Paul W. Sternberg - US grants

DESCRIPTION: This application is to study pattern formation during development of the nematode vulva. Previous work has shown that the product of the lin-3 gene, an EGF homolog, acts as a secreted morphogen in this system. A morphogen is defined as a molecule whose spatial distribution contributes to development of biological pattern by dictating alternate cell responses in a concentration or dose-dependent manner. How this comes about is not known in any growth factor system. One general aim of the experiments proposed here is to understand the mechanism by which different levels of lin-3 activity determine three alternative responses in vulva precursor cells (VPC's). A second general aim is to understand how lin-3 signalling acts in the context of a network of several additional patterning forming mechanisms known to act in the vulva. One ultimate goal is to explain the precision with which VPC cell fates are specified. The role of the lin-3 ligand itself in induction of two different cell fates will be examined by determining whether there is more than one form of the lin-3 ligand, each with a different effect on VPC's, and by testing whether concentration, timing, or duration of lin- 3 activity is important in VPC response. The level at which different qualitative or quantitative signals have their effect in the responding cell will be examined by analyzing mutant forms of the let-23 receptor, to determine whether the signalling pathway branches at this point, and by examining the effects of altering dosage or activity of known downstream components such as ras and raf. To determine whether the patterning function of the lin-3-let-23 signal is reinforced by differing responsiveness of VPC's (that is, by a prepattern), the effects on VPC response of mutations in HOM-C genes will be determined. The time during which VPC's are competent to respond to signal will be determined, as well as the effects of additional signalling pathways on VPC responsiveness, including the lin-12 pathway and several known negative regulators of let- 23. Finally, experiments will be carried out to separate the effects on VPC's of the lin-3 signal and the lin-12-mediated lateral signal. VPC induction will be studied in double lin- 12/glp-1 mutants in mosaics to test whether differing levels of lin-3 activity alone are sufficient to dictate alternate VPC fates. Likewise, the patterning functions of the lin-12 pathway in the absence of lin-3 induction will be studied. Finally, experiments to test competition between these pathways are proposed.

This is a PYI award. Dr. Sternberg will be ivestigating the molecular genetics of development in the nematode, Caenorhabditis elegans.

DESCRIPTION (provided by applicant): This program is for predoctoral training of biological science PhD students for research careers in Cellular and Molecular Biology. This interdisciplinary program involves students and 40 faculty members from the Divisions of Biology, Chemistry, and Engineering. It is a continuation of a training program supported at Caltech for the past 31 years by NIH. Subjects of special emphasis within Cellular and Molecular Biology include genetics and genomics, regulation of gene expression, signal transduction, eukaryotic cell biology, synthetic biological circuits, biopolymers, and protein and cell structure. Interaction between the Divisions is evidenced by students who, although earning their PhD in one Division, carry out their thesis research mentored by a faculty member of another Division; by joint courses; by a less-formal interaction including research collaborations, and by interdisciplinary graduate programs in BioEngineering and in Biochemistry & Molecular Biophysics. The major components of the training activities are: 1) each student's individual research program, guided by faculty members and carried out within a group of other students and postdoctoral fellows having related interests; 2) core graduate courses including courses in bioinformatics and writing; 3) preparation for candidacy examinations; 4) formal and informal an seminars and group meetings; 5) a course in responsible conduct of research, and 6) a research seminar during which CMB students present their own research. Predoctoral trainees are admitted to graduate study in each option based on highly selective admissions criteria, especially high quantitative aptitude and strong motivation for research. Trainees will be selected from admitted students, and will be those who have a primary interest in research in Cellular and Molecular biology. Trainees are expected to pursue research careers that require training in Cellular and Molecular Biology; the superb record of our past trainees supports this expectation. Facilities are located in a complex of adjacent buildings. Multi-user facilities include cell sorting, biological imaging including cryoelectron microscopy, NMR and mass spectrometry, monoclonal antibody production, high throughput DMA sequencing, animal care and production of transgenic mice. RELEVANCE: Cellular and Molecular Biology will continue to underlie the major advances in understanding of human health and disease that can be expected in the next decades. Young researchers trained in this area will make substantial contributions to human welfare. We will help train the next generation of cell and molecular biologists, those who make fundamental, mechanistic insights using both classic and cutting edge methodology and technology, borrowing appropriately from a variety of scientific and engineering disciplines.

Caenorhabditis elegans is a major model system for basic biological and biomedical research and the first animal for which there is a complete description of its genome, anatomy and development. Three years of funding is requested to extend an existing database, ACeDB, into WormBase, a Model Organism Database (MOD), with complete coverage of core genomic, genetic, anatomical and functional information about this nematode. Such a database is necessary to allow the entire biomedical research community as well as C. elegans researchers to make full use of the 97,000,000 basepair genomic sequence, with its 19,000 genes, and the results of intensive molecular genetic analysis of C. elegans. The two top priorities will thus be data curation and user interface. WormBase will include up-to-date annotation of the genomic sequence, the current genetic and physical maps and many experimental data connected to the function and interactions of cells and genes, as well as development and organismal behavior. Direct access to the sources of biological material, such as the strain collection of the Caenorhabditis Genetics Center and direct links to data sets maintained by others will be provided. Data will be recovered from the existing resources, from direct contribution of the individual laboratories, and from the literature. While WormBase will act as a central forum through which every laboratory will be able to contribute constructively to the global effort to fully comprehend this metazoan organism, WormBase professional curators will ensure detailed attribution of data sources and check consistency and integrity. To facilitate communication WormBase will use wherever possible terminology and style concordant with other model organism databases. WormBase will be Web-based and easy to use. The underlying database manager will remain the object-based Acedb database system, which can also be used locally on any platform. Minor enhancements to Acedb will meet the changing priorities of the data sets. Coordination of the project and the main curation site will be at Caltech under the supervision of a C. elegans biologist. Curation and annotation of genomic sequence will take place at the two sequencing centers, the Sanger Centre and Washington University, that generated the entire genome sequence. The Montpellier team will develop interfaces to new large-scale projects such as systematic inactivation of genes, systematic analysis of gene expression, and the large scale cDNA project of Kohara. Development of new user interfaces will take place at Cold Spring Harbor, currently providing Web-based access to ACeDB.

DESCRIPTION (Adapted from the applicant's abstract): Research on the nematode worm Caenorhabditis elegans ranges from global problems such as neural circuitry and function of an entire nervous system and the organization of a whole genome, to mechanistic studies of gene expression, regulation of signal transduction pathways, control of cell fate and cell death during development, synaptic organization, and aging. Study of C. elegans development and behavior has proven useful for studies of genes involved in human health and disease as well as being a model for nematodes that are animal parasites and plant pests. The applicants request funds to help cover costs and travel of participants to attend the 2001 International C. elegans Meeting to be held at UCLA in June 2001. The format of the meeting will be altered to respond to the growth of the field: some parallel sessions will be held and workshops will be given their own time slots. Previous C. elegans meetings have led to the exchange of knowledge, ideas, methods, mutants, and clones, and have been vital in fostering the sense of excitement, collegiality and cooperativity that characterize this field.

Caenorhabditis elegans is a major model system for basic biological and biomedical research and the first animal for which there is a complete description of its genome, anatomy and development. Three years of funding is requested to extend an existing database, ACeDB, into WormBase, a Model Organism Database (MOD), with complete coverage of core genomic, genetic, anatomical and functional information about this nematode. Such a database is necessary to allow the entire biomedical research community as well as C. elegans researchers to make full use of the 97,000,000 basepair genomic sequence, with its 19,000 genes, and the results of intensive molecular genetic analysis of C. elegans. The two top priorities will thus be data curation and user interface. WormBase will include up-to-date annotation of the genomic sequence, the current genetic and physical maps and many experimental data connected to the function and interactions of cells and genes, as well as development and organismal behavior. Direct access to the sources of biological material, such as the strain collection of the Caenorhabditis Genetics Center and direct links to data sets maintained by others will be provided. Data will be recovered from the existing resources, from direct contribution of the individual laboratories, and from the literature. While WormBase will act as a central forum through which every laboratory will be able to contribute constructively to the global effort to fully comprehend this metazoan organism, WormBase professional curators will ensure detailed attribution of data sources and check consistency and integrity. To facilitate communication WormBase will use wherever possible terminology and style concordant with other model organism databases. WormBase will be Web-based and easy to use. The underlying database manager will remain the object-based Acedb database system, which can also be used locally on any platform. Minor enhancements to Acedb will meet the changing priorities of the data sets. Coordination of the project and the main curation site will be at Caltech under the supervision of a C. elegans biologist. Curation and annotation of genomic sequence will take place at the two sequencing centers, the Sanger Centre and Washington University, that generated the entire genome sequence. The Montpellier team will develop interfaces to new large-scale projects such as systematic inactivation of genes, systematic analysis of gene expression, and the large scale cDNA project of Kohara. Development of new user interfaces will take place at Cold Spring Harbor, currently providing Web-based access to ACeDB.

DESCRIPTION: (provided by applicant) Caenorhabditis elegans is a major model system for basic biological and biomedical research and the first animal for which there is a complete description of its genome, anatomy and development. Five years of funding is requested to maintain and expand WormBase, a Model Organism Database (MOD), with complete coverage of core genomic, genetic, anatomical and functional information about this nematode. Such a database is necessary to allow the entire biomedical research community as well as C. elegans researchers to make full use of the 100 Mb genomic sequence, with its 19,500 genes, the 108 Mb sequence of C. briggsae, and the results of intensive molecular genetic analysis of C. elegans. The two top priorities will be intensive data curation and user interface improvement. WormBase will include up-to-date annotation of the genomic sequence, the current genetic and physical maps and many experimental data connected to the function and interactions of cells and genes, as well as development and organismal behavior. Direct access to the sources of biological material, such as the strain collection of the Caenorhabditis genetics Center and direct links to data sets maintained by others will be provided. Data will be recovered from the existing resources, from direct contribution of the individual laboratories, and from the literature. While WormBase will act as a central forum through which every laboratory will be able to contribute constructively to the global effort to fully comprehend this metazoan organism, WormBase professional curators will ensure detailed attribution of data sources and check consistency and integrity. To facilitate communication WormBase will use wherever possible terminology and style concordant with other model organism databases. WormBase will be Web based and easy to use. Multiple databases will be used for data management; the object-based Acedb database system will be used for integration, and this integrated database plus "slave" relational databases will be used to drive the website. Coordination of the project and the main curation site will be at Caltech under the supervision of a C. elegans biologist. Curation and annotation of genomic sequence will take place at the two sequencing centers, the Sanger Institute and Washington University that generated the entire genome sequence. Development of enhanced user interfaces will take place at Cold Spring Harbor. WormBase will work with other MODs to develop shared schema and software (the Generic Model Organism Database project), and shared ontologies (Gene Ontology Consortium).

[unreadable] DESCRIPTION (provided by applicant): [unreadable] [unreadable] An information retrieval and extraction system that processes the full text of biological papers will be [unreadable] developed. A prototype system has been in operation at WormBase for over a year, used by C. elegans [unreadable] researchers as well as WormBase biological curators, and has recently been implemented for yeast at SGD. The system, called Textpresso, separates text into sentences, and labels words and phrases according to an ontology (an organized lexicon), and allows queries to be performed on a database of labeled sentences. The current ontology comprises 37 categories of terms, such as "gene," "regulation," "method," etc. Extraction of particular biological facts, such as gene-gene interactions, can be accelerated significantly by ontologies, with Textpresso automatically performing nearly as well as expert curators to identify sentences; in searches for two uniquely named genes and an interaction term, the ontology confers a threefold increase of search efficiency. This system will be further developed in three ways. First, the core system will be refined and altered to allow expansion to multiple domains of interest, e.g., model organisms, human disease. Simple modifications to the system and website functionality will be made, including synonym, search phrases, and case-sensitivity. A software package for local installation will be supported. The project team will maintain the Textpresso site (www.textpresso.org). which will include C. elegans and pilot systems, but software package will be available for installation of Textpresso at local sites, e.g., SGD, Flybase etc. Second, the ontology will be structured somewhat more deeply and lexica expanded for organism and field [unreadable] specific terms. Third, algorithms for information extraction will be implemented. One approach will be the implementation of similarity measures using categories (high level nodes) of the Textpresso ontology to reduce the dimensionality of associated vector spaces. A second approach will be the development of hidden Markov models to fill slots of a fact template based on the marked-up text. Information extracted will be presented to the user or expert curator. [unreadable] [unreadable] Public Description: The quality and pace of research depends upon rapid access to published information. This project will provide researchers with a search engine that rapidly gives them detailed, technical information they want by indexing the complete text of research articles. [unreadable] [unreadable] [unreadable]

DESCRIPTION (provided by applicant): The nematode C. elegans has powerful genetics, a well-described nervous system, and a complete genome sequence;thus, it is well suited to analysis of behavior and development at the molecular and cellular levels. In particular, the ability to functionally map the influence of particular genes to specific behavioral consequences makes it possible to use genetic analysis to functionally dissect the molecular mechanisms underlying poorly understood aspects of nervous system function. However, many genes with critical roles in neuronal function have effects on behavior that to a casual observer appear very subtle or difficult to describe precisely. Therefore, to fully realize the potential of C. elegans for the genetic analysis of nervous system function, it is necessary to develop sophisticated methods for the rapid and consistent quantitation of mutant phenotypes, especially those related to behavior. The goal of this proposed work is to develop computer vision tools for quantitatively characterizing the phenotypic patterns caused by mutations or pharmacological treatments in C. elegans. By making it possible to precisely characterize the behavioral phenotypes of mutants with abnormal locomotion or egglaying, these tools will be particularly useful for correlating specific neurotransmission defects with characteristic behavioral patterns. These analytical tools will also be used to generate a comprehensive database containing complex behavioral data on a large set of mutant strains. This database will make it possible to identify groups of mutants and pharmacological treatments that have similar effects on behavior or development. With the accumulation of increasing phenotypic data on known mutants, it should ultimately be possible to record from unknown mutant or drug-treated animals and make informed initial hypotheses about the functions of uncharacterized genes and the targets of uncharacterized drugs.

Access to Information; Adopted; Algorithms; Animal Model; Animal Models and Related Studies; Arabidopsis; Biological; Biological databases; Body of uterus; Brachydanio rerio; C elegans; C.elegans; Caenorhabditis elegans; Categories; Cells; Code; Coding System; Collaborations; Common Rat Strains; Computer Programs; Computer software; Corpus; Corpus Uteri; Danio rerio; Data; Data Banks; Data Bases; Databank, Electronic; Databanks; Database, Electronic; Databases; Development; Disease; Disorder; Documentation; Drosophila; Drosophila genus; Figs; Figs - dietary; Fruit Fly, Drosophila; Gene Action Regulation; Gene Expression; Gene Expression Regulation; Gene Proteins; Gene Regulation; Gene Regulation Process; Gene Transcription; Genes; Genetic Transcription; Genome; Goals; Human Biology; Individual; Information Retrieval; Investigators; Label; Language; Life; Literature; Mammals, Rats; Measures; Methods; Methods and Techniques; Methods, Other; Modification; Names; Ontology; Operation; Operative Procedures; Operative Surgical Procedures; Organism; Paper; Process; Protein Gene Products; Publishing; RNA Expression; Rat; Rattus; Regulation; Research; Research Personnel; Researchers; Retrieval, Data; S cerevisiae; Saccharomyces cerevisiae; Site; Software; Speed; Speed (motion); Staging; Structure; Surgical; Surgical Interventions; Surgical Procedure; System; System, LOINC Axis 4; TXT; Techniques; Text; Training Support; Transcription; Transcription, Genetic; Uterine Body; Work; Yeast, Baker's; Yeast, Brewer's; Yeasts; Zebra Danio; Zebra Fish; Zebrafish; base; clinical data repository; clinical data warehouse; computer program/software; data repository; disease/disorder; fruit fly; gene function; gene interaction; genome sequencing; human disease; improved; indexing; interest; living system; markov model; model organism; outreach to information; prototype; relational database; software systems; surgery; vector

[unreadable] DESCRIPTION (provided by applicant): Caenorhabditis elegans is a major model system for basic biological and biomedical research and the first animal for which there is a complete description of its genome, anatomy and development, and some information about each of its ~22,000 genes. Five years of funding is requested to maintain and expand WormBase, a Model Organism Database (MOD), with complete coverage of core genomic, genetic, anatomical and functional information about this and other nematodes. Such a database is necessary to allow the entire biomedical research community to make full use of nematode genomic sequences. The two top priorities will be intensive data curation and user interface improvement. WormBase will include up-to-date annotation of the genomic data, the current genetic and physical maps and many experimental data such as genome-scale datasets connected to the function and interactions of cells and genes, as well as development, physiology and behavior. Direct access to the sources of biological material, such as the strain collection of the Caenorhabditis Genetics Center and direct links to data sets maintained by others will be provided. Data will be recovered from the existing resources, from direct contribution of the individual laboratories, and from the literature. While WormBase will act as a central forum through which every laboratory will be able to contribute constructively to the global effort to fully comprehend this metazoan organism, WormBase professional curators will ensure detailed attribution of data sources and check consistency and integrity. To facilitate communication, WormBase will use technology, terminology and style concordant with other databases wherever possible. WormBase will maintain ontologies for nematode anatomy and phenotypes. WormBase will be Web-based and easy to use. Multiple relational databases will be used for data management; the object-based Acedb database system will be used for integration, and this integrated database plus "slave" relational databases will be used to drive the website. Coordination of the project and the main curation site will be at Caltech under the supervision of a C. elegans biologist. Curation and annotation of genomic sequence will take place at the centers - the Sanger Institute and Washington University - that generated the entire genome sequence. Oxford University will maintain genetic nomenclature. Nematodes (roundworms) are major parasites of humans, livestock and crops, and extension of WormBase to broader coverage of nematode genomics will facilitate research into the diagnosis and treatment of nematode-based disease. Studies of C. elegans have informed us of basic principles of normal development and the molecular basis of aging, cancer, nicotine addiction, as well as a variety of fundamental biological processes such as cell migration, cell differentiation and cell death. [unreadable] [unreadable] [unreadable] [unreadable]

DESCRIPTION (provided by applicant): Cis-acting regulatory elements control gene expression and are involved in all aspects of development, behavior and physiology; but no cis-regulatory element map yet exists for any metazoan genome. We therefore propose to identify genome-wide cis-regulatory elements in C. elegans. Among existing model organisms, C. elegans offers a strong combination of biological properties, transgenic technology, comparisons to genomes in four sibling species, and critical computational and bioinformatic infrastructure. We intend to find genomic regulatory elements in genes with widely varying expression patterns, gene functions, and cis-element content that drive expression in diverse developmental stages, cell types and physiological conditions. A pipeline of genomic predictions followed by efficient transgenic reporter assays will allow us to generate and analyze 10 DNA constructs each week. In year 1 we plan to identify hundreds of regulatory elements, with higher numbers in following years as we become better at predicting functional elements. Predicted elements will be assigned statistical scores based on the quality of their supporting computational and experimental data. We will also use chromatin immunoprecipitation analyzed by intense sequencing (ChIP-seq) to find regulatory modules, and compare its accuracy in finding functional sequences to that of predictions based on comparative genomics. The first round of our results from direct tests of predicted elements and ChIP-seq will be combined with external data from modENCODE to improve our predictive algorithms for later cycles of genome-wide element prediction. Our data will be released promptly to WormBase, and all our computational tools are freely available with full source code.

DESCRIPTION (provided by applicant): Complex genetic networks underlie human disease and health. The construction of genetic networks is now a standard technique in simple cells such as yeast and cultured mammalian cells. Network inference for multicellular organisms is promising especially but one challenge is to parse the network into functional pathways as opposed to just connected graphs, and a second challenge is to analyze networks for complex phenotypes such as neuronal function and behavior. Our goal is to use C. elegans as a model to learn how to accomplish this task, meanwhile generating a network that will inform human genetics. In particular, we will continue to exploit our semi-automated locomotion analysis system (WormTracker) to obtain a phenotypic profile for a large set of genes. Genes will be interrogated using available loss-of- function mutations. The genes examined will include all relevant neuronal genes, as well as genes that encode chromatin modifying proteins and transcription factors. Computational clustering of transcriptional regulators or chromatin modifying proteins with neuronal effector genes will infer regulatory relationships among genes. In addition to locomotion on food, we will also score locomotion off food, and both during crawling and swimming. We will cluster the phenotypes to infer genetic modules, and expand these modules using other available genome- scale data such as gene expression data. To obtain a drug-gene network, we will profile a representative set of drugs and compare them to gene phenotypic profiles. We will test predictions of the drug-gene network by testing particular drug-gene interactions. To refine the genetic network, we will develop additional phenotypic profiling methods, and apply to genes, drugs and gene-drug interaction to split the network into regions of phenotype space. These assays will include quantitative, automated analysis of the rate and variation in pharyngeal pumping using microfluidic devices, established assays for pharmacological effects on male tail posture and spicule protraction to sample genetic effects on the more complex male nervous system, and panels of chemoattractants and repellants to monitor sensory responses. We will leverage our results by integrating what will an extensive data set on quantitative behavioral phenotypes with existing information that allow genetic network inference (expression data, in vitro binding, Gene Ontology annotations, Chromatin immunoprecipitation data, etc.) imported from WormBase. Software and protocols for hardware construction will be freely available from laboratory websites. PUBLIC HEALTH RELEVANCE: Complex genetic networks underlie human disease and health but are a challenge to elucidate. We will use the model organism C. elegans to elucidate genetic networks underlying behavior by efficiently obtaining quantitative behavioral data on mutant strains that are defective in single genes using automated, machine vision systems. The quantitative data will be used to computationally infer genetic networks including genes that function in the nervous system and those that regulate other genes. The data and inferences will be publically available through the Neuroscience Information Framework and WormBase;the software for machine vision will be freely available for download.

DESCRIPTION (provided by applicant): This is an application for support of a conference sponsored by the Genetics Society of America (GSA) entitled Model Organisms to Human Biology: Cancer Genetics, to be held in Washington, DC on June 17-20, 2012. The GSA believes that in this age it is important to convene a meeting that brings together investigators who study model organisms with investigators who study important problems in human biology and disease. This combination promotes a dynamic forum for the exchange of results and ideas between scientists who do not normally interact. Research on model organisms has provided the foundation for our modern-day understanding of human biology, ranging from elucidating the mechanisms for transcriptional regulation to the discoveries that provided the basis for genome-wide association studies of complex human traits. Moreover, these studies, along with more recent cancer genome sequencing projects, have revealed the remarkable extent to which organisms are highly conserved for most fundamental aspects of cellular growth, and how model organism research is directly relevant to understanding human tissue development, physiology, and pathology. However, we still need to learn how best to apply model organisms across the entire spectrum of phylogeny to aspects of cancer biology for which evolution has suited them. These challenges require active discussion among biologists who normally move in different circles. We believe this meeting fills a significant gap in what is available to the scientific community. We also believe that this meeting can act as a catalyst for the type of interdisciplinary initiatives that the NIH encourages and that many see as a source of future advances in cancer biology and medicine. Each session will include two invited speakers (who also serve as session co-chairs) divided between those with a primarily model organism focus or a human/mammalian focus. In addition, four shorter talks will be chosen from the submitted abstracts, to provide opportunities younger investigators to present their work and to enable inclusion of late-breaking stories of special interest. Finally, there will be three keynote talks y world-renowned scientists (Bert Vogelstein, Eric Lander, and Angelika Amon). The meeting is expected to attract approximately 500 people. It will be held at the Omni Shoreham in Washington, DC. All meeting attendees, except local scientists, will be housed on-site and will take most meals together, to stimulate maximal interaction among them. The hotel is accessible to the handicapped and efforts have been made to encourage participation of women and under-represented minorities. The fee structure for the meeting is designed to encourage participation of young scientists. PUBLIC HEALTH RELEVANCE: Progress in understanding human disease and in developing treatments often comes from developing more easily studied model organisms (e.g., yeast, worms, flies, zebrafish, mouse). Genomics has taught us that many important disease processes take place in a much wider group of model organisms than was previously known. This meeting will catalyze scientific exchange and new collaborations between cancer biologists and model organism biologists, which will accelerate progress in understanding the fundamental biology of cancer, and provide the basis for novel approaches to cancer prevention and treatment.

In this project, the PIs will directly measure the metabolism and thermogenesis of nematode soil worm Caenorhabditis elegans (C. elegans) and other model organisms by recording the heat production of the organisms by a microfluidic calorimeter. The calorimeter is based on the microfluidic calorimeter platform developed at Caltech and will have superior performance, including a power resolution at 2% of single worm power generation, a response time of 0.5s and on-chip worm incubation enabling continuous monitoring of a worms activity for over 48 hours. C. elegans will serve as the major target because it is an important model organism that has been extensively used in biological research. In this program thermogenesis in these manipulated worms will be employed to differentiate metabolic pathways and study longevity. First, a number of small molecule inhibitors specific to different biochemical pathways, such as Cyclohexamine (targets Ribosomes) and Actinomycin D (targets RN Polymerases I, II & III), will be used to investigate the contribution of these pathways to metabolism, which will provide a clearer picture of the relative contribution of several important biochemical pathways to overall metabolism in C. elegans. Next, the effect of diet and starvation on the metabolism of adult worms will be studied during their development. Finally, the relation between metabolism and longevity for worms with life-extending genetic mutations will be investigated. The PI and co-PI are committed to dissemination of the technology, outreach and education. The Kavli Nanoscience Institute at Caltech is capable of moderate-scale production of devices. The PI and Co-PI have actively participated in Caltech's Summer Undergraduate Research Program (SURF) and Minority Undergraduate Research Program (MURF) for the past two decades. The co-PI has also has a track record of mentoring high school students, a number of whom have been included as co-authors on papers in top journals based on their summer and after-school research.

PROJECT SUMMARY Because of the staggering complexity of biological systems, biomedical research is becoming increasingly dependent on knowledge stored in a computable form. The Gene Ontology (GO) is by far the largest knowledgebase of how genes function, and has become a critical component of the computational infrastructure enabling the genomic revolution. It has become nearly indispensible in the interpretation of large- scale molecular measurements in biological research. Crucially, for human health research, GO is also one of a suite of complementary ontologies constructed in such as way to maximally promote interoperability and comparability of data sets. It represents the gene functions and biological processes that are perturbed in human disease, e.g. via the links from Human Phenotype Ontology (HPO) class abnormality of lipid metabolism, defined in relation to the GO class lipid metabolic process (GO_0006629), researchers or clinicians can find the set of genes that are known to be involved in this process. GO is a knowledge resource that can be statistically mined, either standalone or in combination with data from other knowledge resources, which enables experts to discover connections and form new hypotheses from the biological networks GO represents. All knowledge in GO is represented using semantic web technologies and so is amenable to computational integration and consistency checking. The proposed GO knowledge environment will enable a wider community of scientists to contribute to, and to utilize, a common, computable representation of biology. To ensure the knowledge environment meets the requirements of biomedical researchers, we will: a) deliver a comprehensive, detailed, computable knowledgebase of gene function, encoded in the Gene Ontology and annotations (computer-readable statements about the how specific genes function), focusing on human biology; b) provide a ?hub? for a broad community of scientists to collaboratively extend, correct and improve the knowledgebase; c) ensure the GO knowledge resource is of the highest quality with regards to depth, breadth and accuracy; d) facilitate the transfer of insights obtained from studies of non-human organisms, such as the mouse and zebrafish, to human biology; and e) enable the scientific community to use the knowledgebase in analyses of large-scale genetic and -omics data. Our aims reflect the essential requirements for realizing the overarching objectives for a biomedical data resource: efficiently capturing and integrating biological knowledge and adhering to the highest possible standard for accuracy and detail; constructing and providing a robust, flexible, powerful, and extensible technological infrastructure available not only for internal use but just as easily by the wider community; and lastly, leveraging state-of-the-art social media, web services and other technologies to disseminate the GO resource to the entire biomedical research community.

DESCRIPTION (provided by applicant): WormBase Is the major publicly available database of information related to Caenorhabditis elegans, an important organism for basic biomedical research, and other nematodes of medical and agricultural importance. Although a crucial daily resource for members of the C. elegans research field, our users extend to the larger parasitology, biomedical, and bioinformatics research communities. WormBase acts as a central forum through which every research group can contribute to the global effort to comprehend nematode genomes. Most users access WormBase via the Internet (www.wormbase.orq). While some install the database locally. WormBase offers extensive coverage of C. elegans core genomic, genetic, anatomical and functional information, allowing the biomedical community to fully utilize the results of intensive molecular genetic analyses and functional genomic studies of this organism in the study of human disease. These data include all available nematode genomic data (such as genome sequence, transcripts and cis-regulatory sites prioritized by species), large-scale functional genomic datasets, the function and interactions of genes and gene products as they relate to development, physiology and behavior, and biological reagents and their source information. WormBase comprises a set of databases storing a wide range of biological information; a website that allows users to access stored information and precomputed analyses based on these data; and tools for programmatic access such as an application programming interface, a data mining platform, and bulk downloads. Curation activities include extraction and integration of information from the literature (assisted by the use of information retrieval tools), incorporation of large-scale datasets from a range of research projects, and gene model verification from experimental data. We will curate hundreds of nematode genome sequences, annotations and core genetic information as well as data on gene function, pathways and transcriptional regulatory networks for C. elegans and select other species. We will expand tools available for data mining, workflow management, visualization, and community annotation, and integrate, store and distribute data in a maintainable, interoperable and scalable system. The project team involves three sites: Caltech primarily curates functional information; EBI carries out sequence-based curation and builds databases for public release; and OICR develops and supports the web presence and visualization. The three sites work closely together and share tasks to ensure timely incorporation, storage and display of information. RELEVANCE Nematodes (roundworms) are major parasites of humans, livestock and crops, and understanding how to control them is a major world health and economic challenge. One species of nematode, C. elegans, is extensively used for basic biomedical research to elucidate how networks of genes affect cells, organs and a whole animal's development, physiology and behavior. WormBase collects, stores and displays information about the genomes and genes of C. elegans and other nematodes to facilitate research about this numerous and important group of animals.

Project Summary Cell adhesion is crucial aspect of development, fertilization, tissue homeostasis, protection from and interaction with other organisms. Many adhesion proteins have been intensively studied for decades and it was an open question whether we have sufficient knowledge of adhesion, given the large number of interacting proteins and interactions involved in adhesion. LINKIN is a conserved, transmembrane protein that we found to be involved in cell adhesion, suggesting that by studying LINKIN and its interacting proteins we can define a new cellular pathway involved in cell adhesion. The striking conservation of LINKIN sequence and gene copy number across eukaryotic evolution suggests a critical role in development. We discovered LINKIN's role in cell adhesion in the context of C. elegans development, specifically the attachment of the migrating linker cell to the vas deferens, which provides a powerful assay for its structure, function and interactions. We identified interacting proteins in human cells and provided evidence for similar molecular interactions in both organisms. We identified the RUVBL1 and RUVBL2 AAA-ATPases, and ?-tubulin as cytoplasmic interactors of LINKIN, suggesting a role for LINKIN in regulating microtubule dynamics, but further investigation is required to connect LINKIN to other interactors and signaling pathways. We propose to further characterize LINKIN's role in cell adhesion in order to connect this new adhesion molecule to other known (or unknown) cellular pathways. A major limitation of human genetic, genomic and systems biology approach is our understanding of the function of many genes. By discovering a new pathway, we will increase the likelihood that genomic, clinical and genetic studies will be interpretable. We will analyze the function and interactors of both the extracellular and intracellular domains of LINKIN. Using evolutionary conservation as a guide we will mutate conserved residues in C. elegans LINKIN and test their function in transgenic worms. We will use human LINKIN proteins with cognate mutations in cell lines for immunoprecipitation and quantitative mass spectrometry proteomics to identify physiologically relevant interacting proteins. We will test the function of interacting proteins identified by the proteomics in C. elegans and cell lines. We will also use C. elegans genetics to screen prioritized candidates for a role in adhesion using the linker cell attachment assay. Candidates will be prioritized by expression in the linker cell, for which we have a deep transcriptomic profile, predictions of encoding transmembrane or secreted proteins, phylogenetic co-occurrence as well as network predictions of interactions based on orthologous proteins in other intensively-studied organisms. In this way, we will identify the portions of LINKIN that are crucial to its function in adhesion and physiologically-relevant interacting proteins both on other cells and same cell that likely mediate adhesion, and in the cytoplasm that implement the adhesive and cytoskeletal interactions. This validated set of functionally interacting proteins will define a new pathway of cellular adhesion and inform a variety of human genetic studies in normal development and disease states.

Project Summary/Abstract C. elegans is a premier model organism that has proven highly useful for discovery of gene function and embedding genes into functional pathways, many of which were discovered in this transparent animal and are conserved in humans. In addition, other nematodes are crucial parasites of humans, infecting roughly a third of the world's population and plant-parasitic nematodes are recognized as one of the greatest threats to crops throughout the world. Despite these extensive ties to human health and disease, nematode specific genes are vastly understudied. We will use the latest CRISPR technology to knockout genes and provide a set of high value genetic tools to the communities of C. elegans researchers, human geneticists, and parasitic nematologists. Targets chosen will be 1000 C. elegans orthologs of genes implicated in human disease as well as 500 conserved genes about which essentially nothing is known, and 500 nematode-specific genes present in human parasites. We will develop an efficient pipeline of gene disruption that includes target choice, oligonucleotide design and ordering, molecular biology, microinjection into worms, selection or screening of conversion events, homozygosing or balancing alleles and verification. Edited strains will be grossly phenotyped and deposited in the CGC for distribution and advertised though the CGC and WormBase websites. We will begin by evaluating two approaches. One approach selects for gene conversion and disruption using a selectable insertion cassette; the other uses insertion of GFP as a zero-length translation fusion and will be screened by PCR. Over the first year we will identify and focus on the approach that is of higher throughput. We will continuously refine targeting methods and improve the pipeline to increase the range and efficiency as well as decrease the cost of production. We will develop Cas9 variants to increase the availability of editing sites within genes. We will develop a PCR bridge method to allow cloning free addition of homology arms. To efficiently screen for in frame GFP edits we will develop a low cost ELISA assay for GFP. Finally, we will also explore using the transcriptional activator Gal4 as a marker. This is a multi-PI project which includes the lead-PIs of the CGC, of WormBase and of the Knockout Consortium; two of the PIs have made important contributions to CRISPR technology development in C. elegans.

Project Summary/Abstract The Streamlined capture and curation of unpublished data project will establish a new data capture and dissemination paradigm that automatically and simultaneously captures and ingests biomedical data into authoritative repositories and publishes them in an online, open access journal `Micropublication: biology'. This new platform will introduce a curation paradigm shift, allowing authors to directly submit the output of their research into pre-designed intelligent web forms. Upon submission, these forms will seamlessly integrate, atomize, and submit metadata into authoritative data repositories enhancing the efficiency and accuracy of curation. Simultaneously, the process will automatically generate a `publication-like' PDF file that will be publishable and citable according to findable, accessible, interoperable and reproducible (FAIR) data principles. We call these single result experiments, streamlined with no narrative ?micropublications?, ideal for among other things, results that often go unpublished. Authors will preserve provenance and establish credit for their research and the automated flow of data they submit will be made publicly accessible in established and authoritative data repositories such as the Model Organism Database (MOD) members of the Allied Genome Resources (AGR): FlyBase, Mouse Genome Database (MGI), Rat Genome Database (RGD), Saccharomyces Genome Database (SGD), WormBase, Zebrafish Model Organism Database (ZFIN), for further re-use. Through the aforementioned repositories, all submitted metadata will automatically be integrated with existing datasets that have been manually extracted from the literature for almost 2 decades. These data will be peer reviewed ensuring they are of high quality and that they meet community standards. Micropublications will be citable, discoverable, and will comply with the Minimum Information Standards for scientific data reporting. In addition, researchers will be able to share both positive and negative data with the scientific community, fulfilling funding agencies' requirements to share all data coming from publicly funded research. After establishing this data retrieval/publication pipeline with WormBase first, and AGR member databases, we will work to expand to non-member, but otherwise critical biomedical model organism databases, such as Xenbase (Xenopus laevis and tropicalis Database), DictyBase (Dictyostelium discoideum database), PomBase (Schizosaccharomyces pombe Database), among others.

Project Summary Understanding the molecular and cellular basis for behavior depends on a rigorous assessment of the contributions of different neuron types. Progress in elucidating neural circuits for behaviors is often hampered by a lack of genetic tools for efficiently generating animals with cell-type specific expression of genes that can be used to perturb or monitor neuronal activity, such as optogenetic tools, tetanus toxin, and GCaMP. Also, there has been steady progress in optogenetics and genetically-encoded sensors such as GCaMP calcium indicators, but it is impractical to rebuild hundreds of strains inserting each improved version into a repertoire of expression vectors. One elegant method that addresses both issues simultaneously is to use a bipartite expression system, which separates the cell-type control from the effector, and thus a set of cell-type specific drivers can be reused with different versions of effectors (e.g., GCaMP6 versus GCaMP3). Conversely, a set of strains might be made with a promoter that directs expression in two or more cell types; if a more specific regulatory sequence is identified, then all the constructs have to be rebuilt. With a bipartite system, construction of a single Driver with the new regulatory sequence can easily combined with all the available Effectors to efficiently generate the strains needed. allows use of all the Effectors. For example, Drosophila researchers have made great use of the Gal4-UAS system in which a transcriptional activator protein (Gal4) is expressed in the cell type(s) of interest and binds to its target sequence ? the UAS ? to direct expression of an effector gene of interest. This scheme allows many combinations of specifically expressed genes to be built from a much smaller number of transgenes. However, Caenorhabditis elegans has not had such a system until our recent development of the cGAL system, an optimized Gal4-UAS system. One key feature of our implementation is the use of the DNA-binding domain of the Gal4 protein from a yeast species whose optimal growth temperature matches that of C. elegans, thereby allowing more efficient target gene activation. We also showed that the cGAL system can be applied to functional studies in C. elegans. We propose to construct an initial neuronal cGAL toolkit, and apply it to one circuit as proof of principle. The chosen circuit is male mating behavior, arguably the most complex of C. elegans behaviors as it involves almost the entire nervous system and a complex series of steps each involving sensory-motor integration. While the roles of many male specific neurons have been identified, the roles of non-sex-specific neurons have not; our approach will make the cGAL reagents that render all of the non-sex-specific neurons tractable to analysis in a systematic way. At the end of two years, we will have fully introduced a useful bipartite expression system to the C. elegans community and refined our understanding of innate behavior.

Project Summary WormBase is the major publicly available database of information related to Caenorhabditis elegans, an important organism for basic biomedical research, and other nematodes of medical and agricultural signficance. Although a crucial daily resource for members of the C. elegans research field, our users extend to the larger parasitology, biomedical, and bioinformatics research communities. WormBase acts as a central forum through which every research group can contribute to the global effort to comprehend nematode genomes and biology. Most users access WormBase via the Internet (www.wormbase.org); some install the database locally. WormBase offers extensive coverage of C. elegans core genomic, genetic, anatomical and functional information, allowing the biomedical community to fully utilize the results of intensive molecular genetic analyses and functional genomic studies of this organism in the study of human disease. These data include all available nematode genomic data (such as genome sequence, transcripts and cis-regulatory sites prioritized by species), large-scale functional genomic datasets, the function and interactions of genes and gene products as they relate to development, physiology and behavior, and biological reagents and their source information. WormBase comprises a set of databases storing a wide range of biological information; a website that allows users to access stored information and precomputed analyses based on these data; and tools for programmatic access such as an application programming interface, a data mining platform, and bulk downloads. Curation activities include extraction and integration of information from the literature (assisted by the use of information retrieval tools), incorporation of large-scale datasets from a range of research projects, and gene model verification from experimental data. We will curate many nematode genome sequences, along with their annotations and core genetic information, as well as data on gene function, pathways and transcriptional regulatory networks for C. elegans and select other species. We will expand tools available for data mining, workflow management, visualization, and community annotation, and integrate, store and distribute data in a maintainable, interoperable and scalable system. The project team involves three sites: Caltech primarily curates functional information and develops ontologies; EBI carries out sequence-based curation and builds databases for public release; and OICR develops and supports the web presence and visualization. The three sites work closely together and share tasks to ensure timely incorporation, storage and display of information, as well as user outreach and education.

Project Summary Understanding how neural circuits create animal behavior requires knowing the system-wide activity patterns that connect sensory experience to motor activities, all within the full set of feedback loops by which actuated motor decisions modulate the animal's perceptions of itself and the outside world during naturally executed and unrestrained behaviors. Mechanistic understanding further requires interpretation of system-wide activity patterns in terms of the connectivity, synaptic, and cellular properties of all relevant neurons. Modeling requires comprehensive mapping of the salient dimensions of sensory input and motor output, as well as how high- dimensional neural activity patterns are properly projected, by decision-making and the internal constraints of the nervous system and motor system, into the fewer dimensions that characterize any animal's observed behavior. Such models are facilitated by using animals where entire brain and motor circuits can be mapped and interrogated with full molecular and cellular resolution. Here, we will use the mating behavior of the male C. elegans as such a paradigm. The mating behavior of C. elegans is a critically important and goal-directed task that occurs in natural environments and is robustly executed in the laboratory. Males use a specialized circuit of ~100 neurons ? sensory neurons, interneurons, neuromodulatory, and motor neurons ? all contained within the male tail ganglia to locate hermaphrodites, locate the vulva along the hermaphrodite's body, and initiate and complete insemination. A diverse set of mechanosensory, chemosensory, and pheromone sensing neurons are used to recognize the shape, texture, and chemical signature of the hermaphrodite body. Several neurons are specialized to detect fiducial points along the hermaphrodite body. The male implicitly uses an internal representation of the size, shape, and predictable behaviors of the hermaphrodite to positively recognize the hermaphrodite, infer its own position along the hermaphrodite, and execute an optimal movement strategy to maintain contact with the hermaphrodite and find and penetrate the vulva. It is now possible to record neural activity from the entire set of neurons in the male tail with high temporal resolution and complete cellular resolution. We will couple experiments, modern data analysis and modeling methods, and cellular and molecular genetic perturbations to elucidate the full set of sensorimotor events that organize the mating behavior. We will develop a realistic model of the circuit that integrates the observable behavioral algorithms with the connectivity and activity patterns of the male tail ganglion. We will apply genetic tools to identify and elucidate each sensory neuron type, and how it affects each aspect of decision-making by downstream interneurons and motor neurons. We will characterize key synaptic properties by molecular dissection of neurotransmitter and receptor types. We will store this comprehensive neurophysiological and neurogenetic data in online project databases connected to our computational models that will allow the wider community to view and probe our data-driven modeling eff ort.

Project Summary Animal brains integrate information to make crucial developmental and behavioral decisions. The brain adapts to life experiences by anatomical, functional, and molecular changes, but understanding the strategic value of these changes requires a comprehensive model that interconnects neural circuits and behavioral dynamics. To develop such models, it is useful to start with animals where entire brain circuits can be interrogated with full molecular, synaptic, and cellular resolution across development. A key decision made by Caenorhabditis elegans is whether to enter immediate reproductive development in good environments or diapause under poor environments. Environmental quality is assessed by a number of defined ethologically relevant signals: quantity and quality of food, population density via defined chemical social cues, and environmental stressors. This decision involves ~5% of the compact C. elegans nervous system, with at least five types of sensory neurons and five types of interneurons, yet is tractable enough to allow a comprehensive analysis. We will tightly couple modeling and experiment, designing perturbations and analyses to elucidate the pertinent dynamics of the decision-making. We will develop, test, and refine a model of the decision circuit starting with an algorithmic model based on decision theory and proceeding towards a circuit model that connects individual neurons and molecules to the decision circuit. We will apply recently molecular genetic tools for circuit manipulation and interrogation, define the transcriptomes of key cell types in the circuit to identify potential neuromodulatory inputs into the computation at longer time scales, and test how changes in the connectome caused by the decision modulate circuit dynamics and behavior. By functional imaging of the decision-making circuit, we will quantify total information flow throughout the worm nervous system that leads to the developmental decision. We will use a tracking microscope to optically record the dynamics of the decision-making circuit from sensory inputs to the brain starting from birth. We will use microfluidic and optogenetic rigs to control multidimensional sensory inputs on the 0.01-100 minute time scale to monitor and manipulate the decision-making circuit in real time. We will correlate neurophysiological analysis with endpoint analysis to map the dynamics of the developmental decision. We will enhance tools for efficient circuit analysis and define relevant neuromodulatory connections. To determine what neural circuit changes occur during and after the decision, we will use high-throughput methods in ssEM to reconstruct the connectome of animals, before, during, and after the decision is made. We will correlate functional imaging and anatomy to determine the functional basis of behavioral variation at all developmental stages. We will use single neuron microdissection to obtain gene expression profiles for about 10 neuron types that are key to the circuit of interest. We will store data in a project database, and visualize the system, results of simulations, and data including neural connectivity data in a 3D model through a network graph viewer and ontology-based browser.

Project Summary The Alliance of Genome Resources (the Alliance) is a ?knowledge commons? for expertly curated genomic data and annotations provided by model organism databases (MODs) and the Gene Ontology Consortium (GOC). Our mission is to facilitate the use of model organisms to understand human biology and disease. The Alliance is organized as two interconnected functional units: Alliance Central and Alliance Knowledge Centers. Alliance Central is responsible for development and maintenance of the software platform and shared modular infrastructure and for the coordination of data harmonization activities across the Knowledge Centers. Alliance Knowledge Centers such as the MODs and the GOC are responsible for expert curation and for submission of data to Alliance Central using common data formats. Knowledge Centers also are responsible for organism- specific user support activities, resources, and user access to data not yet supported by Alliance Central. This U24 application seeks support for the activities of Alliance Central. The proposal reflects a new and transformational approach to modernizing the MOD/GOC ecosystem, increasing the impact and utility of essential community genome resources, and optimizing operational efficiencies for knowledgebases. The aims build on the significant accomplishments we achieved as a consortium since we launched the Alliance in 2016, including: a common management and governance structure, Working Groups, multiple channels for communications among consortium members, infrastructure for coordinated software development and version control, data sharing with the NIH Data Commons Pilot initiative, the development of a common set of orthologs, the release of the Alliance web site and APIs, and successful development of software components that have been adopted by both Alliance members and external resources. Our focus for Specific Aim 1 will be on implementing a shared platform for ingesting, storing, and harmonizing data for MODs. We will continue our long-standing commitment to data management practices that align with FAIR principles. In Specific Aim 2 we describe our plans to implement common methods, including well-documented APIs, for access to model organism data and annotations. The deliverables for this aim will foster widespread adoption and use of Alliance data and resources for the development of new applications for biological discovery and translational research. In Specific Aim 3 we describe our plans to implement a framework to support the development and deployment of software applications, workflows, and analysis tools that use model organism data and annotations. The enhanced functionality for comparative genomics fostered by these innovations will empower the biomedical research community to leverage knowledge across multiple organisms for hypothesis generation and pattern discovery. Finally, in Specific Aim 4 we describe the management and organization of the Alliance as well as the planned activities of our centralized user support helpdesk.

Project Summary Acetylcholine (ACh) is an ancient signaling molecule found in many organisms including bacteria, protozoa, plants, and animals. ACh detection through nicotinic and muscarinic receptors occurs in many human organs besides the nervous system but these much less studied than its neuronal function. One of the non-synaptic functions of ACh signaling is in cell migration during normal development. For example, smooth muscle cells, epithelial keratinocytes, and mesenchymal stem cells migrate in response to ACh, but a detailed mechanistic understanding of how this signaling is utilized in migration, particularly in vivo, is not available. We have developed a unique system with which to study the role of Ach signaling in cell migration in vivo. The C. elegans linker cell (LC) is a specialized epithelial cell that leads the migration of the developing male gonad. We found through single-cell transcriptomics that the LC expresses many neuronal receptors and ion channels, leading to the hypothesis that the LC uses neuronal cues for its migration. We will investigate the role of acetylcholine signaling in the LC because we observed migration defects in mutants lacking particular muscarinic and nicotinic receptors. We will initially focus on the only muscarinic receptor expressed in the LC, GAR-3, that we found to activate changes in cell orientation. We will in parallel investigate the function of the multiple nicotinic receptors in LC migration and potential cooperation between the receptor types. The LC reverses its orientation from the posterior to anterior in response to excess ACh signaling induced by treatment with the acetylcholinesterase inhibitor aldicarb, an assay we will use to identify the downstream components of the GAR-3 pathway in the LC. Since downstream targets of the branching gar-3 signaling pathway have been identified in other contexts (e.g., synaptic transmission), we will test mutants of those genes to identify the specific downstream pathway used to modulate LC orientation. To investigate the role of ACh distribution, we will reprogram the fate of neurons in the ventral nerve cord (VNC) to create artificial anterior/posterior ACh gradients to investigate how ACh distribution and amount affects LC migration. We will collaborate to use Correlation Electron Microscopy to examine GAR- 3 localization relative to the ultrastructure of LC and surrounding tissue at high resolution. We will reuse these assays to study potential effects of six nicotinic receptor subunits.

Summary/Abstract This project will make the model organism data and curation in the Alliance of Genome Resources ? which harmonizes and integrates information from mouse, rat, zebrafish, Drosophila, C. elegans and budding yeast ? readily available for Alzheimer's Disease (AD) researchers. This information notably includes gene function, interaction with AD associated genes; relevant models of disease, gene function and variant effect. The entire user experience ? from home page, to search, to gene and variant pages, as well as the information in each display widget and analysis tools ? will be tailored to the AD researcher. The Alliance now has about 3000 genes from six species that have annotations to AD, but this is embedded in over 120,000 genes in the Alliance purview, and thus prioritization will save time and attention, providing up to a 40-fold enrichment of information. To support an AD specific web portal, algorithms will be developed and deployed that prioritize, based on AD-relevance, information to be displayed and search results. Search of the portal will prioritize AD-relevant entities and terms. Information and the order of display will prioritize AD researcher interests. Algorithmically-generated summaries of gene function will focus on AD-relevant information. An AD-focused literature search and text-mining system will be implemented.

Project Summary To extract greater value from extensive but disparate and siloed data relevant to neural circuits, we will leverage the ontologies, bioinformatics, and curation of the Alliance of Genome Resources to derive an artificial intelligence (AI) ready knowledge graph. Participation of a computational neuroscientist who uses AI for neural circuit analyses will help specify the form of the knowledge graph, demonstrate the utility of the graphs, extend the graphs from a focus on the well-defined nervous system of Caenorhabditis elegans to the similarly well- defined mouse retina, and connect with neuroscience researchers who are starting to applying AI to neural circuits. Known entities (such as neurons, small molecules, and neuropeptides) and Ontologies (anatomy, relations, and experimental evidence) provide the underlying data of the graph. Curated assertions provide the knowledge, e.g., synaptic or functional connections between neurons, neuropeptide has a specific receptor, or a neuropeptide is expressed in a specific neuron). In this graph model, entities are the nodes, ontological relationships are the edges. These provide an inferred knowledge graph supported by evidence backed assertions. This type of knowledge graph can be applied to biological pathways that are based on phenotype observations including expression, neuronal activity and organismal behavior rather than physical interactions or enzymatic activities such as those used to describe biochemical pathways. To accomplish generation of knowledge graphs, we will refine the relevant vocabularies to focus on relations used in neural circuit research, we will adjust existing infrastructure to handle the appropriate ontologies, data models, and curation tools for neural circuit data, and we will incentivize expert contributions by arranging short reviews coupled to computable assertions. The knowledge graph will be used by local AI experts, published on the internet, and tested by a hackathon.

Project Summary Biological knowledgebases are a critical resource for researchers and accelerate scientific discoveries by providing manually curated, machine-readable data collections. However, the aggregation and manual curation of biological data is a labor-intensive process that relies almost entirely on professional biocurators. Two approaches have been advanced to help with this problem: natural language processing (NLP; text mining (TM) and machine learning (ML)) and engagement of researchers (community curation). However, neither of these approaches alone is sufficient to address the critical need for increased efficiency in the biocuration process. Our solution to these challenges is an NLP-enhanced community curation portal, Author Curation to Knowledgebase (ACKnowledge). The ACKnowledge system, currently implemented for the C. elegans literature, couples statistical methods and text mining algorithms to enhance community curation of research articles. We propose to strengthen and expand ACKnowledge by including other species into our pipeline, incorporating more sophisticated machine learning models, and presenting sentence-level entity and concept extraction for more detailed author curation. In addition, we will develop an Author Curation Portal (ACP) to allow authors to easily upload and curate their own documents. Taken together, these enhancements will allow us to maximize community curation efforts by leveraging author expertise in multiple areas of biology, while at the same time supporting authors with as much AI-assisted curation as possible. This reciprocal interaction will improve not only the content of knowledgebases, but the AI methods themselves, as we will receive valuable feedback on our models. By developing an Author Curation Portal, we will further empower authors to participate in the curation process and alert knowledgebases to key information that can, and should, be readily discoverable in accordance with FAIR (Findable, Accessible, Interoperable, and Reusable) data principles.

All animals, including humans live in association with microbes and parasites that can promote health and cause disease. The mechanisms by which animals communicate with microbes and parasites to block, initiate, maintain, and dissolve such associations are just beginning to be uncovered. Because these mechanisms are often conserved across biology, they can be investigated using model animals such as roundworms, or nematodes, which associate with microbes and are themselves parasites. This project will develop new experimental tools in roundworms that have developed partnerships, or symbioses, with specific bacteria. Together these roundworms and their bacterial partners infect and kill insects, using them as a food source. Developing new tools to study this elegant animal-bacterium system will help expand our understanding how animals and bacteria form partnerships, and how they work together to parasitize other animals. The tools and knowledge gained in this project will be rapidly shared with the community of researchers involved in drug discovery, agricultural control of crop pests, and in the study of parasitism, infectious disease, beneficial microbiome function, and fundamental cell, molecular, developmental, and evolutionary biology. As part of this project, undergraduates will be involved in a discovery-based microbiology lab where they will practice isolating and identifying new insect-killing roundworms from the environment. Young people (K-12) and educators will be engaged through collaboration with the Science Journal for Kids, where a basic curriculum and summary of key research findings will be developed for classroom use.

Entomopathogenic nematodes in the genera Heterorhabditis and Steinernema are mutualistically associated with bacteria in the genera Photorhabdus and Xenorhabdus, respectively. The nematode-bacterium symbiotic pair obligately parasitizes insects as a nutrient source for reproduction and has utility as a biological control agent for agricultural insect pests and as a source of novel compounds. The entomopathogenic pair and their insect hosts are models to understand fundamental biological principles, including the evolution and molecular and cellular basis of mutualistic and antagonistic organismal interactions. Numerous features make this system an excellent experimental model including ease and cost of husbandry, fast generation time, and optical transparency. Although genetic techniques have been developed for representative bacterial symbiotic partners and insect hosts, to date there have been no broadly adopted, reliable genetic modification tools in either Steinernema or Heterorhabditis nematodes. This inability to interrogate nematode gene function has hobbled full use of this system to yield much-needed insights into parasitism, animal microbiome interactions, and other areas. Here we propose to capitalize on a recently isolated Steinernema nematode that has promising characteristics for development of genetic tools, including hermaphroditic reproduction, amenability to long-term freezing, healthy development on agar bacterial lawns, resilience to microinjection, and significant pathogenicity to lab insects and agricultural pests. By fully sequencing the genomes and developing genetic techniques and tools for both nematode and symbiont, including CRISPR-Cas9 genome editing in the nematode, and creating an arrayed mutant library for the bacterium, our team will help realize the full potential of this elegant animal-microbe model system.

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.

PROJECT SUMMARY The Alliance of Genome Resources (the Alliance) is a ?knowledge commons? for expertly curated genomic data and annotations by model organism databases (MODs) and the Gene Ontology Consortium (GOC). Our mission is to facilitate the use of model organisms to understand human biology and disease. The Alliance is organized as two interconnected functional units: Alliance Central and Alliance Knowledge Centers. Alliance Central is responsible for development and maintenance of the software platform and shared modular infrastructure and for the coordination of data harmonization activities across the Knowledge Centers. Alliance Knowledge Centers such as the MODs and the GOC are responsible for expert curation and for submission of data to Alliance Central using common data formats. Knowledge Centers also are responsible for organism- specific user support activities, resources, and user access to data not yet supported by Alliance Central. The data management principles of the Alliance align well with the principles represented by FAIR principles (Findability, Accessibility, Interoperability, Reusability) and operational approaches reflected in the TRUST principles (Transparency, Responsibility, User focus, Sustainability and Technology). The focus for the administrative supplement in response to NOT-OD-21-089, includes the following aims: (1) address areas of improvement documented for the Alliance of Genome Resources (Alliance) in a FAIRShake assessment conducted under the auspices of the NIH Common Fund Data Ecosystem Project, (2) complete the Alliance's application to obtain Core Trust Seal certification, and (3) update information about the data and annotation licensing terms at the Alliance hosted on the (Re)usable Data Project (RDP). We will also participate in the workshops and meetings described in NOT-OD-21-089 which will allow the Alliance to compare the metrics/indicators we use to evaluate the impact of our resource to those of other relevant data resources and to adapt our metrics as needed to conform to new community standards or trends. The outcomes of the proposed work align well with the intent of NOT-OD-21-089 to increase the compliance of community data resources with FAIR and TRUST principles that are foundational to a modern data science ecosystem for the biomedical research community.