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Articles 1 - 30 of 36
Full-Text Articles in Physical Sciences and Mathematics
Distributions Of Krill And Antarctic Silverfish And Correlations With Environmental Variables In The Western Ross Sea, Antarctica, L. Brynn Davis, Eileen E. Hofmann, John M. Klinck, Andrea Piñones, Michael S. Dinniman
Distributions Of Krill And Antarctic Silverfish And Correlations With Environmental Variables In The Western Ross Sea, Antarctica, L. Brynn Davis, Eileen E. Hofmann, John M. Klinck, Andrea Piñones, Michael S. Dinniman
CCPO Publications
Antarctic krill Euphausia superba, crystal krill E. crystallorophias, and Antarctic silverfish Pleuragramma antarctica are key mid-trophic level species in the Ross Sea, connecting primary production to the upper trophic levels. Distributions of these species were constructed from observations made in the western Ross Sea from 1988 to 2004. Distributions of environmental conditions were obtained from a 5-km resolution circulation model (temperature, mixed layer depth, surface speed) and satellite-derived observations (chlorophyll, sea ice cover). A hierarchy of statistical methods determined correlations and relationships between species and environmental conditions. Each species occupies a localized habitat defined by different environmental characteristics. …
Molecular Geometries And Other Properties Of H2o⋯Agi And H3n⋯Agi As Characterised By Rotational Spectroscopy And Ab Initio Calculations, Chris Medcraft, Eva Gougoula, Dror M. Bittner, John C. Mullaney, Susana Blanco, David P. Tew, Nicholas R. Walker, Anthony C. Legon
Molecular Geometries And Other Properties Of H2o⋯Agi And H3n⋯Agi As Characterised By Rotational Spectroscopy And Ab Initio Calculations, Chris Medcraft, Eva Gougoula, Dror M. Bittner, John C. Mullaney, Susana Blanco, David P. Tew, Nicholas R. Walker, Anthony C. Legon
Chemistry & Biochemistry Faculty Publications
The rotational spectra of H3N⋯AgI and H2O⋯AgI have been recorded between 6.5 and 18.5 GHz by chirped-pulse Fourier-transform microwave spectroscopy. The complexes were generated through laser vaporisation of a solid target of silver or silver iodide in the presence of an argon gas pulse containing a low concentration of the Lewis base. The gaseous sample subsequently undergoes supersonic expansion which results in cooling of rotational and vibrational motions such that weakly bound complexes can form within the expanding gas jet. Spectroscopic parameters have been determined for eight isotopologues of H3N⋯AgI and six isotopologues of …
The Effects Of Climate On Radial Growth Of Disjunct Northern White Cedar (Thuja Occidentalis L.) In Virginia, Joshua A. Kincaid
The Effects Of Climate On Radial Growth Of Disjunct Northern White Cedar (Thuja Occidentalis L.) In Virginia, Joshua A. Kincaid
Virginia Journal of Science
Understanding the geographic range and growth of species is essential for effective land management in a landscape affected by anthropogenic activity and climate change. Climate change is expected to alter the distribution and growth of many tree species in eastern North America, including northern white cedar (Thuja occidentalis L.). This research examined the effects of climate on radial growth of T. occidentalis in disjunct populations south of its continuous range margin in eastern North America. A T. occidentalis tree-ring chronology was developed and examined for growth-climate interactions. Mean sensitivity of the T. occidentalis chronology was within the range of …
Life History And Management Methods For Blueline Tilefish (Caulolatilus Microps) From The United States Mid-Atlantic Region, Michael A. Schmidtke
Life History And Management Methods For Blueline Tilefish (Caulolatilus Microps) From The United States Mid-Atlantic Region, Michael A. Schmidtke
OES Theses and Dissertations
Blueline tilefish (Caulolatilus microps) have recently undergone an increase in landings from waters off the US Mid-Atlantic region (Virginia-Massachusetts). Currently, life history characteristics of blueline tilefish in this area are undescribed. Additionally, appropriate indices of population abundance are not available for this region, necessitating the use of data-limited management methods to set restrictions for harvest of blueline tilefish in this area. This dissertation describes growth and reproductive characteristics of blueline tilefish caught off the coast of Virginia and explores improvements of data-limited management methods that have been applied to blueline tilefish in the US Mid-Atlantic. Blueline tilefish from …
Population Structure Of Lethrinus Lentjan (Lethrinidae, Percoidei) Across The South China Sea And The Philippines Is Detected With Lane-Affected Radseq Data, Ellen E. Biesack
Population Structure Of Lethrinus Lentjan (Lethrinidae, Percoidei) Across The South China Sea And The Philippines Is Detected With Lane-Affected Radseq Data, Ellen E. Biesack
Biological Sciences Theses & Dissertations
Southeast Asia includes the Coral Triangle, a marine biodiversity hotspot that supports important fishery resources experiencing varied threats. Patterns of speciation and population structure in the Coral Triangle have been examined to test hypotheses relating to the historical geologic processes that may have influenced this biodiversity phenomenon. This study investigates the genetic population structure of the Pink-ear Emperor Snapper, Lethrinus lentjan (Lacepède, 1802), across the Philippines and the South China Sea. The species is fished throughout the Coral Triangle by subsistence and commercial fishers and their landings have been in decline for several years, which could be indicative of depleted …
Marine Reserves Promote Coral Reef Resilience By Mitigating Human Impacts Through The Restoration Of Parrotfish Populations, Increasing Their Reproductive Output And Seeding Neighboring Overfished Reefs, Brian L. Stockwell
Biological Sciences Theses & Dissertations
Coral reefs are some of the most productive ecosystems on the planet, providing fisheries resources for over a billion people with billions of dollars in revenue from tourism for developing nations. Coral reefs are under threat from overfishing and water pollution, resulting in less productive algae dominated reefs. Marine reserves are widely expected to promote the resilience of reefs by protecting and increasing the abundance of herbivorous fishes that can graze on algae, therefore directly or indirectly preventing coral to algal phase shifts. However, the ability of marine reserves to mitigate human impacts, restore herbivorous fish populations and seed nearby …
A Synergistic Approach For Evaluating Climate Model Output For Ecological Applications, Rachel D. Cavanagh, Eugene J. Murphy, Thomas J. Bracegirdle, John Turner, Cheryl A. Knowland, Stuart P. Corney, Walker O. Smith Jr., Claire M. Waluda, Nadine M. Johnston, Richard G. J. Bellerby, Eileen E. Hofmann
A Synergistic Approach For Evaluating Climate Model Output For Ecological Applications, Rachel D. Cavanagh, Eugene J. Murphy, Thomas J. Bracegirdle, John Turner, Cheryl A. Knowland, Stuart P. Corney, Walker O. Smith Jr., Claire M. Waluda, Nadine M. Johnston, Richard G. J. Bellerby, Eileen E. Hofmann
CCPO Publications
Increasing concern about the impacts of climate change on ecosystems is prompting ecologists and ecosystem managers to seek reliable projections of physical drivers of change. The use of global climate models in ecology is growing, although drawing ecologically meaningful conclusions can be problematic. The expertise required to access and interpret output from climate and earth system models is hampering progress in utilizing them most effectively to determine the wider implications of climate change. To address this issue, we present a joint approach between climate scientists and ecologists that explores key challenges and opportunities for progress. As an exemplar, our focus …
Large Marine Protected Areas Represent Biodiversity Now And Under Climate Change, T. E. Davies, S. M. Maxwell, K. Kaschner, C. Garilao, N. C. Ban
Large Marine Protected Areas Represent Biodiversity Now And Under Climate Change, T. E. Davies, S. M. Maxwell, K. Kaschner, C. Garilao, N. C. Ban
Biological Sciences Faculty Publications
Large marine protected areas (>30,000 km2) have a high profile in marine conservation, yet their contribution to conservation is contested. Assessing the overlap of large marine protected areas with 14,172 species, we found large marine protected areas cover 4.4% of the ocean and at least some portion of the range of 83.3% of the species assessed. Of all species within large marine protected areas, 26.9% had at least 10% of their range represented, and this was projected to increase to 40.1% in 2100. Cumulative impacts were significantly higher within large marine protected areas than outside, refuting the …
Perspective: The Physics, Diagnostics, And Applications Of Atmospheric Pressure Low Temperature Plasma Sources Used In Plasma Medicine, M. Laroussi
Electrical & Computer Engineering Faculty Publications
Low temperature plasmas have been used in various plasma processing applications for several decades. But it is only in the last thirty years or so that sources generating such plasmas at atmospheric pressure in reliable and stable ways have become more prevalent. First, in the late 1980s, the dielectric barrier discharge was used to generate relatively large volume diffuse plasmas at atmospheric pressure. Then, in the early 2000s, plasma jets that can launch cold plasma plumes in ambient air were developed. Extensive experimental and modeling work was carried out on both methods and much of the physics governing such sources …
Multi-Material Mesh Representation Of Anatomical Structures For Deep Brain Stimulation Planning, Tanweer Rashid
Multi-Material Mesh Representation Of Anatomical Structures For Deep Brain Stimulation Planning, Tanweer Rashid
Computational Modeling & Simulation Engineering Theses & Dissertations
The Dual Contouring algorithm (DC) is a grid-based process used to generate surface meshes from volumetric data. However, DC is unable to guarantee 2-manifold and watertight meshes due to the fact that it produces only one vertex for each grid cube. We present a modified Dual Contouring algorithm that is capable of overcoming this limitation. The proposed method decomposes an ambiguous grid cube into a set of tetrahedral cells and uses novel polygon generation rules that produce 2-manifold and watertight surface meshes with good-quality triangles. These meshes, being watertight and 2-manifold, are geometrically correct, and therefore can be used to …
Determining Critical Internesting And Foraging Habitats For The Conservation Of Sea Turtles In Gabon, Africa Using Satellite Tracking And Stable Isotope Analysis, Tiffany M. Dawson
Determining Critical Internesting And Foraging Habitats For The Conservation Of Sea Turtles In Gabon, Africa Using Satellite Tracking And Stable Isotope Analysis, Tiffany M. Dawson
Biological Sciences Theses & Dissertations
Understanding the horizontal and vertical habitat of olive ridley sea turtles (Lepidochelys olivacea), a threatened species, is critical for determining regions of protection that may effectively reduce bycatch, the largest threat to this species. Satellite transmitters were used to determine the movement and dive behavior of 21 female olive ridley turtles tagged in Pongara National Park, Gabon during the 2012, 2013, and 2015 nesting seasons. A switching state space model was used to filter the tracking data and categorize the internesting and post-nesting movements. Gridded utilization distribution (UD) home range analysis of tracking data revealed that the entire core habitat …
Link Between Local Phenology And Climate Change, Blake Steiner, Tatyana Lobova
Link Between Local Phenology And Climate Change, Blake Steiner, Tatyana Lobova
Virginias Collegiate Honors Council Conference
The SouthEast Virginia Phenology Project was initiated as collaboration between Norfolk Botanical Garden and Old Dominion University in 2010 to document phenology of seven native plants and potential effects of the climate change on their life cycle. The air temperature in Norfolk has increased on average by 0.02ºC per year since 1980. Four out of seven of taxonomically diverse plant species (Mayapple, Flowering Dogwood, Highbush Blueberry, and Common ButtonBush) exhibited significant sensitivity to warming temperatures. Of these four, only Common Buttonbush (Cephalanthus occidentalis) had shown significant phenophases shift. Specifically, first flowering and first fruiting dates had shifted 2.7 …
Management Strategy Evaluation For The Atlantic Surfclam (Spisula Solidissima) Using A Spatially Explicit, Vessel-Based Fisheries Model, Kelsey M. Kuykendall, Eric N. Powell, John M. Klink, Paula T. Moreno, Robert T. Leaf
Management Strategy Evaluation For The Atlantic Surfclam (Spisula Solidissima) Using A Spatially Explicit, Vessel-Based Fisheries Model, Kelsey M. Kuykendall, Eric N. Powell, John M. Klink, Paula T. Moreno, Robert T. Leaf
CCPO Publications
The commercially valuable Atlantic surfclam (Spisula solidissima) is harvested along the northeastern continental shelf of the United States. Its range has contracted and shifted north, driven by warmer bottom water temperatures. Declining landings per unit of effort (LPUE) in the Mid-Atlantic Bight (MAB) is one result. Declining stock abundance and LPUE suggest that overfishing may be occurring off New Jersey. A management strategy evaluation (MSE) for the Atlantic surfclam is implemented to evaluate rotating closures to enhance Atlantic surfclam productivity and increase fishery viability in the MAB. Active agents of the MSE model are individual fishing vessels with …
Characterization And Analysis Of Real-Time Capillary Convective Pcr Toward Commercialization, Xianbo Qiu, Shiyin Zhang, Lanju Mei, Di Wu, Ke Li, Shengxiang Ge, Xiangzhong Ye, Ningshao Xia, Michael G. Mauk
Characterization And Analysis Of Real-Time Capillary Convective Pcr Toward Commercialization, Xianbo Qiu, Shiyin Zhang, Lanju Mei, Di Wu, Ke Li, Shengxiang Ge, Xiangzhong Ye, Ningshao Xia, Michael G. Mauk
Mechanical & Aerospace Engineering Faculty Publications
Almost all the reported capillary convective polymerase chain reaction (CCPCR) systems to date are still limited to research use stemming from unresolved issues related to repeatability, reliability, convenience, and sensitivity. To move CCPCR technology forward toward commercialization, a couple of critical strategies and innovations are discussed here. First, single- and dual-end heating strategies are analyzed and compared between each other. Especially, different solutions for dual-end heating are proposed and discussed, and the heat transfer and fluid flow inside the capillary tube with an optimized dual-end heating strategy are analyzed and modeled. Second, real-time CCPCR is implemented with light-emitting diode and …
Experimental Impacts Of Climate Warming And Ocean Carbonation On Eelgrass Zostera Marina, Richard C. Zimmerman, Victoria J. Hill, Malee Jinuntuya, Billur Celebi, David Ruble, Miranda Smith, Tiffany Cedeno, W. Mark Swingle
Experimental Impacts Of Climate Warming And Ocean Carbonation On Eelgrass Zostera Marina, Richard C. Zimmerman, Victoria J. Hill, Malee Jinuntuya, Billur Celebi, David Ruble, Miranda Smith, Tiffany Cedeno, W. Mark Swingle
OES Faculty Publications
CO2 is a critical and potentially limiting substrate for photosynthesis of both terrestrial and aquatic ecosystems. In addition to being a climate-warming greenhouse gas, increasing concentrations of CO2 will dissolve in the oceans, eliciting both negative and positive responses among organisms in a process commonly known as ocean acidification. The dissolution of CO2 into ocean surface waters, however, also increases its availability for photosynthesis, to which the highly successful, and ecologically important, seagrasses respond positively. Thus, the process might be more accurately characterized as ocean carbonation. This experiment demonstrated that CO2 stimulation of primary production enhances …
Multiple Mating By Females In The Chesapeake Bay Blue Crab Callinectes Sapidus Population, S. Wells, J. Mcconaugha, L. Horth
Multiple Mating By Females In The Chesapeake Bay Blue Crab Callinectes Sapidus Population, S. Wells, J. Mcconaugha, L. Horth
OES Faculty Publications
Mature females of the Chesapeake Bay (USA) blue crab Callinectes sapidus population mate multiple times. Microsatellite DNA analysis of sperm stored in the spermathecae has shown that virtually all (~97%, 104 out of 107) females collected in a 2009−2010 study mated with at least 2 males. Enumeration of stored sperm revealed that despite multiple mating, some females did not have enough sperm to fulfill their lifetime reproductive potential, suggesting that female blue crabs may experience varying levels of sperm limitation. This could result from multiple factors. The average body size of males in the population has decreased, which reduces the …
Fish Spawning Aggregations: Where Well-Placed Management Actions Can Yield Big Benefits For Fisheries And Conservation, Brad Erisman, William Heyman, Shinichi Kobara, Tal Ezer, Simon Pittman, Octavio Aburto-Oropeza, Richard S. Nemeth
Fish Spawning Aggregations: Where Well-Placed Management Actions Can Yield Big Benefits For Fisheries And Conservation, Brad Erisman, William Heyman, Shinichi Kobara, Tal Ezer, Simon Pittman, Octavio Aburto-Oropeza, Richard S. Nemeth
CCPO Publications
Marine ecosystem management has traditionally been divided between fisheries management and biodiversity conservation approaches, and the merging of these disparate agendas has proven difficult. Here, we offer a pathway that can unite fishers, scientists, resource managers and conservationists towards a single vision for some areas of the ocean where small investments in management can offer disproportionately large benefits to fisheries and biodiversity conservation. Specifically, we provide a series of evidenced-based arguments that support an urgent need to recognize fish spawning aggregations (FSAs) as a focal point for fisheries management and conservation on a global scale, with a particular emphasis placed …
Development Of An Age-Frequency Distribution For Ocean Quahogs Arctica Islandica On Georges Bank, Sara M. Pace, Eric N. Powell, Roger Mann, M. Chase Long, John M. Klinck
Development Of An Age-Frequency Distribution For Ocean Quahogs Arctica Islandica On Georges Bank, Sara M. Pace, Eric N. Powell, Roger Mann, M. Chase Long, John M. Klinck
CCPO Publications
Ocean quahogs [Arctica islandica (Linnaeus, 1769)] are the longest-lived, noncolonial animal known today, with a maximum life span exceeding 500 y. Ocean quahogs are a commercially important bivalve, inhabiting the continental shelf of the North Atlantic Basin. Although considerable information exists on the growth and physiology of A. islandica, limited information is available regarding recruitment; accordingly, sustainably managing the fishery is a challenge. To investigate long-term recruitment trends, the age of ocean quahogs from Georges Bank which were fully recruited to the commercial fishery (>80 mm shell length) was determined by analysis of annual growth lines in …
Impact Of Disease On The Survival Of Three Commercially Fished Species, John M. Hoenig, Maya L. Groner, Matthew W. Smith, Wolfgang K. Vogelbein, David M. Taylor, Donald F. Landers Jr., John T. Swenarton, David T. Gauthier
Impact Of Disease On The Survival Of Three Commercially Fished Species, John M. Hoenig, Maya L. Groner, Matthew W. Smith, Wolfgang K. Vogelbein, David M. Taylor, Donald F. Landers Jr., John T. Swenarton, David T. Gauthier
Biological Sciences Faculty Publications
Recent increases in emergent infectious diseases have raised concerns about the sustainability of some marine species. The complexity and expense of studying diseases in marine systems often dictate that conservation and management decisions are made without quantitative data on population-level impacts of disease. Mark-recapture is a powerful, underutilized, tool for calculating impacts of disease on population size and structure, even in the absence of etiological information. We applied logistic regression models to mark-recapture data to obtain estimates of disease-associated mortality rates in three commercially important marine species: snow crab (Chionoecetes opilio) in Newfoundland, Canada, that experience sporadic epizootics …
The Conservation Status Of Marine Biodiversity Of The Pacific Islands Of Oceania, H. Pippard, G. M. Ralph, M. S. Harvey, K. E. Carpenter, J. R. Buchanan, D. W. Greenfield, H. D. Harwell, H. K. Larson, A. Lawrence, C. Linardich, K. Matsuura, H. Motomura, T. A. Munroe, R. F. Myers, B. C. Russell, W. F. Smith-Vaniz, J. C. Vié, R. R. Thaman, J. T. Williams
The Conservation Status Of Marine Biodiversity Of The Pacific Islands Of Oceania, H. Pippard, G. M. Ralph, M. S. Harvey, K. E. Carpenter, J. R. Buchanan, D. W. Greenfield, H. D. Harwell, H. K. Larson, A. Lawrence, C. Linardich, K. Matsuura, H. Motomura, T. A. Munroe, R. F. Myers, B. C. Russell, W. F. Smith-Vaniz, J. C. Vié, R. R. Thaman, J. T. Williams
Biological Sciences Faculty Publications
The Pacific Islands of Oceania are small islands and atolls occurring over a vast expanse of ocean that are characterized by immense biodiversity and endemism. This project represents a major expansion of the coverage of the Pacific Islands’ marine biodiversity on the IUCN Red List of Threatened Species. The threats to Pacific Island marine biodiversity are many. Results from IUCN Red List initiatives such as this can guide decision-making and conservation prioritization of Pacific Island governments, non-governmental organizations (NGOs) and the private sector. By shaping regional and national policies with these data in mind, priority sites for maintaining marine biodiversity …
The Conservation Status Of Marine Bony Shorefishes Of The Greater Caribbean, Kent E. Carptenter, Christi Linardich, Gina Ralph, N. Cox, D. R. Robertson, H. Harwell, A. Acero P., W. Anderson Jr., F. Barthelat, J. -L. Bouchereau, J. J. Brown, J. Buchanan, D. Buddo, B. Collette, M. Comeros-Raynal, M. Craig, M. Curtis, T. Defex, J. Dooley, W. Driggers Iii, C. Elfes Livsey, T. Fraser, R. Gilmore Jr., L. Grijalba Bendeck, A. Hines, R. Kishore, K. Lindeman, J. -P. Maréchal, J. Mceachran, R. Mcmanus, J. Moore, T. Munroe, H. Oxenford, F. Pezold, F. Pina Amargós, A. Polanco Fernandez, B. Polidoro, C. Pollock, R. Robins, B. Russell, C. Sayer, S. Williams
The Conservation Status Of Marine Bony Shorefishes Of The Greater Caribbean, Kent E. Carptenter, Christi Linardich, Gina Ralph, N. Cox, D. R. Robertson, H. Harwell, A. Acero P., W. Anderson Jr., F. Barthelat, J. -L. Bouchereau, J. J. Brown, J. Buchanan, D. Buddo, B. Collette, M. Comeros-Raynal, M. Craig, M. Curtis, T. Defex, J. Dooley, W. Driggers Iii, C. Elfes Livsey, T. Fraser, R. Gilmore Jr., L. Grijalba Bendeck, A. Hines, R. Kishore, K. Lindeman, J. -P. Maréchal, J. Mceachran, R. Mcmanus, J. Moore, T. Munroe, H. Oxenford, F. Pezold, F. Pina Amargós, A. Polanco Fernandez, B. Polidoro, C. Pollock, R. Robins, B. Russell, C. Sayer, S. Williams
Biological Sciences Faculty Publications
The greater Caribbean biogeographic region covered in this report (representing 38 countries and territories) encompasses an outstanding marine bony shorefish richness of approximately 1,360 species, with many (53%) being endemic. This report provides an overview of the conservation status of greater Caribbean shorefishes, with detailed information available through the IUCN Red List, and gives recommendations.
Informing Marine Protected Area Designation And Management For Nesting Olive Ridley Sea Turtles Using Satellite Tracking, Tiffany M. Dawson, Angela Formia, Pierre D. Agamboué, Georges M. Asseko, François Boussamba, Floriane Cardiec, Emmanuel Chartrain, Philip D. Doherty, J. Michael Fay, Brendan J. Godley, Francis Lambert, Brice D. Koumba Mabert, Jean C. Manfoumbi, Kristian Metcalfe, Gianna Minton, Ivan Ndanga, Jacob Nzegoue, Carmen K. Kouerey Oliwina, Philippe Du Plessis, Guy-Philippe Sounguet, Dominic Tilley, Matthew J. Witt, Sara M. Maxwell
Informing Marine Protected Area Designation And Management For Nesting Olive Ridley Sea Turtles Using Satellite Tracking, Tiffany M. Dawson, Angela Formia, Pierre D. Agamboué, Georges M. Asseko, François Boussamba, Floriane Cardiec, Emmanuel Chartrain, Philip D. Doherty, J. Michael Fay, Brendan J. Godley, Francis Lambert, Brice D. Koumba Mabert, Jean C. Manfoumbi, Kristian Metcalfe, Gianna Minton, Ivan Ndanga, Jacob Nzegoue, Carmen K. Kouerey Oliwina, Philippe Du Plessis, Guy-Philippe Sounguet, Dominic Tilley, Matthew J. Witt, Sara M. Maxwell
Biological Sciences Faculty Publications
Understanding the horizontal and vertical habitat of olive ridley sea turtles (Lepidochelys olivacea), a threatened species, is critical for determining regions for protection and relevant gear modifications that may effectively reduce bycatch, the largest threat to this species. Satellite transmitters were used to determine the movement and dive behavior of 21 female olive ridley turtles tagged in Pongara National Park, Gabon during the 2012, 2013, and 2015 nesting seasons. A switching state-space model was used to filter the tracking data and categorize the internesting and post-nesting movements. Gridded utilization distribution (UD) home range analysis of tracking data revealed …
Rapid Adaptive Responses To Climate Change In Corals, Gergely Torda, Jennifer M. Donelson, Manuel Aranda, Daniel J. Barshis, Line Bay, Michael L. Berumen, David G. Bourne, Neal Cantin, Sylvain Foret, Mikhail Matz
Rapid Adaptive Responses To Climate Change In Corals, Gergely Torda, Jennifer M. Donelson, Manuel Aranda, Daniel J. Barshis, Line Bay, Michael L. Berumen, David G. Bourne, Neal Cantin, Sylvain Foret, Mikhail Matz
Biological Sciences Faculty Publications
Pivotal to projecting the fate of coral reefs is the capacity of reef-building corals to acclimatize and adapt to climate change. Transgenerational plasticity may enable some marine organisms to acclimatize over several generations and it has been hypothesized that epigenetic processes and microbial associations might facilitate adaptive responses. However, current evidence is equivocal and understanding of the underlying processes is limited. Here, we discuss prospects for observing transgenerational plasticity in corals and the mechanisms that could enable adaptive plasticity in the coral holobiont, including the potential role of epigenetics and coral-associated microbes. Well-designed and strictly controlled experiments are needed to …
Eukaryotic Microbes, Principally Fungi And Labyrinthulomycetes, Dominate Biomass On Bathypelagic Marine Snow, Alexander B. Bochdansky, Melissa A. Clouse, Gerhard J. Herndl
Eukaryotic Microbes, Principally Fungi And Labyrinthulomycetes, Dominate Biomass On Bathypelagic Marine Snow, Alexander B. Bochdansky, Melissa A. Clouse, Gerhard J. Herndl
OES Faculty Publications
In the bathypelagic realm of the ocean, the role of marine snow as a carbon and energy source for the deep-sea biota and as a potential hotspot of microbial diversity and activity has not received adequate attention. Here, we collected bathypelagic marine snow by gentle gravity filtration of sea water onto μm filters from similar to 1000 to 3900 m to investigate the relative distribution of eukaryotic microbes. Compared with sediment traps that select for fast-sinking particles, this method collects particles unbiased by settling velocity. While prokaryotes numerically exceeded eukaryotes on marine snow, eukaryotic microbes belonging to two very distant …
Fit To Predict? Ecoinformatics For Predicting The Catchability Of A Pelagic Fish In Near Real-Time, Kylie L. Scales, Elliot L. Hazen, Sara M. Maxwell, Heidi Dewar, Suzanne Kohin, Michael G. Jacox, Christopher A. Edwards, Dana K. Briscoe, Larry B. Crowder, Rebecca L. Lewison, Steven J. Bograd
Fit To Predict? Ecoinformatics For Predicting The Catchability Of A Pelagic Fish In Near Real-Time, Kylie L. Scales, Elliot L. Hazen, Sara M. Maxwell, Heidi Dewar, Suzanne Kohin, Michael G. Jacox, Christopher A. Edwards, Dana K. Briscoe, Larry B. Crowder, Rebecca L. Lewison, Steven J. Bograd
Biological Sciences Faculty Publications
The ocean is a dynamic environment inhabited by a diverse array of highly migratory species, many of which are under direct exploitation in targeted fisheries. The timescales of variability in the marine realm coupled with the extreme mobility of ocean-wandering species such as tuna and billfish complicates fisheries management. Developing ecoinformatics solutions that allow for near real-time prediction of the distributions of highly mobile marine species is an important step towards the maturation of dynamic ocean management and ecological forecasting. Using 25 years (1990-2014) of NOAA fisheries' observer data from the California drift gillnet fishery, we model relative probability of …
Phytoplankton Plastid Proteomics: Cracking Open Diatoms To Understand Plastid Biochemistry Under Iron Limitation, Skyler J. Nunn, Phoebe Dreux Chappell, Kristofer Gomes, Anasthasia Bonderenko, Bethany D. Jenkins, Brook L. Nunn
Phytoplankton Plastid Proteomics: Cracking Open Diatoms To Understand Plastid Biochemistry Under Iron Limitation, Skyler J. Nunn, Phoebe Dreux Chappell, Kristofer Gomes, Anasthasia Bonderenko, Bethany D. Jenkins, Brook L. Nunn
OES Faculty Publications
Diatoms, such as Thalassiosira pseudonana, are important oceanic primary producers, as they sequester carbon dioxide (CO₂) out of the atmosphere, die, and precipitate to the ocean floor. In many areas of the world’s oceans, phytoplankton, such as diatoms, are limited in growth by the availability of iron (Fe). Fe is an essential nutrient for phytoplankton, as it is central in the electron transport chain component of photosynthesis. Through this study, we examined if Fe-limitation makes a significant difference in the proteins expressed within the chloroplast, the power source for diatoms. Here, we utilized a new plastid isolation technique specific …
Modeling Beta-Traces For Beta-Barrels From Cryo-Em Density Maps, Dong Si, Jing He
Modeling Beta-Traces For Beta-Barrels From Cryo-Em Density Maps, Dong Si, Jing He
Computer Science Faculty Publications
Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although ά-helices can be detected from density maps at 5-8 angstrom resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands. The variety of shapes of β-sheets adds the complexity of β-strands detection from density maps. We propose a new approach to model traces of β-strands for β-barrel density regions that are extracted from cryo-EM density maps. In the test containing eight β-barrels extracted from experimental cryo-EM density maps at 5.5 angstrom-8.25 angstrom resolution, StrandRoller detected about 74.26% of the amino acids in the β-strands …
Comparing An Atomic Model Or Structure To A Corresponding Cryo-Electron Microscopy Image At The Central Axis Of A Helix, Stephanie Zeil, Julio Kovacs, Willy Wriggers, Jing He
Comparing An Atomic Model Or Structure To A Corresponding Cryo-Electron Microscopy Image At The Central Axis Of A Helix, Stephanie Zeil, Julio Kovacs, Willy Wriggers, Jing He
Computer Science Faculty Publications
Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM …
An Effective Computational Method Incorporating Multiple Secondary Structure Predictions In Topology Determination For Cryo-Em Images, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Stephanie Zeil, Kamal Al Nasr, Jing He
An Effective Computational Method Incorporating Multiple Secondary Structure Predictions In Topology Determination For Cryo-Em Images, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Stephanie Zeil, Kamal Al Nasr, Jing He
Computer Science Faculty Publications
A key idea in de novo modeling of a medium-resolution density image obtained from cryo-electron microscopy is to compute the optimal mapping between the secondary structure traces observed in the density image and those predicted on the protein sequence. When secondary structures are not determined precisely, either from the image or from the amino acid sequence of the protein, the computational problem becomes more complex. We present an efficient method that addresses the secondary structure placement problem in presence of multiple secondary structure predictions and computes the optimal mapping. We tested the method using 12 simulated images from alpha-proteins and …
Upscaling Stem To Community-Level Transpiration For Two Sand-Fixing Plants: Salix Gordejevii And Caragana Microphylla, Limin Duan, Yang Li, Xue Yan, Tingxi Liu, Xixi Wang
Upscaling Stem To Community-Level Transpiration For Two Sand-Fixing Plants: Salix Gordejevii And Caragana Microphylla, Limin Duan, Yang Li, Xue Yan, Tingxi Liu, Xixi Wang
Civil & Environmental Engineering Faculty Publications
The information on transpiration is vital for sustaining fragile ecosystem in arid/semiarid environment, including the Horqin Sandy Land (HSL) located in northeast China. However, such information is scarce in existing literature. The objectives of this study were to: (1) measure sap flow of selected individual stems of two sand-fixing plants, namely Salix gordejevii and Caragana microphylla, in HSL; and (2) upscale the measured stem-level sap flow for estimating the community-level transpiration. The measurements were done from 1 May to 30 September 2015 (i.e., during the growing season). The upscaling function was developed to have one dependent variable, namely sap …