Unusual Predation Attempts of Polar Bears on Ringed Seals in the Southern Beaufort Sea: Possible Significance of Changing Spring Ice Conditions

In April and May 2003 through 2006, unusually rough and rafted sea ice extended for several tens of kilometres offshore in the southeastern Beaufort Sea from about Atkinson Point to the Alaska border. Hunting success of polar bears (Ursus maritimus) seeking seals was low despite extensive searching for prey. It is unknown whether seals were less abundant in comparison to other years or less accessible because they maintained breathing holes below rafted ice rather than snowdrifts, or whether some other factor was involved. However, we found 13 sites where polar bears had clawed holes through rafted ice in attempts to capture ringed seals (Phoca hispida) in 2005 through 2006 and another site during an additional research project in 2007. Ice thickness at the 12 sites that we measured averaged 41 cm. These observations, along with cannibalized and starved polar bears found on the sea ice in the same general area in the springs of 2004 through 2006, suggest that during those years, polar bears in the southern Beaufort Sea were nutritionally stressed. Searches made farther north during the same period and using the same methods produced no similar observations near Banks Island or in Amundsen Gulf. A possible underlying ecological explanation is a decadal-scale downturn in seal populations. But a more likely explanation is major changes in the sea-ice and marine environment resulting from record amounts and duration of open water in the Beaufort and Chukchi seas, possibly influenced by climate warming. Because the underlying causes of observed changes in polar bear body condition and foraging behaviour are unknown, further study is warranted.En avril et en mai des années 2003 à 2006, de la glace de mer inhabituellement raboteuse et entassée s’est étendue sur plusieurs dizaines de kilomètres au large du sud-est de la mer de Beaufort, à partir de la pointe Atkinson environ jusqu’à la frontière de l’Alaska. Les ours polaires (Ursus maritimus) avaient donc du mal à attraper des phoques malgré la chasse intense. On ne sait pas si les phoques s’y trouvaient en moins grande abondance par rapport aux autres années ou s’ils étaient moins accessibles parce qu’ils maintenaient des trous d’air sous la glace entassée plutôt que dans les congères, ou si un autre facteur entrait en jeu. Cependant, de 2005 à 2006, on a repéré 13 endroits où les ours polaires avaient griffé des trous dans la glace entassée pour essayer d’attraper les phoques annelés (Phoca hispida), puis un autre endroit dans le cadre d’un autre projet de recherche en 2007. Aux 12 endroits mesurés, l’épaisseur de la glace atteignait 41 cm en moyenne. Ces observations, en plus des observations d’ours polaires cannibalisés et d’ours polaires affamés trouvés sur la glace de mer dans à peu près la même région du printemps 2004 au printemps 2006, laissent croire que pendant ces années, les ours polaires du sud de la mer de Beaufort éprouvaient du stress alimentaire. Des recherches effectuées plus au nord pendant cette même période, recherches réalisées à l’aide des mêmes méthodes, n’ont pas permis d’aboutir à des observations similaires près de l’île de Banks ou du golfe Amundsen. Du point de vue écologique, une explication sous-jacente consisterait en un fléchissement décadaire des populations de phoques. Cependant, une explication plus plausible consisterait en des changements majeurs caractérisant la glace de mer et le milieu marin découlant de quantités et de durées records d’eau libre dans les mers de Beaufort et de Chukchi, ce qui pourrait être le résultat du réchauffement climatique. Puisqu’on ne connaît pas les causes sous-jacentes des changements observés sur le plan de l’état du corps et des comportements alimentaires des ours polaires, des recherches plus poussées pourraient être justifiées

KinImmerse: Macromolecular VR for NMR ensembles

<p>Abstract</p> <p>Background</p> <p>In molecular applications, virtual reality (VR) and immersive virtual environments have generally been used and valued for the visual and interactive experience – to enhance intuition and communicate excitement – rather than as part of the actual research process. In contrast, this work develops a software infrastructure for research use and illustrates such use on a specific case.</p> <p>Methods</p> <p>The Syzygy open-source toolkit for VR software was used to write the KinImmerse program, which translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment) or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE.</p> <p>Results</p> <p>In addition to molecular visualizations and navigation, KinImmerse provides a set of research tools for manipulation, identification, co-centering of multiple models, free-form 3D annotation, and output of results. The molecular research test case analyzes the local neighborhood around an individual atom within an ensemble of nuclear magnetic resonance (NMR) models, enabling immersive visual comparison of the local conformation with the local NMR experimental data, including target curves for residual dipolar couplings (RDCs).</p> <p>Conclusion</p> <p>The promise of KinImmerse for production-level molecular research in the DiVE is shown by the locally co-centered RDC visualization developed there, which gave new insights now being pursued in wider data analysis.</p

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu

“Cross” Supermicelles via the Hierarchical Assembly of Amphiphilic Cylindrical Triblock Comicelles

Self-assembled “cross” architectures are well-known in biological systems (as illustrated by chromosomes, for example); however, comparable synthetic structures are extremely rare. Herein we report an in depth study of the hierarchical assembly of the amphiphilic cylindrical P–H–P triblock comicelles with polar (P) coronal ends and a hydrophobic (H) central periphery in a selective solvent for the terminal segments which allows access to “cross” supermicelles under certain conditions. Well-defined P–H–P triblock comicelles M­(PFS-<i>b</i>-PtBA)-<i>b</i>-M­(PFS-<i>b</i>-PDMS)-<i>b</i>-M­(PFS-<i>b</i>-PtBA) (M = micelle segment, PFS = polyferrocenyldimethylsilane, PtBA = poly­(<i>tert</i>-butyl acrylate), and PDMS = polydimethylsiloxane) were created by the living crystallization-driven self-assembly (CDSA) method. By manipulating two factors in the supermicelles, namely the H segment-solvent interfacial energy (through the central H segment length, <i>L</i>₁) and coronal steric effects (via the PtBA corona chain length in the P segment, <i>L</i>₂ related to the degree of polymerization DP₂) the aggregation of the triblock comicelles could be finely tuned. This allowed a phase-diagram to be constructed that can be extended to other triblock comicelles with different coronas on the central or end segment where “cross” supermicelles were exclusively formed under predicted conditions. Laser scanning confocal microscopy (LSCM) analysis of dye-labeled “cross” supermicelles, and block “cross” supermicelles formed by addition of a different unimer to the arm termini, provided complementary characterization to transmission electron microscopy (TEM) and dynamic light scattering (DLS) and confirmed the existence of these “cross” supermicelles as kinetically stable, micron-size colloidally stable structures in solution

Monodisperse Cylindrical Micelles and Block Comicelles of Controlled Length in Aqueous Media

Cylindrical block copolymer micelles have shown considerable promise in various fields of biomedical research. However, unlike spherical micelles and vesicles, control over their dimensions in biologically relevant solvents has posed a key challenge that potentially limits in depth studies and their optimization for applications. Here, we report the preparation of cylindrical micelles of length in the wide range of 70 nm to 1.10 μm in aqueous media with narrow length distributions (length polydispersities <1.10). In our approach, an amphiphilic linear-brush block copolymer, with high potential for functionalization, was synthesized based on poly­(ferrocenyldimethylsilane)-<i>b</i>-poly­(allyl glycidyl ether) (PFS-<i>b</i>-PAGE) decorated with triethylene glycol (TEG), abbreviated as PFS-<i>b</i>-(PEO-<i>g</i>-TEG). PFS-<i>b</i>-(PEO-<i>g</i>-TEG) cylindrical micelles of controlled length with low polydispersities were prepared in <i>N</i>,<i>N</i>-dimethylformamide using small seed initiators via living crystallization-driven self-assembly. Successful dispersion of these micelles into aqueous media was achieved by dialysis against deionized water. Furthermore, B–A–B amphiphilic triblock comicelles with PFS-<i>b</i>-poly­(2-vinylpyridine) (P2VP) as hydrophobic “B” blocks and hydrophilic PFS-<i>b</i>-(PEO-<i>g</i>-TEG) “A” segments were prepared and their hierarchical self-assembly in aqueous media studied. It was found that superstructures formed are dependent on the length of the hydrophobic blocks. Quaternization of P2VP was shown to cause the disassembly of the superstructures, resulting in the first examples of water-soluble cylindrical multiblock comicelles. We also demonstrate the ability of the triblock comicelles with quaternized terminal segments to complex DNA and, thus, to potentially function as gene vectors

Low-cost, Transportable Hydrogen Fueling Station for Early FCEV Adoption

Thousands of public hydrogen fueling stations are needed to support the early Fuel Cell Electric Vehicle (FCEV) market in the U.S.; there are currently 12. The California state government has been the largest investor of the hydrogen fueling infrastructure funding 9 permanent stations currently open to the public with 48 more in development costing anywhere from $1.8M-$5.5M each. To attract private investors and decrease dependence on government funding, a low-cost, mobile hydrogen dispensing system must be developed. This paper describes a transportable hydrogen fueling station that has been designed for $423,000 using off-the-shelf components, less than 23$9.62/kg. This paper presents the mechanical design and operation of the fueling station. A complete report including an economic analysis and safety features is available at: http://hydrogencontest.org/pdf/2014/WSU_2014_HEF_CONTEST.pdf

Identification of furfural resistant strains of Saccharomyces cerevisiae and Saccharomyces paradoxus from a collection of environmental and industrial isolates

Background Fermentation of bioethanol using lignocellulosic biomass as a raw material provides a sustainable alternative to current biofuel production methods by utilising waste food streams as raw material. Before lignocellulose can be fermented it requires physical, chemical and enzymatic treatment in order to release monosaccharides, a process that causes the chemical transformation of glucose and xylose into the cyclic aldehydes furfural and hydroxyfurfural. These furan compounds are potent inhibitors of Saccharomyces fermentation, and consequently furfural tolerant strains of Saccharomyces are required for lignocellulosic fermentation. Results This study investigated yeast tolerance to furfural and hydroxyfurfural using a collection of 71 environmental and industrial isolates of the baker’s yeast Saccharomyces cerevisiae and its closest relative Saccharomyces paradoxus. The Saccharomyces strains were initially screened for growth on media containing 100 mM glucose and 1.5 mg ml-1 furfural. Five strains were identified that showed a significant tolerance to growth in the presence of furfural and these were then screened for growth and ethanol production in the presence of increasing amounts (0.1-4 mg ml-1) of furfural. Conclusions Of the five furfural tolerant strains S. cerevisiae NCYC 3451 displayed the greatest furfural resistance, and was able to grow in the presence of up to 3.0 mg ml-1 furfural. Furthermore, ethanol production in this strain did not appear to be inhibited by furfural, with the highest ethanol yield observed at 3.0 mg ml-1 furfural. Although furfural resistance was not found to be a trait specific to any one particular lineage or population, three of the strains were isolated from environments where they might be continually exposed to low levels of furfural through the on-going natural degradation of lignocelluloses, and would therefore develop elevated levels of resistance to these furan compounds. Thus these strains represent good candidates for future studies of genetic variation relevant to understanding and manipulating furfural resistance and in the development of tolerant ethanologenic yeast strains for use in bioethanol production from lignocellulose processing

A comparison of postrelease survival parameters between single and mass stranded delphinids from Cape Cod, Massachusetts, U.S.A.

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Marine Mammal Science 32 (2016): 161–180, doi:10.1111/mms.12255.The viability of healthy single stranded dolphins as immediate release candidates has received little attention. Responders have been reluctant to release lone delphinids due to their social needs, even when they pass the same health evaluations as mass stranded animals. This study tracked postrelease success of 34 relocated and released satellite tagged delphinids from single and mass strandings. Three postrelease survival parameters (transmission duration, swim speed, and daily distance) were examined to evaluate whether they differed among single stranded/single released (SS/SR), mass stranded/single released (MS/SR), or mass stranded/mass released (MS/MR) dolphin groups. Comparisons were also made between healthy and borderline release candidates. Satellite tags transmitted for a mean of 21.2 d (SD = 19.2, range = 1–79), daily distance traveled was 42.0 km/d (11.25, 20.96–70.72), and swim speed was 4.3 km/h (1.1, 2.15–8.54). Postrelease parameters did not differ between health status groups, however, SS/SR dolphins transmitted for a shorter mean duration than MS/MR and MS/SR groups. Postrelease vessel-based surveys confirmed conspecific group location for two healthy, MS/SR dolphins. Overall, these results support the potential to release healthy stranded single delphinids; however, further refinement of health assessment protocols for these challenging cases is needed.National Oceanic and Atmospheric Administration's National Marine Fisheries Service (NOAA NMFS); John H. Prescott Marine Mammal Rescue Assistance Program Grant Numbers: NA11NMF4390078, NA11NMF4390079, NA11NMF439009

Age-Dependent Changes in the Proteome Following Complete Spinal Cord Transection in a Postnatal South American Opossum (Monodelphis domestica)

Recovery from severe spinal injury in adults is limited, compared to immature animals who demonstrate some capacity for repair. Using laboratory opossums (Monodelphis domestica), the aim was to compare proteomic responses to injury at two ages: one when there is axonal growth across the lesion and substantial behavioural recovery and one when no axonal growth occurs. Anaesthetized pups at postnatal day (P) 7 or P28 were subjected to complete transection of the spinal cord at thoracic level T10. Cords were collected 1 or 7 days after injury and from age-matched controls. Proteins were separated based on isoelectric point and subunit molecular weight; those whose expression levels changed following injury were identified by densitometry and analysed by mass spectrometry. Fifty-six unique proteins were identified as differentially regulated in response to spinal transection at both ages combined. More than 50% were cytoplasmic and 70% belonged to families of proteins with characteristic binding properties. Proteins were assigned to groups by biological function including regulation (40%), metabolism (26%), inflammation (19%) and structure (15%). More changes were detected at one than seven days after injury at both ages. Seven identified proteins: 14-3-3 epsilon, 14-3-3 gamma, cofilin, alpha enolase, heart fatty acid binding protein (FABP3), brain fatty acid binding protein (FABP7) and ubiquitin demonstrated age-related differential expression and were analysed by qRT-PCR. Changes in mRNA levels for FABP3 at P7+1day and ubiquitin at P28+1day were statistically significant. Immunocytochemical staining showed differences in ubiquitin localization in younger compared to older cords and an increase in oligodendrocyte and neuroglia immunostaining following injury at P28. Western blot analysis supported proteomic results for ubiquitin and 14-3-3 proteins. Data obtained at the two ages demonstrated changes in response to injury, compared to controls, that were different for different functional protein classes. Some may provide targets for novel drug or gene therapies