Kwangwon Lee - US grants

Most eukaryotic organisms display cellular and behavioral rhythms with a period of approximately 24 hours. These rhythms are collectively called the biological or circadian "clock", and this clock influences many of an organism's activities, such as the sleep/wake cycle in humans. Through genetic, biochemical, molecular, and genomic studies, the filamentous fungus Neurospora crassa has served as an excellent model system for unraveling many biological mysteries. Due to the commonality of the core mechanisms of the circadian clock in eukaryotes, understanding the clock in Neurospora should improve our understanding of its functioning and biological consequences in a wide range of organisms. The goal of this project is the molecular characterization of two major quantitative trait loci (QTLs) that contribute to circadian rhythms. The project should provide insights into the biology of both the circadian clock and quantitative trait loci.

This research will be integrated into a new laboratory module for the investigator's "Circadian Rhythms" course. The laboratory module will provide undergraduate students - science majors and non-majors alike - with an opportunity for hands-on experience in the experimental characterization of the fungal circadian clock, along with insights into the nature and study of quantitative traits. This will be an invaluable learning experience for these students, and will help them develop into the intellectually informed, scientifically sophisticated citizens that the nation needs.

This Major Research Instrumentation (MRI) grant provides funding to acquire a high-performance computing cluster to support computational biology and affiliated research in the newly formed Center for Computational and Integrative Biology (CCIB) at Rutgers University-Camden (RUC). The CCIB brings together an inter-disciplinary group of faculty from the departments of Biology, Mathematics, Computer Science, Physics, and Chemistry, with a number of compute-intensive, data-driven projects. This proposed acquisition will contribute to, and substantially improve, the computing power available to CCIB projects, affecting both computational and experimental research efforts in up to 20 laboratories at RUC. The cluster will power a large multi-departmental project focused on the development of a common computational platform for multi-purpose modeling of networks and pathways and will significantly facilitate research on (a) how the development of complex body patterns in biological organisms is controlled; (b) mechanisms of biological rhythms and clocks; (c) how normally-occurring random fluctuations (noise) can enhance biological signaling; (d) analysis of biological images and (e) mining the rapidly expanding world store of genomic data.

The computing cluster will significantly strengthen a new interdisciplinary graduate program in CCIB at RUC, and will also strongly contribute to inter-disciplinary curricular development as part of Q-STEP, an innovative NSF program designed to increase the numbers undergraduates completing degrees in the sciences and mathematics at RUC. The state-of-the-art facility will thus form an integral component of extensive computational training for some 20 doctoral and 60 Masters students of CCIB to be enrolled over the next six years, and for Masters students in the existing RUC programs. The research and educational projects enabled by this acquisition will contribute to the mission of RUC to engage the surrounding community the impoverished urban area of Camden, NJ. The remarkable recent success of RUC programs in increasing participation of talented students from populations underrepresented in undergraduate science, technology, engineering, and mathematics (STEM) disciplines will allow CCIB to recruit exceptionally talented students from those populations. The CCIB will strongly encourage the participation of graduate students in a long-running outreach program to the local community. The proposed management plan foresees providing access to the cluster for external users. Minority-serving organizations, as well as research institutions and industrial partners, particularly start-ups collaborating with the CCIB, will be given preference. The computing cluster will enable CCIB to broaden and strengthen collaborations with other research and medical institutions in the area, contributing to the creation of a regional hotspot in southern New Jersey for life science and biomedical research, stimulating the biotechnology industry, and enhancing employment opportunities for the residents of southern New Jersey and its vicinity (Pennsylvania and Delaware).

? DESCRIPTION (provided by applicant) Most living organisms on earth are adapted to a 24 hr cycling environment due to the rotation of the earth. An organism knows the time of the day and prepares the incoming abiotic and biotic stresses, and also utilizes the expected changes of ambient environment. This time-measuring mechanism in an organism is an important biological function for its survival in nature. The observable biological rhythm with about a 24 hr period is collectively called circadian rhythm, and the underlying molecular mechanism of circadian rhythm is called the circadian clock. It has been suggested in different model organisms that circadian rhythm is a fitness trait. However, we still lack knowledge in regards to how circadian clock achieves the fitness advantage. Researchers in the proposal have identified Continent-Specific-Clock-Variation in Neurospora discreta species complex Phylogenetic Species 4b (PS4b) in strains collected in North American strains in comparison to strains collected from other continents, and proposed to characterize how allelic variations of the adaptive gene causes variation of the clock phenotype to adapt to their unique habitat using genetics, genomics, proteomics, and computational biology tools. They will generate allele-swap strains where their genotype is identical, except the continent-specific allele of the candidate gene. The fitness value of the candidate gene will be tested by measuring the number of progeny under different habitat conditions. The successful outcome of the proposed study will allow us an insight on how a local adaption of circadian rhythm of an organism influences the organism's fitness.

Project Summary 1. Goal and Objectives The goal for the Rutgers MARC U-STAR program is to recruit talented students from underrepresented groups to train them for competitive graduate programs. The success of our program will be measured by the following measurable objectives; A. Recruitment and Training 1. Development of an efficient and sustainable system to recruit qualifying MARC scholars. 2. Development of a rigorous academic and research training program. 3. Development of a list of workshops and events for academic skills/professional training. 4. Development of a comprehensive support system for RUC MARC scholars. B. Outcome Measures of the RUC MARC Training: 1. The number of RUC MARC scholars completing their baccalaureate degrees in a biomedically- relevant field. 2. The number of RUC MARC scholars applying to, being accepted by, and matriculating into Ph.D., M.D.-Ph.D. or other combined professional degree-Ph.D. graduate programs. 3. The number of MARC scholars that persist in and complete graduate training. 4. The number of publications by RUC MARC scholars during the training and after graduation. 5. The number of grants awarded to RUC MARC scholars during the training and after graduation. 2. Rationale and design of the research training program Rutgers MARC U-STAR program will be developed by extending the existing research-focused curricular system at RUC. Strengthening undergraduate research and advancing faculty research excellence are important components of the RUC strategic plan and this campus commitment to research will ensure a successful MARC U-STAR program. 3. Key activities in the training plan. Pre-MARC program: ? Exploring Careers in Biology ? Statistics for Biological Research (Experimental Design and Biostatistics) ? Principles and Practices of Biological Research (Original research for all sophomores) ? Workshops on academic skills and professional development ? MARC seminars MARC program: ? Independent Research course (491/492) in junior year and Thesis Honor (495/499) in senior year ? Two summer research internships ? Honors Science Writing course and Bioethics course 4. Duration of grant support. We are seeking five years of support. 5. Projected number of MARC trainees and intended trainee outcomes. Number of MARC scholars We will recruit 3 students per cohort for the first two years, and 5 students per cohort for the last three years; total of 21 students for the first cycle of funding. Outcomes of the Training a) 100% of MARC U-STAR trainees will graduate with a bachelor's degree in a STEM field. b) At least 60% of MARC U-STAR trainees, within three years of graduation, will matriculate into a biomedical Ph.D. or combined M.D./Ph.D. program at a research-intensive institution. c) At least 80% of those matriculates will remain in the graduate program by the end of the current funding period.