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Open Access Publications from the University of California


To meet the challenges of marine conservation, the Center for Marine Biodiversity and Conservation (CMBC) was established at the Scripps Institution of Oceanography (SIO) in May 2001. Its goals are:

  • Investigation: Assess the state of marine ecosystems now and in the past and develop predictive models for the future
  • Education: Train new marine biodiversity and conservation scientists in the United States and around the world
  • Integration: Develop novel interdisciplinary approaches linking the biological, physical, social and informatic sciences
  • Communication: Increase public understanding of scientific issues and provide sound scientific analyses to policy makers
  • Application: Design technically sophisticated, regionally appropriate strategies to prevent and reverse biodiversity collapse

Dr. Lisa Levin, Director

Center for Marine Biodiversity and Conservation

There are 278 publications in this collection, published between 2001 and 2020.
Capstone Papers (222)

The Issues of Solid Waste Management on Small Islands: Malapascua Island Philippines as a Case Study

The issues, that small islands face, regarding the disposal and management of their solid waste are serious. Although not all small islands face the same problems, it is worth looking at one island in particular as a case study to get a better understanding of some of these issues. Malapascua Island in the Philippines, a small island, has over a very short time gone through a period of rapid development due to tourism. Malapascua Island’s solid waste disposal

infrastructure has not kept up with this rapid development. The management and disposal of solid waste has now become a serious issue that needs addressing. Malapascua’s current issues create a platform for the study of the causes as well as possible solutions to the issue of solid waste management. The approach taken is to describe well-developed solid waste management systems contrasted with the current problems faced on Malapascua to examine if there is any way of adapting modern systems to serve Malapascua’s current and future needs.

A Scientist’s Guide to Philanthropy: Bridging the Gap between Marine Conservation Biologists & Funding

This capstone report involves the relationship between marine conservation biologists and funding. The goal is to help scientists pitch their projects in a way that compels potential philanthropists dedicated to ocean conservation to financially contribute by investigating transferable communication tools that scientists can utilize. This has been done through conducting interviews with various marine foundations and institutions’ program departments. Upon conducting extensive research in marine fundraising, it becomes clear that there has been a shift in the philanthropic landscape that requires scientists and labs to think differently about cultivating relationships with donors. Ocean science research has been reliant upon now dwindling large scale financial support from federal agencies. This research highlights the importance of cultivating relationships with philanthropists and marine conservation foundations through new and different communication approaches.

"CONNECTIVITY": A Documentary/Series of Transmedia Research Projects

This project is a transmedia research series that is captured in the stunning format of Ultra-High Definition, or 4k. We explore how life on Planet Ocean, and specifically around the Pacific basin, is inseparably intertwined. Scripps scientists are interviewed about their respective fields of research, and weigh in on their interests, concerns, and the broader scale implications of their work in oceanography. Common anthropogenic stressors take many forms but for this documentary will include (1) Near coastal land development can increase siltation and nutrient loading, which can smother sensitive coral reefs (2) Unsustainable fishing practices are depleting fish stocks in many areas around the Pacific (3) Plastic micro-particles are accumulating in the subtropical oceanic gyres, and overall ocean health is declining (4) Changing ocean chemistry (ocean acidification) is having a direct effect on aqua farms on the Pacific Northwest Coast (5) Whales and fisheries interact, from humpbacks to false killer whales (6) Acoustic soundscapes - from deep ocean ecosystems to shallow reef environments and how sound may be affecting biodiversity (7) Human use of oil-based products is causing increasingly less subtle planetary shifts, adding toxicity to the ecosystem and fueling climate change.

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Conference Reports (4)

Conference Report: Marine Biodiversity in the Present:The Known, Unknown and Unknowable

Funded by the Alfred P. Sloan Foundation's, Known, Unknown and Unknowable project. This is the first in a series of three conferences held at Scripps Institution of Oceanography to explore the structure and knowledge of marine systems. The report describes how the conference was organized and the results of the conference.

Marine Biodiversity: Using the Past to Inform the Future

This report covers the second conference supported by the Alfred P. Sloan Foundation's Known, Unknown and Unknowable Program. The conference goal is to explore the structure and limits to knowledge of marine ecosystems and implications of the state of our knowledge to research, policy and society at large.

This conference highlighted the importance of understanding past ecosystems and how they have changed, and asked how we can make use of this historical perspective to better understand the present and to safeguard and manage to future.

The future of marine biodiversity: The Known Unknown and Unknowable

The reports on the third in a series of conferences funded by the Alfred P. Sloan Foundation's, Known, Unknown and Unknowable program. The purpose of the conference was to explore two main aspects of marine biodiversity in the near (2020) future: (a) projections on anthropogenic drivers and (b)projections on impacts on marine biodiversity.

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Information Series (4)

Snapshot Assessment Protocol (SnAP): Guidelines, Tools, and Tips for RapidlyCharacterizing Small-Scale Fisheries.

Recognizing the need for improved coordination, the Small-scale and Artisanal Fisheries Research Network (SAFRN), at the Scripps Institution of Oceanography’s Center for Marine Biodiversity and Conservation (CMBC), was established in 2010 by graduate students as an interdisciplinary hub of students, researchers, and faculty studying small-scale fisheries (SSF). Our goals are to: enhance communication and collaboration across disciplines, projects, and sectors; share research guidelines and methodologies; and connect research to meaningful management actions.SAFRN has developed the Snapshot Assessment Protocol (SnAP), an interdisciplinary, standardized toolkit for describing SSF holistically, including ecological, social, cultural, economic, and governance-related aspects of these fisheries and the related communities. SnAP is a key part of our 2011-2012 project, “Coordinating Research for Sustaining Artisanal Fisheries”, funded by the Waitt Foundation.

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Other Recent Work (38)

Emperor penguins breeding on iceshelves.

We describe a new breeding behaviour discovered in emperor penguins; utilizing satellite and aerial-survey observations four emperor penguin breeding colonies have been recorded as existing on ice-shelves. Emperors have previously been considered as a sea-ice obligate species, with 44 of the 46 colonies located on sea-ice (the other two small colonies are on land). Of the colonies found on ice-shelves, two are newly discovered, and these have been recorded on shelves every season that they have been observed, the other two have been recorded both on ice-shelves and sea-ice in different breeding seasons. We conduct two analyses; the first using synthetic aperture radar data to assess why the largest of the four colonies, for which we have most data, locates sometimes on the shelf and sometimes on the sea-ice, and find that in years where the sea-ice forms late, the colony relocates onto the ice-shelf. The second analysis uses a number of environmental variables to test the habitat marginality of all emperor penguin breeding sites. We find that three of the four colonies reported in this study are in the most northerly, warmest conditions where sea-ice is often sub-optimal. The emperor penguin's reliance on sea-ice as a breeding platform coupled with recent concerns over changed sea-ice patterns consequent on regional warming, has led to their designation as "near threatened" in the IUCN red list. Current climate models predict that future loss of sea-ice around the Antarctic coastline will negatively impact emperor numbers; recent estimates suggest a halving of the population by 2052. The discovery of this new breeding behaviour at marginal sites could mitigate some of the consequences of sea-ice loss; potential benefits and whether these are permanent or temporary need to be considered and understood before further attempts are made to predict the population trajectory of this iconic species.

Integration of Genomic Data with NMR Analysis Enables Assignment of the Full Stereostructure of Neaumycin B, a Potent Inhibitor of Glioblastoma from a Marine-Derived Micromonospora.

The microbial metabolites known as the macrolides are some of the most successful natural products used to treat infectious and immune diseases. Describing the structures of these complex metabolites, however, is often extremely difficult due to the presence of multiple stereogenic centers inherent in this class of polyketide-derived metabolites. With the availability of genome sequence data and a better understanding of the molecular genetics of natural product biosynthesis, it is now possible to use bioinformatic approaches in tandem with spectroscopic tools to assign the full stereostructures of these complex metabolites. In our quest to discover and develop new agents for the treatment of cancer, we observed the production of a highly cytotoxic macrolide, neaumycin B, by a marine-derived actinomycete bacterium of the genus Micromonospora. Neaumycin B is a complex polycyclic macrolide possessing 19 asymmetric centers, usually requiring selective degradation, crystallization, derivatization, X-ray diffraction analysis, synthesis, or other time-consuming approaches to assign the complete stereostructure. As an alternative approach, we sequenced the genome of the producing strain and identified the neaumycin gene cluster ( neu). By integrating the known stereospecificities of biosynthetic enzymes with comprehensive NMR analysis, the full stereostructure of neaumycin B was confidently assigned. This approach exemplifies how mining gene cluster information while integrating NMR-based structure data can achieve rapid, efficient, and accurate stereostructural assignments for complex macrolides.

6-Bromoindole Derivatives from the Icelandic Marine Sponge Geodia barretti: Isolation and Anti-Inflammatory Activity.

An UPLC-qTOF-MS-based dereplication study led to the targeted isolation of seven bromoindole alkaloids from the sub-Arctic sponge Geodia barretti. This includes three new metabolites, namely geobarrettin A⁻C (1⁻3) and four known compounds, barettin (4), 8,9-dihydrobarettin (5), 6-bromoconicamin (6), and l-6-bromohypaphorine (7). The chemical structures of compounds 1⁻7 were elucidated by extensive analysis of the NMR and HRESIMS data. The absolute stereochemistry of geobarrettin A (1) was assigned by ECD analysis and Marfey's method employing the new reagent l-Nα-(1-fluoro-2,4-dinitrophenyl)tryptophanamide (l-FDTA). The isolated compounds were screened for anti-inflammatory activity using human dendritic cells (DCs). Both 2 and 3 reduced DC secretion of IL-12p40, but 3 concomitantly increased IL-10 production. Maturing DCs treated with 2 or 3 before co-culturing with allogeneic CD4⁺ T cells decreased T cell secretion of IFN-γ, indicating a reduction in Th1 differentiation. Although barettin (4) reduced DC secretion of IL-12p40 and IL-10 (IC50 values 11.8 and 21.0 μM for IL-10 and IL-12p40, respectively), maturing DCs in the presence of 4 did not affect the ability of T cells to secrete IFN-γ or IL-17, but reduced their secretion of IL-10. These results indicate that 2 and 3 may be useful for the treatment of inflammation, mainly of the Th1 type.

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