Nutrient Improvements in Chesapeake Bay: Direct Effect of Load Reductions and Implications for Coastal Management

In Chesapeake Bay in the United States, decades of management efforts have resulted in modest reductions of nutrient loads from the watershed, but the corresponding improvements in estuarine water quality have not consistently followed. Generalized additive models were used to directly link river flows and nutrient loads from the watershed to nutrient trends in the estuary on a station-by-station basis, which allowed for identification of exactly when and where responses are happening. Results show that Chesapeake Bay’s total nitrogen and total phosphorus conditions are mostly improving after accounting for variation in freshwater flow. Almost all of these improving nutrient concentrations in the estuary can be explained by reductions in watershed loads entering through 16 rivers and 145 nearby point sources, with the nearby point source reductions being slightly more effective at explaining estuarine nutrient trends. Overall, these two major types of loads from multiple locations across the watershed are together necessary and responsible for the improving estuarine nutrient conditions, a finding that is highly relevant to managing valuable estuarine resources worldwide

Modeling Possible Cooling-Water Intake System Impacts on Ohio River Fish Populations

To assess the possible impacts caused by cooling-water intake system entrainment and impingement losses, populations of six target fish species near power plants on the Ohio River were modeled. A Leslie matrix model was constructed to allow an evaluation of bluegill, freshwater drum, emerald shiner, gizzard shad, sauger, and white bass populations within five river pools. Site-specific information on fish abundance and length-frequency distribution was obtained from long-term Ohio River Ecological Research Program and Ohio River Sanitation Commission (ORSANCO) electrofishing monitoring programs. Entrainment and impingement data were obtained from 316(b) demonstrations previously completed at eight Ohio River power plants. The model was first run under a scenario representative of current conditions, which included fish losses due to entrainment and impingement. The model was then rerun with these losses added back into the populations, representative of what would happen if all entrainment and impingement losses were eliminated. The model was run to represent a 50-year time period, which is a typical life span for an Ohio River coal-fired power plant. Percent changes between populations modeled with and without entrainment and impingement losses in each pool were compared to the mean interannual coefficient of variation (CV), a measure of normal fish population variability. In 6 of the 22 scenarios of fish species and river pools that were evaluated (6 species × 5 river pools, minus 8 species/river pool combinations that could not be evaluated due to insufficient fish data), the projected fish population change was greater than the expected variability of the existing fish population, indicating a possible adverse environmental impact. Given the number of other variables affecting fish populations and the conservative modeling approach, which assumed 100% mortality for all entrained fish and eggs, it was concluded that the likelihood of impact was by no means assured, even in these six cases. It was concluded that in most cases, current entrainment and impingement losses at six Ohio River power plants have little or no effect at the population level

Variable climatic conditions dominate recent phytoplankton dynamics in Chesapeake Bay

Variable climatic conditions strongly influence phytoplankton dynamics in estuaries globally. Our study area is Chesapeake Bay, a highly productive ecosystem providing natural resources, transportation, and recreation for nearly 16 million people inhabiting a 165,000-km2 watershed. Since World War II, nutrient over-enrichment has led to multiple ecosystem impairments caused by increased phytoplankton biomass as chlorophyll-a (chl-a). Doubled nitrogen (N) loadings from 1945–1980 led to increased chl-a, reduced water clarity, and low dissolved oxygen (DO), while decreased N loadings from 1981–2012 suggest modest improvement. The recent 30+ years are characterized by high inter-annual variability of chl-a, coinciding with irregular dry and wet periods, complicating the detection of long-term trends. Here, we synthesize time-series data for historical and recent N loadings (TN, NO2 + NO3), chl-a, floral composition, and net primary productivity (NPP) to distinguish secular changes caused by nutrient over-enrichment from spatio-temporal variability imposed by climatic conditions. Wet years showed higher chl-a, higher diatom abundance, and increased NPP, while dry years showed lower chl-a, lower diatom abundance, and decreased NPP. Our findings support a conceptual model wherein variable climatic conditions dominate recent phytoplankton dynamics against a backdrop of nutrient over-enrichment, emphasizing the need to separate these effects to gauge progress toward improving water quality in estuaries

An assessment of histone-modification antibody quality

We have tested the specificity and utility of more than 200 antibodies raised against 57 different histone modifications in Drosophila melanogaster, Caenorhabditis elegans and human cells. Although most antibodies performed well, more than 25% failed specificity tests by dot blot or western blot. Among specific antibodies, more than 20% failed in chromatin immunoprecipitation experiments. We advise rigorous testing of histone-modification antibodies before use, and we provide a website for posting new test results (http://compbio.med.harvard.edu/antibodies/)

An assessment of histone-modification antibody quality

We have tested the specificity and utility of more than 200 antibodies raised against 57 different histone modifications in Drosophila melanogaster, Caenorhabditis elegans and human cells. Although most antibodies performed well, more than 25% failed specificity tests by dot blot or western blot. Among specific antibodies, more than 20% failed in chromatin immunoprecipitation experiments. We advise rigorous testing of histone-modification antibodies before use, and we provide a website for posting new test results (http://compbio.med.harvard.edu/antibodies/)

DNaseI Hypersensitivity and Ultraconservation Reveal Novel, Interdependent Long-Range Enhancers at the Complex Pax6 Cis-Regulatory Region

The PAX6 gene plays a crucial role in development of the eye, brain, olfactory system and endocrine pancreas. Consistent with its pleiotropic role the gene exhibits a complex developmental expression pattern which is subject to strict spatial, temporal and quantitative regulation. Control of expression depends on a large array of cis-elements residing in an extended genomic domain around the coding region of the gene. The minimal essential region required for proper regulation of this complex locus has been defined through analysis of human aniridia-associated breakpoints and YAC transgenic rescue studies of the mouse smalleye mutant. We have carried out a systematic DNase I hypersensitive site (HS) analysis across 200 kb of this critical region of mouse chromosome 2E3 to identify putative regulatory elements. Mapping the identified HSs onto a percent identity plot (PIP) shows many HSs correspond to recognisable genomic features such as evolutionarily conserved sequences, CpG islands and retrotransposon derived repeats. We then focussed on a region previously shown to contain essential long range cis-regulatory information, the Pax6 downstream regulatory region (DRR), allowing comparison of mouse HS data with previous human HS data for this region. Reporter transgenic mice for two of the HS sites, HS5 and HS6, show that they function as tissue specific regulatory elements. In addition we have characterised enhancer activity of an ultra-conserved cis-regulatory region located near Pax6, termed E60. All three cis-elements exhibit multiple spatio-temporal activities in the embryo that overlap between themselves and other elements in the locus. Using a deletion set of YAC reporter transgenic mice we demonstrate functional interdependence of the elements. Finally, we use the HS6 enhancer as a marker for the migration of precerebellar neuro-epithelium cells to the hindbrain precerebellar nuclei along the posterior and anterior extramural streams allowing visualisation of migratory defects in both pathways in Pax6(Sey/Sey) mice