Preliminary assessment of benthic macrofauna community within intertidal mudflats, Lake Rudee, Virginia Beach, Virginia

The goal of this assessment was to evaluate the proposed dredging site at Lake Rudee to determine whether the natural resources within the proposed dredge area were of sufficient value that the permitting agency might require further data to be collected to aid in determining whether to grant a dredging permit or how much mitigation to require

From eFish to RecFish - Progress towards Developing an App that Engages Recreational Anglers as Community Scientists

The success of the Cornell Lab of Ornithology with eBird and its associated apps demonstrates the potential value in engaging recreational enthusiasts as community scientists through the use of a cell phone application (hereafter “app”). However, significant differences exist between the recreational angler community and the birding community making it necessary to further investigate the feasibility of engaging recreational anglers as community scientists using an app. The funds awarded through the VIMS Dean and Director’s Innovation Fund were used to: 1) assess the existing landscape of for-profit fishing apps and not-for-profit efforts to use recreational anglers as community scientists, 2) explore current app technologies for potential inclusion in a recreational fishing app, 3) explore potential external funding sources, and 4) determine a preliminary feature set for inclusion in an app for recreational anglers

OmniMerge: A Systematic Approach to Constrained Conformational Search

OmniMerge performs a systematic search to enumerate all conformations of a molecule (at a given level of torsion-angle resolution) that satisfy a set of local geometric constraints. Constraints would typically come from NMR experiments, but applications such as docking or homology modeling could also give rise to similar constraints. The molecule to be searched is partitioned into small subchains so that the set of possible conformations for the whole molecule may be constructed by merging the feasible conformations for the subchain parts. However, instead of using a binary tree for straightforward divide-and-conquer, OmniMerge defines a sub-problem for every possible subchain of the molecule. Searching every subchain provides a counter-intuitive advantage: with every possible subdivision available for merging, one may choose the most favorable merge for each subchain, particularly for the bottleneck chain(s). Improving the bottleneck step may therefore cause the whole search to be completed more quickly. Finally, to discard infeasible conformations more rapidly, OmniMerge filters the solution set of each subchain based on compatibility with the solutions sets of all overlapping subchains. These two innovations—choosing the most favorable merges and enforcing consistency between overlapping subchains—yield significant improvements in run time. By determining the extent of structural variability permitted by a set of constraints, OmniMerge offers the potential to aid error analysis and improve confidence for NMR results on peptides and moderate-sized molecules.Singapore-MIT Alliance (SMA

Assessment of benthic macrofauna community within intertidal mudflats - Hurds Cove, Lynnhaven River, Virginia

A total of 30 samples were collected from eight locations in Hurds Cove, Lynnhaven River, VA. All samples were rinsed over a 500-μm mesh sieve and all material retained on the sieve was analyzed to determine benthic macrofaunal community identity, abundance and biomass. With the exception of one sample with relatively high biomass (50.68 g AFDW m-2) attributable to a single (Rangia cuneata), biomass across all locations was low, ranging from 0.16-0.67 g AFDW m-2. At five of the eight locations, all measurable biomass was contributed by polychaete worms. At the other three locations, polychaetes accounted for 45-57% of total biomass. At two locations, isopods contributed \u3e25% biomass and, at one location, decapod crustaceans accounted for 13.7% of the total biomass. Polychaetes and/or ostracods were the most abundant organisms in all locations. However, despite being abundant, ostracod biomass was below detection limits

Oyster reef ecosystem services: Macrofauna utilization of restored oyster reefs - Harris Creek, Maryland, USA

Oyster reefs provide habitat for a variety of macrofauna species. Our studies focused on the relationship between oyster tissue biomass density and reef-associated macrofauna biomass density. Studies were conducted in 2015-2017 and sites encompassed the majority of the area in which restoration activities were conducted with the Harris Creek Oyster Sanctuary in Maryland. Results presented in this report focus on: 1) interactions between oyster biomass density and season in determining macrofauna biomass, 2) responses of macrofauna to oyster biomass densities below “threshold” levels (0-14.9 g DW m-2) and between threshold and “target” levels (15-49.9 g DW m-2) defined in the success metrics for the Harris Creek restoration effort, 3) the role of tray-scale (0.1 m2), plot-scale (10 m2), and reef-scale oyster biomass density in determining associated macrofauna biomass, and 4) larger scale patterns in macrofauna biomass density within the creek

Integrated assessment of oyster reef ecosystem services: Quantifying Denitrification Rates and Nutrient Fluxes

Measurements of nutrient exchange were made in restored oyster reefs and creek sediments in 2014 and 2015 in Harris Creek, Maryland, USA. Rates of ammonium, nitrate and di-nitrogen fluxes were much higher in reef environments than in sediments, and rates of oxygen uptake reflected high inputs of biodeposits. The rate of denitrification was related to oyster biomass and oyster numbers. The shallow nature of the restoration allows light to reach the bottom and benthic microalgal photosynthesis affects the net nutrient exchange with the bottom. After several years, oyster restoration has increased denitrification in Harris Creek, though observations in mature upper Choptank restored reefs are higher. The trajectory of increase of the nutrient ecosystem services is positive and will be followed over time

An updated model for estimating the TMDL-related benefits of oyster reef restoration Harris Creek, Maryland, USA

In 2014, a user-friendly, web-accessible model was developed that allowed restoration practitioners and resource managers to easily estimate the TMDLrelated benefits of oyster reef (Crassostrea virginica) restoration per unit area, run restoration scenarios in Harris Creek, MD to optimize restoration planning and implementation, and calculate the benefits of the chosen plan. The model was rooted in scientifically defensible data and was readily transferrable to systems throughout the Chesapeake Bay and Eastern Shore. The model operated in five vertically well-mixed boxes along the main axis of the creek. Exchanges among creeks were computed using a tidal prism approach and were compared to exchanges provided from a high resolution 3D hydrodynamic model. Watershed inputs for the model were obtained for the Harris Creek sub-watershed from the Phase V Chesapeake Bay Program Watershed Model. The base model simulated daily concentrations over an annual cycle of chlorophyll-a, dissolved inorganic nitrogen (N) and phosphorus (P), dissolved oxygen, total suspended solids, the biomass of benthic microalgae, and the water column and sediment pools of labile organic carbon (C) and associated N and P. Water quality data for model forcing and calibration were obtained from the Chesapeake Bay Program, the Choptank Riverkeeper, the University of Maryland Center for Environmental Science, and the Maryland Department of Natural Resources. An oyster sub-model was coupled to this base model to compute the volume of water filtered, removal of phytoplankton, suspended solids, and associated nutrients via filtration, recycling of nutrients and consumption of oxygen by oyster respiration, production of feces, N and P accumulation in oyster tissues and shell, oyster-enhanced denitrification, and N and P burial associated with restored reefs. The completed model was served online and operated through a web browser, enabling users to conduct scenario analysis by entering box-specific values for acres restored, restored oyster density, and restored oyster size, as well as the economic value of associated N and P removal. The updated model incorporates all aspects of the previous model but replaces oyster related data collected outside Harris Creek with site-specific data, and now includes restored oyster populations and water quality data through 2016. It also incorporates the impacts of two common, reef-associated filter feeding organisms: the hooked mussel Ischadium recurvum and the sea squirt Molgula manhattensis. Additional data collected in Harris Creek and incorporated into the model include: biomass of benthic microalgae, biogeochemical fluxes in relation to oyster biomass, and the biomass density and distribution of the dominant non-oyster reef filter feeders (I. recurvum, and M. manhattensis). The revised model incorporates an improved estimate of annual oyster growth, uses an improved method for estimating N and P sequestered in tissues and shells, and accounts for the prerestoration oyster population in Harris Creek. The model also incorporates data on the filtration capacity of I. recurvum and M. manhattensis in relation to C. virginica collected as part of a previous study (not in Harris Creek) by Kellogg and Newell (unpublished data)

Systematic conformational search with constraint satisfaction

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2002.Includes bibliographical references (p. 170-177).Determining the conformations of biological molecules is a high scientific priority for biochemists and for the pharmaceutical industry. This thesis describes a systematic method for conformational search, an application of the method to determining the structure of the formyl-Met-Leu-Phe-OH (fMLF)peptide by solid-state NMR spectroscopy, and a separate project to determine the structure of a protein-DNA complex by X-ray crystallography. The purpose of the systematic search method is to enumerate all conformations of a molecule (at a given level of torsion angle resolution) that satisfy a set of local geometric constraints. Constraints would typically come from NMR experiments, but applications such as docking or homology modelling could also give rise to similar constraints. The molecule to be searched is partitioned into small subchains so that the set of possible conformations for the whole molecule may be constructed by merging the feasible conformations for the parts. However, instead of using a binary tree for straightforward divide-and-conquer, four innovations are introduced: (1) OMNIMERGE searches a subproblem for every possible subchain of the molecule. Searching every subchain provides the advantage that every possible merge is available; by choosing the most favorable merge for each subchain, the bottleneck subchain(s) and therefore the whole search may be completed more efficiently. (2) A cost function evaluates alternative divide-and-conquer trees, provided that a preliminary OMNIMERGE search of the molecule has been completed. Then dynamic programming determines the optimal partitioning or "merge-tree" for the molecule; this merge-tree can be used to improve the efficiency of future searches.(cont.) (3) PROPAGATION shares information by enforcing arc consistency between the solution sets of overlapping subchains. By filtering the solution set of each subchain, infeasible conformations are discarded rapidly. (4) An A* function prioritizes each subchain based on estimated future costs. Subchains with sufficiently low priority can be skipped, which improves efficiency. A common theme of these four ideas is to make good choices about how to break the large search problem into lower-dimensional subproblems. These novel algorithms were implemented and the effectiveness of each is demonstrated on a well-constrained peptide with 40 degrees of freedom.by Lisa Tucker-Kellogg.Ph.D

Environmental and Ecological Benefits and Impacts of Oyster Aquaculture Chesapeake Bay, Virginia, USA

To better quantify the ecological benefits and impacts of oyster aquaculture, we sampled water quality, sediment quality, benthic macrofaunal communities and oysters at four oyster aquaculture sites located on the western shore of Chesapeake Bay in Virginia, USA. At each site, we collected samples from within the footprint of the aquaculture cages and from nearby areas with similar physical and environmental conditions but far enough away to be minimally influenced by aquaculture operations. Data collected from the water column included chlorophyll concentrations, turbidity, pH, dissolved oxygen concentrations, light attenuation, particle concentration, median particle size, total suspended solids and their organic content, and dissolved nutrient concentrations. Sediment and macrofauna community data collected included sediment grain size and organic content and macrofauna identity, abundance, biomass and species richness. In addition to assessing the potential impacts of oyster aquaculture on the water column and benthos, we also assessed differences in the oysters harvested Environmental and ecological benefits and impacts of oyster aquaculture at each site and estimated the total amount of nitrogen and phosphorus harvested at each site. Differences in water quality, sediment quality, and macrofauna community structure between areas within and outside the farm footprint were rare and of small magnitude and varying direction (i.e. negative versus positive impact) when they did occur. Aquaculture sites varied by an order of magnitude in size, annual harvest and harvest per unit area. They also varied by an order of magnitude in the total amount of nitrogen (N) and phosphorus (P) harvested per unit area. In contrast to the negative environmental impacts associated with other forms of animal protein production for human consumption, oyster harvest from aquaculture sites studied here resulted in the removal of 21-372 lbs. of N and 3-49lbs of P per farm per year