Molecular insights into RBR E3 ligase ubiquitin transfer mechanisms

National Institute of General Medical Sciences R01 GM0880555T32 GM007270, Francis Crick Institute FCI01, Cancer Research UK, Medical Research Council U117565398, Wellcome Trus

Refining the model of barrier island formation along a paraglacial coast in the Gulf of Maine

Author Posting. © The Author(s), 2012. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Marine Geology 307-310 (2012):40-57, doi:10.1016/j.margeo.2012.03.001.Details of the internal architecture and local geochronology of Plum Island, the longest barrier in the Gulf of Maine, has refined our understanding of barrier island formation in paraglacial settings. Ground-penetrating radar and shallow-seismic profiles coupled with sediment cores and radiocarbon dates provide an 8000-year evolutionary history of this barrier system in response to changes in sediment sources and supply rates as well as variability in the rate of sea-level change. The barrier sequence overlies tills of Wisconsinan and Illinoian glaciations as well as late Pleistocene glaciomarine clay deposited during the post-glacial sea-level highstand at approximately 17 ka. Holocene sediment began accumulating at the site of Plum Island at 7–8 ka, in the form of coarse fluvial channel-lag deposits related to the 50-m wide erosional channel of the Parker River that carved into underlying glaciomarine deposits during a lower stand of sea level. Plum Island had first developed in its modern location by ca. 3.6 ka through onshore migration and vertical accretion of reworked regressive and lowstand deposits. The prevalence of southerly, seaward-dipping layers indicates that greater than 60% of the barrier lithosome developed in its modern location through southerly spit progradation, consistent with a dominantly longshore transport system driven by northeast storms. Thinner sequences of northerly, landward-dipping clinoforms represent the northern recurve of the prograding spit. A 5–6-m thick inlet-fill sequence was identified overlying the lower stand fluvial deposit; its stratigraphy captures events of channel migration, ebb-delta breaching, onshore bar migration, channel shoaling and inlet infilling associated with the migration and eventual closing of the inlet. This inlet had a maximum cross-sectional area of 2800 m2 and was active around 3.5–3.6 ka. Discovery of this inlet suggests that the tidal prism was once larger than at present. Bay infilling, driven by the import of sediment into the backbarrier environment through tidal inlets, as well as minor sediment contribution from local rivers, led to a vast reduction in the bay tidal prism. This study demonstrates that, prior to about 3 ka, Plum Island and its associated marshes, tidal flats, and inlets were in a paraglacial environment; that is, their main source of sediment was derived from the erosion and reworking of glaciogenic deposits. Since that time, Plum Island has been in a state of dynamic equilibrium with its non-glacial sediment sources and therefore can be largely considered to be in a stable, “post-paraglacial” state. This study is furthermore the first in the Gulf of Maine to show that spit accretion and inlet processes were the dominant mechanisms in barrier island formation and thus serves as a foundation for future investigations of barrier development in response to backbarrier infilling.This study was funded by the Minerals Management Service (now the “Bureau of Ocean Energy Manegement, Regulation and Enforcement”), the USGS Eastern Geology and Paleoclimate Science Center, the USGS National Cooperative Geologic Mapping Program (State Map), a Geological Society of America (GSA) Student Research Grant, the American Association of Petroleum Geologists (AAPG) Grants-in-Aid program, and the Boston University Undergraduate Research Opportunities Program (UROP). Additionally, E. Carruthers was funded in part by the Clare Booth Luce Summer Research Fellowship and C. Hein was funded by the National Science Foundation (NSF) Graduate Research Fellowship

Distributed subglacial discharge drives significant submarine melt at a Greenland tidewater glacier

Submarine melt can account for substantial mass loss at tidewater glacier termini. However, the processes controlling submarine melt are poorly understood due to limited observations of submarine termini. Here at a tidewater glacier in central West Greenland, we identify subglacial discharge outlets and infer submarine melt across the terminus using direct observations of the submarine terminus face. We find extensive melting associated with small discharge outlets. While the majority of discharge is routed to a single, large channel, outlets not fed by large tributaries drive submarine melt rates in excess of 3.0 m d−1 and account for 85% of total estimated melt across the terminus. Nearly the entire terminus is undercut, which may intersect surface crevasses and promote calving. Severe undercutting constricts buoyant outflow plumes and may amplify melt. The observed morphology and melt distribution motivate more realistic treatments of terminus shape and subglacial discharge in submarine melt models

Comparison of measurements from different radio-echo sounding systems and synchronization with the ice core at Dome C, Antarctica

We present a compilation of radio-echo sounding (RES) measurements of five radar systems (AWI, BAS, CReSIS, INGV and UTIG) around the EPICA Dome C (EDC) drill site, East Antarctica. The aim of our study is to investigate the differences of the various systems in their resolution of internal reflection horizons (IRHs) and bedrock topography, penetration depth, and quality of imaging the basal layer. We address the questions of the compatibility of existing radar data for common interpretation, and the suitability of the individual systems for Oldest Ice reconnaissance surveys. We find that the most distinct IRHs and IRH patterns can be identified and transferred between most data sets. Considerable differences between the RES systems exist in range resolution and depiction of the basal layer. Considering both aspects, which we judge as crucial factors in the search for old ice, the CReSIS and the UTIG systems are the most valuable ones. In addition to the RES data set comparison we calculate a synthetic radar trace from EDC density and conductivity profiles. We identify ten common IRHs in the measured RES data and the synthetic trace. The reflection-causing conductivity sections are determined by sensitivity studies with the synthetic trace. In this way, we accomplish an accurate two-way travel time to depth conversion for the reflectors, without having to use a precise velocity-depth function that would accumulate depth uncertainties with increasing depth. The identified IRHs are assigned with the AICC2012 time scale age. Due to the isochronous character of these conductivity-caused IRHs, they are a means to extend the Dome C age structure by tracing the IRHs along the RES profiles

A “How-To” Guide for Designing Judgment Bias Studies to Assess Captive Animal Welfare

Robust methods to assess nonhuman animal emotion are essential for ensuring good welfare in captivity. Cognitive bias measures such as the judgment bias task have recently emerged as promising tools to assess animal emotion. The simple design and objective response measures make judgment bias tasks suitable for use across species and contexts. In reviewing 64 studies published to date, it emerged that (a) judgment biases have been measured in a number of mammals and birds and an invertebrate; (b) no study has tested judgment bias in any species of fish, amphibian, or reptile; and (c) no study has yet investigated judgment bias in a zoo or aquarium. This article proposes that judgment bias measures are highly suitable for use with these understudied taxa and can provide new insight into welfare in endangered species housed in zoos and aquariums, where poor welfare impacts breeding success and, ultimately, species survival. The article includes a “how-to” guide to designing judgment bias tests with recommendations for working with currently neglected “exotics” including fishes, amphibians, and reptiles

Rapid and High-Throughput pan-Orthopoxvirus Detection and Identification using PCR and Mass Spectrometry

The genus Orthopoxvirus contains several species of related viruses, including the causative agent of smallpox (Variola virus). In addition to smallpox, several other members of the genus are capable of causing human infection, including monkeypox, cowpox, and other zoonotic rodent-borne poxviruses. Therefore, a single assay that can accurately identify all orthopoxviruses could provide a valuable tool for rapid broad orthopovirus identification. We have developed a pan-Orthopoxvirus assay for identification of all members of the genus based on four PCR reactions targeting Orthopoxvirus DNA and RNA helicase and polymerase genes. The amplicons are detected using electrospray ionization-mass spectrometry (PCR/ESI-MS) on the Ibis T5000 system. We demonstrate that the assay can detect and identify a diverse collection of orthopoxviruses, provide sub-species information and characterize viruses from the blood of rabbitpox infected rabbits. The assay is sensitive at the stochastic limit of PCR and detected virus in blood containing approximately six plaque-forming units per milliliter from a rabbitpox virus-infected rabbit

New Particle-Induced Single Event Latchup Mechanism Observed in a Cryogenic CMOS Readout Integrated Circuit

No abstract availabl

The Natural Products Atlas 2.0 : a database of microbially-derived natural products

Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019. This paper reports the release of a new version of the database which includes a full RESTful application programming interface (API), a new website framework, and an expanded database that includes 8128 new compounds, bringing the total to 32 552. In addition to these structural and content changes we have added full taxonomic descriptions for all microbial taxa and have added chemical ontology terms from both NP Classifier and ClassyFire. We have also performed manual curation to review all entries with incomplete configurational assignments and have integrated data from external resources, including CyanoMetDB. Finally, we have improved the user experience by updating the Overview dashboard and creating a dashboard for taxonomic origin. The database can be accessed via the new interactive website at https://www.npatlas.org.Peer reviewe