216 Jewish Hospital of St. Louis

https://digitalcommons.wustl.edu/bjc_216/1091/thumbnail.jp

Barnes Hospital Bulletin

https://digitalcommons.wustl.edu/bjc_barnes_bulletin/1199/thumbnail.jp

An eDNA Assay to Monitor a Globally Invasive Fish Species from Flowing Freshwater

Ponto-Caspian gobies are a flock of five invasive fish species that have colonized freshwaters and brackish waters in Europe and North America. One of them, the round goby Neogobius melanostomus, figures among the 100 worst invaders in Europe. Current methods to detect the presence of Ponto-Caspian gobies involve catching or sighting the fish . These approaches are labor intense and not very sensitive. Consequently, populations are usually detected only when they have reached high densities and when management or containment efforts are futile. To improve monitoring, we developed an assay based on the detection of DNA traces (environmental DNA, or eDNA ) of Ponto-Caspian gobies in river water. The assay specifically detects invasive goby DNA and does not react to any native fish species . We apply the assay to environmental samples and demonstrate that parameters such as sampling depth, sampling location, extraction protocol, PCR protocol and PCR inhibition greatly impact detection. We further successfully outline the invasion front of Ponto-Caspian gobies in a large river, the High Rhine in Switzerland, and thus demonstrate the applicability of the assay to lotic environments. The eDNA assay requires less time, equipment, manpower, skills, and financial resources than the conventional monitoring methods such as electrofishing, angling or diving. Samples can be taken by untrained individuals, and the assay can be performed by any molecular biologist on a conventional PCR machine. Therefore, this assay enables environment managers to map invaded areas independently of fishermen's' reports and fish community monitorings

Reconstructing the Cosmic Expansion History with a Monotonicity Prior

The cosmic expansion history, mapped by the Hubble parameter as a function of redshift, offers the most direct probe of the dark energy equation of state. One way to determine the Hubble parameter at different redshifts is essentially differentiating the cosmic age or distance with respect to redshift, which may incur large numerical errors with observational data. Taking the scenario that the Hubble parameter increases monotonically with redshift as a reasonable prior, we propose to enforce the monotonicity when reconstructing the Hubble parameter at a series of redshifts. Tests with mock type Ia supernova (SN Ia) data show that the monotonicity prior does not introduce significant biases and that errors on the Hubble parameter are greatly reduced compared to those determined with a flat prior at each redshift. Results from real SN Ia data are in good agreement with those based on ages of passively evolving galaxies. Although the Hubble parameter reconstructed from SN Ia distances does not necessarily provide more information than the distances themselves do, it offers a convenient way to compare with constraints from other methods. Moreover, the monotonicity prior is expected to be helpful to other probes that measure the Hubble parameter at multiple redshifts (e.g., baryon acoustic oscillations), and it may be generalized to other cosmological quantities that are reasonably monotonic with redshift.Comment: 10 pages, 7 figures, 3 tables; v3 added Monte Carlo analysis results; accepted for publicatio

RRS James Cook Cruise JC120 15 Apr - 19 May 2015. Manzanillo to Manzanillo, Mexico. Managing Impacts of Deep-seA resource exploitation (MIDAS): Clarion-Clipperton Zone North Eastern Area of Particular Environmental Interest

RRS James Cook Cruise JC120 was part of the Managing Impacts of Deep-seA resource exploitation (MIDAS) European Union Framework Programme 7 Project. It was jointly funded by the UK Natural Environment Research Council. JC120 was the first UK science cruise to the Clarion Clipperton Zone (CCZ) in the northern equatorial Pacific, an area likely to be targeted for deep-sea mining for polymetallic nodules. This cruise visited the north easternmost Area of Particular Environmental Importance (APEI). There are a total of nine of these APEIs situated to the north and south of the mining claim areas defined by the International Seabed Authority (ISA) across the CCZ. The APEIs have been delineated by the ISA as part of their environmental management plan for the CCZ and are designed to protect representative species and habitats for the CCZ. The APEIs have been designed based on surface ocean characteristics and the topography of the seafloor, estimated from satellite altimetry. At present there has been virtually no sampling of seafloor habitats or species in the APEIs. The NERC cruise aimed to change that. The cruise studied a representative area of the APEI in great detail at high resolution and over a variety of scales. This characterised the habitats, biology, physical and chemical conditions - adding important information about the CCZ in general and making a detailed baseline assessment for this area, which can be compared to other sites and used as a barometer of change in the deep sea associated with mining activities. The NERC cruise JC120 used a variety of tools for assessment of this >4000m deep area of the CCZ. Shipboard mapping of depth and backscatter were carried out (EM12). The autonomous underwater vehicle (AUV) Autosub6000 carried out wide-area acoustic surveys (Edgetech Side-scan sonar, EM2040 Multibeam Bathymetry and sub-bottom profiler), collected seabed photographs and made physical measurements of the water column of the APEI. There were also more detailed HD video and photographic surveys of the seafloor using the HyBIS vehicle. Sediment samples (megacore, boxcore and gravity core), water samples (CTD) and biological samples (Agassiz Trawl) were also collected

Distinct oceanic microbiomes from viruses to protists located near the Antarctic Circumpolar Current

Microbes occupy diverse ecological niches and only through recent advances in next generation sequencing technologies have the true microbial diversity been revealed. Furthermore, lack of perceivable marine barriers to genetic dispersal (i.e., mountains or islands) has allowed the speculation that organisms that can be easily transported by currents and therefore proliferate everywhere. That said, ocean currents are now commonly being recognized as barriers for microbial dispersal. Here we analyzed samples collected from a total of six stations, four located in the Indian Ocean, and two in the Southern Ocean. Amplicon sequencing was used to characterize both prokaryotic and eukaryotic plankton communities, while shotgun sequencing was used for the combined environmental DNA (eDNA), microbial eDNA (meDNA), and viral fractions. We found that Cyanobacteria dominated the prokaryotic component in the South-West Indian Ocean, while γ-Proteobacteria dominated the South-East Indian Ocean. A combination of γ- and α-Proteobacteria dominated the Southern Ocean. Alveolates dominated almost exclusively the eukaryotic component, with variation in the ratio of Protoalveolata and Dinoflagellata depending on station. However, an increase in haptophyte relative abundance was observed in the Southern Ocean. Similarly, the viral fraction was dominated by members of the order Caudovirales across all stations; however, a higher presence of nucleocytoplasmic large DNA viruses (mainly chloroviruses and mimiviruses) was observed in the Southern Ocean. To our knowledge, this is the first that a statistical difference in the microbiome (from viruses to protists) between the subtropical Indian and Southern Oceans. We also show that not all phylotypes can be found everywhere, and that meDNA is not a suitable resource for monitoring aquatic microbial diversity

Support for Integrated Ecosystem Assessments of NOAA’s National Estuarine Research Reserves System (NERRS), Volume I: The Impacts of Coastal Development on the Ecology and Human Well-being of Tidal Creek Ecosystems of the US Southeast

A study was conducted, in association with the Sapelo Island and North Carolina National Estuarine Research Reserves (NERRs), to evaluate the impacts of coastal development on sentinel habitats (e.g., tidal creek ecosystems), including potential impacts to human health and well-being. Uplands associated with southeastern tidal creeks and the salt marshes they drain are popular locations for building homes, resorts, and recreational facilities because of the high quality of life and mild climate associated with these environments. Tidal creeks form part of the estuarine ecosystem characterized by high biological productivity, great ecological value, complex environmental gradients, and numerous interconnected processes. This research combined a watershed-level study integrating ecological, public health and human dimension attributes with watershed-level land use data. The approach used for this research was based upon a comparative watershed and ecosystem approach that sampled tidal creek networks draining developed watersheds (e.g., suburban, urban, and industrial) as well as undeveloped sites. The primary objective of this work was to clearly define the relationships between coastal development with its concomitant land use changes and non-point source pollution loading and the ecological and human health and well-being status of tidal creek ecosystems. Nineteen tidal creek systems, located along the southeastern United States coast from southern North Carolina to southern Georgia, were sampled during summer (June-August), 2005 and 2006. Within each system, creeks were divided into two primary segments based upon tidal zoning: intertidal (i.e., shallow, narrow headwater sections) and subtidal (i.e., deeper and wider sections), and watersheds were delineated for each segment. In total, we report findings on 24 intertidal and 19 subtidal creeks. Indicators sampled throughout each creek included water quality (e.g., dissolved oxygen concentration, salinity, nutrients, chlorophyll-a levels), sediment quality (e.g., characteristics, contaminants levels including emerging contaminants), pathogen and viral indicators, and abundance and genetic responses of biological resources (e.g., macrobenthic and nektonic communities, shellfish tissue contaminants, oyster microarray responses). For many indicators, the intertidally-dominated or headwater portions of tidal creeks were found to respond differently than the subtidally-dominated or larger and deeper portions of tidal creeks. Study results indicate that the integrity and productivity of headwater tidal creeks were impaired by land use changes and associated non-point source pollution, suggesting these habitats are valuable early warning sentinels of ensuing ecological impacts and potential public health threats. For these headwater creeks, this research has assisted the validation of a previously developed conceptual model for the southeastern US region. This conceptual model identified adverse changes that generally occurred in the physical and chemical environment (e.g., water quality indicators such as indicator bacteria for sewage pollution or sediment chemical contamination) when impervious cover levels in the watershed reach 10-20%. Ecological characteristics responded and were generally impaired when impervious cover levels exceed 20-30%. Estimates of impervious cover levels defining where human uses are impaired are currently being determined, but it appears that shellfish bed closures and the flooding vulnerability of headwater regions become a concern when impervious cover values exceed 10-30%. This information can be used to forecast the impacts of changing land use patterns on tidal creek environmental quality as well as associated human health and well-being. In addition, this study applied tools and technologies that are adaptable, transferable, and repeatable among the high quality NERRS sites as comparable reference entities to other nearby developed coastal watersheds. The findings herein will be of value in addressing local, regional and national needs for understanding multiple stressor (anthropogenic and human impacts) effects upon estuarine ecosystems and response trends in ecosystem condition with changing coastal impacts (i.e., development, climate change). (PDF contaions 88 pages

RRS Discovery Cruise DY032, 20 Jun - 07 Jul 2014. Cruise to the Porcupine Abyssal Plain sustained observatory

The Porcupine Abyssal Plain Observatory is a sustained, multidisciplinary observatory in the North Atlantic coordinated by the National Oceanography Centre, Southampton. For over 20 years the observatory has provided key time-series datasets for analysing the effect of climate change on the open ocean and deep-sea ecosystems. As is normally the case during cruises which are needed to refurbish the observatory, a wide range of other activities were carried out during the cruise. The main mooring Ocean Data Acquisition System (ODAS) buoy had ceased transmitting data in March 2015, so a high priority was to recover the buoy and its stored data and this was successfully achieved. In addition, we recovered a set of sediment traps which had been collecting sinking material in the lower part of the water column for the previous 12 months and deployed a new set. These are the autonomous systems, but as is usually the case with our trips to PAP, we carried out various other activities and in this case we investigated the degradation of particles as they sink. Our colleagues from MIO in France carry out sophisticated interrogation using radiolabelling. The Bathysnap time-lapse camera system which had been taking photos of the seabed at 4800m was recovered to give an assessment of the behaviour of the benthic animals and how the seabed appearance changes in response to deposition of material. A new module was deployed. Temporal variability of the water column and seabed fauna - a task which is difficult or impossible to do autonomously was assessed using nets and cores