CURRICULAR AND PEDAGOGICAL INNOVATIONS IN QUANTITATIVE BIOLOGY
Qiu Weigang
Hunter Collegecity: New York country: United States (us)
Grant 5T36GM078001-04 from National Institute Of General Medical Sciences
Abstract: Current undergraduate biological sciences curricula do not provide adequate computational / quantitative training for students who are interested in pursuing careers in biomedical research. Hunter College of the City University of New York (CUNY) will address this lack of training by broadening and implementing a curricular transformation in biology and related sciences begun during its Phase I project, named the Quantitative Biology (QuBi) initiative. QuBi´s interdisciplinary faculty panel´s first aim will integrate computational and quantitative biology content into 26 different courses serving approximately 6,500 registrants per year across the Biology, Chemistry, Computer Science, Mathematics and Statistics departments. Several of these modified courses will introduce our undergraduates to the field of bioinformatics, and QuBi anticipates that up to 20 students per year will pursue the new bioinformatics options and concentrations developed during Phase I. QuBi´s second aim is to establish an enduring educational infrastructure for producing quantitative biologists at Hunter by training our science faculty in new pedagogical approaches such as problem-based learning (PBL), collaborative course development and collaborative teaching. Our faculty will attend educational conferences and participate in summer workshops run by pedagogical experts. All knowledge acquired during this initiative will be shared with faculty across Hunter. QuBi´s third aim, to build a critical mass of quantitative biology students, is vital for the success of the Phase II project. The QuBi team will collaborate with the College´s existing successful science-related educational programs (MARC, MBRS/RISE, HHMI, NSF CSEMS and CollegeNow) for student outreach at both the high school and the college level. The success of the proposed curricular transformation at Hunter College will have a major impact on increasing the number of quantitatively trained biologists, especially minority scientists, at Hunter and across CUNY, since the Hunter curricular activities will be shared with other CUNY campuses. Relevance to Public Health The amount of biological information available today, such as human genome sequences and health statistics, is increasing exponentially. The computational and quantitative sciences are therefore playing an increasingly important role in disease prevention and treatment. The proposed project will produce a future generation of scientists with the quantitative skills required for biomedical research in the 21st century
Keywords: Address; Arts; base; Behavioral Research; Bioinformatics; Biological; Biological Sciences; Biology; Biomedical Research; career; CCL7 gene; Chemistry; Cities; college; Commit; computer science; Computers; design; Development; disorder prevention; Educational aspects; Educational Curriculum; Educational process of instructing; Educational workshop; Enrollment; Ensure; Evaluation; Exposure to; Faculty; Future Generations; genome sequencing; Genomics; Goals; Health; high school; Human Genome; Human Resources; improved; innovation; interest; Knowledge; literacy; Mathematics; meetings; member; Minority; Minority Groups; Names; New York; next generation; novel; organizational structure; Outcome; outreach; Phase; physical science; Play; Problem-Based Learning; programs; public health medicine (field); Recording of previous events; Recruitment Activity; Research Infrastructure; Research Personnel; Role; role model; Running; Science; Scientist; skills; Specialist; statistics; Students; success; symposium; System; Training; Training and Infrastructure; Underrepresented Minority; Universities; university student; Woman; Work
Project start date: 2008-07-01
Project end date: 2013-06-30
Budget start date: 1-JUL-2011
Budget end date: 30-JUN-2012
PFA/PA: RFA-GM-06-005
5T36GM078001-04 (2011): $259327
Sponsored Links Excellgen http://Excellgen.com
Grants awarded to Qiu Weigang
COMPARATIVE GENOMICS OF MAJOR CLONAL GROUPS OF A LYME DISEASE PATHOGEN
Qiu Weigang
Hunter Collegecity: New York country: United States (us)
Grant 5SC3GM083722-04 from National Institute Of General Medical Sciences
Abstract: Lyme disease is the most prevalent and a fast spreading vector-borne infectious disease in the U.S. It is caused by a spirochetal bacterium Borrelia burgdorferi and transmitted by the deer tick Ixodes scapularis. At least 15 genetically distinct clonal groups of the Lyme disease pathogen are circulating in the northeastern U.S., where over 80% of the Lyme disease cases are reported annually. These clonal groups differ in their wildlife prevalence and human pathogenecity. In 2006, a group of six investigators including the PI have initiated a NIH/NIAID-funded 2-year project producing the whole-genome sequences of 17 B. burgdorferi isolates, with the goal of identifying the genetic basis of clone variations in environmental invasiveness and human virulence. Here, the PI proposes a study to complete the goal of the NIAID whole-genome sequencing project by performing the comparative genome analysis of 12 most common clonal groups. Specific aims are First, we will identify strain-specific genome changes in a phylogenetic framework. We will identify and align the main chromosomes, orthologous plasmids, and orthologous coding sequences. We will infer a genome-based phylogeny based on chromosomal DNA sequences, so that the strain differences in genome content, genome organization, and DNA sequences can be mapped to different stages during the evolutionary diversification of these clonal groups. Second, we will distinguish more consequential (e.g., adaptive) genomic changes from the lesser (e.g., random) ones by testing for the influence of natural selection. We will identify intergenic sequences important for gene regulation by their sequence conservation, genes critical for B. burgdorferi adaptation (e.g., surface lipoproteins conferring escape from host immunity) by their high non-synonymous nucleotide substitution rates relative to the synonymous rates, genes associated with initial adaptive clonal divergence by comparing the most recently diverged sister clones. Third, we will develop and maintain a website to facilitate the public dissemination of B. burgdorferi comparative genome information, such as genomic changes specific to a high-virulence clonal group. It is unknown why some strains of the Lyme disease bacteria are more pathogenic than others. We will compare the genomes of high- and low-virulence strains to identify the genes contributing to pathogenecity. Virulence-related genome elements are prime targets for designing therapeutics and vaccines
Keywords: Affect; Antigens; Bacteria; base; Be++ element; Beryllium; Bioinformatics; Black-legged Tick; Borrelia burgdorferi; Borrelia burgdorferi Group; career; Case Study; Centers for Disease Control and Prevention (U.S.); Characteristics; Chromosome Mapping; Chromosomes; Code; Collaborations; college; Communities; comparative; comparative genomics; Complex; Data; Deer Tick; design; Development; Disease; DNA Sequence; Elements; Evolution; Functional RNA; Funding; gene conservation; Gene Expression Regulation; Gene Family; Genes; Genetic; Genome; genome sequencing; Genomics; geographic difference; Goals; Homologous Gene; Human; Imagery; Immunity; improved; Individual; Infection; Inflammatory; Informatics; Intergenic Sequence; Internet; Joints; Lead; Lipoproteins; Lyme Disease; Maps; Molecular; Mutation; National Institute of Allergy and Infectious Disease; Natural Selections; Neuraxis; North America; Nucleotides; Open Reading Frames; Order Spirochaetales; Outcome; pathogen; Pathogenesis; Phenotype; Phylogenetic Analysis; Phylogeny; Plasmids; Population; preference; Prevalence; Qualifying; Regulator Genes; Relative (related person); Research; Research Infrastructure; Research Personnel; Retrieval; Sequence Alignment; Single Nucleotide Polymorphism; Sister; Skin; Specificity; Staging; success; Sum; Surface; Testing; therapeutic vaccine; Ticks; Tissues; tool development; United States; United States National Institutes of Health; Variant; Vector-transmitted infectious disease; Vertebral column; Vertebrates; Virulence; web site; Width; Work; Yang
Project start date: 2008-04-01
Project end date: 2012-03-31
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
PFA/PA: PAR-06-493
5SC3GM083722-04 (2011): $102600