Carbonate-Based Fluorescent Chemical Tool for Uncovering Carboxylesterase 1 (CES1) Activity Variations in Live Cells.

Carboxylesterase 1 (CES1) plays a key role in the metabolism of endogenous biomolecules and xenobiotics including a variety of pharmaceuticals. Despite the established importance of CES1 in drug metabolism, methods to study factors that can vary CES1 activity are limited with only a few suitable for use in live cells. Herein, we report the development of FCP1, a new CES1 specific fluorescent probe with a unique carbonate substrate constructed from commercially available reagents. We show that FCP-1 can specifically report on endogenous CES1 activity with a robust fluorescence response in live HepG2 cells through studies with inhibitors and genetic knockdowns. Subsequently, we deployed FCP-1 to develop a live cell fluorescence microscopy-based approach to identify activity differences between CES1 isoforms. To the best of our knowledge, this is the first application of a fluorescent probe to measure the activity of CES1 sequence variants in live cells.

A Fluorescent Probe with Improved Water Solubility Permits the Analysis of Protein S-Depalmitoylation Activity in Live Cells.

S-Palmitoylation is an abundant lipid post-translational modification that is dynamically installed on and removed from target proteins to regulate their activity and cellular localization. A dearth of tools for studying the activities and regulation of protein S-depalmitoylases, thioesterase "erasers" of protein cysteine S-palmitoylation, has contributed to an incomplete understanding of the role of dynamic S-palmitoylation in regulating proteome lipidation. Recently, we developed "depalmitoylation probes" (DPPs), small molecule probes that become fluorescent upon S-depalmitoylase enzymatic activity. To be suitable for application in live cells, the first-generation DPPs relied on a shorter lipid substrate (C8 vs naturally occurring C16), which enhanced solubility and cell permeability. However, the use of an unnatural lipid substrate on the probes potentially limits the utility of the approach. Herein, we present a new member of the DPP family, DPP-5, which features an anionic carboxylate functional group that increases the probe water solubility. The enhanced water solubility of DPP-5 permits the use of a natural, palmitoylated substrate (C16), rather than a surrogate lipid. We show that DPP-5 is capable of monitoring endogenous S-depalmitoylases in live mammalian cells and that it can reveal changes in S-depalmitoylation levels due to lipid stress. DPP-5 should prove to be a useful new tool for probing the regulation of proteome lipidation through dynamic S-depalmitoylation.

Coral reefs for coastal protection: A new methodological approach and engineering case study in Grenada.

Coastal communities in tropical environments are at increasing risk from both environmental degradation and climate change and require urgent local adaptation action. Evidences show coral reefs play a critical role in wave attenuation but relatively little direct connection has been drawn between these effects and impacts on shorelines. Reefs are rarely assessed for their coastal protection service and thus not managed for their infrastructure benefits, while widespread damage and degradation continues. This paper presents a systematic approach to assess the protective role of coral reefs and to examine solutions based on the reef's influence on wave propagation patterns. Portions of the shoreline of Grenville Bay, Grenada, have seen acute shoreline erosion and coastal flooding. This paper (i) analyzes the historical changes in the shoreline and the local marine, (ii) assess the role of coral reefs in shoreline positioning through a shoreline equilibrium model first applied to coral reef environments, and (iii) design and begin implementation of a reef-based solution to reduce erosion and flooding. Coastline changes in the bay over the past 6 decades are analyzed from bathymetry and benthic surveys, historical imagery, historical wave and sea level data and modeling of wave dynamics. The analysis shows that, at present, the healthy and well-developed coral reefs system in the southern bay keeps the shoreline in equilibrium and stable, whereas reef degradation in the northern bay is linked with severe coastal erosion. A comparison of wave energy modeling for past bathymetry indicates that degradation of the coral reefs better explains erosion than changes in climate and historical sea level rise. Using this knowledge on how reefs affect the hydrodynamics, a reef restoration solution is designed and studied to ameliorate the coastal erosion and flooding. A characteristic design provides a modular design that can meet specific engineering, ecological and implementation criteria. Four pilot units were implemented in 2015 and are currently being field-tested. This paper presents one of the few existing examples available to date of a reef restoration project designed and engineered to deliver risk reduction benefits. The case study shows how engineering and ecology can work together in community-based adaptation. Our findings are particularly important for Small Island States on the front lines of climate change, who have the most to gain from protecting and managing coral reefs as coastal infrastructure.

Avoiding a crisis of motivation for ocean management under global environmental change.

Climate change and ocean acidification are altering marine ecosystems and, from a human perspective, creating both winners and losers. Human responses to these changes are complex, but may result in reduced government investments in regulation, resource management, monitoring and enforcement. Moreover, a lack of peoples' experience of climate change may drive some towards attributing the symptoms of climate change to more familiar causes such as management failure. Taken together, we anticipate that management could become weaker and less effective as climate change continues. Using diverse case studies, including the decline of coral reefs, coastal defences from flooding, shifting fish stocks and the emergence of new shipping opportunities in the Arctic, we argue that human interests are better served by increased investments in resource management. But greater government investment in management does not simply mean more of "business-as-usual." Management needs to become more flexible, better at anticipating and responding to surprise, and able to facilitate change where it is desirable. A range of technological, economic, communication and governance solutions exists to help transform management. While not all have been tested, judicious application of the most appropriate solutions should help humanity adapt to novel circumstances and seek opportunity where possible.

Upgrading Marine Ecosystem Restoration Using Ecological-Social Concepts.

Conservation and environmental management are principal countermeasures to the degradation of marine ecosystems and their services. However, in many cases, current practices are insufficient to reverse ecosystem declines. We suggest that restoration ecology, the science underlying the concepts and tools needed to restore ecosystems, must be recognized as an integral element for marine conservation and environmental management. Marine restoration ecology is a young scientific discipline, often with gaps between its application and the supporting science. Bridging these gaps is essential to using restoration as an effective management tool and reversing the decline of marine ecosystems and their services. Ecological restoration should address objectives that include improved ecosystem services, and it therefore should encompass social-ecological elements rather than focusing solely on ecological parameters. We recommend using existing management frameworks to identify clear restoration targets, to apply quantitative tools for assessment, and to make the re-establishment of ecosystem services a criterion for success.

The value of marsh restoration for flood risk reduction in an urban estuary.

The use of nature-based solutions (NBS) for coastal climate adaptation has broad and growing interest, but NBS are rarely assessed with the same rigor as traditional engineering solutions or with respect to future climate change scenarios. These gaps pose challenges for the use of NBS for climate adaptation. Here, we value the flood protection benefits of stakeholder-identified marsh restoration under current and future climate change within San Francisco Bay, a densely urbanized estuary, and specifically on the shores of San Mateo County, the county most vulnerable to future flooding in California. Marsh restoration provides a present value of $21 million which increases to over $100 million with 0.5 m of sea level rise (SLR), and to about $500 million with 1 m of SLR. There are hotspots within the county where marsh restoration delivers very high benefits for adaptation, which reach $9 million/hectare with likely future sea level and storm conditions. Today's investments in nature and community resilience can result in increasing payoffs as climate change progresses and risk increases.

Tuning reactivity of diphenylpropynone derivatives with metal-associated amyloid-ß species via structural modifications.

A diphenylpropynone derivative, DPP2, has been recently demonstrated to target metal-associated amyloid-ß (metal-Aß) species implicated in Alzheimer's disease (AD). DPP2 was shown to interact with metal-Aß species and subsequently control Aß aggregation (reactivity) in vitro; however, its cytotoxicity has limited further biological applications. In order to improve reactivity toward Aß species and lower cytotoxicity, along with gaining an understanding of a structure-reactivity-cytotoxicity relationship, we designed, prepared, and characterized a series of small molecules (C1/C2, P1/P2, and PA1/PA2) as structurally modified DPP2 analogues. A similar metal binding site to that of DPP2 was contained in these compounds while their structures were varied to afford different interactions and reactivities with metal ions, Aß species, and metal-Aß species. Distinct reactivities of our chemical family toward in vitro Aß aggregation in the absence and presence of metal ions were observed. Among our chemical series, the compound (C2) with a relatively rigid backbone and a dimethylamino group was observed to noticeably regulate both metal-free and metal-mediated Aß aggregation to different extents. Using our compounds, cell viability was significantly improved, compared to that with DPP2. Lastly, modifications on the DPP framework maintained the structural properties for potential blood-brain barrier (BBB) permeability. Overall, our studies demonstrated that structural variations adjacent to the metal binding site of DPP2 could govern different metal binding properties, interactions with Aß and metal-Aß species, reactivity toward metal-free and metal-induced Aß aggregation, and cytotoxicity of the compounds, establishing a structure-reactivity-cytotoxicity relationship. This information could help gain insight into structural optimization for developing nontoxic chemical reagents toward targeting metal-Aß species and modulating their reactivity in biological systems.

Reactivity of diphenylpropynone derivatives toward metal-associated amyloid-ß species.

In Alzheimer's disease (AD), metal-associated amyloid-ß (metal-Aß) species have been suggested to be involved in neurotoxicity; however, their role in disease development is still unclear. To elucidate this aspect, chemical reagents have been developed as valuable tools for targeting metal-Aß species, modulating the interaction between the metal and Aß, and subsequently altering metal-Aß reactivity. Herein, we report the design, preparation, characterization, and reactivity of two diphenylpropynone derivatives (DPP1 and DPP2) composed of structural moieties for metal chelation and Aß interaction (bifunctionality). The interactions of these compounds with metal ions and Aß species were confirmed by UV-vis, NMR, mass spectrometry, and docking studies. The effects of these bifunctional molecules on the control of in vitro metal-free and metal-induced Aß aggregation were investigated and monitored by gel electrophoresis and transmission electron microscopy (TEM). Both DPP1 and DPP2 showed reactivity toward metal-Aß species over metal-free Aß species to different extents. In particular, DPP2, which contains a dimethylamino group, exhibited greater reactivity with metal-Aß species than DPP1, suggesting a structure-reactivity relationship. Overall, our studies present a new bifunctional scaffold that could be utilized to develop chemical reagents for investigating metal-Aß species in AD.

Human carboxylesterases and fluorescent probes to image their activity in live cells.

Human carboxylesterases (CESs) are serine hydrolases that are responsible for the phase I metabolism of an assortment of ester, amide, thioester, carbonate, and carbamate containing drugs. CES activity is known to be influenced by a variety of factors including single nucleotide polymorphisms, alternative splicing, and drug-drug interactions. These different factors contribute to interindividual variability of CES activity which has been demonstrated to influence clinical outcomes among people treated with CES-substrate therapeutics. Detailed exploration of the factors that influence CES activity is emerging as an important area of research. The use of fluorescent probes with live cell imaging techniques can selectively visualize the real-time activity of CESs and have the potential to be useful tools to help reveal the impacts of CES activity variations on human health. This review summarizes the properties of the five known human CESs including factors reported to or that could potentially influence their activity before discussing the design aspects and use considerations of CES fluorescent probes in general in addition to highlighting several well-characterized probes.

Resistance, resilience, and recovery of salt marshes in the Florida Panhandle following Hurricane Michael.

Characterizing the fragility, resistance, and resilience of marshes is critical for understanding their role in reducing storm damages and for helping to manage the recovery of these natural defenses. This study uses high-resolution aerial imagery to quantify the impacts of Hurricane Michael, a category 5 hurricane, on coastal salt marshes in the Florida Panhandle, USA. Marsh damage was classified into several categories, including deposition of sediment or wrack, fallen trees, vegetation loss, and conversion to open water. The marshes were highly resistant to storm damages even under extreme conditions; only 2% of the 173,259 km2 of marshes in the study area were damaged-a failure rate much lower than that of artificial defenses. Marshes may be more resistant than resilient to storm impacts; damaged marshes were slow to recover, and only 16% of damaged marshes had recovered 6 months after landfall. Marsh management mattered for resistance and resilience; marshes on publicly-managed lands were less likely to be damaged and more likely to recover quickly from storm impacts than marshes on private land, emphasizing the need to incentivize marsh management on private lands. These results directly inform policy and practice for hazard mitigation, disaster recovery, adaptation, and conservation, particularly given the potential for more intense hurricane landfalls as the climate changes.

Emerging Solutions to Return Nature to the Urban Ocean.

Urban and periurban ocean developments impact 1.5% of the global exclusive economic zones, and the demand for ocean space and resources is increasing. As we strive for a more sustainable future, it is imperative that we better design, manage, and conserve urban ocean spaces for both humans and nature. We identify three key objectives for more sustainable urban oceans: reduction of urban pressures, protection and restoration of ocean ecosystems, and support of critical ecosystem services. We describe an array of emerging evidence-based approaches, including greening grayinfrastructure, restoring habitats, and developing biotechnologies. We then explore new economic instruments and incentives for supporting these new approaches and evaluate their feasibility in delivering these objectives. Several of these tools have the potential to help bring nature back to the urban ocean while also addressing some of the critical needs of urban societies, such as climate adaptation, seafood production, clean water, and recreation, providing both human and environmental benefits in some of our most impacted ocean spaces.

The Global Flood Protection Benefits of Mangroves.

Coastal flood risks are rising rapidly. We provide high resolution estimates of the economic value of mangroves forests for flood risk reduction every 20 km worldwide. We develop a probabilistic, process-based valuation of the effects of mangroves on averting damages to people and property. We couple spatially-explicit 2-D hydrodynamic analyses with economic models, and find that mangroves provide flood protection benefits exceeding $US 65 billion per year. If mangroves were lost, 15 million more people would be flooded annually across the world. Some of the nations that receive the greatest economic benefits include the USA, China, India and Mexico. Vietnam, India and Bangladesh receive the greatest benefits in terms of people protected. Many (>45) 20-km coastal stretches particularly those near cities receive more than $US 250 million annually in flood protection benefits from mangroves. These results demonstrate the value of mangroves as natural coastal defenses at global, national and local scales, which can inform incentives for mangrove conservation and restoration in development, climate adaptation, disaster risk reduction and insurance.

Assessing the effects of using high-quality data and high-resolution models in valuing flood protection services of mangroves.

The rate of change on coastlines is accelerating from climate change and coastal development. Coastal flooding is a particularly pressing and increasing problem, which affects hundreds of millions of people and damages trillions of US$ in property. Scientists, practitioners and managers must be able to quickly assess flood risk and identify appropriate adaptation and risk reduction measures often with limited data and tools, particularly in developing countries. To inform these decision-making processes, we identify how sensitive flood risk and adaptation analyses are to changes in the resolution of data and models. We further do these comparisons in the context of assess the benefits of an ecosystem-based approach for risk reduction. There is growing interest in these ecosystem-based approaches as cost effective measures for adaptation and risk reduction. We assess flood risks from tropical cyclones and the flood risk reduction benefits provided by mangroves in Pagbilao (the Philippines). Then, we also compare risks and risk reduction (benefits) using different quality data and models, to identify where to invest in in new modeling and data acquisition to improve decision-making. We find that coastal flood risk valuation improves by using high resolution topography and long time series of data on tropical cyclones, while flood reduction benefits of mangroves are better valued by using consistent databases and models along the whole process rather than investing in single measures.

Development of a Split Esterase for Protein-Protein Interaction-Dependent Small-Molecule Activation.

Split reporters based on fluorescent proteins and luciferases have emerged as valuable tools for measuring interactions in biological systems. Relatedly, biosensors that transduce measured input signals into outputs that influence the host system are key components of engineered gene circuits for synthetic biology applications. While small-molecule-based imaging agents are widely used in biological studies, and small-molecule-based drugs and chemical probes can target a range of biological processes, a general method for generating a target small molecule in a biological system based on a measured input signal is lacking. Here, we develop a proximity-dependent split esterase that selectively unmasks ester-protected small molecules in an interaction-dependent manner. Exploiting the versatility of an ester-protected small-molecule output, we demonstrate fluorescent, chemiluminescent, and pharmacological probe generation, each created by masking key alcohol functional groups on a target small molecule. We show that the split esterase system can be used in combination with ester-masked fluorescent or luminescent probes to measure protein-protein interactions and protein-protein interaction inhibitor engagement. We demonstrate that the esterase-based reporter system is compatible with other commonly used split reporter imaging systems for the simultaneous detection of multiple protein-protein interactions. Finally, we develop a system for selective small-molecule-dependent cell killing by unmasking a cytotoxic molecule using an inducible split esterase. Presaging utility in future synthetic biology-based therapeutic applications, we also show that the system can be used for intercellular cell killing via a bystander effect, where one activated cell unmasks a cytotoxic molecule and kills cells physically adjacent to the activated cells. Collectively, this work illustrates that the split esterase system is a valuable new addition to the split protein toolbox, with particularly exciting potential in synthetic biology applications.

Species recovery and recolonization of past habitats: lessons for science and conservation from sea otters in estuaries.

Recovering species are often limited to much smaller areas than they historically occupied. Conservation planning for the recovering species is often based on this limited range, which may simply be an artifact of where the surviving population persisted. Southern sea otters (Enhydra lutris nereis) were hunted nearly to extinction but recovered from a small remnant population on a remote stretch of the California outer coast, where most of their recovery has occurred. However, studies of recently-recolonized estuaries have revealed that estuaries can provide southern sea otters with high quality habitats featuring shallow waters, high production and ample food, limited predators, and protected haul-out opportunities. Moreover, sea otters can have strong effects on estuarine ecosystems, fostering seagrass resilience through their consumption of invertebrate prey. Using a combination of literature reviews, population modeling, and prey surveys we explored the former estuarine habitats outside the current southern sea otter range to determine if these estuarine habitats can support healthy sea otter populations. We found the majority of studies and conservation efforts have focused on populations in exposed, rocky coastal habitats. Yet historical evidence indicates that sea otters were also formerly ubiquitous in estuaries. Our habitat-specific population growth model for California's largest estuary-San Francisco Bay-determined that it alone can support about 6,600 sea otters, more than double the 2018 California population. Prey surveys in estuaries currently with (Elkhorn Slough and Morro Bay) and without (San Francisco Bay and Drakes Estero) sea otters indicated that the availability of prey, especially crabs, is sufficient to support healthy sea otter populations. Combining historical evidence with our results, we show that conservation practitioners could consider former estuarine habitats as targets for sea otter and ecosystem restoration. This study reveals the importance of understanding how recovering species interact with all the ecosystems they historically occupied, both for improved conservation of the recovering species and for successful restoration of ecosystem functions and processes.

Comparing the cost effectiveness of nature-based and coastal adaptation: A case study from the Gulf Coast of the United States.

Coastal risks are increasing from both development and climate change. Interest is growing in the protective role that coastal nature-based measures (or green infrastructure), such as reefs and wetlands, can play in adapting to these risks. However, a lack of quantitative information on their relative costs and benefits is one principal factor limiting their use more broadly. Here, we apply a quantitative risk assessment framework to assess coastal flood risk (from climate change and economic exposure growth) across the United States Gulf of Mexico coast to compare the cost effectiveness of different adaptation measures. These include nature-based (e.g. oyster reef restoration), structural or grey (e.g., seawalls) and policy measures (e.g. home elevation). We first find that coastal development will be a critical driver of risk, particularly for major disasters, but climate change will cause more recurrent losses through changes in storms and relative sea level rise. By 2030, flooding will cost $134-176.6 billion (for different economic growth scenarios), but as the effects of climate change, land subsidence and concentration of assets in the coastal zone increase, annualized risk will more than double by 2050 with respect to 2030. However, from the portfolio we studied, the set of cost-effective adaptation measures (with benefit to cost ratios above 1) could prevent up to $57-101 billion in losses, which represents 42.8-57.2% of the total risk. Nature-based adaptation options could avert more than $50 billion of these costs, and do so cost effectively with average benefit to cost ratios above 3.5. Wetland and oyster reef restoration are found to be particularly cost-effective. This study demonstrates that the cost effectiveness of nature-based, grey and policy measures can be compared quantitatively with one another, and that the cost effectiveness of adaptation becomes more attractive as climate change and coastal development intensifies in the future. It also shows that investments in nature-based adaptation could meet multiple objectives for environmental restoration, adaptation and flood risk reduction.

The global flood protection savings provided by coral reefs.

Coral reefs can provide significant coastal protection benefits to people and property. Here we show that the annual expected damages from flooding would double, and costs from frequent storms would triple without reefs. For 100-year storm events, flood damages would increase by 91% to $US 272 billion without reefs. The countries with the most to gain from reef management are Indonesia, Philippines, Malaysia, Mexico, and Cuba; annual expected flood savings exceed $400 M for each of these nations. Sea-level rise will increase flood risk, but substantial impacts could happen from reef loss alone without better near-term management. We provide a global, process-based valuation of an ecosystem service across an entire marine biome at (sub)national levels. These spatially explicit benefits inform critical risk and environmental management decisions, and the expected benefits can be directly considered by governments (e.g., national accounts, recovery plans) and businesses (e.g., insurance).

Michael addition-based probes for ratiometric fluorescence imaging of protein S-depalmitoylases in live cells and tissues.

The reversible modification of cysteine residues through thioester formation with palmitate (protein S-palmitoylation) is a prevalent chemical modification that regulates the function, localization, and stability of many proteins. Current methods for monitoring the "erasers" of S-palmitoylation, acyl-protein thioesterases (APTs), rely on destructive proteomic methods or "turn-on" probes, precluding deployment in heterogeneous samples such as primary tissues. To address these challenges, we present the design, synthesis, and biological evaluation of Ratiometric Depalmitoylation Probes (RDPs). RDPs respond to APTs with a robust ratiometric change in fluorescent signal both in vitro and in live cells. Moreover, RDPs can monitor endogenous APT activities in heterogeneous primary human tissues such as colon organoids, presaging the utility of these molecules in uncovering novel roles for APTs in metabolic regulation.

Correction: Michael addition-based probes for ratiometric fluorescence imaging of protein S-depalmitoylases in live cells and tissues.

[This corrects the article DOI: 10.1039/C7SC02805A.].

The Value of Coastal Wetlands for Flood Damage Reduction in the Northeastern USA.

As exposure to coastal hazards increases there is growing interest in nature-based solutions for risk reduction. This study uses high-resolution flood and loss models to quantify the impacts of coastal wetlands in the northeastern USA on (i) regional flood damages by Hurricane Sandy and (ii) local annual flood losses in Barnegat Bay in Ocean County, New Jersey. Using an extensive database of property exposure, the regional study shows that wetlands avoided $625 Million in direct flood damages during Hurricane Sandy. The local study combines these models with a database of synthetic storms in Ocean County and estimates a 16% average reduction in annual flood losses by salt marshes with higher reductions at lower elevations. Together, the studies quantify the risk reduction ecosystem services of marsh wetlands. Measuring these benefits in collaboration with the risk modelling industry is crucial for assessing risk accurately and, where appropriate, aligning conservation and risk reduction goals.