ICBG - International Cooperative Biodiversity Group (Indonesia)

A. SPECIFIC AIMS (TOP )
We have established a cooperative group of scientists from several institutions in the U.S. and Indonesia to address the interdependence of biodiversity exploration and discovery of potential applications in energy and human health. This group possesses the capacity to support sustainable use of biodiversity resources and to devise a framework of partnerships to accomplish our goals. We will survey the biological diversity present in several taxonomic groups at selected sites on the island of Sulawesi, Indonesia, and to explore these organisms for natural products with applications to specific human health issues and development of bioenergy resources. The taxonomic groups to be surveyed include vascular plants, invertebrate animals, including insects and other arthropods, vertebrate animals, including birds and small mammals, and selected microbes, including filamentous fungi, yeasts, and bacteria. Screening for health and energy solutions will focus primarily on microbes, but plants for which promising ethnobotanical data exist will also be included in the screening for novel therapeutic agents. The health issues for which we intend to seek such agents include cancer, addictions, and immune disorders, including HIV/AIDS. The energy applications screening will focus on isolating and identifying microbes that produce either high levels of lipids or cellulase enzymes. In addition to the health and energy applications, the surveys will improve our understanding of the biodiversity of Sulawesi, an island with a complex geological and biotic history, rich species diversity in several taxonomic groups, and high species endemism, and will be used to promote conservation and bioresource planning and policy in Indonesia.

Specific aims for this group are:

Specific Aim 1: To perform biodiversity surveys of selected bacteria, fungi, plants, arthropods, and vertebrates in three lowland and one upland rain forest sites on southeastern Sulawesi, Indonesia, and to enrich collections of these organisms in museums in Indonesia and the U.S. These intensive surveys will add significant detail to knowledge of the biota of this relatively little-explored region.
Specific Aim 2: To screen biological materials (bacteria, fungi, plants, insects) isolated in the course of this study for novel products, including novel bioenergy applications. The primary focus of these studies will be bacteria, filamentous fungi, and yeasts isolated from plants, insects, and soils collected under Specific Aim 1.
Specific Aim 3: To screen selected biological materials — primarily fungi and plants — isolated in the course of this study for novel products, including novel therapeutics for treatment of cancer, novel therapeutics for treatment of addictions, novel therapeutics for treatment of immune system disorders, such as HIV/AIDS, and to isolate and identify therapeutically active substances and conduct preclinical studies with purified natural products. The primary focus of these studies will be filamentous fungi and yeasts isolated from plants, insects, and soils collected under Specific Aim 1, but plants for which ethnobotanical information indicate potential promising medicinal value will also be included.
Specific Aim 4: To compare levels of biological diversity in several taxonomic groups mentioned in Specific Aim 1 among the three lowland and one upland forest sites and use that information to develop recommendations for strategies to conserve biodiversity. Based on information gained from the inventories of bacteria, fungi, plants, insects, and vertebrates on alpha and gamma diversity in those groups, we will develop multi-metric diversity models that provide an ecological basis for watershed reserve design, which will, in turn, be used to provide guidelines for development of new nature reserves in this region.
Specific Aim 5: To develop and encourage local conservation planning, education, and outreach efforts that are ecologically, economically, and socio-politically sound and effective. Working with Indonesian scientists from several institutions and national and local government officials, we will develop a series of workshops, town hall–style meetings and discussions, and multimedia instructional materials to communicate information gained in Specific Aims 1-4 and to promote dialogue about how to most effectively implement the conservation strategies from Specific Aim 4.
Specific Aim 6: To develop effective international agreements related to sharing and development of biogenetic resources. Working collaboratively with Indonesian and U.S. scientists, representatives from the technology transfer offices of the Indonesian Institute of Sciences (LIPI) and the U.S. institutions (UC Davis, UC Berkeley, and UC San Francisco) involved in this project, and representatives of the private companies with which we are forming partnerships, we will develop model materials transfer agreements and contractual agreements that ensure that: (a) all organisms collected during the course of this study will remain the property of the Indonesian people; (b) all products resulting from research conducted on those organisms will be freely shared with scientists at LIPI and the other Indonesian institutions involved (Ministry of Forestry, Bandung Institute of Technology); and (c) rigorous ethical guidelines, such as those prescribed by the Convention on Biological Diversity (UNEP-CBD, 1994), are adhered to strictly. Additional international bodies, such as the Swiss Academy of Sciences and associated United Nations agencies, will provide guidance throughout the process.

Structure of Program to Achieve the Specific Aims

In order to address the goals described above, we have assembled a multi-disciplinary, multi-institutional, international team, organized into six Associate Programs (AP). The structure of and relationships among these programs and the personnel associated with them are illustrated in Figure 1.

Associate Program 1, Macro-organism Surveys, will be based at LIPI in Indonesia and led by Dr. Elizabeth Widjaja. This program will be charged with taking the lead on collection of plants and invertebrate animals, including insects and other arthropods. Teams of scientists from Indonesia and the U.S. will participate in field collecting trips scheduled at different times of year during Years 1-3 of the project. Specimens will be deposited in museums in Indonesia and the U.S., including those at LIPI and UC Davis. Activities in Associate Program 2, Microbial Surveys, based at UC Davis and led by Dr. Kate Scow, will be tightly correlated with those of AP1. Indonesian and U.S. microbiologists and mycologists will join the teams described above to participate in field expeditions. Soil, root, and leaf litter samples will be collected along with the macro-organisms listed above. Bacteria, yeasts, and filamentous fungi will be cultured from these samples and from the plants, insects, and vertebrates collected under AP1. Microbes will be cultured in Indonesia and duplicate cultures will be shipped to the U.S. to be deposited in collections, and for further study under APs 3 and 4. In both APs 1 and 2, ethnobiological data will be collected, when possible, in order to help guide the screening activities in AP4. Together, APs 1 and 2 will address Specific Aim 1, will provide APs 3 and 4 the materials needed to address Specific Aims 2 and 3, respectively, and the data needed by AP5 to address Specific Aim 5.

Associate Program 3, Discovery of Energy Solutions, will address Specific Aim 2, and Associate Program 4, Discovery of Human Health Solutions, will address Specific Aim 3. As a result of interaction with private industries, APs 3 and 4 will also help address Specific Aim 6.

Associate Program 5, Conservation Research and Vertebrate Survey, will use information provided by APs 1 and 2, as well as inventories and collections of selected vertebrates, to address Specific Aim 4, and will provide information to AP6 in order to address Specific Aim 5. Associate Program 6, Conservation Partnerships, Training, and Ethics, will draw on information from all APs, especially AP5, to address Specific Aim 5. This AP will also provide analyses and interpretations of experiences of APs 2 and 3 needed to address Specific Aim 6.

B. BACKGROUND AND SIGNIFICANCE (TOP )
B.1. General Background The International Cooperative Biodiversity Group (ICBG) program provides an extraordinary opportunity to bring together in a single project, focused on one geographic region, research in areas of study that, while universally recognized as complementary, are generally pursued under separate auspices and only brought together after the results are published. Specifically, the program fosters the development of groups that will coordinate efforts to investigate biodiversity of particular taxonomic groups, explore the potential value of substances produced by a subset of those taxa to address pressing human concerns, and develop effective, economically and ecologically sound strategies to promote conservation of the biodiversity on which the project is based. As an interdisciplinary team with collective interests in biodiversity, ecology, and the use of natural products to address energy and health issues, we have been strongly motivated to develop a project that meets the requirements of the ICBG program. We have developed a multi-faceted group program that will be the first to simultaneously address all of these objectives on the island of Sulawesi, a global hotspot of biodiversity. Our collaboration occurs at a seminal moment in the development of US government funding emphases, Indonesian government foreign outreach activities, and international conventions governing access to, and use of biodiversity. This project is optimally poised to make significant, positive contributions via a multitiered strategy combining multi-kingdom field surveys with sophisticated laboratory techniques and industrial applications.

B.2. Why Sulawesi? Our project represents one of the largest proposed multi-agency collaborations in US history to inventory biodiversity in Indonesia, a tropical island nation with a fascinating and complex biogeographic history, and a region that harbors tremendous biological diversity which, as in many other tropical regions, is being lost at an alarming rate as human populations and concomitant development grow and expand. The Indonesian archipelago contains some of the most species-rich rainforests in the world, yet these are undergoing rapid destruction. Many species of ecological and economic significance are likely to go extinct before their systematics and biology are studied scientifically. In addition, organisms that produce substances with potential value to humans, such as potential sources of new pharmaceuticals, are likely to be lost forever. The Indonesian region lies at the crossroads of the two major biotas of the world, which originated from the northern and southern supercontinents Laurasia and Gondwanaland, respectively. This history has contributed to the region’s current richness in biodiversity. The interaction between these biotas has been enormously complex due to the geological upheaval caused by collision of the Indian/Australian and Asian tectonic plates. Current interest in the biogeography of Indonesia is intense and research crosses disciplinary boundaries (Metcalfe et al., 2001), but the evolutionary history of the biota is poorly understood (Turner et al., 2001).

The island of Sulawesi, the focal region for this project, is the largest island within the biodiversity hotspot known as Wallacea, which includes Indonesia’s central islands. According to the classification of Wikramanayake et al. (2002), Sulawesi encompasses two ecoregions: Sulawesi Lowland Tropical Forest and Sulawesi Montate Tropical Forest, both of which will be surveyed in this project. Both of these ecoregions are rated by Wikramanayake et al. (2002) as “globally outstanding” in their biological distinctiveness, harboring high degrees of species endemism, and of “critical” conservation status. We have chosen to place greatest emphasis on lowland forests because their easier accessibility renders them somewhat more urgently threatened by logging activities (Wikramanayake et al. 2002).

Sulawesi is rich in biodiversity and high in species endemism in several taxonomic groups (Whitten et al. 2002), but only a small portion of the diversity has been well documented and studied. Several recent efforts by scientists from LIPI in Indonesia and from research institutions in The Netherlands, the UK, Japan, and Denmark have helped begin to fill the enormous gaps in our knowledge of Sulawesi’s flora and fauna, but much work remains to be done. It is therefore clear that any new inventories and collections made from Sulawesi, such as those proposed here, will contribute significantly to our understanding of the biodiversity of the island, as well as to the biodiversity of Indonesia in general. Such information is essential for developing effective policies to conserve species, ecosystems, and valuable genetic resources, which are threatened by habitat destruction due to logging and mining activities accompanying rapid population growth. In spite of those threats, Cannon et al. (2005, 2007) suggest that Sulawesi’s vegetation still remains in relatively good condition, with large areas of old-growth forest still intact. They emphasize the urgency of developing policies to protect those areas and the importance of educational programs to ensure that those policies are enforced. Microbial communities, in particular, have received little attention, and are a primary focus of this proposal.

B.3. Why UC Davis and LIPI? UC Davis is ideally suited to serve as the lead institution on this project. Our research and graduate training programs in ecology in general, and conservation biology in particular, have been consistently rated among the best in the country in recent years. We have assembled an international interdisciplinary team to address the objectives of this project. The members of our team based at UC Davis include an enthoecologist with extensive field experience in Indonesia, a microbial ecologist, a mycologist, and the faculty and staff who are responsible for the management of the campus’s botanical, entomological, vertebrate, and yeast collections, all of whom also have extensive experience with collections-based research. Our collaborators at UC Berkeley and UC San Francisco have extensive experience with isolation and identification of therapeutically active substances from natural sources, and with conducting preclinical tests of those substances to establish their efficacy in addressing all three disease areas covered by this proposal — namely cancer, neurological disorders, and immune system disorders. In recognition of the importance of this project as an interdisciplinary program, the College of Agriculture and Environmental Sciences and the Office of Research at UC Davis together will make a commitment of $170,470 to support personnel and purchase equipment to be used in this project (see Budget Justification for APs 2 and 3 and supporting Letter from Barry Klein, Vice Chancellor for Research at UC Davis).

In addition, we have enjoined the participation of Indonesian scientists based at three major research institutions: Lembaga Ilmu Penegetahuan Indonesia (LIPI – the Indonesian Institute of Sciences), Departemen Kehutanan Republik Indonesia (MoF -the Indonesian Ministry of Forestry), and Institut Teknologi Bandung (ITB- Bandung Institute of Technology), whose collective areas of interest and expertise encompass the full range of objectives for the project, ensuring that Indonesian counterparts are fully involved in all of our APs and engaged in addressing all of our specific aims. As a non-departmental body directly under the President of Indonesia, LIPI is a neutral body and is, therefore, the appropriate contact point for large-scale cooperative research projects. It is also part of LIPI’s mandate to invite researchers from universities and other research institutes to participate in such projects. Thus, LIPI will serve as the lead institution for this project in Indonesia and our AP1, Macro-organism Inventories, will be based there.

While subgroups of us have worked together effectively in the past, this will be the first effort to bring together the entire team. As described in Section D below, development and maintenance of a common project database and website, regular communications and meetings among all project participants, and establishment of a project Advisory Board will be used to build, strengthen, and reinforce team cohesiveness. We have also established plans to develop partnerships with private companies interested in commercial development of natural products with applications to human health (e.g., Bionovo) or energy (e.g., Novozymes, LS9). These partnerships will help ensure that the model guidelines developed under Specific Aim 6 are viable from an industry perspective, and that the economic potentials of natural products identified in this study are eventually realized following those guidelines.

A major strength of this project lies in the interactive synergy between the participants and the APs. This project integrates unique skills and knowledge from a range of disciplines and agencies to address a chain of interrelated issues, such as assessment of the conservation status of the forests of Sulawesi, identification of the trees of economic and ecological importance in those forests, identification of the insects that infest and damage those trees, isolation and identification of the microbes present in the insects’ guts, and discovery of the microbial enzymes that degrade the different forms of cellulose present in the different tree species. The outcomes will be numerous and significant, including improved understanding of Sulawesi’s biodiversity as represented in several taxonomic groups, and of the ecological associations among those organisms, representative collections of those organisms, guidelines for effective conservation strategies, culture collections useful for screening for a broad variety of applications, identification of novel enzymes and oleaginous microbes with applications to energy needs, and isolation of therapeutic substances that will be useful for addressing significant human health challenges throughout the world.

B.4. Focal Energy and Human Health Issues. In AP3, we will focus on low-cost, high-benefit primary screening methods and focused secondary screening methods to identify microbes with characteristics valuable for energy solutions. We will identify microbes that accumulate high levels of lipids, which will be useful for conversion of plant matter to fuels, such as biodiesel and hydrocarbons. We will also use a combination of culture-dependent and culture-independent methods to identify novel cellulase enzymes. The cost of cellulase is a primary factor limiting the economic viability of cellulosic ethanol as a biofuel.

The targets for pharmaceutical discovery and development in AP4 are therapies for human cancers, immune deficiencies, and chemical addiction. Taken together, the major maladies in these groups, including lung cancer, HIV/AIDS, and alcoholism as the most important examples, have devastating impacts on billions of people worldwide, especially in developing countries. The search for these pharmaceuticals will focus on the little explored but rich fungal and floristic populations of Indonesia, and will employ state-of-the-art chemical and biological methods in the hands of experienced investigators to accomplish the project goals.

We have chosen to focus on HIV/AIDS as one of the targets for therapeutic screening due to the local importance of this disease in Indonesia. The incidence of HIV/AIDS infections has grown rapidly in this region in recent years, due to a combination of late recognition of the need for health control measures of growing populations of sex workers, and lack of adequate access to existing treatments for those in need (Ruxungtham et al. 2004). Our proposed studies to identify immune enhancers from fungi will contribute to the critical need for safer, more potent vaccines against HIV/AIDS.

B.5. Expected Significance Based on information presented in the foregoing sections, we are confident that the results of this project will provide substantial contributions in all of the following areas:

Understanding of biodiversity present in southeastern Sulawesi in a broad range of taxonomic groups;
Discovery of ecological relationships among specific plants, insects, and microbes;
Enrichment of museum collections of those taxonomic groups in the U.S. and Indonesia;
Description of novel species;
Identification of therapeutically active substances derived from Sulawesi’s microbial and botanical diversity with potential for treatment of cancer, neurological disorders, and/or immune disorders;
Identification of substances derived from Sulawesi’s microbial diversity with potential application in sustainable energy production;
Development of effective biodiversity conservation strategies for southeastern Sulawesi, with possible broader application to other areas of Indonesia;
Development of effective outreach and education programs to promote those conservation strategies;
Establishment of models for effective and equitable international collaborative partnerships; and
Establishment of models for ethical and sustainable international sharing of biogenetic resources of economic value.

C. PRELIMINARY STUDIES (TOP )
C.1. Qualifications of Project Personnel Each AP includes individuals with experience in interdisciplinary and international collaborative research. Although not all of us have worked in Indonesia in the past, we are confident that our collective experience and expertise make our team ideally qualified to complete this project effectively and expeditiously. In addition, as mentioned above, we have developed a team and a research plan in which the participation of both U.S. and Indonesian scientists is incorporated into all phases of the project (Fig. 1), ensuring that the spirit and practice of international collaboration and cooperation will be fully integrated into all of our efforts. The following paragraphs summarize the expertise and past relevant experience of the AP leaders and several of the other key personnel involved in the project.

Daniel Potter, Principal Investigator for the project and leader of the UC Davis portion of AP1, is Professor in the Department of Plant Sciences, Plant Systematist in the Agricultural Experiment Station, and Director of the Herbarium at UC Davis. His research centers on phylogeny, taxonomy, and evolution of crop plants and their wild relatives. He is interested in the interplay between natural and anthropogenic factors in shaping the evolutionary patterns and processes in plants. Recent projects have included leading a multi-investigator revision of the infrafamilial classification of the economically important family Rosaceae, and leading a collaborative study of phylogenetic relationships across the large genus Prunus, emphasizing the tropical Southeast Asian taxa that have been poorly represented in past systematic studies of the group. That project will involve field work to collect specimens in Indonesia, including Sulawesi, where several of these species are found. Dr. Potter has conducted field research in several other Old and New World tropical areas, including Brazil, Costa Rica, Jamaica, several countries in sub-Saharan Africa, and Aldabra Atoll in the Seychelles, where he held the position of Conservation Officer in 1992. Besides directorship of the UC Davis Herbarium, his previous leadership experience has included organizing an International Meeting of Sapotaceae Researchers held in Costa Rica in 2005, and chairing several committees on the UC Davis campus, most significantly, the Undergraduate Council (2005-2007), a campus-wide committee that deals with complex and sometimes controversial issues related to undergraduate education. Dr. Potter has taught courses in plant systematics and ethnobotany, and interdisciplinary seminars dealing with complex ethical, environmental, and social issues.

Elizabeth A. Widjaja, leader of AP1, is a botanist based at LIPI’s Herbarium Bogoriense in Bogor, Indonesia. An expert in the grass family, Poaceae, especially the bamboos, she has done extensive collecting and field work in Malaysia, New Guinea, and throughout Indonesia, and has contributed more than 5000 specimens to the collections of Herbarium Bogoriense as a result, with duplicates distributed to the National Herbarium of the Netherlands, Kew Herbarium, and Smithsonian Herbarium. Dr. Widjaja has participated in international collaborative research and training programs, including training of young researchers in the Philippines. Also participating as co-Investigators in AP1 are botanist Dr. Teguh Triono, ethnobotanist Dr. Eko B. Walujo, a specialist in earthworms Dr. Hari Nugroho, and entomologist Dr. Rosichon Ubaidillah, all based at LIPI. In addition, Dr. Widjaja will coordinate the participation of 14 Indonesian scientists (10 from LIPI and 2 each from ITB and MoF), including botanists, entomologists, and microbiologists, in the field expeditions to conduct the surveys under APs 1 and 2.

Three other UC Davis-based scientists will be key participants in AP1. Steve Heydon, Senior Museum Scientist in the Bohart Museum of Entomology at UC Davis, has extensive experience in leading or participating in foreign collecting efforts including trips to Central and South America, Southeast Asia, Africa, and Papua New Guinea. Three of these expeditions involved general insect surveys with conservation implications, similar to what is proposed herein for Sulawesi. Dr. Heydon is one of two or three world experts in his family of specialty—the Pteromalidae (Hymenoptera: Chalcidoidea). He has published generic level keys or reviews of the pteromalid faunas of the Nearctic and Neotropical Regions, as well as China. Two other recent publications have dealt with specific genera of the Oriental and Australasian biogeographic regions. Lynn Kimsey, Professor of Entomology and Director of the Bohart Museum, UC Davis, studies the systematics of members of the aculeate wasp families Chrysididae and Tiphiidae. There is a large diversity of chrysidid species in the subfamily Amiseginae and Loboscelidiidae in IndoAustralia. Dr. Kimsey has monographed the world Chrysididae, and she is in the process of doing the same for the family Tiphiidae. She has already described a number of species from the region and is studying the phylogenetic relationships among the genera and species found from Reunion to Australia. She has seen many specimens from the region, including New Guinea, Thailand, Halmahera, northern Australia, Malaysia, and Borneo, but little in between. Sulawesi is a critical faunistic gap to be filled as it is a major biogeographic link between New Guinea/Australia and the Sunda Platform. The tiphiid and chrysidid wasps of Sulawesi are essential unknown. Ellen Dean, curator and former director of the herbarium at UC Davis, was responsible for overseeing the design and construction of the new UC Davis herbarium facility, completed in 2004. Dr. Dean has extensive experience in herbarium specimen processing and curation at the New York Botanical Garden (processing of neotropical plants), UC Berkeley, and UC Davis. She has field experience in Costa Rica (two months), Nicaragua (two weeks), Mexico (two years), and the continental U.S., especially California (20 years). Dr. Dean’s research focuses on plant systematics and taxonomy and ethnobotany. She has focused on systematics and pollination biology of a group of Mexican species of the genus Lycianthes (Solanaceae), which has resulted in her describing several new species. In her role at the UC Davis Herbarium, she performs plant identifications for farm advisors, veterinarians, medical doctors, researchers, and the general public. She also leads field trips and teaches workshops and courses on plant identification.

Kate Scow, leader of AP2, is Professor of Soil Science and a Soil Microbial Ecologist in the department of Land, Air, and Water Resources at UC Davis, and is also past director of the Kearney foundation of Soil Science. Dr. Scow’s research covers a broad range of interactions between microorganisms and their environment. One focus of her research is on the biodegradation, bioremediation, and impacts of environmental pollutants in soil. Other areas of interest include broad-scale ecological questions, such as impacts of invasive plants and influence of agricultural practices on soil communities and processes. Also participating in AP2 are Dr. Maman Turjaman, of the Forest Microbiology Laboratory at MoF, Kyria Boundy- Mills (see below), and David Rizzo, Professor of Plant Pathology at UC Davis, whose research focuses on mycology, forest pathology, and fungal diseases of woody plants, as well as fungal ecology and systematics. Dr. Rizzo has expertise in the isolation, cultivation, and identification of a variety of fungi, including filamentous fungi. Dr. Nathan Schiff, of the Center for Bottomland Hardwoods Research of the USDA, brings to the project a unique combination of expertise in filamentous fungi associated with wood-boring insects, knowledge of cellulose degradation processes, and extensive past field experience in the New and Old World tropics, including Southeast Asia. Insect-associated microbes isolated in this project will have a high chance of harboring potent novel cellulases with potential value in energy applications.

Kyria Boundy-Mills, participant in AP2 and leader of AP3, is curator of the Phaff Yeast Culture Collection in the Department of Food Science and Technology, UC Davis. Dr. Boundy-Mills manages the collection, containing over 7,000 independently isolated wild-type yeast cultures and several dozen filamentous fungi, which is well suited as a source of diverse microbial strains for screening and will serve as an established archive for microbes isolated during the course of this project. In the last five years, Dr. Boundy-Mills has successfully screened over 1,000 isolates in the Phaff collection for a variety of energy-related capabilities, including tolerance of ethanol and other solvents, production of novel cellulases, and production of nextgeneration biofuels, such as higher alcohols. She has built relationships with several biotechnology companies who have funded these projects, and others have provided valuable advice and feedback. Over the last four years, Dr. Boundy-Mills has worked closely with UC Davis entomologists studying insect-associated yeasts, and the effects of these yeasts on insect behavior. In the course of this work, she has isolated and identified over 700 yeast strains from olive fly (Bactrocera oleae) and fruit fly (Drosophila melanogaster). Dr. Boundy- Mills will work closely with Dr. Irnayuli Sitepu of the Forest Microbiology Laboratory of MoF. Dr. Sitepu’s research has focused on plant-microbe interactions, particularly on rhizobacteria associations with Leguminosae and Dipterocarpaceae, and she maintains active ties with Japanese scientists working in bioscience, biotechnology, and agrochemistry.

L. F. Bjeldanes, leader of AP4, is Professor of Toxicology at UC Berkeley. Dr. Bjeldanes is a trained organic chemist with 35 years experience in studies of the biological effects of plant substances, most recently with phytochemicals that exhibit cancer therapeutic and preventive activities. He has conducted screening studies to isolate and identify mutagenic and carcinogenic substances from filamentous fungi, and to isolate and characterize selective estrogen receptor agonists from herbs. For the last 20 years, his research has focused on the identification and modes of action of anticancer and immune enhancing substances from food plants. He has published over 120 peer-reviewed research papers. Dr. Bjeldanes will work closely with Dr. Isao Kubo, UC Berkeley, an expert in the area of natural products chemistry and studies of insect feeding deterrents from plants; Dr. Selena Bartlett, Director of the Preclinical Development group at the Gallo Research Center at UC San Francisco, an expert in all aspects of G protein-coupled receptor (GPCR) heterodimer assay development, who has established new preclinical animal models of addiction and recently identified a new compound for alcohol dependence that is entering clinical trials in 2008; and Dr. Euis Holisotan Hakim, Professor of Natural Products Chemistry at ITB. Her research group is actively engaged in research in three major areas, namely the chemistry of lauraceous, moraceous, and dipterocarpaceous plants of the Indonesian rainforest. Their work has been supported by numerous national and international grants, and has resulted in over 350 publications. Dr. Hakim is Head of the Indonesian Society of Natural Products Chemistry. Her team has collaborated extensively with international colleagues, including scientists in Japan, New Zealand, France, and Italy.

Andy Engilis, leader of AP5, is curator of the UC Davis Wildlife and Fisheries Museum. Dr. Engilis has led research and planning efforts spanning taxonomy, conservation biology, environmental policy and planning, and biodiversity (faunal) inventories. He has over 20 years experience working in the field of conservation biology, conservation planning, habitat restoration, endangered species recovery, and testing theory related to biodiversity. The forum for his work is international in scope, being either directly involved or providing oversight to students and colleagues. He has worked with birds and mammals of tropical rainforests in Papua New Guinea, Central America, and South America. His international experience in conservation, restoration ecology, and policy spans western North America, Central America, South America, Australasia, and Africa. Engilis holds an appointment as Research Affiliate of the Bishop Museum Department of Natural Sciences, where he continues to conduct research in Hawaii and Papua New Guinea.

Jeanine Pfeiffer, leader of AP6, has maintained active research and training programs in Indonesia since 1993 in the fields of agriculture, conservation, forestry, and ethnobiology. Dr. Pfeiffer served as a special advisor to LIPI’s Center for Plant Conservation (Indonesian Botanic Gardens) from 1993-1998, and as a consultant to MoF conservation, production, and research programs from 1993 to the present. Linguistically and socio-politically fluent in Indonesian and American institutional culture, Dr. Pfeiffer provides critical liaison and coordination support for the extensive network of U.S.- and Indonesia-based researchers and practitioners involved in the project. Dr. Pfeiffer routinely holds training and evaluation workshops for a wide network of Indonesian collaborators in field research methodologies, applied conservation, scientific writing, and international collaboration and ethics. Her expertise in institutional capacity building, participatory research methods, and gender and multi-cultural relations will facilitate equitable partnership development among the twenty-some agencies involved in the project. Dr. Pfeiffer’s eighteen years of experience in administering large-scale qualitative and quantitative socio-economic surveys and monitoring and evaluation systems will contribute to the development of proactive, multi-faceted feedback and reporting mechanisms within the project. Dr. Pfeiffer will work closely with Mr. Wahjudi Wardojo of the Forestry Research and Development Agency (FORDA) of MoF, who has 25 years experience in executive-level government positions, most recently as the Secretary General (second-in-command) of MoF and the Director General of FORDA. Mr. Wardojo has also served as Section and Division Head of national government units overseeing agricultural and forestry production and trade, forest protection, nature conservation, administration, and facilities management. Mr. Wardojo has developed several inter-agency and international partnerships related to forest conservation, and has acted as Delegation Team Leader for Indonesia to international meetings on biosphere reserves, forest management, and climate change. Mr. Wardojo currently serves on the Board of Trustees for the Center for International Forestry Research (CIFOR), headquartered in Bogor, Indonesia.

C.2. Advisory Board. Due to the complex interdisciplinary, international nature of this project, which spans basic and applied research, training, and outreach, policy-making, and partnerships among research institutions, government agencies, and private companies, it is essential that we establish an international Advisory Board that will provide feedback and guidance throughout the duration of this project. Several individuals have already agreed to serve on this Advisory Board (see Supporting Letters in the Appendix). They are:

Dr. Chuck Cannon, Professor, Chinese Academy of Sciences, based at Xishuangbanna Tropical Botanic Garden, Yunnan, China, has extensive experience studying the vegetation of Sulawesi and is the first author on the recent, very thorough reports on the subject that will provide the framework for the survey work proposed here. He is continuing to develop more detailed analyses of Sulawesi’s vegetation, while pursuing new research that is increasingly concerned with developing solutions to challenges facing biodiversity conservation in Southeast Asia, including Indonesia.

Dr. Jonathan Eisen, Professor, UC Davis Genome Center and Section of Evolution and Ecology and Department of Medical Microbiology and Immunology, conducts research that links evolution, genomics and microbiology. Of particular relevance to our proposal, he can offer advice and expertise related to sampling of mixed microbial communities, especially for metagenomic analysis, including design of sampling and sequencing procedures, and mining of the metagenomic data for novel cellulase enzyme genes.

Mr. Rafael Gacel, UC Davis Innovation Access, will help to facilitate materials transfer agreements for organisms to be transferred from Indonesia to the U.S. for further research, and contractual arrangements with private companies interested in the commercial development of products derived from those organisms. His presence on the Advisory Board is crucial to ensure open communication among all interested parties regarding these issues.

Dr. Stephen Gaimari, Program Supervisor (Entomology) and Co-Curator of California State Collection of Arthropods, California Department of Food and Agriculture, is a specialist in systematics of flies in the family Lauxaniidae, a group of very high diversity and endemism in Indonesia These insects are a major component of the saprophagous fauna in wet-forest ecosystems, and are likely responsible for a large portion of forest litter turnover. They could therefore prove to be important indicators of habitat health with implications for habitat conservation. Including this group in our entomological surveys will be of great value to our project, as will Dr. Gaimari’s interests and expertise.

Dr. Andrew Hargadon, Associate Professor and Director of the Center for Entrepreneurship and Director of the Energy Efficiency Center in the Graduate School of Management, UC Davis, has expertise in technology and innovation management, entrepreneurship, and the commercialization of science and technology. His research is focused on the point at which technology and innovation meet, particularly for sustainable technologies. He will contribute to this project by providing advice on the analysis and development of the commercial potential of green technologies, and their transfer to the business sector for implementation.

Prof. Dr. Endang Sukara, Deputy Chairman of the Indonesian Institute of Sciences (LIPI) and Chairman for MAB-UNESCO National Committee for Indonesia. Due to his leadership role at LIPI, Dr. Sukara will be a crucial member of our Advisory Board in determining how best to keep our project in line with LIPI’s goals and priorities for biodiversity exploration and conservation. He will also assist us with negotiating exchanges of materials, such as specimens between Indonesia and the U.S., and helping us to ensure that all relevant regulations are observed and that appropriate international ethical standards are upheld in all aspects of the project.

Dr. Sharon Shoemaker, Professor of Food Science and Technology, UC Davis, has over 30 years experience studying cellulases, focal enzymes for the screening activities of AP3, from both basic and applied perspectives. She was also the founding executive director of the California Institute of Food and Agricultural Research at UC Davis and, in that role, she was responsible for bringing in as members several private companies involved in the commercialization of ceulluases. She can therefore offer us excellent advice and guidance on both the scientific and the business-related aspects of this project.

Dr. Tamas Torok, Staff Scientist, Microbiologist, Center for Environmental Biotechnology Lawrence Berkeley National Laboratory, has expertise related to several of our proposed aims. Over the last ten years, Dr. Torok has led international expeditions, collected environmental samples, and isolated microorganisms, including filamentous fungi, yeasts, and bacteria, from Lake Baikal in Siberia, the deserts of Uzbekistan, the Caucasus mountains in Georgia, and extreme environments in Tajikistan and the Kamchatka peninsula in Russia. He has also worked with samples from various closed military basis in the U.S., the Chernobyl Exclusion Zone in Ukraine, and Puerto Rico. He has collaborated with major U.S. and multinational industrial partners, including American Home Products, DuPont, Diversa Corporation, New England BioLabs, SibEnzyme, Maxygen, and NovaCal Pharmaceuticals, screening microorganisms for novel biotechnology applications from agriculture to bio-medicine. Dr. Torok will offer helpful suggestions regarding national and international microbial surveys and screening for natural products with therapeutic and energy applications, including advice on obtaining necessary permits, methods of preserving and shipping microbes, and following international bioethical standards, such as those laid out in the Convention on Biological Diversity. He will also assist us with interactions with industrial partners who may be stakeholders in the results of our research.

Dr. Robert Voeks, Professor of Geography, California State University, Fullerton, studies cultural ecology, ethnobotany, tropical forest ecology, and biogeography in Africa, Brazil, and Borneo. He has roughly twenty years experience carrying out research on tropical ethnobotany, medicinal plant species, and traditional healing systems, especially in Malaysia, Brunei, and Brazil. He will be valuable in advising on the botanical sampling and ethnomedical censusing. He will be able to advise on ethnobotanical inventory methods, especially appropriate community and habitat sampling strategies, as well as elucidating culturally relevant concepts of disease etiology and healing procedures.

We will also invite the following individuals to serve on the Advisory Board, in order to ensure representation of all three of the Indonesian research institutions at which our project participants are based: Dr. Akhmaloka, Dean, Faculty of Mathematics and Natural Sciences, ITB; Ir. Anwar, MSc., Director of Forest and Nature Conservation Research and Development Center, FORDA, MoF.

D. RESEARCH METHODS (TOP )
D.1. Selection of Survey Sites The specific localities to be surveyed will be selected based on both scientific and logistical considerations. First, we have decided to focus our efforts in southeastern Sulawesi (the province of Sulawesi Tenggara), one of the least-studied areas on the island faunally and floristically, and one that encompasses a variety of substrates over a range of elevations and includes significant areas of intact forest with potential for designation as protected areas. Second, because our primary interest is the biodiversity of relatively poorly studied lowland (below 1000 m altitude) tropical forests of Sulawesi, which occupy only a small portion of the island’s total area and which are considered highly threatened due to logging and lack of enforcement of conservation laws in the limited protected areas, three such sites will be surveyed. One upland (above 1000m altitude) forest site will also be included in order to allow us to make comparisons of levels of overall diversity in various taxonomic groups, diversity of organisms yielding natural products with potential applications in human health and bioenergy, and conservation status of forests at different elevations. Finally, from a logistical standpoint, in order to complete the planned number of field expeditions (see AP1), we need to select sites that can all be accessed in the course of a single four- to six-week expedition.

A comprehensive survey of the flora of Sulawesi was completed by The Nature Conservancy (Bogor, Java) and Texas Tech University and is available online (Cannon et al 2005). Based on their analysis of the flora of Sulawesi they could divide the soils into four types: a general soil type they called intermediate, and three “extreme” soil types that supported distinctive floras: limestone, ultramafic, and alluvial. On top of this, they had four elevational classes: lowland (0–850m), upland (850–1500m), montane (1500–2200m), and tropalpine (above 2200m). Then there were some miscellaneous classes, such as karst, wetlands, and mangroves. Using satellite imaging and other remote sensing technologies, as well as site visits, they produced maps of the different forest types as well as indications of the relative condition of the forest: old growth, good forest (some evidence of shifting cultivation but no roads), fair forest (evidence of roads, selective logging or intensive shifting agriculture visible, but with at least half the forest cover intact), poor forest (less than half forest cover), and open areas/converted forests (little or no forest cover left).

Using these maps, and taking into account the amount of collecting effort expended in various parts of Sulawesi, the number of different forest types available, forest condition, and certainly logistics, we identified the region around the town of Kolaka as our target study area (Fig. 2). Kolaka is located on the western side of the southeastern peninsula. There is regular ferry service to Kolaka from the southern province and Ujung Padang, the main transport hub into Sulawesi. This will simplify the movement of large numbers of people, as well as dangerous goods, such as alcohol and cyanide, needed for collecting.

A coastal road extends northwest from Kolaka that passes through a series of villages and near the towns of Wawo, connects with a road going over a range of mountains (Peg. Mengkoka). Contiguous forest on intermediate soils is available along this road from about 150 to 1,650 meters. Research sites along the road can be established in the lowland, upland, and montane zones as defined by Cannon et al. (2005). The highest elevations in the area are 2,790 meters and support a small island of Tropalpine forest. A second area of interest is along a road that runs southeast from Kolaka toward the villages of Bauia and Benua. This road runs through a large patch of good lowland intermediate forest and passes near a patch of old growth forest on mafic soils. This patch of forest is just outside the boundaries of Rawa–Aopa National Park. A research camp in this mafic forest would expand the variety of habitats surveyed and provide information about whether this area should be included in Rawa–Aopa. This national park also contains one of the best areas of wetlands in Sulawesi.

In summary, the Kolaka vicinity has substantial patches of all the major plant communities found in Sulawesi except mangroves and the communities on alluvial soils. Good quality forest on alluvial soils is exceedingly rare in Sulawesi. The forests have road access, but they do not seem to have suffered from widespread clearing spreading out from these roads. According to Cannon et al. (2005), “very little is known about the vegetation communities of this bioregion…The scattered pieces of karst and mafic soils probably provide a stepping stone across the bioregion into the larger areas to the north and may harbor endemic species. The vast area of good quality forest along the northern margin is primarily lowland and upland intermediate forests, making this a highly valuable [region] for conservation purposes.”

Figure 2. Proposed area for biodiversity surveys (APs 1, 2, and 5), with potential sampling sites indicated.

D.2. Summary of Methods for Each Associate Program Associate Program 1: Macro-organism inventories. Leader: Elizabeth Widjaja, LIPI. This program will be charged with taking the lead on collection of plants and invertebrates. A team of scientists based in Indonesia will undertake two visits in each of Years 1and 2 and one visit in Year 3 to each of the four survey sites. Scientists from UC Davis will join these efforts once in each of these years. These trips will be conducted in different months each year to ensure that all periods of annual seasonal climatic variation ate included. An additional visit in Year 3 will be made to work on processing and distribution of specimens collected in previous expeditions. All specimens will be deposited at LIPI, with duplicates to be sent to UC Davis for deposition in the herbarium of the UC Davis Center for Plant Diversity (DAV) and the UC Davis Bohart Museum of Entomology. Local guides participating in the collection activities will be interviewed to gather information about human uses of any of the plants collected, especially medicinal uses. Based on these ethnobotanical data, some plants will be included in the screening activities described in AP 4, the primary emphasis of which will be microbes. In particular, plants with known medicinal uses, especially species that have not been previously subjected to laboratory analyses, will be included in the human health screening.

Associate Program 2: Microbial surveys. Leader: Kate Scow, UC Davis. Activities in this program will be tightly correlated with those of AP1. Indonesian and U.S. microbiologists and mycologists will join the teams described above to participate in field expeditions. Soil, root, and leaf litter samples will be collected along with the macro-organisms listed above. Bacteria, yeasts, and filamentous fungi will be cultured from these samples, and from the plants, insects, and vertebrates collected under AP1. A major focus will be microbes associated with wood-feeding insects. Initial culturing will be conducted at LIPI and at the MoF Forest Microbiology Laboratory in Indonesia. Duplicate cultures will be shipped to the U.S. to be deposited in collections and for further study under APs 3 and 4.

Associate Program 3: Discovery of energy solutions. Leader: Kyria Boundy-Mills, UC Davis. Microbes isolated in AP2, as well as other isolates from the Phaff Yeast Culture Collection, will be screened for their potential utility in biofuels applications. The two specific targets are novel cellulase homologs for improved degradation of lignocellulosic biomass and oleaginous microbes to be used for production of biodiesel or other long-chain liquid fuels. Strains will be screened for cellulase, xylanase, and glucanase activity using AZCLconjugated substrates, for presence of cellulase genes using PCR, and for elevated lipid content using fluorescent staining. Metagenome sequences of microbes in the gut of wood-feeding insects, if performed through the Joint Genome Institute Community Sequencing Project, will also be searched for novel cellulases. In addition, dried preparations of many of the same microorganisms will be prepared for use in AP4, which concerns analysis for novel therapeutics.

Associate Program 4: Discovery of human health solutions. Leader: L. F. Bjeldanes, UC Berkeley. Using high-throughput cell-based assays for potential pharmaceuticals with activities against cancer, immune deficiency, and neurological disorders, natural products will be purified and identified from filamentous fungi, yeast, and selected medicinal plants collected on Sulawesi under APs 1 and 2. Cellular and molecular studies of modes of action of active products will be conducted using a set of tumor cell lines that reflect the most prevalent cancers in the developed world, including cancers of the lung, colon, breast, and prostate gland. In addition, in vivo studies of anticancer potential of these purified products will be conducted in rodent xenograft models. Following initial high-throughput assay in cultured dendritic cells, additional assays of immune activation will be conducted by looking for IL-1 mRNA expression, CC chemokine receptor-7 expression, and T-cell–stimulatory capacity, as well as in vivo testing of immune enhancement activities of these purified products in rodents. Following an initial screen of extracts using a high-throughput G protein-coupled receptor (GPCR) calcium fluorescence assay, follow-up studies in rodents will be conducted, targeting GPCRs that are primarily affected by anxiety, stress, pain, and alcoholism.

Associate Program 5: Conservation research and vertebrate survey. Leader: Andy Engilis, UC Davis. Surveys of terrestrial vertebrates will be conducted in the areas surveyed under APs 1 and 2, and the information will be pooled with data on diversity of plants and invertebrates produced by those programs to make comparisons of biodiversity in and among lowland, mid, and high altitude primary forest. The combined data will also be used to develop multi-metric diversity models that provide an ecological basis for watershed reserve design. The results will be used to support conservation planning intended to minimize forest fragmentation and to develop landscape conservation recommendations for forest preservation and reserve design.

Associate Program 6: Conservation partnerships, training, and ethics. Leader: Jeanine Pfeiffer, UC Davis. The task of this program is to coordinate, monitor, and expand the interagency relationships within Indonesia developed during the proposal planning process and strengthening links between U.S. and Indonesian scientists. Building on the close collaborative links established during the proposal writing process, AP6 will set up web-based communication and conferencing software to create an inter-agency communication network (IACN), enabling a continuous feedback loop among the partners involved in Programs 1-5. Recognizing the importance of routine mechanisms for project assessment, AP6 institutionalizes project evaluation and reporting by organizing annual coordinating meetings that will be held in association with yearly steering committee meetings on a rotational basis at the key Indonesian institutions (LIPI, ITB, and MoF), with teleconference links to UC Davis, UC Berkeley, and other U.S. affiliates. Acknowledging the unique body of collective expertise held by project investigators and collaborators, AP6 facilitates a two-way, interactive training curriculum by organizing onsite field courses, specialized workshops, and guest lectures, which will be videotaped, subtitled, and uploaded to the project website in widely accessible electronic formats. In cooperation with experienced international bodies (e.g., the Swiss Academy of Science; Expert and Working Groups associated with the UN CBD Secretariat), AP6 will assist UC Davis and LIPI officials in developing best practices for incorporating tenets of the Convention on Biological Diversity (UNEP-CBD, 1994) and related international agreements into inter-agency Memoranda of Understanding, Material Transfer Agreements, Mutually Agreed Terms, and Data and Benefit Sharing Agreements. AP6 will also guide AP 1-5 partners in sensitive, respectful engagement with local officials and communities in Sulawesi, in accordance with the principles and practices outlined in the ISE Code of Ethics (International Society of Ethnobiology, 2006), and ensure that contacts with local representatives of administration, government agencies, and research institutions are established and maintained.

D.3. Coordination among Associate Programs The breadth and scope of this project will provide us with powerful tools to address multiple complex questions about Sulawesi’s biodiversity, its potential applications to pressing societal concerns, and the most effective strategies to conserve it, but maximizing the effectiveness of the project will require strong coordination among the different APs. For example, it will be essential to maintain a common relational numbering system for all collections and any products derived from them so that data from all phases of the project — from initial collection and identification of a macro-organism, through isolation and identification of a microbial strain from that macro-organism, to isolation and identification of a therapeutic substance from that microbe — can be easily traced backwards or forwards from any point in the chain.

Three distinct but related strategies will be used to build and reinforce cohesiveness among the different components of this project. First, establishment of a common project database linked to a common project website will facilitate on-line data entry, data-sharing, and general communication among all participants in the project. As members of the ICBG program, we will work with the Fogarty International Center (FIC) program managers to select software for our databasing and data-sharing that is compatible with both our specific requirements for this project, and with the needs of the Global Data Center for the ICBG program (see further details below in section D.5, Data Management). Second, on-line meetings of the PI and all AP leaders and co-investigators will be conducted on a quarterly basis. These online meetings will be facilitated by AP6, and carefully integrated with the annual coordination meetings held by the Indonesian agencies and the Indonesiabased Steering Committee. Third, in order to help provide guidance to this complex project, an international Advisory Board will be established, as described above. Annual reports from each AP leader to the PI, and from the PI to the Advisory Board will describe the progress of each AP, and the Center as a whole, and annual on-line meetings of the PI, AP leaders and co-investigators, and the Advisory Board, will be held one month after the reports are submitted. All annual reports and agendas and minutes of all meetings, including translations into Bahasa Indonesia, will be posted to the project website.

Regular communications and meetings with representatives of our industry partners will also be conducted. These individuals will receive copies of annual reports and will be invited to participate in the annual project meetings, above. In addition, each company will receive more detailed copies of the annual reports from the AP most relevant to its interests (AP3 for energy companies, and AP4 for pharmaceutical companies). When necessary — e.g., as promising products are identified in the later stages of the project — special meetings may be called, to include one or more company representatives and an appropriate subgroup of project investigators and advisors. All project participants and Advisory Board members will be informed of the plans for such meetings, and bilingual agendas and minutes will be posted to the project website. Due to the complex and sensitive nature of discussions related to private companies’ use of products derived from Indonesian biodiversity, all meetings devoted to discussions of these issues will include at least one representative from LIPI, the lead Indonesian institution on the project, and Dr. Pfeiffer, leader of AP6, which is directly concerned with ethical issues, or a delegate designated by her.

International collaborations will be enhanced by visits of U.S. scientists to Indonesia to conduct field work under APs 1, 2, and 5, and by the training activities of AP6. In addition, in each of years 4 & 5, two visiting scholars from Indonesia will be invited to the U.S. for a period of three months to perform research related to this project. In each year, one of these individuals will work with Dr. Kyria Boundy-Mills and co-investigators on AP3 to gain experience in methods for identifying yeasts and filamentous fungi, and screening them for applications to energy issues. The second will work with Dr. Len Bjeldanes and co-investigators at UC Berkeley and UC San Francisco to gain experience in methods for identifying and isolating natural products with therapeutic effects. All visiting scholars will also have ample opportunities to meet with the PI and the other U.S.-based investigators, individually and in group meetings, to discuss the overall project and the relationships among the six APs.

Finally, to build awareness about the scope and complexity of international collaborative research, all senior personnel will be required to participate in at least two programs — one in Year 1 and one in Year 5 — on the international dimensions of conducting research, such as those offered by the National Council of University Research Administrators (NCURA), in which participants are given a chance to ask questions of experts and exchange concerns and ideas in a moderated on-line forum. Such a venue will provide us an excellent opportunity to learn about other projects of similar scope and scale, and to share our own insights, challenges, and lessons learned.

D.4. Overview of Group Timeline (TOP )
In the following table, only major activities of each Associate Program and overall group activities are shown.

E. Data Management: Available Tools: NAPIS (TOP )

F. Announcements (list): (TOP )