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Full-Text Articles in Life Sciences
A Deterministic Model For Understanding Nonlinear Viral Dynamics In Oysters, Qubin Qin, Jian Shen, Kimberly S. Reece
A Deterministic Model For Understanding Nonlinear Viral Dynamics In Oysters, Qubin Qin, Jian Shen, Kimberly S. Reece
VIMS Articles
Contamination of oysters with a variety of viruses is one key pathway to trigger outbreaks of massive oyster mortality as well as human illnesses, including gastroenteritis and hepatitis. Much effort has gone into examining the fate of viruses in contaminated oysters, yet the current state of knowledge of nonlinear virus-oyster interactions is not comprehensive because most studies have focused on a limited number of processes under a narrow range of experimental conditions. A framework is needed for describing the complex nonlinear virus-oyster interactions. Here, we introduce a mathematical model that includes key processes for viral dynamics in oysters, such as …
Antibiotic Resistant Bacteria, Antibiotic Resistance Genes And Potential Drivers In The Aquatic Environments, Shuo Shen
Dissertations
As antibiotic resistance genes in aquatic environment have been increasing across the world, affecting water quality and public health, many studies documented concentrations of antibiotic resistance genes and some studies discussed their potential drivers. However, systematic and quantitative reviews that link antibiotic resistance genes (ARGs) to anthropogenic and environmental factors are limited. Nevertheless, this information will be important for developing regulation policy on controlling antibiotic use and therefore reducing potential risks to antibiotic resistance. I conducted meta-analysis of ARGs concentration at a global scale using Bayesian inference to explore climatic and socio-economic factors as drivers. I found local-scale climatic variables …
An Ecopath With Ecosim Analysis On Offshore Petroleum Platform Influences On Gulf Of Mexico Red Snapper, Valentin Gomez
An Ecopath With Ecosim Analysis On Offshore Petroleum Platform Influences On Gulf Of Mexico Red Snapper, Valentin Gomez
LSU Master's Theses
Offshore oil and gas platforms have had a significant presence in the Gulf of Mexico since the 1950s. An important secondary function of these structures is that they provide artificial habitat to fisheries, most notably Red snapper. Policy changes intended to reduce the risk associated with aging infrastructure have reduced the number of standing platforms from 4044 to 1867 from 2001 to 2018. The effect this loss of habitat has on Red snapper was tested by creating three scenarios of platform changes and modeling the perturbation from 2005 to 2050. The simulation was accomplished using the ecological model Ecopath with …
Multivariate Habitat-Based Predictive Modeling Of Three Demersal Rockfish Species In Central California, Georgia R. Martel
Multivariate Habitat-Based Predictive Modeling Of Three Demersal Rockfish Species In Central California, Georgia R. Martel
Cal Poly Humboldt theses and projects
Accurate, spatially explicit models of rockfish abundance are critical in implementing ecosystem-based management strategies and designating essential fish habitats and marine protected areas. Multibeam bathymetry methods and visual, non-extractive submersible transect surveys were combined to collect environmental variables and fish abundance data at three distinct sites within the study region. Zero-adjusted models were developed using habitat classification analyses of high-resolution (5 m) digital elevation models. Model accuracies were assessed by using a reserved subset of the original datasets. To demonstrate that a model’s predictive power was linked to its spatial origins, Mean Absolute Error and coefficient of determination values were …
Modeling Wind-Induced Waves In The Salish Sea, Zhaoqing Yang, Wei-Cheng Wu, Taiping Wang, Guillaume Mauger, Ruby Leung
Modeling Wind-Induced Waves In The Salish Sea, Zhaoqing Yang, Wei-Cheng Wu, Taiping Wang, Guillaume Mauger, Ruby Leung
Salish Sea Ecosystem Conference
There have been on-going efforts for increasing coastal resilience to the risk of coastal inundation as a result of sea-level rise in Washington. Accurate coastal risk projection depends on detailed and accurate information of sea level rise, including waves and storm surge induced by windstorms. This paper presents a modeling study simulating wind-induced waves in the Salish Sea. A nested-grid modeling approach was used to provide accurate and robust model simulations at various scales. The NOAA NCEP’s WaveWatch III (WW3) model is configured at global and regional scales with wind forcing obtained from the Climate Forecast System Reanalysis (CFSR). For …
An Integrated Environmental And Human Systems Modeling Framework For Puget Sound Restoration Planning, Robert Mckane, Jonathan Halama, Paul Bryce Pettus, Bradley Barnhart, Allen Brookes, Kevin Djang, Tarang Khangaonkar, Isaac Kaplan, Christopher James Harvey, Emily Howe, Phillip S. Levin, Michael W. Schmidt, Raphael Girardin
An Integrated Environmental And Human Systems Modeling Framework For Puget Sound Restoration Planning, Robert Mckane, Jonathan Halama, Paul Bryce Pettus, Bradley Barnhart, Allen Brookes, Kevin Djang, Tarang Khangaonkar, Isaac Kaplan, Christopher James Harvey, Emily Howe, Phillip S. Levin, Michael W. Schmidt, Raphael Girardin
Salish Sea Ecosystem Conference
Local, state, federal, tribal and private stakeholders have committed significant resources to restoring Puget Sound’s terrestrial-marine ecosystem. Though jurisdictional issues have promoted a fragmented approach to restoration planning, there is growing recognition that a more coordinated systems-based restoration approach is needed to achieve recovery goals. This presentation describes our collaborative effort to develop and apply an integrated environmental and human systems modeling framework for the Puget Sound Basin, inclusive of all marine and land areas (1,020 and 12,680 sq. mi.). Our goal is to establish a whole-basin systems modeling framework that dynamically simulates biophysical interactions and transfers (water, nutrients, contaminants, …
Big Sharks In The Salish Sea: Combining Passive Acoustics With The Salish Sea Model To Predict Sixgill Shark (Hexanchus Griseus) Presence, Alli Cramer, Steve Katz, Kelly Andrews, Daniel H. Thornton
Big Sharks In The Salish Sea: Combining Passive Acoustics With The Salish Sea Model To Predict Sixgill Shark (Hexanchus Griseus) Presence, Alli Cramer, Steve Katz, Kelly Andrews, Daniel H. Thornton
Salish Sea Ecosystem Conference
Examination of species-environment relationships that determine broad-scale distribution patterns is a key focus of ecological research. Characterizing animal-habitat associations in the marine environment is particularly challenging given the opacity of the ocean, and addressing this question in marine systems has consequently lagged behind terrestrial systems. In this project, we have leveraged existing data on locations of a large marine predator, the Sixgill Shark, Hexanchus griseus, and linked that with the PNNL’s Salish Sea Model over the domain of shark movement in Puget Sound, Washington state. Twenty-nine Sixgill sharks were tracked from 2005-2009 across 130 hydrophone receivers with tags that reported …
A Modeling Study Of Storm Surge In The Salish Sea, Zhaoqing Yang, Taiping Wang, Ian Miller
A Modeling Study Of Storm Surge In The Salish Sea, Zhaoqing Yang, Taiping Wang, Ian Miller
Salish Sea Ecosystem Conference
The Pacific Northwest coasts are subject to the threat of coastal inundation as a result of storm surge. This snapshot presentation provides an overview of a modeling study of storm surge in the Salish Sea using a high resolution coastal hydrodynamic model. A series of historical storm surge events were identified based on non-tidal residual (NTR) water levels observed at Seattle tide gage. Model simulations corresponding to selected storm surge events were conducted. The Salish Sea storm surge model was validated with both observed tidal and NTR data at NOAA tide gauges in the Salish Sea. Sensitivity analysis on the …
Ecosystem Metabolism Modeling Of Estuaries In Maine: Using Dissolved Oxygen As A Tool For Aquaculture Site Assessment, Katherine Miller
Ecosystem Metabolism Modeling Of Estuaries In Maine: Using Dissolved Oxygen As A Tool For Aquaculture Site Assessment, Katherine Miller
Honors College
The net primary productivity (NPP), also known as the net ecosystem metabolism, of an estuary is a value indicative of the growth and activity of an estuary’s primary producers, relative to the metabolic activity of its consumers. When NPP is high, estuaries exhibit autotrophic conditions that have the capacity to support fruitful bivalve aquaculture. For oyster farmers, the ability to monitor an estuary’s NPP would allow them to predict and prepare for seasonal changes to oyster growth that result from changes to their phytoplankton food source and access to dissolved oxygen (DO). Not only would this aid farmers on site …
Multiscale Habitat Suitability Modeling For Canary Rockfish (Sebastes Pinniger) Along The Northern California Coast, Portia N. Saucedo
Multiscale Habitat Suitability Modeling For Canary Rockfish (Sebastes Pinniger) Along The Northern California Coast, Portia N. Saucedo
Cal Poly Humboldt theses and projects
Detailed spatially-explicit data of the potential habitat of commercially important rockfish species are a critical component for the purposes of marine conservation, evaluation, and planning. Predictive habitat modeling techniques are widely used to identify suitable habitat in un-surveyed regions. This study elucidates the predicted distribution of canary rockfish (Sebastes pinniger) along the largely un-surveyed northern California coast using data from visual underwater surveys and predictive terrain complexity covariates. I used Maximum Entropy (MaxEnt) modelling software to identify regions of suitable habitat for S. pinniger greater than nine cm in total length at two spatial scales. The results of …
Lingcod (Ophiodon Elongatus) Habitat Associations: Implications For Conservation And Management, Megan Bassett
Lingcod (Ophiodon Elongatus) Habitat Associations: Implications For Conservation And Management, Megan Bassett
SNS Master's Theses
Understanding the spatial distribution of marine species and the temporal and spatial scales of the processes that drive those distributions continues to be limited, but is increasingly more critical with the implementation of marine spatial planning. Lingcod (Ophiodon elongatus) are a common demersal fish found from southern Alaska to Baja California, and are exploited both commercially and recreationally across the entirety of their range. Due to stock declines, Lingcod are managed using a variety of fisheries management tools, including spatial management. This study represents a unique in situ investigation of demersal habitat utilization by Lingcod at the southern portion of …
Computer Modeling The Incursion Patterns Of Marine Invasive Species, Matthew W. Johnston
Computer Modeling The Incursion Patterns Of Marine Invasive Species, Matthew W. Johnston
HCNSO Student Theses and Dissertations
Abstract Not Available.
Systematic Ichthyofaunal Surveys In Urban And Non-Urban Watersheds, Eugene G. Maurakis, David V. Grimes, Amanda Schutt, Suzy Short
Systematic Ichthyofaunal Surveys In Urban And Non-Urban Watersheds, Eugene G. Maurakis, David V. Grimes, Amanda Schutt, Suzy Short
Virginia Journal of Science
Objectives were to model fish species richness relative to natural and anthropogenic variables in Quantico Creek, a forested undisturbed stream environment, and Cameron Run, a highly disturbed urban stream environment in the lower Piedmont-Fall Line region of the Potomac River watershed. Species richness in all stream orders (e.g. avg. range=2.5-9.65 in 1st-3rd orders) of Quantico Creek were significantly higher than those (e.g. avg. range=2.1- 7.6 in 1st -4th orders) of Cameron Run. Fish species richness in Quantico Creek watershed can be modeled by eight factors: season, stream order, elevation, river km, stream width and depth, watershed size, and percent of …
Representation Of Bed Stresses Within A Model Of Chesapeake Bay, Courtney K. Harris, J. Paul Rinehimer, Sung-Chan Kim
Representation Of Bed Stresses Within A Model Of Chesapeake Bay, Courtney K. Harris, J. Paul Rinehimer, Sung-Chan Kim
Reports
This project focused on numerical modeling of the Estuarine Turbidity Maximum (ETM) with the goal of improving the representation of the bottom boundary layer and turbulent mixing within the Chesapeake Bay Program’s model [see Cerco and Noel, 2004]. The effort has been part of the EPA’s sediment modeling initiative for the Chesapeake Bay, in coordination with the U.S. Army Corps of Engineers (USACE), Engineering Research and Development Center (ERDC). Research activities focused on the Upper Chesapeake Bay and major tributaries in Maryland (such as the Potomac River); and assisted management of the U.S. EPA TMDL (Total Maximum Daily Load) project …
Development Of Hydrodynamic And Water Quality Models For The Lynnhaven River System, Mac Sisson, Harry V. Wang, Yuepeng Li, Jian Shen, Albert Y. Kuo, Wenping Gong, Mark Brush, Ken Moore
Development Of Hydrodynamic And Water Quality Models For The Lynnhaven River System, Mac Sisson, Harry V. Wang, Yuepeng Li, Jian Shen, Albert Y. Kuo, Wenping Gong, Mark Brush, Ken Moore
Reports
No abstract provided.
Numerical Modeling Scenario Runs To Assess Tss And Chlorophyll Reductions Caused By Ecosystem Restoration, Lynnhaven River, Mac Sisson, Yuepeng Li, Harry V. Wang, Albert Kuo
Numerical Modeling Scenario Runs To Assess Tss And Chlorophyll Reductions Caused By Ecosystem Restoration, Lynnhaven River, Mac Sisson, Yuepeng Li, Harry V. Wang, Albert Kuo
Reports
No abstract provided.
A Numerical Modeling Assessment For The Implementation Of A Runoff Reduction Strategy Plan For The Restoration Of Thalia Creek, Virginia Beach, Mac Sisson, Jian Shen, W. G. Reay, Eduardo J. Miles, Albert Y. Kuo, Harry V. Wang
A Numerical Modeling Assessment For The Implementation Of A Runoff Reduction Strategy Plan For The Restoration Of Thalia Creek, Virginia Beach, Mac Sisson, Jian Shen, W. G. Reay, Eduardo J. Miles, Albert Y. Kuo, Harry V. Wang
Reports
No abstract provided.
Hydrodynamic Modeling For The Proposed Dredging Assessment In Norfolk Harbor Channel, Elizabeth River, Mac Sisson, Harry V. Wang, Jian Shen, Wenping Gong, Albert Y. Kuo
Hydrodynamic Modeling For The Proposed Dredging Assessment In Norfolk Harbor Channel, Elizabeth River, Mac Sisson, Harry V. Wang, Jian Shen, Wenping Gong, Albert Y. Kuo
Reports
No abstract provided.
Upper Ocean Response Of The Mesoamerican Barrier Reef System To Hurricane Mitch And Coastal Freshwater Inputs: A Study Using Sea-Viewing Wide Field-Of-View Sensor (Seawifs) Ocean Color Data And A Nested-Grid Ocean Circulation Model, Jinyu Sheng, Liang Wang, Serge Andrefouet, Chuanmin Hu, Bruce G. Hatcher, Frank E. Muller-Karger, Bjoern Kjerfve, William D. Heyman, Bo Yang
Upper Ocean Response Of The Mesoamerican Barrier Reef System To Hurricane Mitch And Coastal Freshwater Inputs: A Study Using Sea-Viewing Wide Field-Of-View Sensor (Seawifs) Ocean Color Data And A Nested-Grid Ocean Circulation Model, Jinyu Sheng, Liang Wang, Serge Andrefouet, Chuanmin Hu, Bruce G. Hatcher, Frank E. Muller-Karger, Bjoern Kjerfve, William D. Heyman, Bo Yang
Marine Science Faculty Publications
The passage of category‐5 Hurricane Mitch through the Mesoamerican Barrier Reef System (MBRS) in October 1998 was an extreme event with the potential to create unusual patterns of reef connectivity. The impact of this hurricane on the upper ocean of the MBRS is investigated using a triply nested grid ocean circulation modeling system. The model results are validated with contemporaneous ocean color data from the Sea‐viewing Wide Field‐of‐view Sensor (SeaWiFS) satellite and oceanographic measurements in the MBRS. The nested grid system is forced by 6‐hourly National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) winds for the first 294 …
Assessment Of Image Analysis As A Measure Of Scleractinian Coral Growth, Steven K. Gustafson
Assessment Of Image Analysis As A Measure Of Scleractinian Coral Growth, Steven K. Gustafson
USF Tampa Graduate Theses and Dissertations
Image analysis was used to measure basal areas of selected colonies of Montastraea annularis and Porites astreoides, following the colonies over a three-year period from 2002 to 2004. Existing digital images of permanently-marked quadrats in the Caye Caulker Marine Reserve, Belize, were selected based on image quality and availability of images of selected quadrats for all three years. Annual growth rates were calculated from the basal-area measurements. Mean growth rates (radial skeletal extension) for M. annularis and P. astreoides were 0.02 cm yr-1 and -0.20 cm yr-1, respectively. Basal area measurements demonstrated a large degree of variability. Increases were approximately …
Additional Assessments Of The Craney Island Eastward Expansion In The Elizabeth River And Hampton Roads - Hydrodynamic Model Study, Mac Sisson, Harry V. Wang, Ya Ping Wang
Additional Assessments Of The Craney Island Eastward Expansion In The Elizabeth River And Hampton Roads - Hydrodynamic Model Study, Mac Sisson, Harry V. Wang, Ya Ping Wang
Reports
No abstract provided.
The Development Of A Water Quality Model For Baltimore Harbor, Back River, And The Adjacent Upper Chesapeake Bay, Harry V. Wang, Hui Lui, Kyeong Park
The Development Of A Water Quality Model For Baltimore Harbor, Back River, And The Adjacent Upper Chesapeake Bay, Harry V. Wang, Hui Lui, Kyeong Park
Reports
No abstract provided.
Morphology Predicts Suction Feeding Performance In Centrarchid Fishes, Andrew M. Carroll, Peter C. Wainwright, Stephen H. Huskey, David C. Collar, Ralph G. Turingan
Morphology Predicts Suction Feeding Performance In Centrarchid Fishes, Andrew M. Carroll, Peter C. Wainwright, Stephen H. Huskey, David C. Collar, Ralph G. Turingan
Ocean Engineering and Marine Sciences Faculty Publications
Suction feeding fish differ in their capacity to generate subambient pressure while feeding, and these differences appear to relate to morphological variation. We developed a morphological model of force transmission in the fish head and parameterized it with measurements from individual fish. The model was applied to 45 individuals from five species of centrarchid fishes: Lepomis macrochirus, Lepomis punctatus, Lepomis microlophus, Micropterus salmoides and Pomoxis nigromaculatus. Measurements of epaxial cross-sectional area, epaxial moment arm, buccal area and buccal area moment arm were combined to estimate pressure generation capacity for individual fish. This estimation was correlated with pressure measured in fish …
Local And Deep-Ocean Forcing Contributions To Anomalous Water Properties On The West Florida Shelf, Robert H. Weisberg, Ruoying He
Local And Deep-Ocean Forcing Contributions To Anomalous Water Properties On The West Florida Shelf, Robert H. Weisberg, Ruoying He
Marine Science Faculty Publications
Material property distributions on continental shelves result from the mixing and modifications of estuarine and deep-ocean source waters. How this occurs depends on the momentum and buoyancy that are input either locally on the shelf or from the deep-ocean at the shelf break. We address this question of local versus deep-ocean forcing for the West Florida Shelf (WFS) using in situ data and a numerical circulation model. The spring and summer seasons of 1998 and 1999 show distinctively different water properties on the shelf and at the shelf break. We account for these differences by a combination of local forcing, …
Application Of An Integrated Watershed And Tidal Prism Model To The Poquoson Coastal Embayment, Jian Shen, Harry V. Wang, Mac Sisson
Application Of An Integrated Watershed And Tidal Prism Model To The Poquoson Coastal Embayment, Jian Shen, Harry V. Wang, Mac Sisson
Reports
No abstract provided.
Application Of An Integrated Watershed And Tidal Prism Model To Cockrell Creek, Jian Shen, Harry V. Wang, Mac Sisson
Application Of An Integrated Watershed And Tidal Prism Model To Cockrell Creek, Jian Shen, Harry V. Wang, Mac Sisson
Reports
No abstract provided.
Instruction For Using An Integrated Watershed Tidal Prism Modeling System For Simulating Fecal Colifrom, Jian Shen, Mac Sisson, Harry V. Wang
Instruction For Using An Integrated Watershed Tidal Prism Modeling System For Simulating Fecal Colifrom, Jian Shen, Mac Sisson, Harry V. Wang
Reports
No abstract provided.
Basinsim 1.0 A Windows-Based Watershed Modeling Package, Ting Dai, Richard L. Wetzel, Tyler R.L. Christensen, E. Amy Lewis
Basinsim 1.0 A Windows-Based Watershed Modeling Package, Ting Dai, Richard L. Wetzel, Tyler R.L. Christensen, E. Amy Lewis
Reports
BasinSim 1.0 for Windows is the product of a NOAA Coastal Zone Management grant (through the Virginia Coastal Resources Management Program) awarded to Drs. Ting Dai, R. L. Wetzel, I. C. Anderson, and L. W. Haas at the Virginia Institute of Marine Science, College of William and Mary in 1998. Additional support has been provided for the development and testing of this package and production of this user’s guide by grants from Virginia’s Chesapeake Bay Local Assistance Department (CBLAD). BasinSim 1.0 is a desktop simulation system that predicts sediment and nutrient loads for small to mid-sized watersheds. The simulation system …
Modeling Coastal Hydrodynamics And Water Qualityof Kyunggi Bay Korea:Application Of Vims Hem-3d Model, Jian Shen, Chang-Shik Kim, Albert Y. Kuo
Modeling Coastal Hydrodynamics And Water Qualityof Kyunggi Bay Korea:Application Of Vims Hem-3d Model, Jian Shen, Chang-Shik Kim, Albert Y. Kuo
Reports
No abstract provided.
Application Of A Tidal Prism Water Quality Model To Virginia Small Coastal Basins: Poquoson River, Piankatank River, Cherrystone Inlet And Hungars Creek, Albert Y. Kuo, Arthur J. Butt, Sung-Chan Kim, Jing Lin
Application Of A Tidal Prism Water Quality Model To Virginia Small Coastal Basins: Poquoson River, Piankatank River, Cherrystone Inlet And Hungars Creek, Albert Y. Kuo, Arthur J. Butt, Sung-Chan Kim, Jing Lin
Reports
No abstract provided.