organized in specific translocation assemblies in the intermembrane space. Their conformational properties and how these influence the mechanism of assembly remain poorly understood. Moreover, the three-dimensional structure of the TIM10 complex is unknown. We have characterized the structural properties of these proteins in their free and assembled states using NMR, circular dichroism, and small angle x-ray scattering. We show that the free proteins are largely unfolded in their reduced assembly-incompetent state and molten globules in their oxidized assembly-competent state. Tim10 appears less structured than Tim9 in their respective free oxidized forms and undergoes a larger structural change than Tim9 upon complexation. The NMR data here demonstrates unequivocally that only the oxidized states of the Tim9 and Tim10 proteins are capable of forming a complex. Zinc binding stabilizes the reduced state against proteolysis without significantly affecting the secondary structure. Solution x-ray scattering was used to obtain a molecular envelope for the subunits individually and for their fully functional TIM10 complex. Ab initio shape reconstructions based on the scattering data has allowed us to obtain the first low resolution three-dimensional structure of the TIM10 complex. This is a novel structure that displays extensive surface hydrophobicity. The structure also provides an explanation for the escorting function of this non-ATP-powered chaperone particle.     

Distinct signaling pathways regulate differential opioid effects on actin cytoskeleton in malignant MCF7 and nonmalignant MCF12A human breast epithelial cells

The mechanisms through which opioids regulate the activity of malignant breast epithelial cells are currently unknown. In the present study we report the differential actin cytoskeleton reorganization induced by opioids in malignant (MCF7) and nonmalignant (MCF12A) breast epithelial cells expressing functional opioid receptors. Exposure of MCF7 cells to the opioid agonist alpha(s1) casomorphin induced important actin assembly and reorganization, including the formation of filopodia and lamellipodia. In contrast, incubation of MCF12A cells with alpha(s1) casomorphin revealed a partial but transient disassembly of actin microfilaments. Immunoprecipitation and immunoblot analyses showed rapid phosphorylation of focal adhesion kinase (FAK) and vinculin in opioid-treated MCF7 cells. Moreover, FAK associates with phosphatidylinositol-3 (PI-3 kinase), the latter being subsequently phosphorylated and activated. In addition, a substantial activation of the small GTPase Rac1 was observed. Pretreatment of MCF7 cells with the specific PI-3 kinase inhibitor wortmannin abolished both the activation of Rac1 and actin reorganization, while the opioid-induced phosphorylation of FAK and vinculin remained unaffected. Interestingly, in opioid-treated MCF12A cells this signaling cascade remained inactive, while we identified rapid phosphorylation of actin regulating the protein villin. Finally, opioids differentially inhibited cell motility in each cell line. Our data suggest a distinct, opioid-induced, signaling pathway activated in malignant breast epithelial cells, leading to important actin reorganization. These findings may indicate a potential antineoplastic role of opiates, based on the activation of differential signaling mechanisms.     

Wolbachia infections of the whitefly Bemisia tabaci

We report the first systematic survey for the presence of Wolbachia endosymbionts in aphids and whiteflies, particularly different populations and biotypes of Bemisia tabaci. Additional agriculturally important species included were predator species, leafhoppers, and lepidopterans. We used a polymerase chain reaction (PCR)-based detection assay with ribosomal 16S rDNA and Wolbachia cell surface protein (wsp) gene primers. Wolbachia were detected in a number of whitefly populations and species, whitefly predators, and one leafhopper species; however, none of the aphid species tested were found infected. Single, double, and triple infections were detected in some of the B. tabaci populations. PCR and phylogenetic analysis of wsp gene sequences indicated that all Wolbachia strains found belong to group B. Topologies of the optimal tree derived by maximum likelihood (ML) and a ML tree in which Wolbachia sequences from B. tabaci are constrained to be monophyletic are significantly different. Our results indicate that there have been at least four independent Wolbachia infection events in B. tabaci. The importance of the presence of Wolbachia infections in B. tabaci is discussed.     

Drought-induced variations of water relations parameters in Olea europaea

The effects of water stress on water potential components, tissue water content, mean elastic modulus and the osmoregulation capacity of olive (Olea europaea L. cv. Coratina) leaves was determined. Artificial rehydration of olive leaf tissues altered the P-V relationships so that a plateau phenomenon occurred. Points in the P-V curve in the region affected by the plateau, generally up to –0.5 MPa, were corrected for all the samples analyzed. In the corrected P-V relationship, an osmotic adjustment was found in drought-stressed leaf tissues. Osmotic potentials at full turgor (_{0 (sat)}) and osmotic potential at turgor-loss (_{0 (TVT)}) decreased from –2.06±0.01 MPa and –3.07±0.16 MPa in controls to –2.81±0.03 MPa and –3.85±0.12 MPa in most stressed plants. Osmotic adjustment values obtained from the P-V curves agreed with those obtained using an osmometer. An active osmotic adjustment of 1.42 MPa was also observed in 1–4 mm- diameter roots. Mannitol is the main carbohydrate involved in osmotic potential decrease in all treatments. The maximum elastic modulus increased from 11.6±0.95 MPa in the controls to 18.6±0.61 MPa in the most stressed plants.     

Structure of the inclusion complexes of heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin with indole-3-butyric acid and 2,4-dichlorophenoxyacetic acid

The crystal structures of the complexes of heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin with indole-3-butyric acid and with 2,4-dichlorophenoxyacetic acid were studied by X-ray diffraction. The complexes crystallize in the monoclinic P2(1) space group. The host molecules are elliptically puckered and stacked along the a crystal axis, in a head-to-tail fashion, forming columns. One primary methoxy group of the host molecule of the complex with indole-3-butyric acid has the unusual trans-gauche conformation for permethylated CDs. All the secondary O-3-CH(3) methoxy groups, some secondary O-2-CH(3) and some primary methoxy groups pointing inwards the cavity enclose the indole or the 2,4-dichlorophenoxy moieties of the guest molecules inside the cavity, while the chains of the guests protrude between two adjacent host molecules of the columns. The mean planes of the indole and 2,4-dichlorophenoxy moieties of the guests are nearly perpendicular to the mean planes of the elliptical heptagons defined by the O-4n atoms of the hosts. The carboxyl group of the guests form hydrogen bonds with oxygen atoms of the host molecules or with the water molecules found in the space between the complexes of the same column.     

The dynamic dimerization of the yeast ADP/ATP carrier in the inner mitochondrial membrane is affected by conserved cysteine residues

The ADP/ATP carrier (AAC) that facilitates the translocation of ATP made in mitochondria is inserted at the inner mitochondrial membrane by the TIM10-TIM22 protein import system. Here we addressed the state of the AAC precursor during insertion (stage IV of import) and identified residues of the carrier important for dimerization. By a combination of (i) import of a mix of His-tagged and untagged versions of AAC either 35S-labeled or unlabeled, (ii) import of a tandem covalent dimer AAC into wild-type mitochondria, and (iii) import of monomeric AAC into mitochondria expressing only the tandem covalent dimer AAC, we found that the stage IV intermediate is a monomer, and this stage is probably the rate-limiting step of insertion in the membrane. Subsequent dimerization occurs extremely rapidly (within less than a minute). The incoming monomer dimerizes with monomeric endogenous AAC suggesting that the AAC dimer is very dynamic. Conserved Cys residues were found not to affect insertion significantly, but they are crucial for the dimerization process to obtain a functional carrier.     

Assembly of Tim9 and Tim10 into a functional chaperone

The TIM10 complex is localized in the mitochondrial intermembrane space and mediates insertion of hydrophobic proteins at the inner membrane. We have characterized TIM10 assembly and analyzed the structural properties of its subunits, Tim9 and Tim10. Both proteins are alpha-helical with a protease-resistant central domain, and each self-associates to form mainly dimers and trimers in solution. Tim9 and Tim10 bound to one another with submicromolar affinity in equimolar amounts and assembled in a stable, significantly extended complex that was indistinguishable from the native mitochondrial TIM10 complex. Importantly, the reconstituted TIM10 complex is functional because it bound to the physiological substrate ADP/ATP carrier and displayed chaperone activity in refolding the model substrate firefly luciferase. These data demonstrate that the individual subunits can exist as independent, dynamically self-associating proteins. Assembly into the thermodynamically stable hexameric complex is necessary for the TIM10 chaperone function.