Evaluating the efficacy of small-scale marine protected areas for preserving reef health: A case study applying emerging monitoring technology

Marine protected areas (MPAs) are widely used as management tools to conserve species and ecosystems at risk from human impact. Coastal managers often focus MPA designation on biogenic reef environments due to their value and sensitivity to damage. However, difficulties in enforcement and a lack of capacity to adequately monitor MPAs often make it hard for managers to assess the effectiveness of MPAs, particularly in under‐resourced, low‐income coastal countries. Reef community data were collected at three long‐term managed reserves within the Western Visayas region of the central Philippines in order to assess the state of reef community structure inside and outside of these small‐scale locally managed MPAs. In addition, 3D structural data were captured using recently developed 'Structure from Motion' photogrammetry techniques, demonstrating how multiple quantitative metrics of physical structural complexity and health can be recorded in such analyses. These community‐run MPAs were shown to be effective even when small (10–20 ha). Mean fish biomass density was five times greater within present‐day protected sites, alongside significantly increased levels of fish diversity, richness, and size. No significant structural differences were observed inside and outside of MPAs; however, average reef rugosity, height, and roughness were significantly higher in unfished reefs compared to blast‐fished reefs. Reef substrate complexity, coral composition, and level of management, were also shown to structure fish community assemblages, with the link between reef structure and fish richness/abundance disrupted outside of MPAs. The Structure from Motion technique allows a greater range of quantitative morphometrics to be assessed than traditional methods and at relatively low cost. The technique is rapid, non‐destructive and can be archived, increasing the value of data for managers wishing to quantify reef health and efficiently monitor benthic changes through time. We discuss both the limitations and benefits of this technology's future use

Measuring the long-term success of small-scale marine protected areas in a Philippine reef fishery

Tropical coral reefs are subject to multiple pressures from both natural and anthropogenic sources. These pressures have caused widespread declines in reef health, resulting in the increased use of spatial management tools such as marine protected areas (MPAs). MPAs have proven generally effective if well designed and enforced, but there are limited long-term studies investigating how the presence of small-scale MPAs affects fish populations and reef communities. Using a 12-year time series, we found that small-scale (10–50 ha) community-managed MPAs along the Danajon Bank of the Philippines preserved average fish biomass within their boundaries over time relative to surrounding fished reefs. Unprotected areas are, however, showing significant long-term biomass decline. MPAs were also found to preserve more key trophic groups and larger-bodied commercially targeted reef fish families. Fish biomass of piscivore, scavenger and invertivore trophic groups inside individual MPAs is, however, still declining at a similar rate as outside. Surprisingly, long-term benthic cover and growth form composition were not significantly affected overall by MPA presence, despite the sporadic use of highly destructive dynamite fishing in this region. Coral cover has remained historically low (21–28%) throughout the study, following widespread bleaching mortality. While management tempered overall abundance declines, we found that irrespective of MPA presence, there was a generalised decline of both large- and small-bodied fish size groups across the study region, most steeply within the 20–30 cm length fish, and a shift towards proportionally higher abundances of small (5–10 cm) fish. This indicates a combination of over-exploitation, inadequate MPA size and coverage for larger fish, and the lingering effects of the 1998 bleaching event. Generalised shifts in body size and trophic structure reported here could lead to future reductions in fishery productivity and stability and will be further exacerbated unless broader fishery regulations and enforcement is instated

Modified Cav1.4 Expression in the Cacna1fnob2 Mouse Due to Alternative Splicing of an ETn Inserted in Exon 2

The Cacna1fnob2 mouse is reported to be a naturally occurring null mutation for the Cav1.4 calcium channel gene and the phenotype of this mouse is not identical to that of the targeted gene knockout model. We found two mRNA species in the Cacna1fnob2 mouse: approximately 90% of the mRNA represents a transcript with an in-frame stop codon within exon 2 of CACNA1F, while approximately 10% of the mRNA represents a transcript in which alternative splicing within the ETn element has removed the stop codon. This latter mRNA codes for full length Cav1.4 protein, detectable by Western blot analysis that is predicted to differ from wild type Cav1.4 protein in a region of approximately 22 amino acids in the N-terminal portion of the protein. Electrophysiological analysis with either mouse Cav1.4wt or Cav1.4nob2 cDNA revealed that the alternatively spliced protein does not differ from wild type with respect to activation and inactivation characteristics; however, while the wild type N-terminus interacted with filamin proteins in a biochemical pull-down experiment, the alternatively spliced N-terminus did not. The Cacna1fnob2 mouse electroretinogram displayed reduced b-wave and oscillatory potential amplitudes, and the retina was morphologically disorganized, with substantial reduction in thickness of the outer plexiform layer and sprouting of bipolar cell dendrites ectopically into the outer nuclear layer. Nevertheless, the spatial contrast sensitivity (optokinetic response) of Cacna1fnob2 mice was generally similar to that of wild type mice. These results suggest the Cacna1fnob2 mouse is not a CACNA1F knockout model. Rather, alternative splicing within the ETn element can lead to full-length Cav1.4 protein, albeit at reduced levels, and the functional Cav1.4 mutant may be incapable of interacting with cytoskeletal filamin proteins. These changes, do not alter the ability of the Cacna1fnob2 mouse to detect and follow moving sine-wave gratings compared to their wild type counterparts

Assessing ecological resilience to human induced environmental change in shallow lakes

Sudden unpredictable changes in ecosystems are an increasing source of concern because of their inherent unpredictability and the difficulties involved in restoration. Our understanding of the changes that occur across different trophic levels and the form of this change is lacking. This is especially true of large shallow lakes, where characteristics such as fetch and depth are close to theoretical boundary values for hysteretic behaviour. The development of reliable indicators capable of predicting these changes has been the focus of much research in recent years. The success of these early warning indicators (EWIs) has so far been mixed. There remain many unknowns about how they perform under a wide variety of conditions and parameters. Future climate change is predicted to have a wide range of impacts through the interaction of combined pressures, making the understanding of EWIs and the in-lake processes that occur during regime shifts imperative. Loch Leven, Scotland, UK, is a large shallow lake with a history of eutrophication, research and management and as such is an ideal study site to better understand resilience and regime shifts under a range of interacting stressors. The objectives of this research are to: (1) analyse long term data to identify the occurrence of common tipping points within the chemical (water column nutrient concentrations) and biological (macrophytes, phytoplankton, zooplankton) components of the loch, then test these tipping points using five statistical early warning indicators (EWIs) across multiple rolling window sizes; and (2) quantify the changes in lake ecology using a before/after analysis and testing for non-linearity, combined with modelling using the aquatic ecosystem process model PCLake to determine the level of resilience following a regime shift during recovery from eutrophication; (3) using PCLake, examine the sensitivity of Loch Leven to regime shifts in the face of predicted environmental change (e.g. climate change, nutrient pollution). Statistical analysis identified tipping points across all trophic levels included, from physical and chemical variables through to apex predators. The success of EWIs in predicting the tipping points was highly dependent on the number of EWIs used, with window size having a smaller impact. The 45% window size had the highest overall accuracy across all EWIs but only detected 16.5% more tipping points than the window size with the lowest overall accuracy. Differences between individual EWI performance and usage of them as a group was substantial with a 29.7% increase between the two. In both individual and group use of EWIs, false positives (early warning without a tipping point) were more common than true positives (tipping point preceded by EWI), creating significant doubts about their reliability as management tools. Significant change was seen across multiple variables and trophic levels in the before/after analysis following sudden recovery from eutrophication, with most variables also showing evidence of non-linear change. Modelling of responses to nutrient loading for chlorophyll, zooplankton and macrophytes, under states from before and after the shift, indicate hysteresis and thus the presence of feedback mechanisms. The modelling of responses to nutrient loading and predicted climate change in temperature and precipitation demonstrated that increases in temperature and decreases in summer precipitation individually had large impacts on chlorophyll and zooplankton at medium to high phosphorus (P) loads. However, modelling of the combined effects of these changes resulted in the highest lake chlorophyll concentrations of all tested scenarios. At low P loads higher temperatures and increased winter precipitation had the greatest impact on system resilience with a lower Critical Nutrient Load (CNL). The difference between chlorophyll and zooplankton as opposed to macrophytes was in the presence of a lower CNL for the increased winter precipitation-only scenarios which was not seen in the macrophytes. This highlights the potential role of high winter inputs potentially loaded with particulate matter in reducing resilience at lower P loads. This research has highlighted the vulnerability and low resilience of Loch Leven to environmental change. The presence of multiple tipping points and high levels of EWI activity show a high level of flexibility in the system. Coupled with the occurrence of widespread trophic change during a sudden recovery and a small level of hysteresis and high levels of sensitivity to climate change, the low levels of resilience become clear. The impact of lake-specific characteristics such as moderate depth, large fetch and a heterogeneous bed morphology is particularly evident in the limitations on macrophyte cover and the reliance on zooplankton to determine the hysteresis offset (amount of phosphorus (P) loading between the two CNL). The presence of these characteristics can be used to identify other lakes vulnerable to change. Improving the predictive capabilities of resilience indicators such as EWIs, and better understanding of the ecological changes that occur during non-linear change in response to recovery and climate change, can help target relevant ecosystem components for preventative management. These actions may become necessary under even the most conservative estimates of environmental change

Immunogenicity of standard and extended dosing intervals of BNT162b2 mRNA vaccine

Extension of the interval between vaccine doses for the BNT162b2 mRNA vaccine was introduced in the United Kingdom to accelerate population coverage with a single dose. At this time, trial data were lacking, and we addressed this in a study of United Kingdom healthcare workers. The first vaccine dose induced protection from infection from the circulating alpha (B.1.1.7) variant over several weeks. In a substudy of 589 individuals, we show that this single dose induces severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing antibody (NAb) responses and a sustained B and T cell response to the spike protein. NAb levels were higher after the extended dosing interval (6–14 weeks) compared with the conventional 3- to 4-week regimen, accompanied by enrichment of CD4+ T cells expressing interleukin-2 (IL-2). Prior SARS-CoV-2 infection amplified and accelerated the response. These data on dynamic cellular and humoral responses indicate that extension of the dosing interval is an effective immunogenic protocol

Pseudomonas putida AlkA and AlkB Proteins Comprise Different Defense Systems for the Repair of Alkylation Damage to DNA – In Vivo, In Vitro, and In Silico Studies

Alkylating agents introduce cytotoxic and/or mutagenic lesions to DNA bases leading to induction of adaptive (Ada) response, a mechanism protecting cells against deleterious effects of environmental chemicals. In Escherichia coli, the Ada response involves expression of four genes: ada, alkA, alkB, and aidB. In Pseudomonas putida, the organization of Ada regulon is different, raising questions regarding regulation of Ada gene expression. The aim of the presented studies was to analyze the role of AlkA glycosylase and AlkB dioxygenase in protecting P. putida cells against damage to DNA caused by alkylating agents. The results of bioinformatic analysis, of survival and mutagenesis of methyl methanesulfonate (MMS) or N-methyl-N’-nitro-N-nitrosoguanidine (MNNG) treated P. putida mutants in ada, alkA and alkB genes as well as assay of promoter activity revealed diverse roles of Ada, AlkA and AlkB proteins in protecting cellular DNA against alkylating agents. We found AlkA protein crucial to abolish the cytotoxic but not the mutagenic effects of alkylans since: (i) the mutation in the alkA gene was the most deleterious for MMS/MNNG treated P. putida cells, (ii) the activity of the alkA promoter was Ada-dependent and the highest among the tested genes. P. putida AlkB (PpAlkB), characterized by optimal conditions for in vitro repair of specific substrates, complementation assay, and M13/MS2 survival test, allowed to establish conservation of enzymatic function of P. putida and E. coli AlkB protein. We found that the organization of P. putida Ada regulon differs from that of E. coli. AlkA protein induced within the Ada response is crucial for protecting P. putida against cytotoxicity, whereas Ada prevents the mutagenic action of alkylating agents. In contrast to E. coli AlkB (EcAlkB), PpAlkB remains beyond the Ada regulon and is expressed constitutively. It probably creates a backup system that protects P. putida strains defective in other DNA repair systems against alkylating agents of exo- and endogenous origin