Daniel Janies - US grants

This award will fund a three-day symposium in Washington, DC, October 24-26, 2011, bringing together leaders in important fields of mutual interest to Brazil and the United States. These fields include bioenergy, climate change, biodiversity and Amazon studies, plant genomics, urban and area studies, optics and photonics, vaccines and drug discovery, stem cells, and tropical diseases. The event celebrates the 50-year anniversary of the São Paulo Research Foundation (Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP). Brazil is an emerging actor in science and technology as well as financial, agricultural, and energy markets. In addition to these advances, as a large democracy, Brazil is one the United States? critical partners in the world. A joint scientific meeting is fitting to commemorate FAPESP and, moreover, to solidify the future of the US ? Brazil partnership.

Echinoderms include familiar animals such as starfishes, sea urchins, and a wide array of extinct forms stretching back to the Cambrian Period, circa 500 million years ago. Echinoderms share a common ancestor with backboned animals and thus provide a crucial link to understanding a huge portion of the entire tree of life as well as the history of our species. This project, the Echinoderm Tree of Life Project, will resolve the phylogenetic placement of Echinoderms within the tree of life and clarify important unresolved relationships among major echinoderm lineages using data from genetic sequencing and anatomy.

Echinoderms are fascinating, and their unique features, such as mutable ligaments and novel means of detecting light, have biomedical engineering applications. Because research on such marine animals and their adaptations is naturally attractive to young people, excellent students are expected to be recruited and the importance of science will be communicated to a broad audience. Long-term impacts, embodied by scientific publications, textbooks, anatomical and genomic data, and extensive pages in the Tree of Life and Encyclopedia of Life web projects, will provide resources to researchers and educators. Outreach will include videos and broadcasts about marine exploration and applications of fundamental biological research across the biomedical sciences.

DESCRIPTION (provided by applicant): The purpose of the proposed project, entitled The Ohio State University Clinical and Translational Research Informatics Training Program (CTRIP), is to establish a novel and highly impactful Biomedical Informatics training initiative that focuses upon the emergent and rapidly growing sub-domains of Translational Bioinformatics (TBI) and Clinical Research Informatics (CRI). This program will leverage the unique scholarly and environmental strengths present at The Ohio State University Medical Center (OSUMC), and employ two well-established and highly successful pre- and post-doctoral training mechanisms present within The Ohio State University College of Medicine for degree granting purposes. Trainees will be involved in a combination of didactic and application-oriented instruction modalities, and will pursue independent research projects as a capstone to their curricula. The TBI track of the program will specifically focus upon pre-doctoral training, and combine core informatics competencies with a rigorous grounding in the biology of human disease. The CRI track of the program will specifically focus on post-doctoral training for individuals with terminal clinical degrees (e.g., MD, DO, or equivalent), and will similarly combine core informatics competencies with a rigorous grounding in clinical research methodology. The overall training program will house no more than six funded pre- and post-doctoral trainees at any given time. Our intent with the CTRIP program is to utilize an agile and highly innovative curricula development and evaluation plan, thus allowing for constant program optimization and adaptation to evolving trends and developments in the basic and applied Biomedical Informatics knowledge base.

Project Summary Mammals, including humans, cannot regrow lost or damaged body parts. Echinoderms, with whom mammals share a deep common ancestor, can quickly and ef?ciently regenerate numerous body parts including muscular, skeletal, soft, and nervous tissues of appendages and internal organs. The ability of echinoderms to regenerate makes these animals particularly attractive for research in regenerative medicine. However, studies of regeneration in echinoderms has lagged behind other model systems due to the lack of functional genomic tools. Thus our overarching goal is to develop echinoderm model systems for regenerative medicine. To this end, the ?rst aim of this proposal is to ?nish and annotate the genomes of two echinoderm species that have served as proven models for studies of regeneration, including the sea cucumber, Sclerodactyla briareus, and the brittle star, Ophioderma brevispinum. Taken together, these organ- isms exhibit a broad spectrum of regenerative phenomena ranging from morphallactic remodeling through transdifferentiation of the existing tissues, to rapid epimorphic terminal growth. In particular, both animals can regrow their central nervous system. The second aim of our proposal is to adapt modern techniques of functional genomics to studies of adult echinoderm tissues. One sub-Aim here is to be able to experimentally regulate expression of genes of interest in vivo in regenerating animals. The focus of this sub-Aim will be electroporation and viral vector-based delivery of expression constructs into adult echinoderm tissues. Another sub-Aim is to use CRISPR/Cas9 genome editing technology in adult echinoderm tissues in vivo. In order to as- sess the ef?ciency of these functional genomic tools, we will use them to perturb transcription factors that are key regulators of echinoderm neurogenesis. Suppression of expression of these transcription factors is therefore expected to produce a clear phenotype by impairing neural regeneration in both species. The completion of the proposed project will lead to establishment of genomic resources to probe the functional role of known developmental genes, as well as of novel regeneration-associated genes identi?ed in recent high-throughput expression studies, in the spontaneously regenerating cen- tral nervous system. This, in turn, will yield novel insights into the mechanisms of post-traumatic neurogenesis and inform the development of new therapeutic approaches to treat the poorly regener- ating neural injuries in human patients. The research agenda of the proposed project provides a wealth of opportunities. Many of our un- dergraduate and graduate students are the ?rst in their families to have higher education opportunities and these students include many from historically under-represented minority groups.

A diverse team of faculty researchers, research computing, and networking experts from across UNC Charlotte are collaborating to develop and deploy an advanced network for research across the campus. This network dramatically improves digital communication between researchers, scientific instrumentation, visualization workstations, high performance computing (HPC) infrastructure and external collaborators. Access to the advanced network enables higher speed to existing research workflows and allows for new research processes previously unavailable to the team. For example, massive datasets from multiple DNA sequencing instruments are streamed to powerful HPC clusters thus removing data analysis bottlenecks. Research applying motion analysis and artificial intelligence to Future of Work research, natural language processing and cyber physical systems are also supported. Applications include fluid dynamics simulation of airflow, which carries infectious microbes, in public transportation. Research collaborations between UNC Charlotte and other universities is enhanced by speeding acquisition and sharing of research results. Students from varied backgrounds, including UNC Charlotte’s large cohorts from underrepresented groups and first generation college students will work with this state-of-the-art cyberinfrastructure in their coursework and research projects.

The design is a campus wide 100Gb fibre-based network with Science DMZ including a Data Transfer Node enabling data flows separate from the day-to-day traffic of University business. The network is implemented as a spine-leaf architecture with two spines (64x100GbE) interconnected to each other with 100Gb links by MLAG. One spine is placed in the HPC Data Center and the other is placed in a separate campus Data Center. The network has 6 Leafs (32x100 GbE) supporting connectivity between buildings housing academic departments and HPC infrastructure. Performance is monitored and tuned with PerfSonar nodes. Security is monitored through Zeek (40Gb/s) nodes. The network and Science DMZ are tuned and optimized in collaboration between researchers and network architects.

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.