Solution structure of the cyclic peptide contryphan-Vn, a Ca2+-dependent K+ channel modulator

The solution structure of contryphan-Vn, a cyclic peptide with a double cysteine S-S bridge and containing a D-tryptophan extracted from the venom of the cone snail Conus ventricosus, has been determined by NMR spectroscopy using a variety of homonuclear and heteronuclear NMR methods and restrained molecular dynamics simulations. The main conformational features of backbone contryphan-Vn are a type IV beta-turn from Gly 1 to Lys 6 and a type I beta-turn from Lys 6 to Cys 9. As already found in other contryphans, one of the two prolines--the Pro4--is mainly in the cis conformation while Pro7 is trans. A small hydrophobic region probably partly shielded from solvent constituted from the close proximity of side chains of Pro7 and Trp8 was observed together with a persistent salt bridge between Asp2 and Lys6, which has been revealed by the diagnostic observation of specific nuclear Overhauser effects. The salt bridge was used as a restraint in the molecular dynamics in vacuum but without inserting explicit electrostatic contribution in the calculations. The backbone of the unique conformational family found of contryphan-Vn superimposes well with those of contryphan-Sm and contryphan-R. This result indicates that the contryphan structural motif represents a robust and conserved molecular scaffold whose main structural determinants are the size of the intercysteine loop and the presence and location in the sequence of the D-Trp and the two Pro residues.     

Prediction of physical protein-protein interactions

Many essential cellular processes such as signal transduction, transport, cellular motion and most regulatory mechanisms are mediated by protein-protein interactions. In recent years, new experimental techniques have been developed to discover the protein-protein interaction networks of several organisms. However, the accuracy and coverage of these techniques have proven to be limited, and computational approaches remain essential both to assist in the design and validation of experimental studies and for the prediction of interaction partners and detailed structures of protein complexes. Here, we provide a critical overview of existing structure-independent and structure-based computational methods. Although these techniques have significantly advanced in the past few years, we find that most of them are still in their infancy. We also provide an overview of experimental techniques for the detection of protein-protein interactions. Although the developments are promising, false positive and false negative results are common, and reliable detection is possible only by taking a consensus of different experimental approaches. The shortcomings of experimental techniques affect both the further development and the fair evaluation of computational prediction methods. For an adequate comparative evaluation of prediction and high-throughput experimental methods, an appropriately large benchmark set of biophysically characterized protein complexes would be needed, but is sorely lacking.     

Designing connected marine reserves in the face of global warming

Marine reserves are widely used to protect species important for conservation and fisheries and to help maintain ecological processes that sustain their populations, including recruitment and dispersal. Achieving these goals requires well‐connected networks of marine reserves that maximize larval connectivity, thus allowing exchanges between populations and recolonization after local disturbances. However, global warming can disrupt connectivity by shortening potential dispersal pathways through changes in larval physiology. These changes can compromise the performance of marine reserve networks, thus requiring adjusting their design to account for ocean warming. To date, empirical approaches to marine prioritization have not considered larval connectivity as affected by global warming. Here, we develop a framework for designing marine reserve networks that integrates graph theory and changes in larval connectivity due to potential reductions in planktonic larval duration (PLD) associated with ocean warming, given current socioeconomic constraints. Using the Gulf of California as case study, we assess the benefits and costs of adjusting networks to account for connectivity, with and without ocean warming. We compare reserve networks designed to achieve representation of species and ecosystems with networks designed to also maximize connectivity under current and future ocean‐warming scenarios. Our results indicate that current larval connectivity could be reduced significantly under ocean warming because of shortened PLDs. Given the potential changes in connectivity, we show that our graph‐theoretical approach based on centrality (eigenvector and distance‐weighted fragmentation) of habitat patches can help design better‐connected marine reserve networks for the future with equivalent costs. We found that maintaining dispersal connectivity incidentally through representation‐only reserve design is unlikely, particularly in regions with strong asymmetric patterns of dispersal connectivity. Our results support previous studies suggesting that, given potential reductions in PLD due to ocean warming, future marine reserve networks would require more and/or larger reserves in closer proximity to maintain larval connectivity.     

Wheel-running and rest activity pattern interaction in two octodontids (Octodon degus, Octodon bridgesi)

Wheel-running and other non-photic stimuli influence the rest-activity pattern of diurnal and nocturnal mammals. A day to night inversion of phase preference of activity was described among Octodon degus, when exposed to ad-libitum wheel running. We have studied the rest-activity pattern response in presence of ad libitum wheel-running in wild-captured male individuals from two species of genus Octodon: O. degus (n = 9, crepuscular-diurnal) and O. bridgesi (n = 3, nocturnal). After two months of habituation to laboratory conditions, recordings were performed in isolation chambers under a 12:12 light-dark schedule with or without access to a running wheel. Actograms were constructed from data obtained by an automated acquisition system. O. bridgesi were also recorded under constant darkness, with or without access to wheel-running. Entrained to the light-dark schedule, a crepuscular pattern of activity was evident for O. degus, whereas O. bridgesi displayed a robust nocturnal chronotype. The activity of O. degus observed during the dark phase was enhanced when wheel-running was allowed. No significant change in phase preference was observed for O. bridgesi when wheel-running was allowed. A lengthening of endogenous period was observed in O. bridgesi after wheel-running exposure under constant darkness. Nocturnal and diurnal octodontids exhibit different masking responses to wheel-running.     

Winter migration of rockhopper penguins (Eudyptes c. chrysocome) breeding in the Southwest Atlantic: is utilisation of different foraging areas reflected in opposing population trends?

Rockhopper penguins (Eudyptes chrysocome) breeding on Staten Island, Argentina, were satellite tracked in 2002 and 2003 during the onset of their winter migration. After their moult, the dispersal of 24 birds was monitored for a mean period of 50.0±40.3 days. Birds travelled at a mean velocity of 3.1±1.1 km/h. The mean minimum distance travelled was 1,640±1,425 km; the maximum distance to the colony was generally less than 1,000 km, although one bird travelled more than 2,000 km from the colony. The penguins dispersed over an area totalling about 1.3 million km2, ranging from 50 to 62°S and from 49°W in the Atlantic to 92°W in the Pacific, and covering polar, sub-polar and temperate waters in oceanic regions as well as shelf waters. Despite the very wide dispersal, both temporally and spatially, two important wintering grounds for rockhopper penguins from Staten Island could be identified, both located over shelf regions: one extended from Staten Island to the north along the coast of Tierra del Fuego up to the Magellan Strait; the other was located over the Burdwood Bank, an isolated extension of the Patagonian Shelf to the south of the Falkland Islands. The Drake Passage also appeared to be an important area for wintering penguins, although dispersal was far more widely spread. Comparison with data obtained during winter from rockhopper penguins originating from the Falkland Islands showed that the area off the coast of Tierra del Fuego was used more or less exclusively by birds from Staten Island, whereas the Burdwood Bank was shared with penguins coming from southern colonies in the Falkland Islands. The implications of these findings are discussed with regard to (a) opposing population trends of rockhopper penguins in the Southwest Atlantic, and (b) the urgent need to establish adequate conservation measures for species and habitat protection.     

The use of DGGE analyses to explore eastern Mediterranean and Red Sea marine picophytoplankton assemblages

In vast areas of the oceans, most marine photosynthetic production is performed by cells smaller than 2-3 microm (picoplankton). Here, we report on denaturing gradient gel electrophoresis (DGGE) analyses of naturally occurring marine oxygenic picophytoplankton using the conserved photosynthetic psbA gene. The psbA gene proved to be a good indicator for picophytoplankton presence and was shown to work with DGGE. The DGGE results show the distribution of photosynthetic marine groups belonging to cyanobacteria and the eukaryotic prasinophytes (green algae) in the Red and eastern Mediterranean Seas in the seasons examined. The present study demonstrates the value of DGGE as a tool for rapid analyses of natural marine communities of picophytoplankton.     

<Emphasis Type="Italic">M. tuberculosis</Emphasis> genotypic diversity and drug susceptibility pattern in HIV- infected and non-HIV-infected patients in northern Tanzania

Background  

Tuberculosis (TB) is a major health problem and HIV is the major cause of the increase in TB. Sub-Saharan Africa is endemic for both TB and HIV infection. Determination of the prevalence of M. tuberculosis strains and their drug susceptibility is important for TB control.     

The BMP pathway is essential for re-specification and maintenance of the dorsoventral axis in regenerating and intact planarians

The bone morphogenetic protein (BMP) pathway has been shown to play an important role in the establishment of the dorsoventral axis during development in both vertebrate and invertebrate species. In an attempt to unravel the role of BMPs in pattern formation during planarian regeneration, we studied this signaling pathway in Schmidtea mediterranea. Here, we functionally characterize planarian homologues of two key elements of the pathway: Smed-BMP and Smed-Smad1. Whole-mount in situ hybridization showed that Smed-BMP is expressed at the planarian dorsal midline, suggesting a role in dorsoventral patterning, while Smed-Smad1 is widely expressed throughout the mesenchyme and in the central nervous system. RNA interference (RNAi) knockdowns of Smed-BMP or Smed-Smad1 led to the disappearance of dorsal markers along with the ectopic expression of ventral markers on the dorsal side of the treated animals. In almost all cases, a duplicated central nervous system differentiated dorsally after Smed-BMP or Smed-Smad1 RNAi. These defects were observed not only during regeneration but also in intact non-regenerating animals. Our results suggest that the BMP signaling pathway is conserved in planarians and that it plays a key role in the regeneration and maintenance of the dorsoventral axis.