ORCID Profile
0000-0002-6336-3373
Current Organisation
University of Colorado at Boulder
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Publisher: Elsevier BV
Date: 12-2019
DOI: 10.1016/J.MOLCEL.2019.09.012
Abstract: In the arms race against bacteria, bacteriophages have evolved erse anti-CRISPR proteins (Acrs) that block CRISPR-Cas immunity. Acrs play key roles in the molecular coevolution of bacteria with their predators, use a variety of mechanisms of action, and provide tools to regulate Cas-based genome manipulation. Here, we present structural and functional analyses of AcrIIA6, an Acr from virulent phages, exploring its unique anti-CRISPR action. Our cryo-EM structures and functional data of AcrIIA6 binding to Streptococcus thermophilus Cas9 (St1Cas9) show that AcrIIA6 acts as an allosteric inhibitor and induces St1Cas9 dimerization. AcrIIA6 reduces St1Cas9 binding affinity for DNA and prevents DNA binding within cells. The PAM and AcrIIA6 recognition sites are structurally close and allosterically linked. Mechanistically, AcrIIA6 affects the St1Cas9 conformational dynamics associated with PAM binding. Finally, we identify a natural St1Cas9 variant resistant to AcrIIA6 illustrating Acr-driven mutational escape and molecular ersification of Cas9 proteins.
Publisher: Informa UK Limited
Date: 05-1992
Publisher: Ocean Drilling Program
Date: 09-1991
Publisher: Proceedings of the National Academy of Sciences
Date: 08-10-2018
Abstract: We conducted a systematic, high-resolution analysis of bottom trawl fishing footprints for 24 regions on continental shelves and slopes of five continents and New Zealand. The proportion of seabed trawled varied -fold among regions (from 0.4 to 80.7% of area to a depth of 1,000 m). Within 18 regions, more than two-thirds of seabed area remained untrawled during study periods of 2–6 years. Relationships between metrics of total trawling activity and footprint were strong and positive, providing a method to estimate trawling footprints for regions where high-resolution data are not available. Trawling footprints were generally smaller in regions where fisheries met targets for exploitation rates, implying collateral environmental benefits of effective fisheries management.
Publisher: CSIRO Publishing
Date: 2005
DOI: 10.1071/AJ04040
Abstract: The Australian seabed is influenced by extreme weather conditions of various types: cyclones, high tidal ranges, offshore currents and storm waves. In the past two centuries substantial progress in our understanding of the seabed and environmental conditions has been made by studies of the seabed sedimentology, hydrodynamics, and through habitat mapping. As part of the CSIRO Wealth from Oceans Flagship program the authors are involved in a new fiveyear study to investigate and predict the effect of possible climate change scenarios on the seabed in the next 50 years. Those changes will assess undersea infrastructure installations such as pipelines in a changed regime of seafloor stability, burial, erosion and abrasion.As an initial phase of this project the authors have extrapolated the current climatic conditions into the next 50 years. It was found that (under an extension of present day climatic conditions):the majority of terrigenous sediment carried down by major rivers (Murray River, Snowy River, Tamar River, etc) is trapped in the inland lakes or estuaries. Only a marginal fraction of fine grain sediment reaches the continental shelf a high energy wave climate, significant tidal currents, and the frequent surges of wind-driven currents make the local seabed highly mobile and sensitive to the modern hydrodynamic changes. Both results imply that an exposed pipeline may suffer from local scour and fatigue damage due to oscillatory loads induced by vortex shedding behind the pipelines andthere are several high risk zones in the region where turbidity current and submarine slope failure post a great threat to offshore pipelines.The next phase of the project will be to provide testable predictions of the changes under a variety of global warming scenarios.
Publisher: Elsevier BV
Date: 02-1992
Publisher: Scandinavian University Press / Universitetsforlaget AS
Date: 10-1980
Publisher: CSIRO Publishing
Date: 2008
DOI: 10.1071/AJ07011
Abstract: In this paper, the impact of climate change on seabed sediment transport in the north-western region of the Australian Exclusive Economic Zone (EEZ) has been investigated by a state-of-the-art numerical sediment transport model, Sedsim. It links the environmental forces and seabed response into a dynamic sedimentation system. Although numerical implementation of some forcing and responses is approximate, it is a significant step forward in understanding the nature of potential long-term seabed changes as well as in evaluating the likely impact of climate change on the northwest Australian continental shelf. It was found that: the modelled high-energy climate change scenario produced 17% and 38% increases on total volumes of seabed transport in the northern and southern part of the Australian northwest region respectively the Indonesian ThroughFlow (ITF), the Leeuwin Current (LC) and high energy waves (associated with tropical cyclones) play the most important roles in large-scale long-term evolution of the NW seafloor offshore pipeline design could usefully incorporate the changed risk profiles due to long-term non-stationarity of climate-derived forcing processes.
Publisher: Springer Science and Business Media LLC
Date: 05-1988
DOI: 10.1038/333303A0
Publisher: Proceedings of the National Academy of Sciences
Date: 29-10-2018
Abstract: The geological record contains numerous ex les of “greenhouse periods” and ocean acidification episodes, where the spreading of corrosive (CO 2 -enriched) bottom waters enhances the dissolution of CaCO 3 minerals delivered to the seafloor or contained within deep-sea sediments. The dissolution of sedimentary CaCO 3 neutralizes excess CO 2 , thus preventing runaway acidification, and acts as a negative-feedback mechanism in regulating atmospheric CO 2 levels over timescales of centuries to millennia. We report an observation-based indication and quantification of significant CaCO 3 dissolution at the seafloor caused by man-made CO 2 . This dissolution is already occurring at various locations in the deep ocean, particularly in the northern Atlantic and near the Southern Ocean, where the bottom waters are young and rich in anthropogenic CO 2 .
Publisher: Cambridge University Press (CUP)
Date: 1987
DOI: 10.1017/S0263593300011019
Abstract: The dimensional statistics and proximal development characters of the Llanvirnian pendent didymograptid D. murchisoni are defined using the type material from near Builth Wells (Powys) and other collections from Abereiddi Bay (Dyfed). Population variability (as expressed by variation coefficients) in the undeformed faunas amounts to about 10% for the sicula lengths and thecal spacings, but is over 20% (up to 200%) for stipe lengths and ergences. Characters with low variability have greater species-diagnostic value. Proximal development in the species involves a dicalycal th 1 1 and a low origin for that theca from the sicula. The taxa Didymograptus lus, D. nanus, D. geminus, D. geminus latus and D. acutus are varieties within populations of D. murchisoni and are therefore junior synonyms. The resulting rationalised taxonomy allows advances to be made in the use of the species in stratigraphy and tectonics. For ex le, an occurrence of undeformed (pyritised) D. murchisoni in full relief at Abereiddi in the same beds as flattened and deformed faunas, allows a calculation of the absolute three-dimensional strains to be made for the slates there. The strains are strongly flattening (K 0 · 3) and involve volume changes of about −56%. The high dilatation values imply that stylolite and grain-boundary pressure solution operated during the deformations to take the changes in volume beyond what is possible with simple compaction (i.e. porosity reduction).
Publisher: US Geological Survey
Date: 2005
DOI: 10.3133/DS118
Publisher: Society for Sedimentary Geology
Date: 27-02-2018
DOI: 10.2110/JSR.2018.15
Publisher: Acoustical Society of America (ASA)
Date: 10-2017
DOI: 10.1121/1.5014716
Abstract: Biologically colonized seafloors have been difficult to model for their acoustic interaction. The distributions of geoacoustic properties above and beneath the nominal bottom can be extremely complex. We have implemented workflows in software which: (i) efficiently construct many patterns of growth forms, bioturbation, organism aggregations, and flesh-skeleton morphologies, and (ii) submit them to “Eikonal” wavefront acoustic modeling. Ray-based finite-element and statistical methods can, in theory, be applied but they run into problems of the strongly inhomogeneous geoacoustics, ray-chaos (of several causes), absence of a clear ision into the usual rough surface/inhomogeneous volume halfspaces, and heavy computational costs. Wavefront methods, namely, Eikonals implemented via Fast-Marching Algorithms, are able to deal with complex situations—as has been realized lately in deep seismic geophysics, in moving object tracking, and interestingly, in urban settings, for locating gunshots and mapping Wi-fi fields. They also to offer a new way to understand the acoustic backscatter results from multibeam, sidescan and single beam sonar systems over complex biologic seafloor types. This direction of research requires close knowledge of both the “bio” and the “geo” of seafloors.
Publisher: Springer Science and Business Media LLC
Date: 10-01-2013
DOI: 10.1038/SREP01057
Publisher: Informa UK Limited
Date: 05-12-2007
Publisher: US Geological Survey
Date: 2007
DOI: 10.3133/OFR20061195
Publisher: Elsevier BV
Date: 03-2008
Publisher: Springer Science and Business Media LLC
Date: 12-2002
Publisher: Informa UK Limited
Date: 09-1988
Publisher: Elsevier BV
Date: 05-1990
Publisher: CSIRO Publishing
Date: 2009
DOI: 10.1071/MF08049
Abstract: With increasing concerns about climate change and sea-level rise, there is a need for a comprehensive understanding of the sedimentary processes involved in the erosion, transport and deposition of sediment on the continental shelf. In the present paper, long-term and large-scale seabed morphological changes on the south-west Australian continental shelf were investigated by a comprehensive sediment transport model, Sedsim. The investigated area covers the continental shelf and abyssal basins of the south-western region. The regional seabed is sensitive to environmental forces and sediment supply, and most terrigenous sediment carried down by major rivers is trapped in inland lakes or estuaries. Only a small fraction of fine-grain sediment reaches the continental shelf. The simulation has also confirmed that the Leeuwin Current and high-energy waves play the most important roles in regional long-term seabed evolution. Although the numerical implementation only approximates some forcing and responses, it represents a significant step forward in understanding the nature of potential long-term seabed change as a response to possible climate change scenarios. The 50-year forecast on the seabed morphological changes provides a reference for the management of coastal and offshore resources, as well as infrastructure, in a sustainable way.
Publisher: Elsevier BV
Date: 09-2004
Publisher: Springer Science and Business Media LLC
Date: 15-02-2017
Publisher: Elsevier BV
Date: 03-2005
Publisher: American Society of Civil Engineers
Date: 11-05-2007
Publisher: Informa UK Limited
Date: 11-2163
Publisher: Ocean Drilling Program
Date: 08-1989
Publisher: MDPI AG
Date: 06-08-2020
DOI: 10.3390/JMSE8080586
Abstract: Turbidity currents deliver sediment rapidly from the continental shelf to the slope and beyond and can be triggered by processes such as shelf resuspension during oceanic storms mass failure of slope deposits due to sediment- and wave-pressure loadings and localized events that grow into sustained currents via self- lifying ignition. Because these operate over multiple spatial and temporal scales, ranging from the eddy-scale to continental-scale coupled numerical models that represent the full transport pathway have proved elusive though in idual models have been developed to describe each of these processes. Toward a more holistic tool, a numerical workflow was developed to address pathways for sediment routing from terrestrial and coastal sources, across the continental shelf and ultimately down continental slope canyons of the northern Gulf of Mexico, where offshore infrastructure is susceptible to damage by turbidity currents. Workflow components included: (1) a calibrated simulator for fluvial discharge (Water Balance Model - Sediment WBMsed) (2) domain grids for seabed sediment textures (dbSEABED) bathymetry, and channelization (3) a simulator for ocean dynamics and resuspension (the Regional Ocean Modeling System ROMS) (4) A simulator (HurriSlip) of seafloor failure and flow ignition and (5) A Reynolds-averaged Navier–Stokes (RANS) turbidity current model (TURBINS). Model simulations explored physical oceanic conditions that might generate turbidity currents, and allowed the workflow to be tested for a year that included two hurricanes. Results showed that extreme storms were especially effective at delivering sediment from coastal source areas to the deep sea, at timescales that ranged from in idual wave events (~hours), to the settling lag of fine sediment (~days).
Publisher: American Geophysical Union (AGU)
Date: 07-2020
DOI: 10.1029/2020GC008922
Abstract: Loess sediments are windblown silt deposits with, in general, a carbonate grain content of up to 30%. While regionally, loess was reported to increase weathering fluxes substantially, the influence on global weathering fluxes remains unknown. Especially on glacial‐interglacial time scales, loess weathering fluxes might have contributed to land‐ocean alkalinity flux variability since the loess areal extent during glacial epochs was larger. To quantify loess weathering fluxes, global maps representing the loess distribution were compiled. Water chemistry of rivers draining recent loess deposits suggests that loess contributes over‐proportionally to alkalinity concentrations if compared to the mean of alkalinity concentrations of global rivers (~4,110 µeq L −1 for rivers draining loess deposits and ~1,850 µeq L −1 for the total of global rivers), showing comparable alkalinity concentration patterns in rivers as found for carbonate sedimentary rocks. Loess deposits, covering ~4% of the ice‐ and water‐free land area, increase calculated global alkalinity fluxes to the coastal zone by 16%. The new calculations lead to estimating a 4% higher global alkalinity flux during the Last Glacial Maximum (LGM) compared to present fluxes. The effect of loess on that comparison is high. Alkalinity fluxes from silicate‐dominated lithological classes were ~28% and ~30% lower during the LGM than recent (with loess and without loess, respectively), and elevated alkalinity fluxes from loess deposits compensated for this. Enhanced loess weathering d ens due to a legacy effect changes in silicate‐dominated lithologies over the glacial‐interglacial time scale.
Publisher: American Geophysical Union (AGU)
Date: 08-2006
DOI: 10.1029/2006GC001297
Publisher: Esri
Date: 08-06-2016
Publisher: Informa UK Limited
Date: 10-2018
Publisher: Wiley
Date: 2016
Publisher: Informa UK Limited
Date: 10-2018
Publisher: US Geological Survey
Date: 2007
DOI: 10.3133/OFR20061046
Publisher: Geological Society of London
Date: 2006
Location: United Kingdom of Great Britain and Northern Ireland
Start Date: 2016
End Date: 2017
Funder: Volkswagen Foundation
View Funded ActivityStart Date: 2011
End Date: 2012
Funder: Directorate for Geosciences
View Funded ActivityStart Date: 2006
End Date: 2008
Funder: Directorate for Geosciences
View Funded ActivityStart Date: 2013
End Date: 2018
Funder: Directorate for Geosciences
View Funded ActivityStart Date: 2014
End Date: 2018
Funder: Directorate for Computer & Information Science & Engineering
View Funded ActivityStart Date: 2012
End Date: 2013
Funder: Directorate for Geosciences
View Funded ActivityStart Date: 2010
End Date: 2011
Funder: Directorate for Geosciences
View Funded Activity