The restoration of intertidal habitats for non-breeding waterbirds through breached managed realignment

Conservation of intertidal habitats in the UK is vital in order to continue to support nationally and internationally important populations of non-breeding waterbirds. Historic reclamation for agriculture and industry has resulted in the loss and degradation of large areas of these intertidal habitats in estuaries and they continue to be threatened by sea-level rise. Managed realignment is one method which is increasingly being used to restore intertidal habitats. As managed realignment is a relatively new restoration technique, the extent to which knowledge of the biology of estuaries is applicable to managed realignment sites is unclear. Habitat restoration is often unsuccessful or incomplete, so a detailed knowledge of both the natural system and the characteristics of restored systems will usually be necessary to recreate fully-functional estuarine habitats. This thesis focuses on Nigg Bay Managed Realignment Site (Nigg Bay MRS), the first managed realignment site in Scotland, and follows the first four years of ecological development to gain an understanding of how breached realignment can be used to restore intertidal habitats to support non-breeding waterbirds. This thesis has six major aims: (i) to describe the development of saltmarsh, (ii) to describe the development of intertidal flat, (iii) to describe the colonisation by non-breeding waterbirds (iv) to determine how tidal cycle and weather affect patterns of waterbird use, (v) to determine which factors affect the spatial distribution of waders and finally (vi) to determine the patterns of use by individual birds. Four summers after the re-establishment of tidal conditions, almost all of the saltmarsh species recorded on the nearby saltmarsh had colonised Nigg Bay MRS, although recognisable communities had yet to establish. Three winters after the re- establishment of tidal conditions in Nigg Bay MRS, the sediments had a significantly smaller particle size and higher organic matter content compared to the fine sands of the adjacent intertidal flats. The intertidal invertebrate community also differed from the adjacent intertidal flats. Nigg Bay MRS attracted large numbers of non-breeding waterbirds and supported each of the most common wader and wildfowl species present in the wider estuary. Nigg Bay MRS performs a number of important functions for non-breeding waterbirds by: (i) providing a foraging and resting habitat when the tide is absent and intertidal sediments in Nigg Bay are exposed; (ii) providing a foraging resource as the tide passes over the intertidal sediments within the site once the intertidal flats in Nigg Bay are inundated; and (iii) providing a high tide roosting site. On days with low temperatures and high wind speeds, more waterbirds use Nigg Bay MRS, suggesting that it is likely to be providing sheltering benefits. Nigg Bay MRS also provides top-up feeding habitat. The factors that often influence the spatial distributions of waders in estuaries appear to be operating within Nigg Bay MRS. Wader densities are greater on the intertidal flats when they are accessible than on the saltmarsh. Wader densities are also greatest close to creeks and drainage channels, possibly due to higher invertebrate densities, more accessible prey or sheltering benefits. Colour-ringing and radio-tracking of Common Redshank established that Nigg Bay MRS has a subset of regular users, including both adults and juveniles, and the wader assemblage at night may differ from the assemblage during the day. These findings are discussed in terms of the implications for locating, designing and managing future managed realignment projects.EThOS - Electronic Theses Online ServiceRSPB : University of Stirling : SNHGBUnited Kingdo

Immunization with the C-domain of α-toxin prevents lethal infection, localizes tissue injury, and promotes host response to challenge with Clostridium perfringens

© 2004 by the Infectious Diseases Society of America. All rights reserved.Clostridium perfringens gas gangrene is characterized by rapid tissue destruction, impaired host response, and, often, death. Phospholipase C (α-toxin) is the virulence factor most responsible for these pathologies. The present study investigated the efficacy of active immunization with the C-terminal domain of α-toxin (Cpa247–370) in a murine model of gas gangrene. Primary end points of the study were survival, progression of infection, and tissue perfusion. Secondary end points, which were based on findings of histologic evaluation of tissues, included the extent of tissue destruction and microvascular thrombosis, as well as the magnitude of the tissue inflammatory response. Survival among C-domain–immunized animals was significantly greater than that among sham-immunized control animals. Furthermore, immunization with the C-domain localized the infection and prevented ischemia of the feet. Histopathologic findings demonstrated limited muscle necrosis, reduced microvascular thrombosis, and enhanced granulocytic influx in C-domain–immunized mice. We conclude that immunization with the C-domain of phospholipase C is a viable strategy for the prevention of morbidity and mortality associated with C. perfringens gas gangrene

Fatal S. aureus Hemorrhagic Pneumonia: Genetic Analysis of a Unique Clinical Isolate Producing both PVL and TSST-1

In 2008, an unusual strain of methicillin-sensitive Staphylococcus aureus (MSSA68111), producing both Panton-Valentine leukocidin (PVL) and toxic shock syndrome toxin-1 (TSST-1), was isolated from a fatal case of necrotizing pneumonia. Because PVL/TSST-1 co-production in S. aureus is rare, we characterized the molecular organization of these toxin genes in strain 68111. MSSA68111 carries the PVL genes within a novel temperate prophage we call ФPVLv68111 that is most similar, though not identical, to phage ФPVL – a phage type that is relatively rare worldwide. The TSST-1 gene (tst) in MSSA68111 is carried on a unique staphylococcal pathogenicity island (SaPI) we call SaPI68111. Features of SaPI68111 suggest it likely arose through multiple major recombination events with other known SaPIs. Both ФPVLv68111 and SaPI68111 are fully mobilizable and therefore transmissible to other strains. Taken together, these findings suggest that hypervirulent S. aureus have the potential to emerge worldwide

Intrauterine Device Placement During Cesarean Delivery and Continued Use 6 Months Postpartum: A Randomized Controlled Trial

To compare intrauterine device (IUD) use at 6 months postpartum among women who underwent intracesarean delivery (during cesarean delivery) IUD placement versus women who planned for interval IUD placement 6 or more weeks postpartum

Dihydrodinophysistoxin-1 Produced by Dinophysis norvegica in the Gulf of Maine, USA and Its Accumulation in Shellfish

Dihydrodinophysistoxin-1 (dihydro-DTX1, (M-H)−m/z 819.5), described previously from a marine sponge but never identified as to its biological source or described in shellfish, was detected in multiple species of commercial shellfish collected from the central coast of the Gulf of Maine, USA in 2016 and in 2018 during blooms of the dinoflagellate Dinophysis norvegica. Toxin screening by protein phosphatase inhibition (PPIA) first detected the presence of diarrhetic shellfish poisoning-like bioactivity; however, confirmatory analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) failed to detect okadaic acid (OA, (M-H)−m/z 803.5), dinophysistoxin-1 (DTX1, (M-H)−m/z 817.5), or dinophysistoxin-2 (DTX2, (M-H)−m/z 803.5) in samples collected during the bloom. Bioactivity-guided fractionation followed by liquid chromatography-high resolution mass spectrometry (LC-HRMS) tentatively identified dihydro-DTX1 in the PPIA active fraction. LC-MS/MS measurements showed an absence of OA, DTX1, and DTX2, but confirmed the presence of dihydro-DTX1 in shellfish during blooms of D. norvegica in both years, with results correlating well with PPIA testing. Two laboratory cultures of D. norvegica isolated from the 2018 bloom were found to produce dihydro-DTX1 as the sole DSP toxin, confirming the source of this compound in shellfish. Estimated concentrations of dihydro-DTX1 were \u3e0.16 ppm in multiple shellfish species (max. 1.1 ppm) during the blooms in 2016 and 2018. Assuming an equivalent potency and molar response to DTX1, the authority initiated precautionary shellfish harvesting closures in both years. To date, no illnesses have been associated with the presence of dihydro-DTX1 in shellfish in the Gulf of Maine region and studies are underway to determine the potency of this new toxin relative to the currently regulated DSP toxins in order to develop appropriate management guidance

Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9

Thermostable clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas9) enzymes could improve genome-editing efficiency and delivery due to extended protein lifetimes. However, initial experimentation demonstrated Geobacillus stearothermophilus Cas9 (GeoCas9) to be virtually inactive when used in cultured human cells. Laboratory-evolved variants of GeoCas9 overcome this natural limitation by acquiring mutations in the wedge (WED) domain that produce >100-fold-higher genome-editing levels. Cryoelectron microscopy (cryo-EM) structures of the wild-type and improved GeoCas9 (iGeoCas9) enzymes reveal extended contacts between the WED domain of iGeoCas9 and DNA substrates. Biochemical analysis shows that iGeoCas9 accelerates DNA unwinding to capture substrates under the magnesium-restricted conditions typical of mammalian but not bacterial cells. These findings enabled rational engineering of other Cas9 orthologs to enhance genome-editing levels, pointing to a general strategy for editing enzyme improvement. Together, these results uncover a new role for the Cas9 WED domain in DNA unwinding and demonstrate how accelerated target unwinding dramatically improves Cas9-induced genome-editing activity

Evaluation of a clinical decision support strategy to increase seasonal influenza vaccination among hospitalized children before inpatient discharge

Importance: Hospitalized children are at increased risk of influenza-related complications, yet influenza vaccine coverage remains low among this group. Evidence-based strategies about vaccination of vulnerable children during all health care visits are especially important during the COVID-19 pandemic. Objective: To design and evaluate a clinical decision support (CDS) strategy to increase the proportion of eligible hospitalized children who receive a seasonal influenza vaccine prior to inpatient discharge. Design, Setting, and Participants: This quality improvement study was conducted among children eligible for the seasonal influenza vaccine who were hospitalized in a tertiary pediatric health system providing care to more than half a million patients annually in 3 hospitals. The study used a sequential crossover design from control to intervention and compared hospitalizations in the intervention group (2019-2020 season with the use of an intervention order set) with concurrent controls (2019-2020 season without use of an intervention order set) and historical controls (2018-2019 season with use of an order set that underwent intervention during the 2019-2020 season). Interventions: A CDS intervention was developed through a user-centered design process, including (1) placing a default influenza vaccine order into admission order sets for eligible patients, (2) a script to offer the vaccine using a presumptive strategy, and (3) just-in-time education for clinicians addressing vaccine eligibility in the influenza order group with links to further reference material. The intervention was rolled out in a stepwise fashion during the 2019-2020 influenza season. Main Outcomes and Measures: Proportion of eligible hospitalizations in which 1 or more influenza vaccines were administered prior to discharge. Results: Among 17 740 hospitalizations (9295 boys [52%]), the mean (SD) age was 8.0 (6.0) years, and the patients were predominantly Black (n = 8943 [50%]) or White (n = 7559 [43%]) and mostly had public insurance (n = 11 274 [64%]). There were 10 997 hospitalizations eligible for the influenza vaccine in the 2019-2020 season. Of these, 5449 (50%) were in the intervention group, and 5548 (50%) were concurrent controls. There were 6743 eligible hospitalizations in 2018-2019 that served as historical controls. Vaccine administration rates were 31% (n = 1676) in the intervention group, 19% (n = 1051) in concurrent controls, and 14% (n = 912) in historical controls (P \u3c .001). In adjusted analyses, the odds of receiving the influenza vaccine were 3.25 (95% CI, 2.94-3.59) times higher in the intervention group and 1.28 (95% CI, 1.15-1.42) times higher in concurrent controls than in historical controls. Conclusions and Relevance: This quality improvement study suggests that user-centered CDS may be associated with significantly improved influenza vaccination rates among hospitalized children. Stepwise implementation of CDS interventions was a practical method that was used to increase quality improvement rigor through comparison with historical and concurrent controls

RNA signatures allow rapid identification of pathogens and antibiotic susceptibilities

With rising rates of drug-resistant infections, there is a need for diagnostic methods that rapidly can detect the presence of pathogens and reveal their susceptibility to antibiotics. Here we propose an approach to diagnosing the presence and drug-susceptibility of infectious diseases based on direct detection of RNA from clinical samples. We demonstrate that species-specific RNA signatures can be used to identify a broad spectrum of infectious agents, including bacteria, viruses, yeast, and parasites. Moreover, we show that the behavior of a small set of bacterial transcripts after a brief antibiotic pulse can rapidly differentiate drug-susceptible and -resistant organisms and that these measurements can be made directly from clinical materials. Thus, transcriptional signatures could form the basis of a uniform diagnostic platform applicable across a broad range of infectious agents

High-Throughput Analysis of Lung Immune Cells in a Combined Murine Model of Agriculture Dust-Triggered Airway Inflammation With Rheumatoid Arthritis

Rheumatoid arthritis (RA)-associated lung disease is a leading cause of mortality in RA, yet the mechanisms linking lung disease and RA remain unknown. Using an established murine model of RA-associated lung disease combining collagen-induced arthritis (CIA) with organic dust extract (ODE)-induced airway inflammation, differences among lung immune cell populations were analyzed by single cell RNA-sequencing. Additionally, four lung myeloid-derived immune cell populations including macrophages, monocytes/macrophages, monocytes, and neutrophils were isolated by fluorescence cell sorting and gene expression was determined by NanoString analysis. Unsupervised clustering revealed 14 discrete clusters among Sham, CIA, ODE, and CIA+ODE treatment groups: 3 neutrophils (inflammatory, resident/transitional, autoreactive/suppressor), 5 macrophages (airspace, differentiating/recruited, recruited, resident/interstitial, and proliferative airspace), 2 T-cells (differentiating and effector), and a single cluster each of inflammatory monocytes, dendritic cells, B-cells and natural killer cells. Inflammatory monocytes, autoreactive/suppressor neutrophils, and recruited/differentiating macrophages were predominant with arthritis induction (CIA and CIA+ODE). By specific lung cell isolation, several interferon-related and autoimmune genes were disproportionately expressed among CIA and CIA+ODE (e.g. Oasl1, Oas2, Ifit3, Gbp2, Ifi44, and Zbp1), corresponding to RA and RA-associated lung disease. Monocytic myeloid-derived suppressor cells were reduced, while complement genes (e.g. C1s1 and Cfb) were uniquely increased in CIA+ODE mice across cell populations. Recruited and inflammatory macrophages/monocytes and neutrophils expressing interferon-, autoimmune-, and complement-related genes might contribute towards pro-fibrotic inflammatory lung responses following airborne biohazard exposures in setting of autoimmune arthritis and could be predictive and/or targeted to reduce disease burden

Dihydrodinophysistoxin-1 produced by Dinophysis norvegica in the Gulf of Maine, USA and its accumulation in shellfish

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Deeds, J. R., Stutts, W. L., Celiz, M. D., MacLeod, J., Hamilton, A. E., Lewis, B. J., Miller, D. W., Kanwit, K., Smith, J. L., Kulis, D. M., McCarron, P., Rauschenberg, C. D., Burnell, C. A., Archer, S. D., Borchert, J., & Lankford, S. K. Dihydrodinophysistoxin-1 produced by Dinophysis norvegica in the Gulf of Maine, USA and its accumulation in shellfish. Toxins, 12(9), (2020): E533, doi:10.3390/toxins12090533.Dihydrodinophysistoxin-1 (dihydro-DTX1, (M-H)−m/z 819.5), described previously from a marine sponge but never identified as to its biological source or described in shellfish, was detected in multiple species of commercial shellfish collected from the central coast of the Gulf of Maine, USA in 2016 and in 2018 during blooms of the dinoflagellate Dinophysis norvegica. Toxin screening by protein phosphatase inhibition (PPIA) first detected the presence of diarrhetic shellfish poisoning-like bioactivity; however, confirmatory analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) failed to detect okadaic acid (OA, (M-H)−m/z 803.5), dinophysistoxin-1 (DTX1, (M-H)−m/z 817.5), or dinophysistoxin-2 (DTX2, (M-H)−m/z 803.5) in samples collected during the bloom. Bioactivity-guided fractionation followed by liquid chromatography-high resolution mass spectrometry (LC-HRMS) tentatively identified dihydro-DTX1 in the PPIA active fraction. LC-MS/MS measurements showed an absence of OA, DTX1, and DTX2, but confirmed the presence of dihydro-DTX1 in shellfish during blooms of D. norvegica in both years, with results correlating well with PPIA testing. Two laboratory cultures of D. norvegica isolated from the 2018 bloom were found to produce dihydro-DTX1 as the sole DSP toxin, confirming the source of this compound in shellfish. Estimated concentrations of dihydro-DTX1 were >0.16 ppm in multiple shellfish species (max. 1.1 ppm) during the blooms in 2016 and 2018. Assuming an equivalent potency and molar response to DTX1, the authority initiated precautionary shellfish harvesting closures in both years. To date, no illnesses have been associated with the presence of dihydro-DTX1 in shellfish in the Gulf of Maine region and studies are underway to determine the potency of this new toxin relative to the currently regulated DSP toxins in order to develop appropriate management guidance.Partial support for this research was received from the National Oceanic and Atmospheric Administration, National Centers for Coastal Ocean Science Competitive Research, Ecology and Oceanography of Harmful Algal Blooms Program under awards NA17NOS4780184 and NA19NOS4780182 to Juliette Smith (VIMS) and Jonathan Deeds (US FDA), and Prevention, Control, and Mitigation of Harmful Algal Blooms program award NA17NOS4780179 to Stephen Archer. This paper is ECOHAB publication number EC0956