James Hanken - US grants

This proposal examines the origin, differentiation, and morphogenesis of the ossified craniofacial skeleton in the oriental Fire-bellied Toad, Bombina orientalis. It entails (1) documenting the extent of cranial neural crest contribution to the osteocranium, and (2) identifying the roles of four factors that influence the timing and sequence of bone formation, and subsequent skeletal growth and morphogenesis, and other vertebrates. These factors are temperature, epithelial-mesenchymal tissue interactions, thyroid hormone, and the eye. Methods include: identifying results of ablation of restricted portions of the embryonic neural crest on subsequent cranial osteogenesis; quantifying differences in the timing and sequence of ossification among specimens reared at different constant temperatures; documenting the ability of cranial mesenchyme to initiate osteogenesis both in the absence of overlying epidermis and in the presence of trunk (i.e., noncranial) epidermis; examining patterns of ossification in larvae reared in various concentrations of thyroxine; analyzing effects of unilateral removal of the eye on bone growth and morphogenesis, and on adult skull size and shape. Some of these analyses will consider the entire complement of skull bones; others will focus primarily on the frontoparietal, an intramembranous bone that is homologous to the frontal and parietal of other vertebrates. Analytical procedures include whole-mount and serial-section histology of preserved specimens, in vivo bone labelling with Alizarin Red S, and computer-aided, three-dimensional reconstruction of skeletal morphology. Diagnosis of the developmental bases of human congenital skull malformations relies largely on the study of nonhuman vertebrates. An understanding of the mechanisms that control cranial ossification during anuran metamorphosis can serve as a "model system" for the study of craniofacial skeletal development in vertebrates, including man.

Drs. James Hanken and Marvalee Wake propose a half-day symposium at the centennial meeting of the American Society of Zoologists (ASZ) in Boston in December, 1989. The theme of the symposium will be "Experimental Approaches to the Analysis of Form and Function." Two speakers each will address the impact of experimental approaches at the developmental, functional, ecological and evolutionary levels of organization. The specific aims of the symposium are to evaluate the utility of the experimental approach by illustrating the kinds of insights that can be gained, as well as the limitations faced in experimental functional analyses. A Proceedings volume will be published Technological advances in imaging, microsensors and microsurgery, and the resolution of early developmental features have rejuvenated the discipline of functional analysis. These novel sources of data will shed new light on ecological, physiological, and evolutionary issues. The proposed symposium will find a diverse and interested audience at the annual meeting of ASZ.

Direct development is an evolutionarily derived life history mode in vertebrates and invertebrates in which the free living, aquatic larval stage is lost. This project examines the pattern and mechanisms of cranial development in direct developing anurans, and how these differ from those in metamorphosing taxa. Experimental and descriptive methods include immunohistochemistry (to localize the embryonic distribution of type II collagen and visualize the initial skeletal pattern); scanning electron microscopy (to document neural crest morphology and migration); heterospecific transplantation of premigratory cranial neural crest and cranial ectoderm (to examine inductive tissue interactions that underlie the development, and loss, of cranial tissues); in vivo administration of thyroid hormone and TH- blocking agents; TH radioimmunoassay (to measure the contribution of TH from maternal and embryonic sources); and conventional histology. Analyses will focus on Eleutherodactylus coqui (Leptodactylidae), whose ontogeny is among the most derived of any direct developing anuran with respect to the ancestral metamorphic pattern of cranial development. Reference data concerning the ancestral pattern will be obtained from several phylogenetically diverse species,including Bombina orientalis (Discoglossidae), Xenopus laevis (Pipidae), and Rana pipiens (Ranidae). Results will contribute to our understanding of the basis of direct development in amphibians and how this important life history mode has evolved. They also will be used to address a series of issues in developmental and systematic biology, concerning the relation between development and morphological evolution. These include the evolutionary implication of mechanisms of cranial pattern formation; the importance of ontogenetic repatterning vs. heterochrony; the role of inductive tissue interactions; and the hormonal mediation of embryonic development. finally, they will allow comparison of direct development in amphibians with that in other groups with complex life cycles.

9321572 Hanken This proposal outlines a series of descriptive and experimental studies that examine the hormonal mediation of embryonic development in direct-developing anurans. Precocious activity of the thyroid axis is frequently cited as the mechanism underlying direct development, but this has never been fully examined. To test this hypothesis, initial appearance and subsequent development of the thyroid axis in a direct-developing frog will be compared to the patterns observed in metamorphosing frogs. The role of thyroid hormones (TH) in mediating direct development will also be evaluated experimentally by manipulating endogenous hormone levels. Methods include histology (to document thyroid gland and median eminence formation), radioimmunoassay (to determine TH levels through embryonic development), immunocytochemistry (to examine the ontogeny of thyrotropic cells and TH receptor expression), and hormone manipulation (to experimentally examine the roles of TH in direct development). Analyses will focus on embryos of the direct developing frog Eleutherodactylus coqui (Leptodactylidae) derived from an established breeding colony. For comparative purposes, analyses will also include several metamorphosing species, including Leptodactylus albilabris (Leptodactylidae), Bombina orientalis (Discoglossidae), and Xenopus laevis (Pipidae). Results will contribute to our understanding of the endocrine mediation of direct development in amphibians. They also will provide new information on the mechanistic basis underlying life-history evolution. In addition, this study will examine maternal provisioning of hormones in early embryogenesis and development, a process relevant to understanding early development in all classes of vertebrates. ***

9419407 James Hanken The ultimate goal of this research project is to understand the developmental basis of anatomical differences in anatomy of the head among species. The studies focus on a unique population of cells--the neural crest--from which many cranial tissues in vertebrates are derived. The specific contributions of neural crest cells to the skull and cranial musculature in different species will be assessed by labeling these cells with a fluorescent dye early in development, before they begin to migrate throughout the body, and tracking their movement to see which cranial tissues are derived from the labeled cells. The research will also determine whether neural crest cells contain the developmental information that is responsible for anatomical differences among species and document the place and time during development where genes are expressed that might mediate the development and adult fates of neural crest cells. The research will increase our knowledge of the genetic and developmental mechanisms underlying the integrated evolution of complex anatomical structures.

Hanken 9801586 This study will examine the development of the skull in several species of amphibians (frogs). Its main goals are to better understand the molecular and genetic processes that underlie the embryonic development of bone in the heads of vertebrate animals, and how these processes are modified during evolution to achieve diversity of skull size and shape among species. It also will provide greater understanding of the developmental bases for direct development, a widespread but poorly studied life-history mode found in many species of living amphibians, and how direct development evolved from the ancestral, metamorphic life history. Individual analyses will employ several different laboratory procedures. These include labelling embryonic cells with vital dyes and embryonic tissue recombinations (to identify which cells contribute to the adult skull); histology and immunocytochemistry (to study detailed aspects of cranial anatomy); and recombinant DNA technologies, in situ hybridization, and implantation of protein-soaked beads (to identify genes that are involved in bone formation and determine the likely functions of each). By supporting this research, this award also will enhance the education and training of a postgraduate student and better prepare the PI for a career in higher education and biological research.

The Museum of Comparative Zoology at Harvard University houses one of the premier collections of invertebrate fossils in the US. Since its founding by Louis Agassiz in the 1850s, the collection has served as an important resource for researchers from the US and abroad, housing over 10,000 types and more than a million specimens. However, while the collection has not been neglected, neither has it been much improved over the course of the last century. It now falls below the standards that one might expect for a collection of its size and significance. The primary goals for modernization of the invertebrate fossil collection are to assemble together in high security cases the types and other valuable specimens now scattered throughout the collection; to add, replace, and renovate the housing for the remainder of the collection, including installation of compactors; and to computerize the collection into a fully searchable web-based database.

This award provides support for purchase of an Environmental Scanning Electron Microscope (ESEM) equipped with a Peltier cooling stage to be used by at least 13 research groups in the Department of Organismic and Evolutionary Biology and the Department of Molecular and Cellular Biology of Harvard University. This modern, multifunctional instrument will replace an existing, 25-year-old instrument which lacks the capacity for examining fully hydrated materials. The instrument will be available for use by students, research associates and faculty, insuring student training in use of a modern electron microscope. Diverse research in the areas of organismic, evolutionary, and developmental biology will utilize this new equipment. Initial uses include studies of the morphology of sulfur-oxidizing bacteria, determination of the migration pathway of neural crest cells in amphibians, and studies of the mechanisms of xylem embolism repair and root water uptake in plants. Such studies with the level of resolution provided by scanning electron microscopy were not possible until the development of instruments that did not use a low pressure or vacuum in the sample chamber.

The Museum of Comparative Zoology's collection of amphibians and reptiles is one of the world's largest and most important resources for systematic herpetology. Information stored in it is of great scientific value. More than half the world's species are represented, including representatives of all families. It is exceptionally rich in primary type specimens and important historical collections, which have figured prominently in the development of herpetology as a discipline and in the development of faunal work for particular areas or taxonomic groups. The collection is heavily used by the international scientific community, as documented by the high frequency of loan requests, by the large number of primary research publications that are based wholly or in part on MCZ specimens, and by the many visitors who come to work in the collection. The present project would relieve serious overcrowding by the purchase of a compactor system and new cabinets, making this important resource more easily accessible to the community. The project is part of the second phase of a three-phase plan to renovate the physical facilities of the Department of Herpetology and modernize the Department's operations.

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A grant has been awarded to Dr. James Hanken at Harvard University, as part of a four-institution collaboration, to study phylogenetic relationships of the living amphibians and their close fossil relatives. Living Amphibians are a prominent part of the Earth's vertebrate fauna and include three orders: the caecilians (Gymnophiona), salamanders (Caudata), and frogs and toads (Anura). Despite recent advances in discovering and describing their diversity, many critical questions in amphibian evolution remain unresolved and a fresh analysis of evolutionary relationships is needed to take new discoveries into account. Furthermore, the recent decline and apparent extinction of amphibians from many environments makes it urgent that we discover and classify the diversity present today. A team of seven investigators from diverse institutions (University of Texas at Austin, University of California at Berkeley, Harvard University, and the University of Kansas) and their colleagues will collaborate to resolve modern amphibian relationships. Field sampling in biodiversity hotspots will provide materials of new or previously unsampled lineages. Anatomical and morphological data from living and fossil forms will be combined with DNA sequences from a set of defined mitochondrial and nuclear genes for as many species as possible, and will be integrated with existing data sets. Analysis of these large data sets will be used to gain insight into such questions as repeated patterns of evolution, geographic patterns, and rates of evolution. Dr. Hanken and his students and colleagues will focus on morphological and anatomical studies of African frogs and on select groups of Neotropical plethodontid salamanders, as well as contributing to the overall integration of molecular and morphological datasets for phylogenetic analysis.
Understanding the evolutionary history of modern amphibians is critical for developing conservation strategies for amphibians as well as completing the vertebrate portion of the tree of life. The project will involve extensive student training and interaction with US and international colleagues. Communication with the public will utilize web resources, especially AmphibiaWeb, an existing site that will be expanded and further developed to provide information on all species of amphibians for professionals and the public at large. AmphibiaWeb will also provide training opportunities for students and senior professionals to enable them more effectively to communicate their findings.

Harvard University is awarded a grant to develop a networked solution to enable annotation of distributed biological collection data and to share assertions about their quality or usability. Internet inquiries that are posed to multiple datasets may yield varying results depending on the suitability or quality of the targeted data. In some cases it might be possible to inquire of experts or software agents that can assist in determining the fitness for use; in other cases such experts or agents might already have recorded an assessment of the data. However, that information is not typically available to the originator of the query. The proposed system will make these value-added assertions accessible to the end users of biodiversity datasets.

The Filtered Push network uses natural science collections as a reference implementation for a cyberinfrastructure with which any community can render an expert opinion about the quality of data, and the fitness for use of a data set or a subset of records. The emergent knowledgebase of the Filtered Push network supports the ability of interested parties to get immediate or historical access to these annotations, filtered by criteria expressing constraints on their interests. The network can also provide for the automatic execution of scientific workflows triggered by expert commentary, by the introduction or discovery of new data, or by a change in scientific viewpoints. As with the annotations, the outputs of such workflows can be distributed to interested parties, software or human. Filtered Push networks therefore allow for continuous quality control by the scientific community, based on human expertise, statistical or logical machine reasoning or advances in the domain science itself. The Filtered Push project maintains a wiki at http://www.etaxonomy.org/mw/FilteredPush. This project is part of a 10-year effort to digitize and mobilize the scientific information associated with biological specimens held in U.S. research collections. The images and digitized data from this project will be integrated into the online national resource as outlined in the community strategic plan available at http://digbiocol.files.wordpress.com/2010/05/digistratplanfinaldraft.pdf.

Collaborative Research Digitization TCN: Southwest Collections of Arthropods Network (SCAN): A Model for Collections Digitization to Promote Taxonomic and Ecological Research

The Southwest Collections of Arthropods Network (SCAN) brings together 10 diverse arthropod collections at universities and museums throughout the Southwest to create a virtual network of ground dwelling arthropods which are notably responsive to temporal and spatial environmental changes. These 10 collections document much of the Southwest's biodiversity, but currently the data associated with millions of arthropod specimens are not easily accessible. To overcome this, SCAN will develop methods for integrating existing databases, catalogue-image specimens, develop new electronic identification techniques, and produce a virtual library of ground-dwelling arthropods (beetles, grasshoppers, spiders, ants). In addition the project will work with the existing project Filtered Push to increase the capacity of experts to provide remote identifications and annotations of data that can be sent throughout the network.

The comprehensive SCAN online library and expert information will be available to the public as well as professionals in taxonomy, ecology, and climate change science. Smaller institutions will be provided increased access to large data sets for promoting research. The SCAN datasets will support a number of ongoing projects examining the effects of environmental and land-use change on individual arthropod species. By increasing access to this information, SCAN will stimulate new research and increased awareness in biodiversity conservation throughout the region. Over 50 undergraduates also will be trained in cyberinfrastructure, systematics, and ecology. This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biological Collections program and all data resulting from this award will be available through the national resource, iDigBio.org.

Biological collections are an irreplaceable resource that informs our scientific understanding of the history and diversity of life on Earth. The value of these research collections is greatly enhanced when the specimens and data are digitized and made widely and publically available. The biodiversity collections community recently united to develop a ten-year Strategic Plan for establishing a Network Integrated Biocollections Alliance (NIBA), but to date, no detailed community-informed plan has been developed to guide the implementation of that Strategic Plan. The American Institute of Biological Sciences (AIBS) will conduct a workshop of diverse stakeholders with the specific goal of deriving a detailed implementation plan for the NIBA.

A detailed community-informed plan will help the scientific community more effectively curate specimens and data, increase research productivity by improving access to collection resources, develop innovative tools to capture and validate data, develop protocols that enhance the efficiency of digital capture, and provide education and training to develop the biodiversity collections workforce. As data and specimens are captured and made publically available, there will be new opportunities for the public to access and learn about biodiversity and Earth systems, and the plan will recommend methods to promote citizen science activities to expose the public directly to these scientific resources.

The rapid biodiversity change in North America has significant effects on essential ecosystem services, from impact on soil health and nutrient cycling, to agriculture, forestry and water quality. Exploding populations of invasive species threaten fresh water and terrestrial habitats and potentially impact the natural resources of the nation. Easy access to robust, expertly vetted baseline data for species occurrences, abundances, and distribution ranges, and monitoring how these parameters have changed through time, will facilitate the protection of the nation's natural resources, and vastly improve the capacity for effective restoration, land management planning, and conservation management. Numerous undergraduate students will receive training in digitization technologies and a modular exhibit will be developed to engage public interest in biodiversity changes.

Effective monitoring requires easy electronic access to historical specimen baseline information for temporal and regional species diversity comparisons that can facilitate informed land management decisions. Vast amounts of specimen data are housed within the nation's natural history collections, but most of these data are not readily accessible from digital resources. Size and complexity of scientific specimen collections require major technological advances in capturing specimen data. The goal of this four-year collaborative project is the rapid digitization of >2 million specimens and their locality data from ten arthropod and mollusk collections housed at six major US museums in six states (Il, OH, AL,MI, DE, PA). This project will significantly automate specimen data capture by utilizing optical character and voice-recognition technologies. The digitized data from this project will be immediately deployed for habitat-based distribution modeling and analyses.This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biological Collections program and all data resulting from this award will be available through the national resource (iDigBio.org).

The University of Illinois Urbana Champaign and Harvard University are awarded grants to develop software tools for scientific data digitization, sharing, integration and use. The considerable challenge to digitizing natural science collections in the U.S. (and globally) necessitate a focus on both digitization efficiencies and the utility of the generated data. This grant will develop a novel, extensible, open source toolkit (Kurator) for automated and semi-automated workflows with diverse curation services to aid biodiversity research and beyond. This project will enhance discovery and understanding while promoting teaching, training and learning. A postdoctoral fellow will be trained in provenance enhanced workflow technology and contribute to Kurator design and implementation. Principles of data management curation with a focus on provenance will be taught in undergraduate and graduate courses. This project will also enhance infrastructure for research and education through collaborations with iDigBio and the Encyclopedia of Life. Educational modules and outreach activities on data quality and data curation will be developed for undergraduates and high school educators. Several Thematic Collection Networks will provide data via iDigBio for testing to insure dissemination of high quality data. Critical community authority files that do not have associated web services will be made available to the greater community as Kurator actors and services.

Kurator will consist of a user friendly web interface for users to configure and launch workflows while maintaining provenance, and a workflow platform for rapid development of new curation services and workflow variants. The latter will also be used to "wrap" valuable domain authority files that are not currently available as services. New "curator-in-the-loop" workflow technology allows us to directly involve experts in semi automatic curation pipelines, using human interaction actors via FilteredPush, other syndication methods, and discovery environments. Kurator will allow examination of data lineages to facilitate the assessment of credibility, supports repeatability in publication, informs legal proceedings where data are regulated, and provides context for feedback to a given resource. Kurator will facilitate digitization efforts through custom processing of raw data obtained from hardcopy specimen labels against existing services, including taxonomic name resolution, georeferencing, and duplicate specimen detection, as well as newly created customizable actors for appropriate controlled vocabularies to clean the data. Where required, semi-automated services can invoke expert review using annotation services and existing discovery environments. Curation pipelines can be integrated with other workflows for analysis of ecological, evolutionary, phenological, genomic and related data, can be shared or repurposed easily, and can be made accessible for publication.

This project will investigate the genetic factors that cause elaborated bone pattern in fish fins. Bone pattern elaboration results from increases in bone numbers and connections, and such research is important for understanding processes of both evolution and development. In evolution, increase in the number of bones arranged end-to-end helped transform fins into limbs and aided the colonization of land by extinct vertebrates. In development, normal function and movement depends upon formation of the proper bone numbers and connections, and defective development can lead to severe impairment. Currently, the mechanisms that led to elaboration of the fin skeleton to form limbs are unknown. To identify the genetic factors involved, the researchers will study strains of the model species, zebrafish, that have genetic changes that result in the formation of new fin bones. They will also investigate naturally occurring variation in two species, gar and bowfin, that have different numbers of bones extending from the shoulder. These complementary approaches will reveal the mechanisms regulating growth and formation of the skeleton of fins and limbs, and show how simple genetic changes can lead to the formation of limbs from fins. Understanding the mechanisms of bone pattern elaboration and development has implications for human health and developmental abnormalities, and may provide clues for the evolution of life on land. Additionally, the project will provide research opportunities for Native American undergraduates.

While tetrapod vertebrates have increased the number of bones along the proximo-distal (P-D) axis of the limb, teleost fishes such as the zebrafish have reduced the pectoral fin skeleton; only a single long bone is found along the P-D axis. The researchers performed a forward mutagenesis screen in zebrafish and isolated a novel mutant that forms supernumerary bones along the P-D axis of the fin through a process similar to that seen in the development of tetrapod limbs. The proposed research will extend results from mutant analysis to natural populations to determine if the mutation is producing supernumerary bones by activating ancestral genetic mechanisms. Transcriptome profiling by RNA sequencing will be used to compare gene-expression levels in the developing pectoral fins of wild-type and mutant zebrafish, as well as two species that exhibit natural variation in P-D axis elaboration. This analysis will reveal patterns of differential gene expression that correlate with P-D axis elaboration. Differentially expressed genes will be tested in the zebrafish to determine if their modified expression has an effect on fin morphology. This study will elucidate how additive phenotypic changes arise in development and identify candidate pathways by which additional fin/limb bones are formed in both evolution and disease.

This study will clarify the role of thyroid hormone in the development of amphibian limbs. Hormones are substances produced in the body that influences the way the body grows or develops. Thyroid hormone plays an important role in the transition of tadpoles into frogs, especially in limb development. Nearly a third of frog species bypass the tadpole stage and develop directly into frogs and the role of thyroid hormone in the development of these species is not known. This project will test two alternative hypotheses about the role of thyroid hormone in this process. In association with the Harvard Museum of Natural History, this project will also develop several educational activities on amphibian biodiversity for K-12 students, teachers, and parents. Some of these activities can be offered at little cost, which will allow many students to experience wildlife and witness the dramatic transformation of metamorphosis for themselves.

Comparing how thyroid hormone regulates gene activity during limb development between direct-developing and metamorphosing frogs can tell us how fundamental endocrine networks evolve and generate different life cycles. Biphasic frogs (which undergo metamorphosis) require thyroid hormone (TH) for metamorphosis and limb development. This study evaluates the role of TH in limb development in the direct-developing frog Eleutherodactylus coqui for comparison to its role in three biphasic frog taxa (Xenopus laevis, Bombina orientalis, and Dendrobates tinctorius). Next-generation sequencing will be used to characterize and compare the TH-induced molecular phenotype in the developing limb of all four species. This study will provide a basis for further studies of amphibian life history evolution and identify interspecific variation in an otherwise highly conserved molecular mechanism of metamorphosis. Characterizing how one group achieves direct development will provide a comparison for investigating the repeated origins of this life history in other amphibians, and address questions at the intersection of endocrinology, evolution, and development.

This project will investigate the genetic factors that cause elaborated bone pattern in fish fins. Bone pattern elaboration results from increases in bone numbers and connections, and such research is important for understanding processes of both evolution and development. In evolution, increase in the number of bones arranged end-to-end helped transform fins into limbs and aided the colonization of land by extinct vertebrates. In development, normal function and movement depends upon formation of the proper bone numbers and connections, and defective development can lead to severe impairment. Currently, the mechanisms that led to elaboration of the fin skeleton to form limbs are unknown. To identify the genetic factors involved, the researchers will study strains of the model species, zebrafish, that have genetic changes that result in the formation of new fin bones. They will also investigate naturally occurring variation in two species, gar and bowfin, that have different numbers of bones extending from the shoulder. These complementary approaches will reveal the mechanisms regulating growth and formation of the skeleton of fins and limbs, and show how simple genetic changes can lead to the formation of limbs from fins. Understanding the mechanisms of bone pattern elaboration and development has implications for human health and developmental abnormalities, and may provide clues for the evolution of life on land. Additionally, the project will provide research opportunities for Native American undergraduates.

While tetrapod vertebrates have increased the number of bones along the proximo-distal (P-D) axis of the limb, teleost fishes such as the zebrafish have reduced the pectoral fin skeleton; only a single long bone is found along the P-D axis. The researchers performed a forward mutagenesis screen in zebrafish and isolated a novel mutant that forms supernumerary bones along the P-D axis of the fin through a process similar to that seen in the development of tetrapod limbs. The proposed research will extend results from mutant analysis to natural populations to determine if the mutation is producing supernumerary bones by activating ancestral genetic mechanisms. Transcriptome profiling by RNA sequencing will be used to compare gene-expression levels in the developing pectoral fins of wild-type and mutant zebrafish, as well as two species that exhibit natural variation in P-D axis elaboration. This analysis will reveal patterns of differential gene expression that correlate with P-D axis elaboration. Differentially expressed genes will be tested in the zebrafish to determine if their modified expression has an effect on fin morphology. This study will elucidate how additive phenotypic changes arise in development and identify candidate pathways by which additional fin/limb bones are formed in both evolution and disease.

The oVert (openVertebrate) Thematic Collection Network (TCN) will generate and serve high-resolution digital three-dimensional (3D) data for internal anatomy across vertebrate diversity. Via a network of digitization centers across the US, more than 20,000 fluid-preserved specimens representing over 80% of the living genera of vertebrates will be CT-scanned. This will provide broad coverage for exploration and research on all major groups of vertebrates. Contrast-enhanced scans will be generated that reveal soft tissues and organs. This collection of digital imagery and three-dimensional volumes will be open for exploration, download, and use to address questions related to the discovery of new species, documenting patterns of anatomical diversity and growth, and testing hypotheses of function and evolution. The resource will provide unprecedented global access to valuable specimens in US museum collections and will develop best practices and guidelines for high-throughput CT-scanning, including efficient workflows, preferred resolutions, and archival formats that optimize the variety of downstream applications. Museum specialists will be trained on the generation, curation, and distribution of 3D data, researchers in using 3D anatomical data, and high school and undergraduate students in the tools for creating 3D anatomical models. To drive the use of these digital specimens by K-12 STEM educators, teacher-driven workshops that generate freely available lesson plans focused on specific science standards that are based on digital and printed 3D models of specimens in US museum collections.

Data generated by oVert will serve as a catalyst for diverse research projects focused on understanding the vertebrate morphological diversity and will dramatically increase the accessibility of specimens housed in US scientific collections. These anatomical phenotypes represent a common currency that facilitates integration across the fields of taxonomy, evolution, developmental biology, comparative physiology, functional anatomy, paleontology, and ecology. The x-ray computed tomography (CT) scanning gemerates high-resolution digital anatomical data, represented as both 2D image stacks and 3D volumes and surfaces. With these 3D digital specimens, US and international research communities will be able to (1) diagnose, describe, and infer patterns of relationships among both living and extinct vertebrates, (2) test hypotheses of morphological evolution such as patterns of disparity, modularity, and phenotype-environment correlations, (3) develop structure-function models for testing hypotheses about morphological adaptations related to, e.g., feeding and locomotion, and (4) explore relationships between brain and nervous system anatomy and both sensory and musculoskeletal function. The 3D data will be distributed globally through MorphoSource, an on-line data repository for 3D biological specimen data, which will capture standardized metadata, ingest legacy data from previous and existing projects, and will supply media information to data aggregators including iDigBio (www.idigbio.org). Training workshops, both on-site at participating institutions and national society meetings of scientists and educators are planned to foster innovation and capabilities for users of 3D image data.

For two centuries, America has amassed an unparalleled collection of specimens from exploring the world's oceans. They were pulled up with nets, scooped up from seabeds with grabs, and hand-collected by divers, all contributing to a library of biodiversity that captures the state of life in the ocean - year after year, decade after decade. The broadest evolutionary scope of those collections is in the marine invertebrates, animals without backbones - sea stars, corals, worms, jellyfish, crabs, and thousands of other animals. That library of preserved marine invertebrates is our essential guide to the diversity of ocean life across the globe. And because they encapsulate data from the moment they were picked up, these institutional collections also act as a time machine, letting us use the past to understand how our present will become the future. But there is a problem - vast numbers of these specimens are essentially invisible outside of a tiny community of museum specialists. The only record of these specimens' existence is on labels enclosed in the jars with the preserved animals or in paper logbooks on a shelf. These specimens will remain nearly undiscoverable on museum shelves until their core descriptive information is made digitally available. Therefore, this project will create public digital records for over 7.5 million specimens from our nation's legacy of marine exploration, thereby making the immense investment in the specimens' acquisition available to 21st Century biodiversity and ecosystems research. Because these specimens provide a visible and tangible window into our oceans' enchanting biodiversity, this project will involve STEM educators and student educators in the digitization effort, so that they will be able to reflect their science experiences directly back to the classroom. The public will be involved virtually, by contributing transcription of specimen label data.

Digitization of alcohol-preserved marine specimens has never been carried out on this scale. A major challenge lies in the location of the data: written, typed, or printed on labels in the jars with the specimens. In many cases, that will require opening the jar, extracting the label, and either transcribing it directly or photographing it for later transcription - for hundreds of thousands of jars. The immediate participants in this program will digitize most or all of the marine invertebrate collections at nineteen institutions across the country, more than doubling the number of digital records for marine invertebrates in the U.S. All data will be publicly available through existing data portals, including iDigBio.org, using standardized data formats, thereby dramatically enhancing the accessibility of biodiversity data for comprehensive, systems-based analysis of ocean ecosystems.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

This project will enable online access to a unique, irreplaceable resource for comparative studies of the evolution and development of the vertebrate brain. The R. Glenn Northcutt Collection of Comparative Vertebrate Neuroanatomy and Embryology, housed in Harvard’s Museum of Comparative Zoology (MCZ), is the world’s largest and most taxonomically diverse collection of histological preparations of developing and adult vertebrate brains mounted on glass microscope slides. It is of particular interest and relevance to the current generation of neuroscientists who use molecular and genetic approaches to elucidate mechanisms underlying evolutionary innovations, but the slides are fragile and access to them is difficult and time consuming. By utilizing a whole-slide-imaging workflow developed through a novel collaboration with Harvard’s Center for Brain Science, the project will allow professional scientists, educators and students to easily and routinely access the slides’ content via high-resolution digital images. Such access will facilitate use of the slides in research and education and complement novel technologies for studying brain structure, development and function. It will facilitate collaborations between the neuroscience and biodiversity communities and, together with other projects that seek mass digitization and sharing of biological collections, it will enhance the ability of natural history institutions to more fully serve both science and society beyond their traditional constituencies. Indeed, the project’s imaging workflow and associated training components offer an exemplar method for rapid and cost-effective digitization that can be used by other institutions, whose slide holdings number in the millions, most of which remain dark data.

The project will use a high-throughput, semi-automated slide scanner to make high-resolution digital images of the approximately 33,000 glass microscope slides in the Northcutt Collection. When completed, the project will provide online access to approximately 500,000 serial sections and whole-mount preparations of adult brains and embryos of more than 240 genera and 270 species of living vertebrates. A cost-effective whole-slide imaging workflow will be utilized to process as many as 360 slides/week while yielding excellent image resolution (0.2 and 0.4 μm/pixel at 40X and 20X magnification, respectively). A digital image of each slide will be served to potential users via two online portals: MCZbase, the Museum of Comparative Zoology’s permanent specimen database; and MorphoSource, an NSF-supported online repository for specimen digital imagery. Both portals will be configured with Girder and SlideAtlas, two open-source software tools for whole-slide image viewing, downloading and analysis. In addition, for as many as 20 species widely used to teach comparative vertebrate anatomy, digital images of a subset of histological sections labelled to point out principal brain regions will be uploaded to BrainMaps, an online resource for vertebrate neuroanatomy. Finally, the project will produce several resources for training both students and professionals in methods for mass digitization and computer-assisted visualization of slide collections regardless of subject matter. These resources include four “how-to” videos, two online tutorials, undergraduate and graduate student internships and a graduate-level course in museum studies.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.