Omnivory and periphyton mats: uncoupling and quantifying consumer effects in the Florida Everglades

The role of omnivores in structuring communities is poorly understood. I studied the effect of two abundant omnivores, grass shrimp (Palaemonetes paludosas) and eastern mosquitofish (Gambusia holbrooki), on periphyton biomass of the Florida Everglades. I performed field experiments to test for consumer top-down and “complex” top-down effects on periphyton biomass. My experiments suggested that shrimp and mosquitofish had consumptive effects on periphyton but in many instances, periphyton wet weight, AFDM, and chlorophyll a increased significantly with shrimp or fish density, suggesting compensation by nutrient regeneration or trophic cascade processes. I propose that characteristic periphyton mat structure and integrity deters herbivory and affects the outcome of the periphyton-consumer interaction. Results from a descriptive study and a laboratory experiment support this hypothesis. Overall, consumption by shrimp and mosquitofish was significant, but coupled with and sometimes compensated by “complex” top-down effects, making these consumers “functional” omnivores

A comprehensive survey of Douglas Lake, Cheboygan County, MI.

Without knowledge of the natural state of a lake at a given degree of productivity and a profile of its features, it is at best difficult to define what the goal of lake and watershed conservation/management for a lake at that state of development should be. With the objective of developing a full profile of Douglas Lake, Cheboygan County, Michigan, a comprehensive survey was undertaken. The morphometric parameters investigated were a) the method of basin formation, b) morphometry of the lake basin and littoral zone, c) geology underlying the lake basin and watershed, d) underlying soils of the watershed, e) area of the watershed, and f) watershed land use patterns. Physical parameters measured in Douglas Lake included a) depth, b) temperature and summer thermal stratification, c) depth-dependent light intensity, d) conductivity, e) oxygenation, f) chlorophyll a levels, g) alkalinity/hardness, and h) concentrations of nitrogen, phosphorous, and silica (nutrient richness) by strata. Biotic parameters were surveyed by measuring a) the abundance and diversity of non-benthic phytoplankton, b) abundance and diversity of non-benthic zooplanktoon, c) diversity of littoral zone macroinvertebrates, and d) diversity of littoral zone macrophytes. The goal of the survey was to measure the basic morphometric, physical, and biotic parameters of Douglas Lake, analyze the surveyed measurements for their individual indications of trophic status, and ultimately integrate all measurements and analyses to create a picture of the lake's overall productivity. Leeches are usually found under sticks or stones or in the mud on the bottom of lakes, ponds, and streams unless actively in search of food. Of approximately three hundred leeches collected in the Douglas Lake region during June and July, none were found at a depth greater than two feet. The temperature range of the water was between 18 C and 26 C. Gently moving water in protected coves or at the outlets or inlets of lakes is preferred to still water.http://deepblue.lib.umich.edu/bitstream/2027.42/54731/1/3172.pd

Relationships of Native and Exotic Strains of Phragmites australis to Wetland Ecosystem Properties

Invasions by exotic plant species like Phragmites australis can affect wetlands and the services they provide, including denitrification. Native and exotic Phragmites strains were genetically verified in 2002 but few studies have compared their ecosystem effects. We compared relationships between native and exotic Phragmites and environmental attributes, soil nutrient concentrations, and abundance and activity of soil denitrifying bacteria. There were no significant differences for any measured variables between sites with exotic and native strains. However, there were significant positive correlations between native Phragmites stem density and soil nutrient concentrations and denitrification rates. Furthermore, denitrifying bacterial abundance was positively correlated with nitrate concentration and denitrification rates. Additionally, there were significant negative correlations between water levels in native Phragmites sites and native stem density, nutrient concentrations, and denitrification rates. Surprisingly, we found no significant relationships between exotic stem density or water level and measured variables. These results suggest 1) the native strain may have important ecosystem effects that had only been documented for exotic Phragmites, and 2) abiotic drivers such as water level may have mediated this outcome. Further work is needed to determine if the stem density gradients were a consequence, rather than a cause, of pre-existing gradients of abiotic factors

Quantitative RT-PCR profiling of the Rabbit Immune Response: Assessment of Acute Shigella flexneri Infection

Quantitative reverse transcription PCR analysis is an important tool to monitor changes in gene expression in animal models. The rabbit is a widely accepted and commonly used animal model in the study of human diseases and infections by viral, fungal, bacterial and protozoan pathogens. Only a limited number of rabbit genes have, however, been analyzed by this method as the rabbit genome sequence remains unfinished. Recently, increasing coverage of the genome has permitted the prediction of a growing number of genes that are relevant in the context of the immune response. We hereby report the design of twenty-four quantitative PCR primer pairs covering common cytokines, chemoattractants, antimicrobials and enzymes for a rapid, sensitive and quantitative analysis of the rabbit immune response. Importantly, all primer pairs were designed to be used under identical experimental conditions, thereby enabling the simultaneous analysis of all genes in a high-throughput format. This tool was used to analyze the rabbit innate immune response to infection with the human gastrointestinal pathogen Shigella flexneri. Beyond the known inflammatory mediators, we identified IL-22, IL-17A and IL-17F as highly upregulated cytokines and as first responders to infection during the innate phase of the host immune response. This set of qPCR primers also provides a convenient tool for monitoring the rabbit immune response during infection with other pathogens and other inflammatory conditions

Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK.

BACKGROUND: A safe and efficacious vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), if deployed with high coverage, could contribute to the control of the COVID-19 pandemic. We evaluated the safety and efficacy of the ChAdOx1 nCoV-19 vaccine in a pooled interim analysis of four trials. METHODS: This analysis includes data from four ongoing blinded, randomised, controlled trials done across the UK, Brazil, and South Africa. Participants aged 18 years and older were randomly assigned (1:1) to ChAdOx1 nCoV-19 vaccine or control (meningococcal group A, C, W, and Y conjugate vaccine or saline). Participants in the ChAdOx1 nCoV-19 group received two doses containing 5 × 1010 viral particles (standard dose; SD/SD cohort); a subset in the UK trial received a half dose as their first dose (low dose) and a standard dose as their second dose (LD/SD cohort). The primary efficacy analysis included symptomatic COVID-19 in seronegative participants with a nucleic acid amplification test-positive swab more than 14 days after a second dose of vaccine. Participants were analysed according to treatment received, with data cutoff on Nov 4, 2020. Vaccine efficacy was calculated as 1 - relative risk derived from a robust Poisson regression model adjusted for age. Studies are registered at ISRCTN89951424 and ClinicalTrials.gov, NCT04324606, NCT04400838, and NCT04444674. FINDINGS: Between April 23 and Nov 4, 2020, 23 848 participants were enrolled and 11 636 participants (7548 in the UK, 4088 in Brazil) were included in the interim primary efficacy analysis. In participants who received two standard doses, vaccine efficacy was 62·1% (95% CI 41·0-75·7; 27 [0·6%] of 4440 in the ChAdOx1 nCoV-19 group vs71 [1·6%] of 4455 in the control group) and in participants who received a low dose followed by a standard dose, efficacy was 90·0% (67·4-97·0; three [0·2%] of 1367 vs 30 [2·2%] of 1374; pinteraction=0·010). Overall vaccine efficacy across both groups was 70·4% (95·8% CI 54·8-80·6; 30 [0·5%] of 5807 vs 101 [1·7%] of 5829). From 21 days after the first dose, there were ten cases hospitalised for COVID-19, all in the control arm; two were classified as severe COVID-19, including one death. There were 74 341 person-months of safety follow-up (median 3·4 months, IQR 1·3-4·8): 175 severe adverse events occurred in 168 participants, 84 events in the ChAdOx1 nCoV-19 group and 91 in the control group. Three events were classified as possibly related to a vaccine: one in the ChAdOx1 nCoV-19 group, one in the control group, and one in a participant who remains masked to group allocation. INTERPRETATION: ChAdOx1 nCoV-19 has an acceptable safety profile and has been found to be efficacious against symptomatic COVID-19 in this interim analysis of ongoing clinical trials. FUNDING: UK Research and Innovation, National Institutes for Health Research (NIHR), Coalition for Epidemic Preparedness Innovations, Bill & Melinda Gates Foundation, Lemann Foundation, Rede D'Or, Brava and Telles Foundation, NIHR Oxford Biomedical Research Centre, Thames Valley and South Midland's NIHR Clinical Research Network, and AstraZeneca

Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK

Background A safe and efficacious vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), if deployed with high coverage, could contribute to the control of the COVID-19 pandemic. We evaluated the safety and efficacy of the ChAdOx1 nCoV-19 vaccine in a pooled interim analysis of four trials. Methods This analysis includes data from four ongoing blinded, randomised, controlled trials done across the UK, Brazil, and South Africa. Participants aged 18 years and older were randomly assigned (1:1) to ChAdOx1 nCoV-19 vaccine or control (meningococcal group A, C, W, and Y conjugate vaccine or saline). Participants in the ChAdOx1 nCoV-19 group received two doses containing 5 × 1010 viral particles (standard dose; SD/SD cohort); a subset in the UK trial received a half dose as their first dose (low dose) and a standard dose as their second dose (LD/SD cohort). The primary efficacy analysis included symptomatic COVID-19 in seronegative participants with a nucleic acid amplification test-positive swab more than 14 days after a second dose of vaccine. Participants were analysed according to treatment received, with data cutoff on Nov 4, 2020. Vaccine efficacy was calculated as 1 - relative risk derived from a robust Poisson regression model adjusted for age. Studies are registered at ISRCTN89951424 and ClinicalTrials.gov, NCT04324606, NCT04400838, and NCT04444674. Findings Between April 23 and Nov 4, 2020, 23 848 participants were enrolled and 11 636 participants (7548 in the UK, 4088 in Brazil) were included in the interim primary efficacy analysis. In participants who received two standard doses, vaccine efficacy was 62·1% (95% CI 41·0–75·7; 27 [0·6%] of 4440 in the ChAdOx1 nCoV-19 group vs71 [1·6%] of 4455 in the control group) and in participants who received a low dose followed by a standard dose, efficacy was 90·0% (67·4–97·0; three [0·2%] of 1367 vs 30 [2·2%] of 1374; pinteraction=0·010). Overall vaccine efficacy across both groups was 70·4% (95·8% CI 54·8–80·6; 30 [0·5%] of 5807 vs 101 [1·7%] of 5829). From 21 days after the first dose, there were ten cases hospitalised for COVID-19, all in the control arm; two were classified as severe COVID-19, including one death. There were 74 341 person-months of safety follow-up (median 3·4 months, IQR 1·3–4·8): 175 severe adverse events occurred in 168 participants, 84 events in the ChAdOx1 nCoV-19 group and 91 in the control group. Three events were classified as possibly related to a vaccine: one in the ChAdOx1 nCoV-19 group, one in the control group, and one in a participant who remains masked to group allocation. Interpretation ChAdOx1 nCoV-19 has an acceptable safety profile and has been found to be efficacious against symptomatic COVID-19 in this interim analysis of ongoing clinical trials

Descriptive study of the vertical structure of floating algal mats in the Maple River, Cheboygan Co., MI.

Flabs (floating algal benthos; also referred to as floating algal mats) are present in several streams and bodies of water of northern Michigan. They are formed at the benthic surface until an accumulation of oxygen due to photosynthesis and other external forces dislodges them from the bottom and make them float at the surface. Flabs have ecological importance since they serve as microhabitas for different fauna, such as insect larvae, crustaceans, bacteria, etc., and for different algal taxa that might grow better in the conditions provided by the mat (e.g., blue-green filaments like Oscillatoria). They act also as refuges for several organisms in periods of dry downs or adverse conditions, and serve as a food source for the fauna that lives inside them, as well as other animals, such as macroinvertebrates or even fish. They have also been used as indicators of eutrophicatin in some systems since it is this phenomenon that enhances the occurrence of floating algal mats. Several types of floating algal mats have been described for marine and freshwater habitats, and it has been suggested that the flab-forming organisms are blue-green algae. Nevertheless, some other algal taxa, such as diatoms or green algae, have also been observed in the flabs. Since the flabs are cohesively kept together as a separate entity, it should be of interest to assess if any vertical structuring exists in these flabs, such as different algal taxa occupying different layers or zones of the algal mat. Some studies have looked at stratification in algal mats regarding physical parameters such as pH, light, temperature, and oxygen and hydrogen sulfide concentration at microscales. Only a few studies though, have analyzed the vertical structure of species composition in flabs. It is important to realize that the microhabitat that flabs create is a whole microecosystem in its own, and since flabs are dynamic microenvironments capable of supporting a whole array of interactions, much information can be gained by assessing profiles of algal mats.http://deepblue.lib.umich.edu/bitstream/2027.42/54730/1/3171.pdfDescription of 3171.pdf : Access restricted to on-site users at the U-M Biological Station

Decoupling Carbon Effects and UV Protection from Terrestrial Subsidies on Pond Zooplankton

Studies on spatial subsidies have overwhelmingly addressed their trophic nature. However, certain subsidies might affect recipient communities beyond the feeding pathway. Terrestrial colored dissolved organic matter (DOM) is such a subsidy providing a carbon source for bacteria and heterotrophic nanoflagellates which zooplankton can consume (trophic pathway), but also protecting zooplankton against damaging UV radiation through its color (non-trophic pathway). These mechanisms have been quantified separately, but few studies have attempted to decouple them and evaluate their effects in the context of subsidies. In this study, I experimentally isolated the trophic and non-trophic pathways by which DOM (as maple leaf leachate) affects zooplankton, and also addressed how local food resources (i.e., phytoplankton) could mediate the response of zooplankton to DOM subsidies. Terrestrial subsidies (DOM) effectively shielded zooplankton against damaging UV radiation. Local resources (i.e., phytoplankton), however, did not seem to mediate the fitness response of zooplankton to UV radiation. This study also suggested that the carbon in DOM might be slightly detrimental to zooplankton independent of the UV protection effect. High levels of local resources combined with carbon subsidies from DOM did not translate into higher zooplankton survival, presumably because of the detrimental effects of DOM on zooplankton. This study provides further support for the importance of terrestrial subsidies in affecting communities through non-trophic pathways (UV attenuation) and documents that the trophic pathway might be strongly dependent on subsidy quality. Further studies on the role of subsidies that include the less documented non-trophic pathways are needed to improve our mechanistic understanding of how communities and ecosystems respond to spatial subsidies