Heat coma and its relationship to ocean dynamics in the oceanic sea skaters of Halobates (Heteroptera: Gerridae) inhabiting Indian and Pacific Oceans

This study was performed to clarify how weather and current dynamics affect the resistance to temperature change in the oceanic sea skaters, Halobates. Heat coma temperature (HCT) was measured for the adults and 5th instar larvae of four Halobates species collected from a fixed sampling location (12°00′N, 135°00′E ) in western tropical Pacific Ocean and from 13 locations in the eastern area of the India Ocean ranging from 08°00′N-06°00′S and 86°00-76°00′E. Both the gap temperature for heat coma (GTHC, mean±SD: 7.83±1.86 °C, n=32) and the heat coma temperature (HCP, 35.03±1.80 °C, n=32) of individuals collected from the Pacific Ocean, during the first half (10 days) of the sampling period at the fixed sampling point, were significantly higher than those during the second half (GTHC: 5.10±2.05 °C, n=63; HCP: 34.03±2.02 °C, n=63). The reduction in heat tolerance shown in the second half of the 20 day period may have been caused by a decrease in air temperature due to rainfall that occurred around the sampling point accompanied with the arrival of Typhoon No. 6.In the study of individuals collected from the Indian Ocean, significantly higher average GTHCs of >8 °C were recorded for the adult H. micans collected at 02°00′S and 06°00′S (89°00′E) than those at 0°00-8°00′N in the eastern Indian Ocean. Dynamic mixture of water from northern and southern currents occurs at 02°00-6°00′S of the Indian Ocean and might relate to such high heat tolerance.Temperature dynamics in the ocean habitat might directly affect the temperature resistance of the oceanic sea skaters.     

Structural analysis of the N‐terminal fragment of the antiangiogenic protein endostatin: A molecular dynamics study

Endostatin is a potent antiangiogenic protein derived from the noncollagenous domain 1 (NC1) of collagen XVIII. The mechanism by which endostatin exerts its antiangiogenic effect is still incompletely understood. It has been shown that the 27 amino acid N‐terminal fragment of murine endostatin has antitumor, antimigration, and antipermeability activities comparable to the full soluble protein. To understand how this peptide can exert such elaborate function, we performed structural analysis using molecular dynamics to evaluate the behavior of this fragment in aqueous environment. Here, we show that the N‐terminal peptide of murine endostatin is able to assume a well‐defined structure, folding into a zinc‐dependent β‐hairpin conformation. Analyzing the folding mechanism, we were able to understand why the N‐terminal peptide of human endostatin with the same length failed to acquire a stable conformation. Conversely, we were able to predict the successful folding of the R4Q mutant and of a shorter form of the human peptide with 25 residues. Finally, we show that the β‐hairpin conformation assumed by the zinc‐bound peptide of murine endostatin has a high structural similarity with fragments of another family of angiogenesis inhibitors: the integrin‐binding portion of the NC1 domain of collagen IV. Indeed, our docking simulations show that arresten, canstatin, and the endostatin peptide bind to the same spot of αVβ3 integrin, suggesting similar interactions via a common binding site on this receptor. Proteins 2011;. © 2011 Wiley‐Liss, Inc.     

Gap Dynamics in a Seagrass Landscape

We investigated gap dynamics within a shallow subtidal landscape characterized by seagrass vegetation and examined the relationship between gap formation and selected physical factors. The study was conducted over 2 y by using a biannual mapping of seagrass and water depth across an 48,800-m² area in Tampa Bay, Florida. In addition, monthly sediment deposition or erosion was recorded at 96 locations within the landscape. Gaps represented from 2.4% to 5.7% of the seagrass landscape, and all were within monospecific stands of Halodule wrightii. Gaps ranged in size from 10 to 305 m² and most frequently decreased in size over time. Most gaps were small and short lived (less than 6-mo duration), but the second age group most frequently recorded was at least 1.5 y old. No new species of seagrass invaded the gaps with Halodule replacing itself 100% of the time. Gaps were recorded over the entire range of water depths within the landscape. Neither gap area nor persistence of gaps was related to water depth. However gap area was associated positively with the number of extreme sedimentation events. Gaps originated not only from removal of interior vegetation (similar to classic gaps) but also from differential growth of the seagrass margin (similar to edaphic gaps). Distinct seasonal components to the mode of formation were detected with interior-produced gaps originating primarily in the winter and margin gaps most commonly during summer. These results combine to illustrate the importance of large-scale studies with fine-scale resolution for deciphering unique features of seagrass landscape dynamics. Our historical information suggests that a static enumeration of gaps may not provide an accurate assessment of disturbance intensity in this system, and the seagrass mosaic probably is explained best by a combination of disturbance regimes and edaphic factors, such as sediment stability. Moreover, we suggest that even in areas characterized by monospecific stands of vegetation and over short or moderate time periods, gaps indirectly may influence community structure and ecosystem function via modification of habitat arrangement. Received 17 September 1998; accepted 26 April 1999.     

Dynamics in the cyclic Enterobacterial common antigen as studied by <Superscript>13</Superscript>C NMR relaxation

The motional properties of the cyclic enterobacterial common antigen (cECA), consisting of four trisaccharide repeat units, have been investigated by carbon-13 spin relaxation. R₁, R₂ and NOE relaxation parameters have been determined at three magnetic field strengths. The data were interpreted within the model-free framework to include the possibility of motional anisotropy, and overall as well as local dynamical parameters were fitted separately for each ring carbon. The motional anisotropy was addressed by assuming an axially symmetric diffusion tensor, which was fitted from the overall correlation times for each site in the sugar residues using the previously determined crystal structure. The data were found to be in agreement with an oblate shape of the molecule, and the values for D_iso and were in good agreement with translational diffusion data and an estimate based on calculation of the moment of inertia tensor, respectively. The local dynamics in cECA were found to be residue-dependent. Somewhat lower values for the order parameters, as well as longer local correlation times, were observed for the -linked ManNAcA residue compared to the two -linked residues in the trisaccharide repeat unit.     

Structural dynamics of the mitochondrial ADP/ATP carrier revealed by molecular dynamics simulation studies

The mitochondrial adenosine diphosphate/adenosine triphosphate (ADP/ATP) carrier has been recently crystallized in complex with its specific inhibitor carboxyatractyloside (CATR). In the crystal structure, the six-transmembrane helix bundle that defines the nucleotide translocation pathway is closed on the matrix side due to sharp kinks in the odd-numbered helices. The closed conformation is further sealed by the loops protruding into the matrix that interact through an intricate network of charge-pairs. To gain insight into its structural dynamics we performed molecular dynamics (MD) simulation studies of the ADP/ATP carrier with and without its cocrystallized inhibitor. The two trajectories sampled a conformational space around two different configurations characterized by distinct salt-bridge networks with a significant shift from inter- to intrarepeat bonding on the matrix side in the absence of CATR. Analysis of the geometrical parameters defining the transmembrane helices showed that even-numbered helices can undergo a face rotation, whereas odd-numbered helices can undergo a change in the wobble angle with a conserved proline acting as molecular hinge. Our results provide new information on the dynamical properties of the ADP/ATP carrier and for the first time yield a detailed picture of a stable carrier conformation in absence of the inhibitor.     

Radiation damage in the bulk and at the surface

The UK environmental e-science initiative supports the development and modification of simulation tools used to study radiation damage effects. We discuss the development and modification to the DL_POLY molecular dynamics (MD) code. Using the newly developed tools, we study the effects of radiation damage related to the safe encapsulation of highly radioactive materials, including nuclear waste. We address the possible differences between the radiation damage in the bulk and at the surface of a material, and perform MD simulations of energetic events in zircon structure. We find that in the case of readily amorphizable material, the formation of a stable alternative covalent network reduces the possible effect of the surface on the damaged structure.     

Nonlinear acoustics in pant hoots of common chimpanzees (Pan troglodytes): frequency jumps, subharmonics, biphonation, and deterministic chaos

The pant hoot calls produced by common chimpanzees (Pan troglodytes) are multi-call vocalizations that have figured prominently in investigations of acoustic communication in this species. Although pant hoots are predominantly harmonically structured, they can exhibit an acoustic complexity that has recently been linked to nonlinearity in the vocal-fold dynamics underlying typical mammalian sound production. We examined the occurrence of these sorts of nonlinear phenomena in pant hoot vocalizations, contrasting quieter and lower-pitched "introduction" components with loud and high-pitched "climax" calls in the same bouts. Spectrographic evidence revealed four kinds of nonlinear phenomena, including discrete frequency jumps, subharmonics, biphonation, and deterministic chaos. While these events were virtually never observed during the introduction, they occurred in more than half of the climax calls. Biphonation was by far the most common phenomenon, followed by subharmonics, chaos, and frequency jumps. Individual callers varied in the degree to which their climax calls exhibited nonlinear phenomena, but were consistent in showing more biphonation than other forms. These outcomes show that nonlinear phenomena are routinely present in chimpanzee pant hoots, and help lay the foundation for investigating the function of such events.