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

Environmental and ecological benefits and impacts of oyster aquaculture: Addendum

The data described in this addendum are provided to enhance the resolution and/or expand the temporal scope of the information already provided in the final report (Kellogg et al. 2018). High-resolution water quality transect data were collected at all four sites in Summer 2017, at White Stone (Windmill Point site) and Lynnhaven River in Fall 2017, and at White Stone (North Point site) in Spring 2018. During each sampling period, data were collected from multiple transects through and outside of each farm. Resulting data were detrended as needed based on temporal and salinity-related patterns found in data collected outside the farm footprint. Comparison of the resulting data from inside and outside the farm identified significant differences between water quality inside the farm footprint and outside for the majority of site x season combinations for all parameters. However, differences were consistently small enough to have no biologically significant impact, positive or negative, on farm-scale water quality. Benthic macrofaunal communities inside and outside the farms were assessed at White Stone’s Windmill Point site and at the Lynnhaven River site in Fall 2017 and White Stone’s North Point site in Spring 2018. Data on species richness, macrofauna abundance, and macrofauna biomass were compared between samples taken inside the farm footprint and outside the farm footprint for all site x season combinations. These data were compared to data previously reported from Summer 2017 collected at all four aquaculture sites. Overall, patterns in species richness and macrofauna abundance were not consistent across seasons within site, across sites within seasons or within gear type. With the exception of one of the farm sites studied, there was a trend towards increased macrofauna biomass inside the footprint of aquaculture farms. This pattern is consistent with the assumption that food for benthic macrofauna at these sites is enhanced by oyster biodeposition. Overall, we found no biologically significant negative impacts on macrofaunal communities inside aquaculture farms and some evidence that suggests a possible positive impact on benthic macrofauna production

Oyster reef ecosystem services: Finfish utilization and trophic linkages Harris Creek, Maryland, USA

Oyster reefs provide habitat for finfish and their prey. Our project focused on determining the impacts of oyster reef restoration on finfish in the Harris Creek Oyster Sanctuary in the Maryland portion of Chesapeake Bay. As a preliminary step, we examined the utility of using trawls in the place of gillnets to sample finfish but found that trawl samples were also highly variable and that the diets of finfish caught in trawls tended to be different than those caught in gillnets. Based on these findings and the fact that gillnets can be set within reef habitats, all remaining sampling was conducted using gillnets. To assess differences in finfish abundance on oyster reef compared to adjacent non-reef habitats, we used pairs of gillnets to determine catch per unit effort (CPUE). Of the species captured, only white perch showed significantly higher CPUE in reef habitats than in adjacent non-reef habitats. Using only data from on-reef sites, we examined the effect of reef type (restored vs. non-restored) on finfish CPUE. Reef type had no significant effect on CPUE for white perch or striped bass

Integrated assessment of oyster reef ecosystem services: Macrofauna utilization of restored oyster reefs

Within the Harris Creek Oyster Sanctuary in the Maryland portion of Chesapeake Bay, we evaluated relationships between basic oyster reef characteristics and the abundance and biomass of macrofauna. The eight sites selected for these studies included five restored oyster reef sites and three sites suitable for restoration that had not been restored. These sites encompassed a range of oyster biomass density and were spread throughout the sanctuary area. At each site one month prior to each of four sampling periods, divers filled four wire mesh baskets (0.1m2 surface area x 15 cm depth) with material from the site and embedded them so that the surface was flush with the surrounding substratum. In spring, early summer, late summer and fall of 2015, divers collected baskets and returned them to the laboratory where all macrofauna ≥1 mm were collected from each sample and their identity, abundance and biomass were determined. In addition to the abundance and biomass of oysters, we also assessed the amount of surface as the volume of live oysters along with that of any oyster shells whose surface was at least 50% oxic based on coloration (i.e. black shell was presumed to have been buried below the surface in anoxic conditions). Positive relationships were identified for all three reef characteristics and the three major macrofaunal groups examined. In the majority of seasons, the relationship between both biomass and abundance of the hooked mussel, Ischadium recurvum, as a power function of oyster tissue biomass density, oyster abundance per square meter and surface shell volume. The relationship between oyster reef characteristics and the biomass and abundance of the mud crab, Eurypanopeus depressus, and of the naked goby, Gobiosoma bosc, were always positive but were more variable than that for I. recurvum. These data demonstrate that relationships can be found between oyster reef characteristics and macrofauna abundance and biomass. They further demonstrate that, in many cases, simple measures of reef characteristics such as oyster abundance and shell volume can provide predictions of macrofauna abundance and biomass that are comparable to more labor intensive measures such as oyster tissue biomass

Integrated assessment of oyster reef ecosystem services: Fish and crustacean utilization and trophic linkages

Using a regression design that encompassed the continuum of oyster reef biomass density in Harris Creek, MD, from unrestored reefs to those restored reefs with the greatest oyster biomass, we examined finfish and crustacean utilization of these habitats. Of the eight sites studied, three had not been subject to any restoration activities and five had been planted in 2012 with juvenile oysters set on oyster shell. All sites were sampled in April, June, August, and October 2015. During each sampling period, we assessed abundance, total length and biomass of finfish and examined gut contents to assess the diets of selected finfish species. Of the species collected that were likely to use reefs as habitat or a foraging ground, only striped bass and white perch were sufficiently abundant to support robust statistical analyses. Regression analyses found no clear relationship between oyster biomass density and catch per unit effort, total length or biomass for striped bass or white perch. Analyses of the effects of sampling period and restoration status (restored versus non-restored sites) on fish utilization frequently found an effect of sampling period but rarely found an effect of restoration status. In all cases where differences were detected, they suggested greater utilization of non-restored sites. Overall, data were sparse and the power of statistical analyses was low. Analyses of striped bass and white perch diets suggest that they are using oyster reefs as a foraging ground. Although comparisons of the proportion of striped bass and white perch that contained prey in their stomachs found no difference between those caught on restored sites versus non-restored sites, gut contents of both species contained prey taxa that are likely more abundant on restored oyster reefs than nonrestored sites. As a percentage of total prey wet weight, polychaete worms were the most important component of striped bass diets in both April (50%) and August (47%). Of the polychaete worms identifiable to species, 100% were Alitta succinea, a species found in much greater abundance and biomass on restored oyster reefs than on comparable non-restored sites (Kellogg et al. 2013, Rodney and Paynter 2006). White perch diets were dominated by the ascidian Molgula manhattensis (52%), a species generally found in greater abundance on hard substrates including oyster reefs. Of the identifiable species of fish found in the stomachs of striped bass, 93% by weight were naked gobies (Gobiosoma bosc) or striped blennies (Chasmodes bosquianus), two species found in greater abundance and biomass on restored oyster reefs than nonrestored sites in Chesapeake Bay (Kellogg et al. 2013, Rodney and Paynter 2006). For white perch, naked gobies accounted for 95% of the identifiable fish species by weight. Direct comparisons of white perch and striped bass diets to the prey fields at each sampling site will be conducted as part of a companion project also funded by NOAA Chesapeake Bay Office (Award #: NA13NMF4570209: Integrated assessment of oyster reef ecosystem services: Macrofaunal utilization, secondary production and nutrient sequestration). This companion project will also provide data on abundance, biomass and distribution of small, reef-associated species including naked gobies, striped blennies, and oyster toadfish (Opsanus tau)

Scaling Ecosystem Services to Reef Development : Effects of oyster density on nitrogen removal and reef community structure

Eighteen native oyster experimental reefs (16-m2 each) were restored using six oyster densities (0, 10, 25, 50, 100 and 250 adult oysters m-2) with three replicates of each density at each of two sites: one subtidal site in Onancock Creek, Virginia and one intertidal site in Hillcrest Oyster Sanctuary within The Nature Conservancy’s Virginia Coast Reserve. A science-based monitoring program explored quantitative relationships between structural and functional characteristics of these restored reefs. Structural parameters examined included oyster abundance, oyster size/biomass, surface shell volume, reef topographic complexity and sediment characteristics. Functional parameters included denitrification rates and macrofaunal abundance and biomass. Data were collected from the intertidal site during six sampling periods between April 2012 and July 2013 and from the subtidal site in April and June 2012. Relationships between reef structural parameters and functional parameters were complex and variable. As of July 2014, the intertidal reefs continue to serve as a platform for continued studies of the relationships between reef structural and functional characteristics

iAnn: an event sharing platform for the life sciences

Summary: We present iAnn, an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. iAnn allows automatic visualisation and integration of customised event reports. A central repository lies at the core of the platform: curators add submitted events, and these are subsequently accessed via web services. Thus, once an iAnn widget is incorporated into a website, it permanently shows timely relevant information as if it were native to the remote site. At the same time, announcements submitted to the repository are automatically disseminated to all portals that query the system. To facilitate the visualization of announcements, iAnn provides powerful filtering options and views, integrated in Google Maps and Google Calendar. All iAnn widgets are freely available. Availability: http://iann.pro/iannviewer Contact: [email protected]

HNF4A and GATA6 loss reveals therapeutically actionable subtypes in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) can be divided into transcriptomic subtypes with two broad lineages referred to as classical (pancreatic) and squamous. We find that these two subtypes are driven by distinct metabolic phenotypes. Loss of genes that drive endodermal lineage specification, HNF4A and GATA6, switch metabolic profiles from classical (pancreatic) to predominantly squamous, with glycogen synthase kinase 3 beta (GSK3β) a key regulator of glycolysis. Pharmacological inhibition of GSK3β results in selective sensitivity in the squamous subtype; however, a subset of these squamous patient-derived cell lines (PDCLs) acquires rapid drug tolerance. Using chromatin accessibility maps, we demonstrate that the squamous subtype can be further classified using chromatin accessibility to predict responsiveness and tolerance to GSK3β inhibitors. Our findings demonstrate that distinct patterns of chromatin accessibility can be used to identify patient subgroups that are indistinguishable by gene expression profiles, highlighting the utility of chromatin-based biomarkers for patient selection in the treatment of PDAC

Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer

Background and aims: Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress and novel therapeutic response in PC to develop a biomarker driven therapeutic strategy targeting DDR and replication stress in PC. Methods: We interrogated the transcriptome, genome, proteome and functional characteristics of 61 novel PC patient-derived cell lines to define novel therapeutic strategies targeting DDR and replication stress. Validation was done in patient derived xenografts and human PC organoids. Results: Patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, co-segregates with response to platinum (P < 0.001) and PARP inhibitor therapy (P < 0.001) in vitro and in vivo. We generated a novel signature of replication stress with which predicts response to ATR (P < 0.018) and WEE1 inhibitor (P < 0.029) treatment in both cell lines and human PC organoids. Replication stress was enriched in the squamous subtype of PC (P < 0.001) but not associated with DDR deficiency. Conclusions: Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR proficient PC, and post-platinum therapy

Hyperoxemia and excess oxygen use in early acute respiratory distress syndrome : Insights from the LUNG SAFE study

Publisher Copyright: © 2020 The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.Background: Concerns exist regarding the prevalence and impact of unnecessary oxygen use in patients with acute respiratory distress syndrome (ARDS). We examined this issue in patients with ARDS enrolled in the Large observational study to UNderstand the Global impact of Severe Acute respiratory FailurE (LUNG SAFE) study. Methods: In this secondary analysis of the LUNG SAFE study, we wished to determine the prevalence and the outcomes associated with hyperoxemia on day 1, sustained hyperoxemia, and excessive oxygen use in patients with early ARDS. Patients who fulfilled criteria of ARDS on day 1 and day 2 of acute hypoxemic respiratory failure were categorized based on the presence of hyperoxemia (PaO2 > 100 mmHg) on day 1, sustained (i.e., present on day 1 and day 2) hyperoxemia, or excessive oxygen use (FIO2 ≥ 0.60 during hyperoxemia). Results: Of 2005 patients that met the inclusion criteria, 131 (6.5%) were hypoxemic (PaO2 < 55 mmHg), 607 (30%) had hyperoxemia on day 1, and 250 (12%) had sustained hyperoxemia. Excess FIO2 use occurred in 400 (66%) out of 607 patients with hyperoxemia. Excess FIO2 use decreased from day 1 to day 2 of ARDS, with most hyperoxemic patients on day 2 receiving relatively low FIO2. Multivariate analyses found no independent relationship between day 1 hyperoxemia, sustained hyperoxemia, or excess FIO2 use and adverse clinical outcomes. Mortality was 42% in patients with excess FIO2 use, compared to 39% in a propensity-matched sample of normoxemic (PaO2 55-100 mmHg) patients (P = 0.47). Conclusions: Hyperoxemia and excess oxygen use are both prevalent in early ARDS but are most often non-sustained. No relationship was found between hyperoxemia or excessive oxygen use and patient outcome in this cohort. Trial registration: LUNG-SAFE is registered with ClinicalTrials.gov, NCT02010073publishersversionPeer reviewe