Vibrio elicits targeted transcriptional responses from copepod hosts

Author Posting. © The Author(s), 2016. This is the author's version of the work. It is posted here by permission of Federation of European Microbiological Societies for personal use, not for redistribution. The definitive version was published in FEMS Microbiology Ecology 92 (2016): fiw072, doi:10.1093/femsec/fiw072.Copepods are abundant crustaceans that harbor diverse bacterial communities, yet the nature of their interactions with microbiota are poorly understood . Here, we report that Vibrio elicits targeted transcriptional responses in the estuarine copepod Eurytemora affinis. We pre-treated E. affinis with an antibiotic-cocktail and exposed them to either a zooplankton specialist (Vibrio sp. F10 9ZB36) or a free-living species (V. ordalii 12B09) for 24 hours. We then identified via RNA-Seq a total of 78 genes that were differentially expressed following Vibrio exposure, including homologs of C-type lectins, chitin-binding proteins and saposins. The response differed between the two Vibrio treatments, with the greatest changes elicited upon inoculation with V. sp. F10. We suggest that these differentially regulated genes play important roles in cuticle integrity, the innate immune response, and general stress responses, and that their expression may enable E. affinis to recognize and regulate symbiotic vibrios. We further report that V. sp. F10 culturability is specifically altered upon colonization of E. affinis. These findings suggest that rather than acting as passive environmental vectors, copepods discriminately interact with vibrios, which may ultimately impact the abundance and activity of copepod-associated bacteria.2017-04-0

The Differences in Antibiotic Decision-making Between Acute Surgical and Acute Medical Teams: An Ethnographic Study of Culture and Team Dynamics

Background Cultural and social determinants influence antibiotic decision-making in hospitals. We investigated and compared cultural determinants of antibiotic decision-making in acute medical and surgical specialties. Methods An ethnographic observational study of antibiotic decision-making in acute medical and surgical teams at a London teaching hospital was conducted (August 2015–May 2017). Data collection included 500 hours of direct observations, and face-to-face interviews with 23 key informants. A grounded theory approach, aided by Nvivo 11 software, analyzed the emerging themes. An iterative and recursive process of analysis ensured saturation of the themes. The multiple modes of enquiry enabled cross-validation and triangulation of the findings. Results In medicine, accepted norms of the decision-making process are characterized as collectivist (input from pharmacists, infectious disease, and medical microbiology teams), rationalized, and policy-informed, with emphasis on de-escalation of therapy. The gaps in antibiotic decision-making in acute medicine occur chiefly in the transition between the emergency department and inpatient teams, where ownership of the antibiotic prescription is lost. In surgery, team priorities are split between 3 settings: operating room, outpatient clinic, and ward. Senior surgeons are often absent from the ward, leaving junior staff to make complex medical decisions. This results in defensive antibiotic decision-making, leading to prolonged and inappropriate antibiotic use. Conclusions In medicine, the legacy of infection diagnosis made in the emergency department determines antibiotic decision-making. In surgery, antibiotic decision-making is perceived as a nonsurgical intervention that can be delegated to junior staff or other specialties. Different, bespoke approaches to optimize antibiotic prescribing are therefore needed to address these specific challenges

The frequency of item writing flaws in multiple-choice questions used in high stakes nursing assessments

Multiple-choice questions are a common assessment method in nursing examinations. Few nurse educators, however, have formal preparation in constructing multiple-choice questions. Consequently, questions used in baccalaureate nursing assessments often contain item-writing flaws, or violations to accepted item-writing guidelines. In one nursing department, 2770 MCQs were collected from tests and examinations administered over a five-year period from 2001 to 2005. Questions were evaluated for 19 frequently occurring item-writing flaws, for cognitive level, for question source, and for the distribution of correct answers. Results show that almost half (46.2%) of the questions contained violations of item-writing guidelines and over 90% were written at low cognitive levels. Only a small proportion of questions were teacher generated (14.1%), while 36.2% were taken from testbanks and almost half (49.4%) had no source identified. MCQs written at a lower cognitive level were significantly more likely to contain item-writing flaws. While there was no relationship between the source of the question and item-writing flaws, teachergenerated questions were more likely to be written at higher cognitive levels (p < 0.001). Correct answers were evenly distributed across all four options and no bias was noted in the placement of correct options. Further training in item-writing is recommended for all faculty members who are responsible for developing tests. Pre-test review and quality assessment is also recommended to reduce the occurrence of item-writing flaws and to improve the quality of test questions. © 2006 Elsevier Ltd. All rights reserved.postprin

Opportunities for system level improvement in antibiotic use across the surgical pathway

Optimizing antibiotic prescribing across the surgical pathway (before, during, and after surgery) is a key aspect of tackling important drivers of antimicrobial resistance and simultaneously decreasing the burden of infection at the global level. In the UK alone, 10 million patients undergo surgery every year, which is equivalent to 60% of the annual hospital admissions having a surgical intervention. The overwhelming majority of surgical procedures require effectively limited delivery of antibiotic prophylaxis to prevent infections. Evidence from around the world indicates that antibiotics for surgical prophylaxis are administered ineffectively, or are extended for an inappropriate duration of time postoperatively. Ineffective antibiotic prophylaxis can contribute to the development of surgical site infections (SSIs), which represent a significant global burden of disease. The World Health Organization estimates SSI rates of up to 50% in postoperative surgical patients (depending on the type of surgery), with a particular problem in low- and middle-income countries, where SSIs are the most frequently reported healthcare-associated infections. Across European hospitals, SSIs alone comprise 19.6% of all healthcare-acquired infections. Much of the scientific research in infection management in surgery is related to infection prevention and control in the operating room, surgical prophylaxis, and the management of SSIs, with many studies focusing on infection within the 30-day postoperative period. However it is important to note that SSIs represent only one of the many types of infection that can occur postoperatively. This article provides an overview of the surgical pathway and considers infection management and antibiotic prescribing at each step of the pathway. The aim was to identify the implications for research and opportunities for system improvement

Altered gene expression associated with epizootic shell disease in the American lobster, Homarus americanus

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Fish & Shellfish Immunology 29 (2010): 1003-1009, doi:10.1016/j.fsi.2010.08.008.Epizootic shell disease is a poorly understood condition that has significantly affected the American lobster fishery in New England (northeastern US) since the 1990s. Here we present the results of a study to identify changes in gene expression in lobsters exhibiting symptoms of epizootic shell disease. Suppressive subtractive hybridization (SSH) was used to compare gene expression between cDNA pools from diseased (symptomatic) and apparently healthy (asymptomatic) lobsters. Subsequently, quantitative real‐time polymerase chain reaction (qPCR) was used to measure expression of nine genes that were differentially‐expressed in the SSH analysis, in seven tissues (muscle, gill, heart, hepatopancreas, brain, branchiostegite, gonad) dissected from individual symptomatic and asymptomatic lobsters. Expression of arginine kinase (involved in cellular energetics) was significantly decreased in muscle of symptomatic lobsters. Expression of hemocyanin (a respiratory hemolymph protein involved in oxygen transport) was highest in hepatopancreas and showed highly variable expression with a trend toward higher expression in asymptomatic individuals. α2‐Macroglobulin (involved in the innate immune system) was most highly expressed in the ovary, particularly of symptomatic lobsters. The ESTs produced through this study add to the fledgling field of crustacean genomics and revealed three genes that could be further evaluated in lobsters of varying shell disease severity, molt stage, and reproductive condition, for possible implication in epizootic shell disease.Funding for this research was provided by the National Marine Fisheries Service as the ‘New England Lobster Research Initiative: Lobster Shell Disease’ under NOAA grant NA06NMF4720100 to the University of Rhode Island Fisheries Center

Assembly of a reference transcriptome for the gymnosome pteropod Clione limacina and profiling responses to short-term CO2 exposure

© The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Marine Genomics 34 (2017): 39-45, doi:10.1016/j.margen.2017.03.003.The gymnosome (unshelled) pteropod Clione limacina is a pelagic predatory mollusc found in polar and sub-polar regions. It has been studied for its distinctive swimming behavior and as an obligate predator on the closely related thecosome (shelled) pteropods. As concern about ocean acidification increases, it becomes useful to compare the physiological responses of closely-related calcifying and non-calcifying species to acidification. The goals of this study were thus to generate a reference transcriptome for Clione limacina, to expose individuals to CO2 for a period of 3 days, and to explore differential patterns of gene expression. Our Trinity assembly contained 300,994 transcripts of which ~26% could be annotated. In total, only 41 transcripts were differentially expressed following the CO2 treatment, consistent with a limited physiological response of this species to short-term CO2 exposure. The differentially expressed genes identified in our study were largely distinct from those identified in previous studies of thecosome pteropods, although some similar transcripts were identified, suggesting that comparison of these transcriptomes and responses may provide insight into differences in OA responses among phylogenetically and functionally distinct molluscan lineages.A. Thabet is grateful for a fellowship from the Egyptian Culture and Education Bureau and for mentoring from Drs. M.M. Sarhan and M.M. Fouda. Funding for this research was provided by a National Science Foundation grant to Lawson, Maas, and Tarrant (OCE-1316040)

Exploring residents' experiences of mealtimes in care homes: A qualitative interview study.

This is the final version of the article. Available from BioMed Central via the DOI in this record.BACKGROUND: Many interventions aim to alleviate well-documented problems of malnutrition in residential care homes and improve residents' health and wellbeing. Despite some positive findings, little is known about how and why mealtime interventions might be effective, and in particular, what effects residents' experiences of mealtimes have on health outcomes. The aim of this study was to gain an insight into these experiences and explore some of the issues that may impact on residents' enjoyment of meals, and resulting health and wellbeing. METHODS: Semi-structured interviews were conducted with eleven residents from four care homes in the South West UK. Thematic analysis was used to derive content and meaning from transcribed interviews. Interviews were supplemented by researcher observations of mealtimes. RESULTS: The dining experience was a focal point for participants' broader experiences of residing in a care home. Three themes pertaining to residents' experiences were identified: (1) Emotional and psychological connections with other residents; (2) managing competing interests with limited resources; and (3) familiarity and routine. CONCLUSION: Mealtimes are a mainstay of life in a care home through which residents' experiences are characterised, exemplified and magnified. Understanding how residents interact with one another, accommodating their preferences and encouraging autonomy may enhance their mealtime experiences. It may also help to ease the transition from independent-living to life in care, which can be particularly stressful for some residents, and improve health and wellbeing over the long-term.This research was funded by the National Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care South West Peninsula

Developing the 'gripes' tool for junior doctors to report concerns:a pilot study

Background Junior doctors often have concerns about quality and safety but show low levels of engagement with incident reporting systems. We aimed to develop and pilot a web-based reporting tool for junior doctors to proactively report concerns about quality and safety of care, and optimise it for future use. Methods We developed the gripes tool with input from junior doctors and piloted it at a large UK teaching hospital trust. We evaluated the tool through an analysis of concerns reported over a 3-month pilot period, and through interviews with five stakeholders and two focus groups with medical students and junior doctors about their views of the tool. Results Junior doctors reported 111 concerns during piloting, including a number of problems previously unknown to the trust. Junior doctors felt the tool was easy to use and encouraged them to report. Barriers to engagement included lack of motivation of junior doctors to report concerns, and fear of repercussions. Ensuring transparency about who would see reported concerns, and providing feedback across whole cohorts of junior doctors about concerns raised and how these had been addressed to improve patient safety at the trust, were seen having the potential to mitigate against these barriers. Sustainability of the tool was seen as requiring a revised model of staffing to share the load for responding to concerns and ongoing efforts to integrate the tool and data with other local systems for gathering intelligence about risks and incidents. Following piloting the trust committed to continuing to operate the gripes tool on an ongoing basis. Conclusions The gripes tool has the potential to enable trusts to proactively monitor and address risks to patient safety, but sustainability is likely to be dependent on organisational commitment to staffing the system and perceptions of added value over the longer term

De novo transcriptome assembly of the Southern Ocean copepod Rhincalanus gigas sheds light on developmental changes in gene expression

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Berger, C. A., Steinberg, D. K., Copley, N. J., & Tarrant, A. M. De novo transcriptome assembly of the Southern Ocean copepod Rhincalanus gigas sheds light on developmental changes in gene expression. Marine Genomics, (2021): 100835, https://doi.org/10.1016/j.margen.2021.100835.Copepods are small crustaceans that dominate most zooplankton communities in terms of both abundance and biomass. In the polar oceans, a subset of large lipid-storing copepods occupy central positions in the food web because of their important role in linking phytoplankton and microzooplankton with higher trophic levels. In this paper, we generated a high-quality de novo transcriptome for Rhincalanus gigas, the largest—and among the most abundant—of the Southern Ocean copepods. We then conducted transcriptional profiling to characterize the developmental transition between late-stage juveniles and adult females. We found that juvenile R. gigas substantially upregulate lipid synthesis and glycolysis pathways relative to females, as part of a developmental gene expression program that also implicates processes such as muscle growth, chitin formation, and ion transport. This study provides the first transcriptional profile of a developmental transition within Rhincalanus gigas or any endemic Southern Ocean copepod, thereby extending our understanding of copepod molecular physiology.Funding for this project was provided by the National Science Foundation (Grants OPP-1746087 to AMT and OPP-1440435 to DKS)

Life cycle and early development of the thecosomatous pteropod Limacina retroversa in the Gulf of Maine, including the effect of elevated CO2 levels

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Marine Biology 162 (2015): 2235-2249, doi:10.1007/s00227-015-2754-1.Thecosome pteropods are pelagic molluscs with aragonitic shells. They are considered to be especially vulnerable among plankton to ocean acidification (OA), but to recognize changes due to anthropogenic forcing a baseline understanding of their life history is needed. In the present study, adult Limacina retroversa were collected on five cruises from multiple sites in the Gulf of Maine (between 42° 22.1’–42° 0.0’ N and 69° 42.6’–70° 15.4’ W; water depths of ca. 45–260 m) from October 2013−November 2014. They were maintained in the laboratory under continuous light at 8° C. There was evidence of year-round reproduction and an individual life span in the laboratory of 6 months. Eggs laid in captivity were observed throughout development. Hatching occurred after 3 days, the veliger stage was reached after 6−7 days, and metamorphosis to the juvenile stage was after ~ 1 month. Reproductive individuals were first observed after 3 months. Calcein staining of embryos revealed calcium storage beginning in the late gastrula stage. Staining was observed in the shell gland, shell field, mantle, and shell margin in later stages. Exposure of two batches of larvae at the gastrula stage to elevated CO2 levels (800 and 1200 ppm) resulted in significantly increased mortality in comparison with individuals raised under ambient (~400 ppm) conditions and a developmental delay in the 1200 ppm treatment compared with the ambient and 800 ppm treatments.A. Thabet is grateful for a fellowship from the Egyptian Culture and Education Bureau and for mentoring from Drs. S.A. Saber, M.M. Sarhan and M.M. Fouda. Funding for this research was provided by a National Science Foundation grant to Lawson, Maas, and Tarrant (OCE-1316040). Additional support for field sampling was provided by the WHOI Coastal Ocean Institute and Pickman Foundation to Wang, Maas, and Lawson.2016-10-2